http://www2.unil.ch/cbg/api.php?action=feedcontributions&user=Sven&feedformat=atomCBG - User contributions [en]2024-03-29T02:07:52ZUser contributionsMediaWiki 1.31.12http://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2024&diff=6828UNIL BSc course: Bioinformatics for Genomics 20242024-03-19T14:33:36Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:David|David]]<br />
** [[User:Ilaria|Ilaria]]<br />
** [[User:Dennis|Dennis]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Sacha|Sacha]]<br />
** [[User:Leah|Leah]]<br />
<br />
* Schedule<br />
** 27 March 2024: "Measuring and visualising genome-wide gene expression"<br />
*** 8:15-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:15-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: David, Sofia, Leah, Sven)<br />
** 10 April 2024: "Advanced analysis of genome-wide gene expression"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Ilaria, Sacha, Sven)<br />
** 17 April 2024: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1GsazMsMxtEHxWYYMkGXqyb47RJTDsPeR?usp=sharing Tutorial] (Lead: Ilaria, Support: Sacha, Dennis, Leah, Sven)<br />
** 24 April 2024: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1FDlKl1iuNQYb4wc11Lgdj1s98SzfBDOb?usp=sharing Tutorial] (Lead: David, Support: Sofia, Dennis, Leah, Sven)<br />
** 25 April 2024: "Defining and visualising gene networks"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1LpSUx5nQaQCWQXqzWdNfarFA1ha6JMyeC-q5Nf_RfPQ/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1V6iKh0zLhe7Ofxx5aN40MYzNsJ4O3pJk?usp=sharing Tutorial] (Lead: Sofia, Support: David, Dennis, Sacha, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2024&diff=6827UNIL BSc course: Bioinformatics for Genomics 20242024-03-19T14:28:43Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:David|David]]<br />
** [[User:Ilaria|Ilaria]]<br />
** [[User:Dennis|Dennis]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Sacha|Sacha]]<br />
** [[User:Leah|Leah]]<br />
<br />
* Schedule<br />
** 27 March 2024: "Measuring and visualising genome-wide gene expression"<br />
*** 8:15-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:15-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Sofia, Leah, Sven)<br />
** 10 April 2024: "Advanced analysis of genome-wide gene expression"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Sacha, Sven)<br />
** 17 April 2024: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1GsazMsMxtEHxWYYMkGXqyb47RJTDsPeR?usp=sharing Tutorial] (Lead: Ilaria, Support: Dennis, Leah, Sven)<br />
** 24 April 2024: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1FDlKl1iuNQYb4wc11Lgdj1s98SzfBDOb?usp=sharing Tutorial] (Lead: David, Support: Dennis, Leah, Sven)<br />
** 25 April 2024: "Defining and visualising gene networks"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1LpSUx5nQaQCWQXqzWdNfarFA1ha6JMyeC-q5Nf_RfPQ/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1V6iKh0zLhe7Ofxx5aN40MYzNsJ4O3pJk?usp=sharing Tutorial] (Lead: Sofia, Support: Dennis, Sacha, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2024&diff=6826UNIL BSc course: Bioinformatics for Genomics 20242024-03-19T14:27:16Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:David|David]]<br />
** [[User:Ilaria|Ilaria]]<br />
** [[User:Dennis|Dennis]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Sacha|Sacha]]<br />
** [[User:Leah|Leah]]<br />
<br />
* Schedule<br />
** 27 March 2024: "Measuring and visualising genome-wide gene expression"<br />
*** 8:15-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:15-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Leah, Sven)<br />
** 10 April 2024: "Advanced analysis of genome-wide gene expression"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Sacha, Sven)<br />
** 17 April 2024: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1GsazMsMxtEHxWYYMkGXqyb47RJTDsPeR?usp=sharing Tutorial] (Lead: Ilaria, Support: Dennis, Leah, Sven)<br />
** 24 April 2024: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1FDlKl1iuNQYb4wc11Lgdj1s98SzfBDOb?usp=sharing Tutorial] (Lead: David, Support: Dennis, Leah, Sven)<br />
** 25 April 2024: "Defining and visualising gene networks"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1LpSUx5nQaQCWQXqzWdNfarFA1ha6JMyeC-q5Nf_RfPQ/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1V6iKh0zLhe7Ofxx5aN40MYzNsJ4O3pJk?usp=sharing Tutorial] (Lead: Sofia, Support: Dennis, Sacha, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2024&diff=6825UNIL BSc course: Bioinformatics for Genomics 20242024-03-19T13:28:07Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:David|David]]<br />
** [[User:Ilaria|Ilaria]]<br />
** [[User:Dennis|Dennis]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Sacha|Sacha]]<br />
** [[User:Leah|Leah]]<br />
<br />
* Schedule<br />
** 27 March 2024: "Measuring and visualising genome-wide gene expression"<br />
*** 8:15-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:15-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Ilaria, Sacha, Sven)<br />
** 10 April 2024: "Advanced analysis of genome-wide gene expression"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Ilaria, Sacha, Sven)<br />
** 17 April 2024: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1GsazMsMxtEHxWYYMkGXqyb47RJTDsPeR?usp=sharing Tutorial] (Lead: Ilaria, Support: David, Dennis, Leah, Sven)<br />
** 24 April 2024: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1FDlKl1iuNQYb4wc11Lgdj1s98SzfBDOb?usp=sharing Tutorial] (Lead: David, Support: Sofia, Ilaria, Leah, Sven)<br />
** 25 April 2024: "Defining and visualising gene networks"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1LpSUx5nQaQCWQXqzWdNfarFA1ha6JMyeC-q5Nf_RfPQ/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1V6iKh0zLhe7Ofxx5aN40MYzNsJ4O3pJk?usp=sharing Tutorial] (Lead: Sofia, Support: Dennis, Ilaria, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_%22Bioinformatics_for_Genomics%22&diff=6824UNIL BSc course: "Bioinformatics for Genomics"2024-03-19T10:29:20Z<p>Sven: Changed redirect target from UNIL BSc course: Bioinformatics for Genomics 2023 to UNIL BSc course: Bioinformatics for Genomics 2024</p>
<hr />
<div>#REDIRECT[[UNIL_BSc_course:_Bioinformatics_for_Genomics_2024]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2024&diff=6823UNIL BSc course: Bioinformatics for Genomics 20242024-03-19T09:24:56Z<p>Sven: Created page with "This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module. * Course aims: ** Get to know some key bioinformatics methods neces..."</p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:David|David]]<br />
** [[User:Ilaria|Ilaria]]<br />
** [[User:Dennis|Dennis]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Sacha|Sacha]]<br />
** [[User:Leah|Leah]]<br />
<br />
* Schedule<br />
** 27 March 2024: "Measuring and visualising genome-wide gene expression"<br />
*** 8:15-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:15-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Ilaria, Sacha, Sven)<br />
** 10 April 2024: "Advanced analysis of genome-wide gene expression"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Ilaria, Sacha, Sven)<br />
** 17 April 2024: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1GsazMsMxtEHxWYYMkGXqyb47RJTDsPeR?usp=sharing Tutorial] (Lead: Dennis, Support: David, Ilaria, Leah, Sven)<br />
** 24 April 2024: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1FDlKl1iuNQYb4wc11Lgdj1s98SzfBDOb?usp=sharing Tutorial] (Lead: David, Support: Sofia, Ilaria, Leah, Sven)<br />
** 25 April 2024: "Defining and visualising gene networks"<br />
*** 10:15-12:00 [https://docs.google.com/presentation/d/1LpSUx5nQaQCWQXqzWdNfarFA1ha6JMyeC-q5Nf_RfPQ/edit?usp=sharing Lecture] (Sven)<br />
*** 14:15-16:00 [https://colab.research.google.com/drive/1V6iKh0zLhe7Ofxx5aN40MYzNsJ4O3pJk?usp=sharing Tutorial] (Lead: Sofia, Support: Dennis, Ilaria, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Concept&diff=6821Concept2024-03-11T16:28:28Z<p>Sven: </p>
<hr />
<div>'''Background''': Many biological questions can only be addressed with some level of mathematical, statistical or computational expertise. Yet, studies in Life Science traditionally have put less emphasis on mathematical training than other scientific disciplines like physics and engineering. Students of biology should therefore improve their mathematical skills to stay competitive in many fields of biological research.<br />
<br />
'''Goals''': This course aims to improve mathematical and computational skills of undergraduate students in the 3rd year by studying a specific biological questions that requires some mathematical skills.<br />
<br />
'''Contents''': The idea behind this course is that for many students a mathematical concept or tool is best understood in the context of an application. Thus rather than learning an abstract mathematical theory, this course is very applied and the learning process is driven by a biological question. For example, students may be confronted with big datasets (such genomic profiles for thousand of genes in hundreds of samples) and learn how to study such data using approaches like principle component analysis or clustering. Topics like regression analysis may be explored to associate different types of biological observation (e.g. genotypes and some phenotypes). Network concepts and analysis methods are taught in the context of protein interactions or other biological networks. All project include real biological or biomedical data and address questions that are of current research interest, while requiring some non-trivial mathematical analysis whose outcome is open. Students will work in small groups of 2-4 students on projects under the weekly supervision of a teaching assistant (usually a PhD student or post-doc) with regular joint meetings: In the first joint meeting the project choices will be presented, in the second joint meeting students will present their projects and preliminary results, and in the final meeting the completed projects will be presented. <br />
<br />
'''Prerequisites''': All 3rd year students are welcome. Exceptionally we also permit 2nd year students if free places are available. Basic math, stats and programming knowledge is a big plus, but the key requirement is an interest to improve these skills.<br />
<br />
'''Evaluation''': Up 5 points of the final grade are based on the performance in the final presentation. Here we look at the results, the depth of the student teams' analysis, and how well they are presented. 1 point of the final grade is based on the individual study performance throughout the course.<br />
<br />
(back to main page of [[Course: "Solving Biological Problems that require Math"]])</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_%22Solving_Biological_Problems_that_require_Math%22&diff=6820UNIL BSc course: "Solving Biological Problems that require Math"2024-03-11T16:24:45Z<p>Sven: Changed redirect target from UNIL BSc course: Solving Biological Problems that require Math 2023 to UNIL BSc course: Solving Biological Problems that require Math 2024</p>
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<div>#REDIRECT [[UNIL BSc course: Solving Biological Problems that require Math 2024]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=User:Sacha&diff=6819User:Sacha2024-03-11T14:43:33Z<p>Sven: Created page with "Hi. I'm Sacha. More information on me will come soon ... S"</p>
<hr />
<div>Hi.<br />
<br />
I'm Sacha. More information on me will come soon ...<br />
<br />
S</div>Svenhttp://www2.unil.ch/cbg/index.php?title=User:Leah&diff=6818User:Leah2024-03-11T14:42:49Z<p>Sven: </p>
<hr />
<div>Hi.<br />
<br />
I'm Leah. More information on me will come soon ...<br />
<br />
L</div>Svenhttp://www2.unil.ch/cbg/index.php?title=User:Leah&diff=6817User:Leah2024-03-11T14:42:30Z<p>Sven: Created page with "Hi. I'm Leah. More information on me soon ... L"</p>
<hr />
<div>Hi.<br />
<br />
I'm Leah. More information on me soon ...<br />
<br />
L</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Dates_and_Deadlines_2024&diff=6816Dates and Deadlines 20242024-03-08T10:20:48Z<p>Sven: </p>
<hr />
<div>* '''First ''kick-off'' meeting''': Friday, 8. March 2024 at 9:00-12:00 (POL/202)<br />
** The concept of the course will be explained (~15 min)<br />
** The projects will be briefly presented by the respective supervisors (~15 min for each supervisor)<br />
** The course wiki will be explained (~15 min)<br />
<br />
* Students need <br />
** to '''confirm their participation''' in this course by: Monday, 11. March 2024 (midnight),<br />
** to '''form study groups''' of 3-4 students and <br />
** to announce by e-mail the '''three projects they are most interested in working on'''<br />
<br />
* Projects will be assigned no later than: Thursday, 14. March 2024<br />
<br />
* The first session with the supervisors will be arranged per e-mail<br />
<br />
* ''free working & weekly meetings with supervisors'': until the first feedback meeting<br />
<br />
* '''[[Open office for feedback 2024]]''': Friday 22 March 2024 at 9:00-12:00 (GEN 2025.1): Students are invited (but not forced) to see the course coordinator to:<br />
** Report briefly what their project is about and the goals they want to achieve<br />
** Discuss how they want to achieve these goals and what analysis tools they will use<br />
** Highlight any issues or worries about their project that could interfere with their success<br />
<br />
* '''[[Intermediate report meeting 2024]]''': Friday 26 April 2024 at 9:00-12:00 (GEN 2024)<br />
* Students will present their projects highlighting<br />
** reminder of the background of the project<br />
** preliminary results <br />
** the goals they already achieved<br />
<br />
* ''free working & weekly meetings with supervisors'': until end of May 2024<br />
<br />
* '''[[Final report meeting 2024]]''': Friday 31. May 2024 at 9:00-12:00 (GEN 2024)<br />
** Each study group presents their results (Presentations should take 25-30 minutes, including about 5' for questions, and are the basis for the student evaluation)<br />
** Feedback on the course in general<br />
<br />
(Meetings will be arranged freely between students and supervisors.)<br />
<br />
* back to [[UNIL BSc course: Solving Biological Problems that require Math 2024]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Dates_and_Deadlines_2024&diff=6815Dates and Deadlines 20242024-03-08T10:16:49Z<p>Sven: </p>
<hr />
<div>* '''First ''kick-off'' meeting''': Friday, 8. March 2024 at 9:00-12:00 (POL/202)<br />
** The concept of the course will be explained (~15 min)<br />
** The projects will be briefly presented by the respective supervisors (~15 min for each supervisor)<br />
** The course wiki will be explained (~15 min)<br />
<br />
* Students need <br />
** to '''confirm their participation''' in this course by: Monday, 11. March 2024 (midnight),<br />
** to '''form study groups''' of 3-4 students and <br />
** to announce by e-mail the '''three projects they are most interested in working on'''<br />
<br />
* Projects will be assigned no later than: Thursday, 14. March 2024<br />
<br />
* The first session with the supervisors will be arranged per e-mail<br />
<br />
* ''free working & weekly meetings with supervisors'': until the first feedback meeting<br />
<br />
* '''[[Open office for feedback 2024]]''': Friday 22 March 2024 at 9:00-12:00 (GEN 2025.1): Students are invited (but not forced) to see the course coordinator to:<br />
** Report briefly what their project is about and the goals they want to achieve<br />
** Discuss how they want to achieve these goals and what analysis tools they will use<br />
** Highlight any issues or worries about their project that could interfere with their success<br />
<br />
* '''[[Intermediate report meeting 2024]]''': Friday 26 April 2024 at 9:00-12:00 (GEN 2024)<br />
* Students will present their projects highlighting<br />
** reminder of the background of the project<br />
** preliminary results <br />
** the goals they already achieved<br />
<br />
* ''free working & weekly meetings with supervisors'': until end of May 2024<br />
<br />
* '''[[Final report meeting 2024]]''': Friday 31. May 2024 at 9:00-12:00 (GEN 2024)<br />
** Each study group presents their results (Presentations should take 25-30 minutes, including about 5' for questions, and are the basis for the student evaluation)<br />
** Feedback on the course in general<br />
<br />
(Meetings will be arranged freely between students and supervisors.)<br />
<br />
* back to [[UNIL BSc course: Solving Biological Problems that require Math 2023]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Dates_and_Deadlines_2024&diff=6814Dates and Deadlines 20242024-03-08T10:15:36Z<p>Sven: </p>
<hr />
<div>* '''First ''kick-off'' meeting''': Friday, 8. March 2024 at 9:00-12:00 (POL/202)<br />
** The concept of the course will be explained (~15 min)<br />
** The projects will be briefly presented by the respective supervisors (~15 min for each supervisor)<br />
** The course wiki will be explained (~15 min)<br />
<br />
* Students need <br />
** to '''confirm their participation''' in this course by: Monday, 11. March 2024 (midnight),<br />
** to '''form study groups''' of 3-4 students and <br />
** to announce by e-mail the '''three projects they are most interested in working on'''<br />
<br />
* Projects will be assigned no later than: Thursday, 14. March 2024<br />
<br />
* The first session with the supervisors will be arranged per e-mail<br />
<br />
* ''free working & weekly meetings with supervisors'': until the first feedback meeting<br />
<br />
* '''[[Open office for feedback 2024]]''': Friday 22 March 2024 at 9:00-12:00 (GEN 2025.1)<br />
* Students are invited to see the course coordinator to:<br />
** Report briefly what their project is about and the goals they want to achieve<br />
** Discuss how they want to achieve these goals and what analysis tools they will use<br />
** Highlight any issues or worries about their project that could interfere with their success<br />
<br />
* '''[[Intermediate report meeting 2024]]''': Friday 26 April 2024 at 9:00-12:00 (GEN 2024)<br />
* Students will present their projects highlighting<br />
** reminder of the background of the project<br />
** preliminary results <br />
** the goals they already achieved<br />
<br />
* ''free working & weekly meetings with supervisors'': until end of May 2024<br />
<br />
* '''[[Final report meeting 2024]]''': Friday 31. May 2024 at 9:00-12:00 (GEN 2024)<br />
** Each study group presents their results (Presentations should take 25-30 minutes, including about 5' for questions, and are the basis for the student evaluation)<br />
** Feedback on the course in general<br />
<br />
(Meetings will be arranged freely between students and supervisors.)<br />
<br />
* back to [[UNIL BSc course: Solving Biological Problems that require Math 2023]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Dates_and_Deadlines_2024&diff=6813Dates and Deadlines 20242024-03-08T10:14:52Z<p>Sven: Created page with "* '''First ''kick-off'' meeting''': Friday, 8. March 2024 at 9:00-12:00 (POL/202) ** The concept of the course will be explained (~15 min) ** The projects will be briefly pres..."</p>
<hr />
<div>* '''First ''kick-off'' meeting''': Friday, 8. March 2024 at 9:00-12:00 (POL/202)<br />
** The concept of the course will be explained (~15 min)<br />
** The projects will be briefly presented by the respective supervisors (~15 min for each supervisor)<br />
** The course wiki will be explained (~15 min)<br />
<br />
* Students need <br />
** to '''confirm their participation''' in this course by: Monday, 11. March 2024 (midnight),<br />
** to '''form study groups''' of 3-4 students and <br />
** to announce by e-mail the '''three projects they are most interested in working on'''<br />
<br />
* Projects will be assigned no later than: Thursday, 14. March 2024<br />
<br />
* The first session with the supervisors will arranged per e-mail<br />
<br />
* ''free working & weekly meetings with supervisors'': until the first feedback meeting<br />
<br />
* '''[[Open office for feedback 2024]]''': Friday 22 March 2024 at 9:00-12:00 (GEN 2025.1)<br />
* Students are invited to see the course coordinator to:<br />
** Report briefly what their project is about and the goals they want to achieve<br />
** Discuss how they want to achieve these goals and what analysis tools they will use<br />
** Highlight any issues or worries about their project that could interfere with their success<br />
<br />
* '''[[Intermediate report meeting 2024]]''': Friday 26 April 2024 at 9:00-12:00 (GEN 2024)<br />
* Students will present their projects highlighting<br />
** reminder of the background of the project<br />
** preliminary results <br />
** the goals they already achieved<br />
<br />
* ''free working & weekly meetings with supervisors'': until end of May 2024<br />
<br />
* '''[[Final report meeting 2024]]''': Friday 31. May 2024 at 9:00-12:00 (GEN 2024)<br />
** Each study group presents their results (Presentations should take 25-30 minutes, including about 5' for questions, and are the basis for the student evaluation)<br />
** Feedback on the course in general<br />
<br />
(Meetings will be arranged freely between students and supervisors.)<br />
<br />
* back to [[UNIL BSc course: Solving Biological Problems that require Math 2023]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Solving_Biological_Problems_that_require_Math_2024&diff=6812UNIL BSc course: Solving Biological Problems that require Math 20242024-03-08T10:07:50Z<p>Sven: Created page with "* Coordinator: Sven Bergmann * Concept * Useful tools * Dates and Deadlines 2024 * Projects ** Retinal vascular properties & disease (Sofia) ** Top-bottom di..."</p>
<hr />
<div>* Coordinator: [[Sven Bergmann]]<br />
* [[Concept]]<br />
* [[Useful tools]]<br />
* [[Dates and Deadlines 2024]]<br />
<br />
* Projects<br />
** Retinal vascular properties & disease (Sofia) <br />
** Top-bottom differences in retinal vascular properties (Sacha) <br />
** Sex differences in retinal vascular properties (Leah)<br />
** Vascular properties of patients with peripheral artery disease (Michael)<br />
** Vascular properties of plant leaves (Ilaria)<br />
<br />
* Supervisors<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Sacha|Sacha]]<br />
** [[User:Leah|Leah]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Ilaria|Ilaria]]<br />
<br />
* [[Grading]]<br />
* see also [[UNIL BSc course: Solving Biological Problems that require Math 2023]]<br />
* [[How to upload files and edit your project page]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Welcome_info&diff=6802Welcome info2023-10-31T13:48:17Z<p>Sven: </p>
<hr />
<div><br />
This page contains some information you will need to start working at the CBG. Please update it if necessary. In addition, you can read the<br />
'''[[Guidelines for a successful stay at the CBG]]'''<br />
<br />
== '''First steps''' ==<br />
<br />
Once you arrive at the CBG/DBC, here is the list of things you should do first.<br />
<br />
<br />
* '''Building keys and hardware lockers'''<br />
<br />
Ask Michelle N'Cho to get your keys to access the building and your office. Once you have setup your desktop, ask for some cables to lock your hardware.<br />
<br />
<br />
* '''UNIL account'''<br />
You will find here some useful informations concerning [http://www.unil.ch/ci/page88358.html your personal access to the UNIL] and [http://www.unil.ch/ci/page34.html the services] provided.<br />
<br />
Open the [https://www.unil.ch/ci/files/live/sites/ci/files/shared/acces/Creation-Id-V1.12-formulaire.pdf pdf], fill it out, get it signed by your supervisor and send it to the Centre Informatique.<br />
<br />
You will receive by post your username and password to will allow you to use all the services and resources at UNIL.<br />
<br />
* '''Wiki Access'''<br />
Ask [[User:Michael|Michael]] to provide you with a login for the wiki. You should then add yourself to the "people" [[People | page]], and update your personal webpage User:Username, where username is your username.<br />
<br />
* ''' Maling list access'''<br />
Ask [[User:Daniel| Daniel]] to put you on the CBG mailing list and ask Michelle N'Cho to add you to the DBC mailing list.<br />
<br />
* '''Calendar Access'''<br />
Ask any member of the lab to give you the credentials to access the our shared google calendars, one for the CBG and one for the DGM. These calendars allow you to be updated on upcoming events and meetings, as well as when people are away from the lab. <br />
<br />
* '''Campus card (student card)'''<br />
<br />
Fill in the following form [http://www.unil.ch/webdav/site/campuscard/shared/pdf/CC_formulaire_etudiant_nov08.pdf Student Campus Card form] and sent it back to the service des immatriculations at UNIL.<br />
<br />
Please see also section "PhD student and Doctoral Programme" to know how to enrol at UNIL.<br />
<br />
== ''' IT access ''' ==<br />
<br />
*''' Printer''' <br />
<br />
Ask Michelle.<br />
<br />
* '''Access to the servers'''<br />
<br />
Ask [[User:Michael|Michael]] to create you an account on the calculation servers we have here. <br />
<br />
* '''Services au personnel''' <br />
<br />
http://www.unil.ch/ci/page34.html<br />
<br />
* '''UNIL Internal Portal'''<br />
<br />
http://www.unil.ch/interne<br />
<br />
== ''' PhD Student and Doctoral Programme''' ==<br />
<br />
* PhD students have to be registered at UNIL from the beginning until the end of their doctoral studies, meaning until the registration of their thesis at the Bibliothèque Cantonale et Universitaire. All the instructions for the online registration are available [http://www.unil.ch/immat/page83462_en.html here]. Please also note that there are two deadlines for enrollment at the University: Autumn semester (before 31 July) and Spring semester (before 31 January)<br />
<br />
*As a PhD student starting at the CBG, you will then have to complete the PhD Doctoral Programme in Life Science which is about collecting 12 ECTS credits during your PhD by attending courses, conferences, tutorials... Details can be found [http://www.unil.ch/edfbm/page79197.html here].<br />
<br />
* The SIB also provides all along the year [http://www.sib.swiss/training training courses] and once a year a summer shcool is organized by the [http://www.sib.swiss/training/for-sib-phd-students SIB PhD training network] . PhD students can register to those activities and gather credits for the UNIL Doctoral Programme.<br />
<br />
*More info about research and career can be found [https://www.unil.ch/researcher/en/home.html here]<br />
<br />
== ''' SIB affiliation ''' ==<br />
<br />
* As a member of the CBG, you are member of the [http://www.isb-sib.ch/ Swiss Institute of Bioinformatics] . You will have to fill in [http://www2.unil.ch/cbg/images/e/e6/New_arrivals_departures_form.pdf the registration form] according to the instructions. Please note that new arrival or new departure has to be announced by you at the SIB administration.<br />
*Usually at the end of January of each year, the SIB organizes the SIB days (2 days retreat) bringing together all the members of the SIB across Switzerland. Please make sure you register to this event.<br />
<br />
=='''Special foreigners arriving in Switzerland''' ==<br />
<br />
You will find [http://www.unil.ch/bienvenue/page20660_en.html here] the students' handbook, which contains very useful information.<br />
Other basic information can be found at [http://www.unil.ch/bienvenue/page9044_en.html this page].<br />
<br />
* '''Swiss residence permit'''<br />
<br />
You will have to request it from the office of your town of residence. The request is made by our admin.<br />
<br />
*''' Medical care insurances'''<br />
<br />
It's mandatory to have a health insurance once you arrive in Switzerland. <br />
Have a look at the official [http://www.priminfo.ch/praemien/index.php?sprache=f federal list of insurances] and compare the offers with [http://fr.comparis.ch/krankenkassen/default.aspx?tid=googleAd-KK_fr&WT.srch=1&extclient=comparis comparis.ch].<br />
Some additional information about the different health systems can be found in [http://www.frc.ch/pages.php?id=1140 this article] from la fédération romande des consommateurs.<br />
<br />
==''' General info ''' ==<br />
<br />
* '''Coffees'''<br />
<br />
Coffee is free. Hurray!<br />
<br />
* '''Supplies'''<br />
<br />
All kinds of pens, notebooks,Post-it, stamps, envelopes, ... can be provided by our admin).<br />
<br />
* '''Google calendar'''<br />
<br />
We share a google calendar where all kind of infos are written (vacations, conferences, lab meeting...). To get the access, ask any member of the CBG.<br />
<br />
* '''DBC meetings/CBG meetings/Journal clubs'''<br />
<br />
We have a number of regular meetings that include the DGM progress report, CBG group meetings and the [[Journal Club]]. Time and places are indicated on the google calendars.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_Data_Analysis_I_2023&diff=6801UNIL MSc course: Data Analysis I 20232023-09-22T09:53:57Z<p>Sven: </p>
<hr />
<div>'''Introduction'''<br />
This course is for MSc students both from the MLS and BEC master programs. The goal is to review fundamental notions in statistics and show how they are useful for basic data analysis challenges in biology. <br />
<br />
'''Prerequisites'''<br />
Students who follow this course should already have some basic knowledge in statistics and R equivalent to the one achieved by bachelor students at the University of Lausanne. To catch up, if needed, students can participate in dedicated R refresher sessions for Master students by F. Schütz on Wednesday 10:15-12:00 in Gen/C (except 15.11.23 : BIO/Amphi).<br />
<br />
'''Resources'''<br />
The following software is required for this course:<br />
<br />
a recent version of R (in doubt, simply download and install the latest version from the R website at https://stat.ethz.ch/CRAN/ -- many potential problems are solved by simply upgrading to the latest R version)<br />
RStudio (which you can download from http://www.rstudio.com/products/rstudio/download/)<br />
Here are the slides related to the third lecture on Introduction to Regression Analysis <br />
<br />
'''Schedule and content'''<br />
This course is taught in 4 blocks. Each block has 2h frontal lecture:<br />
<br />
* 22.09.2023 9:00-11:00 Basic notions of probability theory, Central Limit Theorem ([https://docs.google.com/presentation/d/12JxTXy-eIRgr-5nnYoPlfLrYU2PFCn6JchC6--X6mzg Slides])<br />
* 29.09.2023 9:00-11:00 Important distributions and tests, sampling and estimates <br />
* 06.10.2023 9:00-11:00 Introduction to linear regression<br />
* 13.10.2023 9:00-11:00 Introduction to mixed models and Cox models<br />
<br />
The lectures are accompanied by supervised exercise sessions (see below).<br />
<br />
'''Exercises and grades'''<br />
This course has no oral or written exam; instead students must submit their solutions to exercises. <br />
<br />
There will be four sets of exercises - one for each session. The exercise corresponding to each session is discussed 11:15-12:00 right after the lecture to make sure all questions are clear. The exercises are due on Thursdays at 22:00, six day after the lecture. They are discussed on the following day in the afternoon at 13:00-14:00.<br />
<br />
For each question we indicate how many points one receives for a correct answer. The grade of each exercise is the sum of these points truncated at 6. The final grade is the average of the grades from the three sets.<br />
<br />
*[https://docs.google.com/document/d/1AHbYft2Lsv9YvAhusYoj2PxEnLXoK_QawtbE9OPnNpg Exercise set #1] (due on 28.09.2023 22:00)<br />
*Exercise set #2 (due on 05.10.2023 22:00)<br />
*Exercise set #3 (due on 12.10.2023 22:00)<br />
*Exercise set #4 (due on 17.10.2023 22:00)<br />
<br />
Submission should be done via Moodle, but you can also send your exercise to Sven.Bergmann@unil.ch in case this does not work.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_Data_Analysis_I_2023&diff=6800UNIL MSc course: Data Analysis I 20232023-09-22T09:52:24Z<p>Sven: </p>
<hr />
<div>'''Introduction'''<br />
This course is for MSc students both from the MLS and BEC master programs. The goal is to review fundamental notions in statistics and show how they are useful for basic data analysis challenges in biology. <br />
<br />
'''Prerequisites'''<br />
Students who follow this course should already have some basic knowledge in statistics and R equivalent to the one achieved by bachelor students at the University of Lausanne. To catch up, if needed, students can participate in dedicated R refresher sessions for Master students by F. Schütz on Wednesday 10:15-12:00 in Gen/C (except 15.11.23 : BIO/Amphi).<br />
<br />
'''Resources'''<br />
The following software is required for this course:<br />
<br />
a recent version of R (in doubt, simply download and install the latest version from the R website at https://stat.ethz.ch/CRAN/ -- many potential problems are solved by simply upgrading to the latest R version)<br />
RStudio (which you can download from http://www.rstudio.com/products/rstudio/download/)<br />
Here are the slides related to the third lecture on Introduction to Regression Analysis <br />
<br />
'''Schedule and content'''<br />
This course is taught in 4 blocks. Each block has 2h frontal lecture:<br />
<br />
* 22.09.2023 9:00-11:00 Basic notions of probability theory, Central Limit Theorem [https://docs.google.com/presentation/d/12JxTXy-eIRgr-5nnYoPlfLrYU2PFCn6JchC6--X6mzg Slides]<br />
* 29.09.2023 9:00-11:00 Important distributions and tests, sampling and estimates Slides<br />
* 06.10.2023 9:00-11:00 Introduction to linear regression Slides<br />
* 13.10.2023 9:00-11:00 Introduction to mixed models and Cox models Slides<br />
<br />
The lectures are accompanied by supervised exercise sessions (see below).<br />
<br />
'''Exercises and grades'''<br />
This course has no oral or written exam; instead students must submit their solutions to exercises. <br />
<br />
There will be four sets of exercises - one for each session. The exercise corresponding to each session is discussed 11:15-12:00 right after the lecture to make sure all questions are clear. The exercises are due on Thursdays at 22:00, six day after the lecture. They are discussed on the following day in the afternoon at 13:00-14:00.<br />
<br />
For each question we indicate how many points one receives for a correct answer. The grade of each exercise is the sum of these points truncated at 6. The final grade is the average of the grades from the three sets.<br />
<br />
*[https://docs.google.com/document/d/1AHbYft2Lsv9YvAhusYoj2PxEnLXoK_QawtbE9OPnNpg Exercise set #1] (due on 28.09.2023 22:00)<br />
*Exercise set #2 (due on 05.10.2023 22:00)<br />
*Exercise set #3 (due on 12.10.2023 22:00)<br />
*Exercise set #4 (due on 17.10.2023 22:00)<br />
<br />
Submission should be done via Moodle, but you can also send your exercise to Sven.Bergmann@unil.ch in case this does not work.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_Data_Analysis_I_2023&diff=6799UNIL MSc course: Data Analysis I 20232023-09-22T09:51:29Z<p>Sven: </p>
<hr />
<div>'''Introduction'''<br />
This course is for MSc students both from the MLS and BEC master programs. The goal is to review fundamental notions in statistics and show how they are useful for basic data analysis challenges in biology. <br />
<br />
'''Prerequisites'''<br />
Students who follow this course should already have some basic knowledge in statistics and R equivalent to the one achieved by bachelor students at the University of Lausanne. To catch up, if needed, students can participate in dedicated R refresher sessions for Master students by F. Schütz on Wednesday 10:15-12:00 in Gen/C (except 15.11.23 : BIO/Amphi).<br />
<br />
'''Resources'''<br />
The following software is required for this course:<br />
<br />
a recent version of R (in doubt, simply download and install the latest version from the R website at https://stat.ethz.ch/CRAN/ -- many potential problems are solved by simply upgrading to the latest R version)<br />
RStudio (which you can download from http://www.rstudio.com/products/rstudio/download/)<br />
Here are the slides related to the third lecture on Introduction to Regression Analysis <br />
<br />
'''Schedule and content'''<br />
This course is taught in 4 blocks. Each block has 2h frontal lecture:<br />
<br />
* 22.09.2023 9:00-11:00 Basic notions of probability theory, Central Limit Theorem <br />
[https://docs.google.com/presentation/d/12JxTXy-eIRgr-5nnYoPlfLrYU2PFCn6JchC6--X6mzg Slides]<br />
* 29.09.2023 9:00-11:00 Important distributions and tests, sampling and estimates Slides<br />
* 06.10.2023 9:00-11:00 Introduction to linear regression Slides<br />
* 13.10.2023 9:00-11:00 Introduction to mixed models and Cox models Slides<br />
<br />
The lectures are accompanied by supervised exercise sessions (see below).<br />
<br />
'''Exercises and grades'''<br />
This course has no oral or written exam; instead students must submit their solutions to exercises. <br />
<br />
There will be four sets of exercises - one for each session. The exercise corresponding to each session is discussed 11:15-12:00 right after the lecture to make sure all questions are clear. The exercises are due on Thursdays at 22:00, six day after the lecture. They are discussed on the following day in the afternoon at 13:00-14:00.<br />
<br />
For each question we indicate how many points one receives for a correct answer. The grade of each exercise is the sum of these points truncated at 6. The final grade is the average of the grades from the three sets.<br />
<br />
[https://docs.google.com/document/d/1AHbYft2Lsv9YvAhusYoj2PxEnLXoK_QawtbE9OPnNpg Exercise set #1] (due on 28.09.2023 22:00)<br />
Exercise set #2 (due on 05.10.2023 22:00)<br />
Exercise set #3 (due on 12.10.2023 22:00)<br />
Exercise set #4 (due on 17.10.2023 22:00)<br />
<br />
Submission should be done via Moodle, but you can also send your exercise to Sven.Bergmann@unil.ch in case this does not work.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_Data_Analysis_I_2023&diff=6798UNIL MSc course: Data Analysis I 20232023-09-22T09:49:01Z<p>Sven: </p>
<hr />
<div>'''Introduction'''<br />
This course is for MSc students both from the MLS and BEC master programs. The goal is to review fundamental notions in statistics and show how they are useful for basic data analysis challenges in biology. <br />
<br />
'''Prerequisites'''<br />
Students who follow this course should already have some basic knowledge in statistics and R equivalent to the one achieved by bachelor students at the University of Lausanne. To catch up, if needed, students can participate in dedicated R refresher sessions for Master students by F. Schütz on Wednesday 10:15-12:00 in Gen/C (except 15.11.23 : BIO/Amphi).<br />
<br />
'''Resources'''<br />
The following software is required for this course:<br />
<br />
a recent version of R (in doubt, simply download and install the latest version from the R website at https://stat.ethz.ch/CRAN/ -- many potential problems are solved by simply upgrading to the latest R version)<br />
RStudio (which you can download from http://www.rstudio.com/products/rstudio/download/)<br />
Here are the slides related to the third lecture on Introduction to Regression Analysis <br />
<br />
'''Schedule and content'''<br />
This course is taught in 4 blocks. Each block has 2h frontal lecture:<br />
<br />
** 22.09.2023 9:00-11:00 Basic notions of probability theory, Central Limit Theorem <br />
[https://docs.google.com/presentation/d/12JxTXy-eIRgr-5nnYoPlfLrYU2PFCn6JchC6--X6mzg Slides]<br />
** 29.09.2023 9:00-11:00 Important distributions and tests, sampling and estimates Slides<br />
** 06.10.2023 9:00-11:00 Introduction to linear regression Slides<br />
** 13.10.2023 9:00-11:00 Introduction to mixed models and Cox models Slides<br />
<br />
The lectures are accompanied by supervised exercise sessions (see below).<br />
<br />
'''Exercises and grades'''<br />
This course has no oral or written exam; instead students must submit their solutions to exercises. <br />
<br />
There will be four sets of exercises - one for each session. The exercise corresponding to each session is discussed 11:15-12:00 right after the lecture to make sure all questions are clear. The exercises are due on Thursdays at 22:00, six day after the lecture. They are discussed on the following day in the afternoon at 13:00-14:00.<br />
<br />
For each question we indicate how many points one receives for a correct answer. The grade of each exercise is the sum of these points truncated at 6. The final grade is the average of the grades from the three sets.<br />
<br />
[|https://docs.google.com/document/d/1AHbYft2Lsv9YvAhusYoj2PxEnLXoK_QawtbE9OPnNpg Exercise set #1] (due on 28.09.2023 22:00)<br />
Exercise set #2 (due on 05.10.2023 22:00)<br />
Exercise set #3 (due on 12.10.2023 22:00)<br />
Exercise set #4 (due on 17.10.2023 22:00)<br />
<br />
<br />
Assignment icon<br />
Submit Exercise set #1 Assignment<br />
Assignment icon<br />
Submit Exercise set #2 Assignment<br />
Assignment icon<br />
Submit Exercise set #3 Assignment<br />
Assignment icon<br />
Submit Exercise set #4</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_MSc_course:_Data_Analysis_I_2023&diff=6797UNIL MSc course: Data Analysis I 20232023-09-22T09:47:00Z<p>Sven: Created page with "'''Introduction''' This course is for MSc students both from the MLS and BEC master programs. The goal is to review fundamental notions in statistics and show how they are use..."</p>
<hr />
<div>'''Introduction'''<br />
This course is for MSc students both from the MLS and BEC master programs. The goal is to review fundamental notions in statistics and show how they are useful for basic data analysis challenges in biology. <br />
<br />
'''Prerequisites'''<br />
Students who follow this course should already have some basic knowledge in statistics and R equivalent to the one achieved by bachelor students at the University of Lausanne. To catch up, if needed, students can participate in dedicated R refresher sessions for Master students by F. Schütz on Wednesday 10:15-12:00 in Gen/C (except 15.11.23 : BIO/Amphi).<br />
<br />
'''Resources'''<br />
The following software is required for this course:<br />
<br />
a recent version of R (in doubt, simply download and install the latest version from the R website at https://stat.ethz.ch/CRAN/ -- many potential problems are solved by simply upgrading to the latest R version)<br />
RStudio (which you can download from http://www.rstudio.com/products/rstudio/download/)<br />
Here are the slides related to the third lecture on Introduction to Regression Analysis <br />
<br />
'''Schedule and content'''<br />
This course is taught in 4 blocks. Each block has 2h frontal lecture:<br />
<br />
22.09.2023 9:00-11:00 Basic notions of probability theory, Central Limit Theorem <br />
[https://docs.google.com/presentation/d/12JxTXy-eIRgr-5nnYoPlfLrYU2PFCn6JchC6--X6mzg Slides]<br />
29.09.2023 9:00-11:00 Important distributions and tests, sampling and estimates Slides<br />
06.10.2023 9:00-11:00 Introduction to linear regression Slides<br />
13.10.2023 9:00-11:00 Introduction to mixed models and Cox models Slides<br />
<br />
The lectures are accompanied by supervised exercise sessions (see below).<br />
<br />
'''Exercises and grades'''<br />
This course has no oral or written exam; instead students must submit their solutions to exercises. <br />
<br />
There will be four sets of exercises - one for each session. The exercise corresponding to each session is discussed 11:15-12:00 right after the lecture to make sure all questions are clear. The exercises are due on Thursdays at 22:00, six day after the lecture. They are discussed on the following day in the afternoon at 13:00-14:00.<br />
<br />
For each question we indicate how many points one receives for a correct answer. The grade of each exercise is the sum of these points truncated at 6. The final grade is the average of the grades from the three sets.<br />
<br />
[[Exercise set #1|https://docs.google.com/document/d/1AHbYft2Lsv9YvAhusYoj2PxEnLXoK_QawtbE9OPnNpg]] (due on 28.09.2023 22:00)<br />
Exercise set #2 (due on 05.10.2023 22:00)<br />
Exercise set #3 (due on 12.10.2023 22:00)<br />
Exercise set #4 (due on 17.10.2023 22:00)<br />
<br />
<br />
Assignment icon<br />
Submit Exercise set #1 Assignment<br />
Assignment icon<br />
Submit Exercise set #2 Assignment<br />
Assignment icon<br />
Submit Exercise set #3 Assignment<br />
Assignment icon<br />
Submit Exercise set #4</div>Svenhttp://www2.unil.ch/cbg/index.php?title=GMM&diff=6796GMM2023-09-18T10:30:06Z<p>Sven: </p>
<hr />
<div>Deletion, insertion and duplication events giving rise to copy number variations (CNVs) have been found genome-wide in the humans and other species.<br />
Such genomic aberrations were identified already more than a decade ago using array-based comparative hybridization. They can also be detected using <br />
data from SNP genotyping arrays, typically by combining the intensities of the two probes for a given SNP and comparing to the same SNP from other arrays (thus deriving a copy number ratio).<br />
Significant shift from the baseline (unit ratio or zero log ratio) reflects copy number changes. Such changes can be identified in many ways, for example, one can use segmentation algorithms to partition the signal then classify such segments into gain, copy neutral and loss status.<br />
Yet, for large datasets, one can take advantage of the signal distribution at each SNP, and cluster each individual from the distribution into a component that would reflect a given copy number change.<br />
<br />
We developed a Gaussian Mixture Model, which detect copy number variation from the distribution of copy number ratios. From the data, it will fit one component for each of the following copy number states: deletion, copy-neutral, 1 and 2 additional copy; with a constraint on the difference between the mixture means. Then for a given individual, it will determine the probabilities for each copy number state and compute the expected copy number (dosage). <br />
<br />
=== License ===<br />
<br />
The GMM algorithm is licensed under the GNU General Public License, version 2 or later. For details, see http://www.gnu.org/licenses/old-licenses/gpl-2.0.html.<br />
<br />
=== Usage ===<br />
<br />
The GMM can be applied to identify CNVs from any rectangular matrix of copy number ratio. <br />
<br />
Format is like : chr pos sample1 sample2 ...<br />
<br />
Fields should be tab-delimited and it assumes data (within chromosome) are sorted by position.<br />
<br />
An example input file is available within the GMM_CNV.zip (see Download section).<br />
<br />
<br />
For '''[http://www.mathworks.com/ Matlab] users''', download the source code and use the callCNVs.m script.<br />
<br />
'''Users without Matlab''', can use the compiled version and the Matlab Component Runtime (MCR). (Please note, we are only providing a compiled Linux x86_64 version for now).<br />
<br />
Then you can use (and edit according to your need) the shell script called "run_CallCNVs.sh" <br />
<br />
sh run_CallCNVs.sh path_to_the_MCR/v79/<br />
<br />
=== Requirements ===<br />
<br />
If you have the MATLAB software, you can directly use the source code.<br />
<br />
Otherwise, you will need to download the Matlab Component Runtime to use the executables (see Download section).<br />
<br />
=== Download ===<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Description <br />
! File Name<br />
! Size <br />
! md5sum<br />
|-<br />
| MCR for 64-bit Linux <br />
| http://www.unil.ch/cbg/homepage/downloads/MCR2007_x86_64.zip|MCR2007_x86_64.zip|/download/MCR2007_x86_64.zip<br />
| 224M<br />
| 451c54a811b3e01402b6a46a1b814c4d <br />
|-<br />
| Linux Executables (+ example input file)<br />
| http://www.unil.ch/cbg/homepage/downloads/GMM_CNV.zip|GMM_CNV.zip|/download/GMM_CNV.zip<br />
| 556k <br />
| bd579f39c340a50de2bb80a649643be3<br />
|-<br />
| Source code<br />
| http://www.unil.ch/cbg/homepage/downloads/GMM_CNV_SOURCE.zip|GMM_CNV_SOURCE.zip|/download/GMM_CNV_SOURCE.zip<br />
| 16k <br />
| 3cb7799bf3e180b33a6742ef382b105e<br />
|-<br />
|-<br />
| Example output files<br />
| http://www.unil.ch/cbg/homepage/downloads/GMM_CNV_outputs.zip|GMM_CNV_outputs.zip|/download/GMM_CNV_outputs.zip<br />
| 460k <br />
| 6b621a6a8e279697f610db35810777ce<br />
|-<br />
|}<br />
<br />
=== Frequently Ask Questions ===<br />
<br />
<br />
<br />
'''* What are the default component the model will try to fit?'''<br />
<br />
The current implementation models deletion, copy neutral, 3 copies and more than 3 copies.<br />
<br />
<br />
'''* What happen if the model fails to fit the data ?'''<br />
<br />
The model will output this warning :<br />
Exiting: Maximum number of iterations has been exceeded - increase MaxIter option.<br />
Missing data will be set as 0. Then the model will analyse the next SNP (if any).<br />
<br />
<br />
'''* I am getting :<br />
Exiting: Maximum number of iterations has been exceeded - increase MaxIter option.<br />
What does this mean?<br />
'''<br />
The model could not find the component separation before reaching its maximal iteration limit.<br />
This can be due to noisy data, or distribution where no such separation exists.<br />
Try increasing :<br />
MAX_FUN_CALL=10000; # nb of optimization function call<br />
MAX_FUN_ITER=5000; # nb of iterations for each optimization function call<br />
But note, this can significantly increase the runtime.<br />
<br />
<br />
'''* Can I apply some extra normalization before fitting the Gaussian Mixture Model?'''<br />
<br />
Yes, by default a Loess smoothing is applied. (This step can be skipped by setting DO_LOESS_SMOOTH=0 in the shell script or setting DO_LOESS=0; in callCNVs.m).<br />
<br />
Since Gaussian Mixture Model can be sensitive to batch effects, it is strongly recommended that adequate normalization is applied before using the model. <br />
note : The loess smoothing will not correct batch effects, but will improve the signal to noise ratio within individual profile. By default, the Loess windows size is 41 SNPs. For higher density arrays (Affymetrix 6.0 or Illumina 1M) such window could be increased. <br />
<br />
<br />
'''* I am getting this error : <br />
error while loading shared libraries: libmwmclmcrrt.so:<br />
cannot open shared object file: No such file or directory<br />
what does it mean?'''<br />
<br />
Most likely your LD_LIBRARY_PATH is not pointing correctly to the MCR.<br />
The run_callCNVs.sh script should do it for you.<br />
<br />
sh run_callCNVs.sh /path-to-my-MCR/v79 test.dat</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Robustness_in_Drosophila_embryo_patterning&diff=6795Robustness in Drosophila embryo patterning2023-09-18T10:29:15Z<p>Sven: </p>
<hr />
<div>[[Category:Homepage]]<br />
<br />
Bicoid (Bcd) is a well studied morphogen involved in the patterning of the anterior-posterior (AP) axis of the Drosophila embryo. Zygotic downstream genes read out this gradient and their expression domains determine the basic body plan of the embryo along this axis. The positions of these domains are remarkably insensitive to fluctuations in the external environment and their relative proportions are maintained across embryos of different sizes. The latter feature is referred to as scaling and occurs within a single species and also across different species. <br />
<br />
Recent experiments also show that the Bicoid gradient itself is rather precise and that its length scale correlates to some extent to the embryo size. These new findings suggest that the precision and scaling of Bcd target genes may, at least in part, be attributed to that of the morphogen gradient itself. Therefore, we investigate single morphogen models that aim at explaining the precision and scaling of Bcd target genes at the level of the morphogen gradient. However, it is likely that other mechanisms (e.g. Bcd interactions with the staufen gene, gap genes interactions, Bcd interactions with maternal Hunchback and the terminal system or bistability ) also contribute to ensure precise domain localization and further increase robustness in AP patterning.<br />
<br />
In our work, we measured precision in more than 150 staining images for the gap genes Krüppel (Kr), Giant (Gt) and Hunchback (Hb), as well as the pair-rule gene Even-skipped (Eve) in embryos with a single, double (wt) and quadruple dose of bcd. Our data indicated that the precision is maximal at mid-embryo as well as position-dependent rather than gene-dependent. This provided independent support for the conclusions drawn from direct measurements of Bcd that the morphogen gradient itself is the main contributor to the precision of the target genes. It motivated our subsequent analytical investigation of noise propagation during Bcd gradient formation within a single-morphogen modeling framework. Our analysis showed that fluctuations in the parameters affecting morphogen production, degradation, diffusion as well as nuclear trapping can give rise naturally to highest precision at mid-embryo, provided the Bcd gradient is decoded at pre-steady state. Finally, we considered a variety of models to investigate the scaling of the morphogen gradient. In order to single out the most likely scenario, we experimentally investigated scaling at the level of the target genes. We observed somewhat elevated scaling for expression domain boundaries in the anterior part of the embryo and almost perfect scaling beyond ~40%L (L is the embryo size). This effect appeared to be position-dependent rather than gene-dependent. Based on these observations, we argue that the formation of the Bcd gradient itself is a main contributor to robust patterning along the anterior-posterior axis and that pre-steady state decoding is an efficient means to increase robustness.<br />
<br />
We also work on the formation of the Bicoid gradient from its mRNA gradient, as suggested by a recent publication. We model the active quasi-random transport of ''bcd'' mRNA from the anterior pole (along a non-polar cortical microtubules network), forming a complex with the mRNA-binding protein Staufen, in a pure diffusive way. Establishment of the Bcd protein gradient arises by local translation from the non-localized and evolving mRNA gradient. <br />
We use a simple and general formalism for the modeling of morphogen gradient formation which allows to obtain explicit analytical solutions in the 1D case. We can also estimate diffusive parameters. The model is also being compared to static source models (without mRNA transport) involving delocalization of the source (step- and Gaussian source).<br />
<br />
== More info ==<br />
* [http://www.nature.com/msb/journal/v6/n1/pdf/msb20107.pdf Precision and scaling in morphogen gradient read-out] Aitana Morton de Lachapelle & Sven Bergmann<br />
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3010118/pdf/msb201086.pdf Pre-steady and stable morphogen gradients: can they coexist?] Aitana Morton de Lachapelle & Sven Bergmann<br />
* Introduction to Systems Biology, Uri Alon<br />
* Developmental Biology, Gilbert<br />
* [http://flymove.uni-muenster.de/ FlyMove]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Welcome_to_the_Computational_Biology_Group!&diff=6794Welcome to the Computational Biology Group!2023-09-18T10:28:18Z<p>Sven: </p>
<hr />
<div>[[Category:Homepage]]<br />
<br />
<!-- __NOTOC__ --><br />
<!-- <newsbulletins>header=NEWS|limit=3</newsbulletins> --><br />
<!-- A history of all news can be found [[History | here]]. --><br />
<br />
[[Image:CBG 2017.png|1200px]]<br />
<br />
== Who are we? ==<br />
The Computational Biology Group (CBG) is a research group embedded in the [http://unil.ch/dbc Department of Computational Biology] at the [http://unil.ch University of Lausanne]. The group consists of [http://www2.unil.ch/cbg/index.php?title=People PhD students and postdocs] and is led by [[user:Sven | Prof. Sven Bergmann]].<br />
<br />
== What are our goals? ==<br />
Our goals are to improve our fundamental understanding of how genetic variability affects phenotypes, to learn about underlying molecular mechanisms, and to make use of our insights to improve the diagnosis, prevention and treatment of disease whenever possible. We are also interested in relatively small biological systems that can be modelled quantitatively, our goal being to understand better the properties that contribute to their robustness and evolvability under changing environmental conditions.<br />
<br />
== What are our research interests? ==<br />
The group works on a broad spectrum of biological topics, from systems biology of development and signal transduction over genomics<br />
to statistical genetics. In recent years our primary focus has been on genome-wide association studies (GWAS) that link genetic variants, such<br />
as single nucleotide polymorphisms (SNP), to organismal traits. The group develops and applies innovative tools for linking association signals<br />
to genes and pathways for single (Pascal) and multiple traits (PascalX). Most analyses use data from the Cohorte Lausannoise (CoLaus),<br />
SKIPOGH and the UK Biobank with a particular interest in high-dimensional phenotypes, such as gene expression, metabolomics, and, most recently, features derived from images.<br />
<br />
Specifically, we lead the interdisciplinary ''VascX SNF Sinergia'' project. Together with three clinical research groups, our goal is to extract vascular parameters from a unique set of cohorts providing several types of retinal and non-retinal vasculature imaging, history of vascular diseases, risk factors and genotypes. Our group is developing state-of-the-art methodologies (including ''Deep Learning'') to quantify how these parameters vary across the subjects of a given cohort and study the similarity between these parameters across the retina, brain and limbs. To this end we are also integrating genetic information to identify genes and biochemical pathways that modulate vessels’ shape and contribute to vascular disease. Finally we develop models that can predict cardiovascular and cerebrovascular disease risk based on the morphology of<br />
retinal vessels. This highly interdisciplinary project will advance our knowledge about the genetic and molecular mechanisms for shaping vasculature. Since retinal imaging is fast and inexpensive, our aim to predict individuals’ risks and detect disease onset early presents a real<br />
prospect of a tangible impact on the societal burden caused by common vascular diseases.<br />
<br />
== How do we work? ==<br />
Most of our work is computational, which means we use computer algorithms to process and analyse data. Our analyses often have a statistical component to evaluate the significance of results. Whenever possible we describe our data using mathematical models. Sometimes these models can be solved analytically, but often we rely on numerical solutions and simulations. Some of our methods have a heuristic component, but we try to evaluate them rigorously and make them as practical as possible. We strongly believe in sharing our analysis tools and Open Science in general. <br />
<br />
Our group seeks an interdisciplinary approach, bridging the traditional gaps between physics, mathematics and biology. Our lab collaborates with experimental and medical research groups.<br />
<br />
== General info on this wiki ==<br />
This wiki is the main instrument to centralize and archive information on and generated by the CBG. Ask [[user:Michael | Michael]] if you have any questions or need an account.<br />
<br />
<br />
<!-- <newsbulletins>header=NEWS|limit=1</newsbulletins> --></div>Svenhttp://www2.unil.ch/cbg/index.php?title=Teaching&diff=6712Teaching2023-05-31T12:10:47Z<p>Sven: </p>
<hr />
<div>'''Teaching statement:''' Giving seminars and courses related to computational biology is a prime objective of the Computational Biology Group. Our aim is to provide biology students at all academic levels with knowledge about basic concepts of computational and quantitative biology. We believe that – at a time where high-throughput genomic technologies are entering more and more into biological and bio-medical research – it is a prerequisite for all students of biology to be exposed to basic tools of large-scale data analysis. Similarly, quantitative assays and imaging allow for mathematical modeling of biological systems in space and time that produces testable hypotheses. Since formal (mathematical and computational) education receives comparatively less emphasis (and interest) in the classical life sciences, educating students in these fields is a major challenge. In our experience a significant number of biology students are uncomfortable in using mathematics, which may be rooted already in their high school education or even before. The frontal courses offered to biology students may help brushing up basic mathematical skills of some students, but are less likely to be effective for many students who have long lost their interest and self-confidence in solving mathematical problems. We thus attempt to provide also alternative approaches, like our annual hands-on [[UNIL BSc course: "Solving Biological Problems that require Math"]] that is directed at undergraduate students (see [[Concept]]).<br />
<br />
----<br />
<br />
= 2023 =<br />
* [[UNIL BSc course: Bioinformatics for Genomics 2023]]<br />
* [[UNIL BSc course: Solving Biological Problems that require Math 2023]]<br />
* [[UNIL MSc course: Data Analysis I 2023]]<br />
<br />
= 2022 =<br />
* [[UNIL BSc course: Bioinformatics for Genomics 2022]]<br />
* [[UNIL BSc course: Solving Biological Problems that require Math 2022]]<br />
* [[UNIL MSc course: Data Analysis I 2022]]<br />
<br />
= 2021 =<br />
* [[UNIL BSc course: Bioinformatics for Genomics 2021]]<br />
* [[UNIL BSc course: Solving Biological Problems that require Math 2021]]<br />
* [[UNIL MSc course: Data Analysis I 2021]]<br />
<br />
= 2020 =<br />
* [[UNIL BSc course: Bioinformatics for Genomics 2020]]<br />
* [[UNIL BSc course: Solving Biological Problems that require Math 2020]]<br />
* [[UNIL MSc course: Data Analysis I 2020]]<br />
* [[UNIL MSc course: Case studies in bioinformatics 2020]]<br />
<br />
= 2019 =<br />
* [[UNIL BSc course: Solving Biological Problems that require Math 2019]]<br />
* [[UNIL MSc course: Case studies in bioinformatics 2019]]<br />
* [[UNIL PhD course: Biology for non-biologists 2019]]<br />
<br />
= 2018 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2018"]]<br />
* [[UNIL MSc course: "Case studies in bioinformatics 2018"]]<br />
* [[UNIL PhD course: "Biology for non-biologists 2018"]]<br />
<br />
= 2017 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2017"]]<br />
* [[UNIL MSc course: "Case studies in bioinformatics 2017"]]<br />
<br />
= 2016 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2016"]]<br />
* [[UNIL MSc course: "Case studies in bioinformatics 2016"]]<br />
<br />
= 2015 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2015"]]<br />
* [[UNIL MSc course: "Case studies in bioinformatics 2015"]]<br />
<br />
= 2014 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2014"]]<br />
* [[SIB course on “Statistical genomics and statistical genetics”]]<br />
* [[UNIL PhD seminar: "Bi-weekly meeting for graduate students in biostatistics and computational biology"]]<br />
<br />
= 2013 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2013"]]<br />
* [[SIB winter-school on “Clinical Bioinformatics”]]<br />
<br />
= 2012 =<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2012"]]<br />
* [[Summerschool of the Max-Weber Stiftung]]<br />
* [[EPFL doctoral course: "Functional Genomics 2012"]]<br />
<br />
= 2011 =<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2011"]] <br />
* [[SystemsX.ch/SIB summer-school ”From Data to Models in Biological Systems”]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2011"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2011"]]<br />
<br />
= 2010 =<br />
* [[UNIL PhD literature seminar: "Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls"]]<br />
* [[UNIL Biomedical Master: "Metabolic diseases 2010"]] <br />
* [[UNIL BSc course: "Experimental design 2010"]] <br />
* [[UNIL BSc course: "GGE course module on Genome-wide association studies"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2010"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2010"]]<br />
<br />
= 2009 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL BSc course: "Experimental design 2009"]] <br />
* [[UNIL MSc course: "Genes: from sequence to function 2009"]]<br />
* [[UNIL BSc course: "Solving Biological Problems that require Math 2009"]]<br />
* [[EPFL doctoral course: "Functional Genomics 2009"]]<br />
<br />
= 2008 =<br />
* [[UNIL PhD literature seminar: "Systematic interpretation of genetic interactions using protein networks"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2008"]]<br />
* [[Summer school course: "Biologie und Medizin im digitalen Zeitalter: Jenseits der Disziplinen"]]<br />
* [[SIB course: "Statistical analysis applied to genome and proteome analyses"]]<br />
<br />
= 2007 =<br />
* [[UNIL PhD literature seminar: "Optimality and evolutionary tuning of the expression level of a protein"]]<br />
* [[UNIL MSc course: "Cartographie, séquençage et structure des génomes 2007"]]<br />
* [[CIG-DGM joint seminar: "Genome-wide Association Studies"]]<br />
<br />
= 2006 =<br />
* [[UNIL PhD literature seminar: "Diffusion and scaling during early embryonic pattern formation"]]<br />
<br />
[[Category:Homepage]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Welcome_info&diff=6704Welcome info2023-05-30T11:15:13Z<p>Sven: </p>
<hr />
<div><br />
This page contains some information you will need to start working at the CBG. Please update it if necessary. In addition, you can read the<br />
'''[[Guidelines for a successful stay at the CBG]]'''<br />
<br />
== '''First steps''' ==<br />
<br />
Once you arrive at the CBG/DBC, here is the list of things you should do first.<br />
<br />
<br />
* '''Building keys and hardware lockers'''<br />
<br />
Ask Stéphanie Scuderi to get your keys to access the building and your office. Once you have setup your desktop, ask for some cables to lock your hardware.<br />
<br />
<br />
* '''UNIL account'''<br />
You will find here some useful informations concerning [http://www.unil.ch/ci/page88358.html your personal access to the UNIL] and [http://www.unil.ch/ci/page34.html the services] provided.<br />
<br />
Open the [https://www.unil.ch/ci/files/live/sites/ci/files/shared/acces/Creation-Id-V1.12-formulaire.pdf pdf], fill it out, get it signed by your supervisor and send it to the Centre Informatique.<br />
<br />
You will receive by post your username and password to will allow you to use all the services and resources at UNIL.<br />
<br />
* '''Wiki Access'''<br />
Ask [[User:Michael|Michael]] to provide you with a login for the wiki. You should then add yourself to the "people" [[People | page]], and update your personal webpage User:Username, where username is your username.<br />
<br />
* ''' Maling list access'''<br />
Ask [[User:Daniel| Daniel]] to put you on the CBG mailing list and ask Michelle N'Cho to add you to the DBC mailing list.<br />
<br />
* '''Calendar Access'''<br />
Ask any member of the lab to give you the credentials to access the our shared google calendars, one for the CBG and one for the DGM. These calendars allow you to be updated on upcoming events and meetings, as well as when people are away from the lab. <br />
<br />
* '''Campus card (student card)'''<br />
<br />
Fill in the following form [http://www.unil.ch/webdav/site/campuscard/shared/pdf/CC_formulaire_etudiant_nov08.pdf Student Campus Card form] and sent it back to the service des immatriculations at UNIL.<br />
<br />
Please see also section "PhD student and Doctoral Programme" to know how to enrol at UNIL.<br />
<br />
== ''' IT access ''' ==<br />
<br />
*''' Printer''' <br />
<br />
Ask Michelle.<br />
<br />
* '''Access to the servers'''<br />
<br />
Ask [[User:Michael|Michael]] to create you an account on the calculation servers we have here. <br />
<br />
* '''Services au personnel''' <br />
<br />
http://www.unil.ch/ci/page34.html<br />
<br />
* '''UNIL Internal Portal'''<br />
<br />
http://www.unil.ch/interne<br />
<br />
== ''' PhD Student and Doctoral Programme''' ==<br />
<br />
* PhD students have to be registered at UNIL from the beginning until the end of their doctoral studies, meaning until the registration of their thesis at the Bibliothèque Cantonale et Universitaire. All the instructions for the online registration are available [http://www.unil.ch/immat/page83462_en.html here]. Please also note that there are two deadlines for enrollment at the University: Autumn semester (before 31 July) and Spring semester (before 31 January)<br />
<br />
*As a PhD student starting at the CBG, you will then have to complete the PhD Doctoral Programme in Life Science which is about collecting 12 ECTS credits during your PhD by attending courses, conferences, tutorials... Details can be found [http://www.unil.ch/edfbm/page79197.html here].<br />
<br />
* The SIB also provides all along the year [http://www.sib.swiss/training training courses] and once a year a summer shcool is organized by the [http://www.sib.swiss/training/for-sib-phd-students SIB PhD training network] . PhD students can register to those activities and gather credits for the UNIL Doctoral Programme.<br />
<br />
*More info about research and career can be found [https://www.unil.ch/researcher/en/home.html here]<br />
<br />
== ''' SIB affiliation ''' ==<br />
<br />
* As a member of the CBG, you are member of the [http://www.isb-sib.ch/ Swiss Institute of Bioinformatics] . You will have to fill in [http://www2.unil.ch/cbg/images/e/e6/New_arrivals_departures_form.pdf the registration form] according to the instructions. Please note that new arrival or new departure has to be announced by you at the SIB administration.<br />
*Usually at the end of January of each year, the SIB organizes the SIB days (2 days retreat) bringing together all the members of the SIB across Switzerland. Please make sure you register to this event.<br />
<br />
=='''Special foreigners arriving in Switzerland''' ==<br />
<br />
You will find [http://www.unil.ch/bienvenue/page20660_en.html here] the students' handbook, which contains very useful information.<br />
Other basic information can be found at [http://www.unil.ch/bienvenue/page9044_en.html this page].<br />
<br />
* '''Swiss residence permit'''<br />
<br />
You will have to request it from the office of your town of residence. The request is made by our admin.<br />
<br />
*''' Medical care insurances'''<br />
<br />
It's mandatory to have a health insurance once you arrive in Switzerland. <br />
Have a look at the official [http://www.priminfo.ch/praemien/index.php?sprache=f federal list of insurances] and compare the offers with [http://fr.comparis.ch/krankenkassen/default.aspx?tid=googleAd-KK_fr&WT.srch=1&extclient=comparis comparis.ch].<br />
Some additional information about the different health systems can be found in [http://www.frc.ch/pages.php?id=1140 this article] from la fédération romande des consommateurs.<br />
<br />
==''' General info ''' ==<br />
<br />
* '''Coffees'''<br />
<br />
Coffee is free. Hurray!<br />
<br />
* '''Supplies'''<br />
<br />
All kinds of pens, notebooks,Post-it, stamps, envelopes, ... can be provided by our admin).<br />
<br />
* '''Google calendar'''<br />
<br />
We share a google calendar where all kind of infos are written (vacations, conferences, lab meeting...). To get the access, ask any member of the CBG.<br />
<br />
* '''DBC meetings/CBG meetings/Journal clubs'''<br />
<br />
We have a number of regular meetings that include the DGM progress report, CBG group meetings and the [[Journal Club]]. Time and places are indicated on the google calendars.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Welcome_info&diff=6703Welcome info2023-05-30T11:13:26Z<p>Sven: </p>
<hr />
<div><br />
This page contains some information you will need to start working at the CBG. Please update it if necessary. In addition, you can read the<br />
'''[[Guidelines for a successful stay at the CBG]]'''<br />
<br />
== '''First steps''' ==<br />
<br />
Once you arrive at the CBG/DBC, here is the list of things you should do first.<br />
<br />
<br />
* '''Building keys and hardware lockers'''<br />
<br />
Ask Stéphanie Scuderi to get your keys to access the building and your office. Once you have setup your desktop, ask for some cables to lock your hardware.<br />
<br />
<br />
* '''UNIL account'''<br />
You will find here some useful informations concerning [http://www.unil.ch/ci/page88358.html your personal access to the UNIL] and [http://www.unil.ch/ci/page34.html the services] provided.<br />
<br />
Open the [https://www.unil.ch/ci/files/live/sites/ci/files/shared/acces/Creation-Id-V1.12-formulaire.pdf pdf], fill it out, get it signed by your supervisor and send it to the Centre Informatique.<br />
<br />
You will receive by post your username and password to will allow you to use all the services and resources at UNIL.<br />
<br />
* '''Wiki Access'''<br />
Ask [[User:Michael|Michael]] to provide you with a login for the wiki. You should then add yourself to the "people" [[People | page]], and update your personal webpage User:Username, where username is your username.<br />
<br />
* ''' Maling list access'''<br />
Ask [[User:Daniel| Daniel]] to put you on the CBG mailing list and ask Michelle N'Cho to add you to the DBC mailing list.<br />
<br />
* '''Calendar Access'''<br />
Ask any member of the lab to give you the credentials to access the our shared google calendars, one for the CBG and one for the DGM. These calendars allow you to be updated on upcoming events and meetings, as well as when people are away from the lab. <br />
<br />
* '''Campus card (student card)'''<br />
<br />
Fill in the following form [http://www.unil.ch/webdav/site/campuscard/shared/pdf/CC_formulaire_etudiant_nov08.pdf Student Campus Card form] and sent it back to the service des immatriculations at UNIL.<br />
<br />
Please see also section "PhD student and Doctoral Programme" to know how to enrol at UNIL.<br />
<br />
== ''' IT access ''' ==<br />
<br />
*''' Printer''' <br />
<br />
Ask Michelle.<br />
<br />
* '''Access to the servers'''<br />
<br />
Ask [[User:Michael|Michael]] to create you an account on the calculation servers we have here. <br />
<br />
* '''Softwares available'''<br />
<br />
To see what sort of softwares are available at UNIL:<br />
<br />
**For PCs: [http://www.vista4beginners.com/Map-Network-Drive Map the following network drive] : \\distripc.unil.ch\soft and connect to it typing ad\username and entering your password (the one from your email account).<br />
<br />
http://www.unil.ch/ci/page33723.html<br />
<br />
**For Macs: Connect to the following server (cmd + k on the Finder window) afp://bigmac.unil.ch using your email username and password.<br />
<br />
* Informatique Service'''<br />
[http://wwwfbm.unil.ch/si/en/ The information technology service of the FBM (SI)] helps to all informatics and computer related problems at the FBM. It's a plate-forme between the departments on the Bugnon-Epalinges site.<br />
<br />
* '''Services au personnel''' <br />
<br />
http://www.unil.ch/ci/page34.html<br />
<br />
* '''UNIL Internal Portal'''<br />
<br />
http://www.unil.ch/interne<br />
<br />
== ''' PhD Student and Doctoral Programme''' ==<br />
<br />
* PhD students have to be registered at UNIL from the beginning until the end of their doctoral studies, meaning until the registration of their thesis at the Bibliothèque Cantonale et Universitaire. All the instructions for the online registration are available [http://www.unil.ch/immat/page83462_en.html here]. Please also note that there are two deadlines for enrollment at the University: Autumn semester (before 31 July) and Spring semester (before 31 January)<br />
<br />
*As a PhD student starting at the CBG, you will then have to complete the PhD Doctoral Programme in Life Science which is about collecting 12 ECTS credits during your PhD by attending courses, conferences, tutorials... Details can be found [http://www.unil.ch/edfbm/page79197.html here].<br />
<br />
* The SIB also provides all along the year [http://www.sib.swiss/training training courses] and once a year a summer shcool is organized by the [http://www.sib.swiss/training/for-sib-phd-students SIB PhD training network] . PhD students can register to those activities and gather credits for the UNIL Doctoral Programme.<br />
<br />
*More info about research and career can be found [https://www.unil.ch/researcher/en/home.html here]<br />
<br />
== ''' SIB affiliation ''' ==<br />
<br />
* As a member of the CBG, you are member of the [http://www.isb-sib.ch/ Swiss Institute of Bioinformatics] . You will have to fill in [http://www2.unil.ch/cbg/images/e/e6/New_arrivals_departures_form.pdf the registration form] according to the instructions. Please note that new arrival or new departure has to be announced by you at the SIB administration.<br />
*Usually at the end of January of each year, the SIB organizes the SIB days (2 days retreat) bringing together all the members of the SIB across Switzerland. Please make sure you register to this event.<br />
<br />
=='''Special foreigners arriving in Switzerland''' ==<br />
<br />
You will find [http://www.unil.ch/bienvenue/page20660_en.html here] the students' handbook, which contains very useful information.<br />
Other basic information can be found at [http://www.unil.ch/bienvenue/page9044_en.html this page].<br />
<br />
* '''Swiss residence permit'''<br />
<br />
You will have to request it from the office of your town of residence. The request is made by our admin.<br />
<br />
*''' Medical care insurances'''<br />
<br />
It's mandatory to have a health insurance once you arrive in Switzerland. <br />
Have a look at the official [http://www.priminfo.ch/praemien/index.php?sprache=f federal list of insurances] and compare the offers with [http://fr.comparis.ch/krankenkassen/default.aspx?tid=googleAd-KK_fr&WT.srch=1&extclient=comparis comparis.ch].<br />
Some additional information about the different health systems can be found in [http://www.frc.ch/pages.php?id=1140 this article] from la fédération romande des consommateurs.<br />
<br />
==''' General info ''' ==<br />
<br />
* '''Coffees'''<br />
<br />
Coffee is free. Hurray!<br />
<br />
* '''Supplies'''<br />
<br />
All kinds of pens, notebooks,Post-it, stamps, envelopes, ... can be provided by our admin).<br />
<br />
* '''Google calendar'''<br />
<br />
We share a google calendar where all kind of infos are written (vacations, conferences, lab meeting...). To get the access, ask any member of the CBG.<br />
<br />
* '''DBC meetings/CBG meetings/Journal clubs'''<br />
<br />
We have a number of regular meetings that include the DGM progress report, CBG group meetings and the [[Journal Club]]. Time and places are indicated on the google calendars.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Welcome_info&diff=6702Welcome info2023-05-30T11:13:02Z<p>Sven: </p>
<hr />
<div><br />
This page contains some information you will need to start working at the CBG. Please update it if necessary. In addition, you can read the<br />
'''[[Guidelines for a successful stay at the CBG]]'''<br />
<br />
== '''First steps''' ==<br />
<br />
Once you arrive at the CBG/DBC, here is the list of things you should do first.<br />
<br />
<br />
* '''Building keys and hardware lockers'''<br />
<br />
Ask Stéphanie Scuderi to get your keys to access the building and your office. Once you have setup your desktop, ask for some cables to lock your hardware.<br />
<br />
<br />
* '''UNIL account'''<br />
You will find here some useful informations concerning [http://www.unil.ch/ci/page88358.html your personal access to the UNIL] and [http://www.unil.ch/ci/page34.html the services] provided.<br />
<br />
Open the [https://www.unil.ch/ci/files/live/sites/ci/files/shared/acces/Creation-Id-V1.12-formulaire.pdf pdf], fill it out, get it signed by your supervisor and send it to the Centre Informatique.<br />
<br />
You will receive by post your username and password to will allow you to use all the services and resources at UNIL.<br />
<br />
* '''Wiki Access'''<br />
Ask [[User:Michael|Michael]] to provide you with a login for the wiki. You should then add yourself to the "people" [[People | page]], and update your personal webpage User:Username, where username is your username.<br />
<br />
* ''' Maling list access'''<br />
Ask [[User:Daniel| Daniel]] to put you on the CBG mailing list and ask Michelle N'Cho to add you to the DBC mailing list.<br />
<br />
* '''Calendar Access'''<br />
Ask any member of the lab to give you the credentials to access the our shared google calendars, one for the CBG and one for the DGM. These calendars allow you to be updated on upcoming events and meetings, as well as when people are away from the lab. <br />
<br />
* '''Campus card (student card)'''<br />
<br />
Fill in the following form [http://www.unil.ch/webdav/site/campuscard/shared/pdf/CC_formulaire_etudiant_nov08.pdf Student Campus Card form] and sent it back to the service des immatriculations at UNIL.<br />
<br />
Please see also section "PhD student and Doctoral Programme" to know how to enrol at UNIL.<br />
<br />
== ''' IT access ''' ==<br />
<br />
*''' Printer''' <br />
<br />
Ask Michelle.<br />
<br />
* '''Access to the servers'''<br />
<br />
Ask [[User:Michael|Michael]] to create you an account on the calculation servers we have here. <br />
We also have a server hosted by vital-it. <br />
<br />
* '''Softwares available'''<br />
<br />
To see what sort of softwares are available at UNIL:<br />
<br />
**For PCs: [http://www.vista4beginners.com/Map-Network-Drive Map the following network drive] : \\distripc.unil.ch\soft and connect to it typing ad\username and entering your password (the one from your email account).<br />
<br />
http://www.unil.ch/ci/page33723.html<br />
<br />
**For Macs: Connect to the following server (cmd + k on the Finder window) afp://bigmac.unil.ch using your email username and password.<br />
<br />
* Informatique Service'''<br />
[http://wwwfbm.unil.ch/si/en/ The information technology service of the FBM (SI)] helps to all informatics and computer related problems at the FBM. It's a plate-forme between the departments on the Bugnon-Epalinges site.<br />
<br />
* '''Services au personnel''' <br />
<br />
http://www.unil.ch/ci/page34.html<br />
<br />
* '''UNIL Internal Portal'''<br />
<br />
http://www.unil.ch/interne<br />
<br />
== ''' PhD Student and Doctoral Programme''' ==<br />
<br />
* PhD students have to be registered at UNIL from the beginning until the end of their doctoral studies, meaning until the registration of their thesis at the Bibliothèque Cantonale et Universitaire. All the instructions for the online registration are available [http://www.unil.ch/immat/page83462_en.html here]. Please also note that there are two deadlines for enrollment at the University: Autumn semester (before 31 July) and Spring semester (before 31 January)<br />
<br />
*As a PhD student starting at the CBG, you will then have to complete the PhD Doctoral Programme in Life Science which is about collecting 12 ECTS credits during your PhD by attending courses, conferences, tutorials... Details can be found [http://www.unil.ch/edfbm/page79197.html here].<br />
<br />
* The SIB also provides all along the year [http://www.sib.swiss/training training courses] and once a year a summer shcool is organized by the [http://www.sib.swiss/training/for-sib-phd-students SIB PhD training network] . PhD students can register to those activities and gather credits for the UNIL Doctoral Programme.<br />
<br />
*More info about research and career can be found [https://www.unil.ch/researcher/en/home.html here]<br />
<br />
== ''' SIB affiliation ''' ==<br />
<br />
* As a member of the CBG, you are member of the [http://www.isb-sib.ch/ Swiss Institute of Bioinformatics] . You will have to fill in [http://www2.unil.ch/cbg/images/e/e6/New_arrivals_departures_form.pdf the registration form] according to the instructions. Please note that new arrival or new departure has to be announced by you at the SIB administration.<br />
*Usually at the end of January of each year, the SIB organizes the SIB days (2 days retreat) bringing together all the members of the SIB across Switzerland. Please make sure you register to this event.<br />
<br />
=='''Special foreigners arriving in Switzerland''' ==<br />
<br />
You will find [http://www.unil.ch/bienvenue/page20660_en.html here] the students' handbook, which contains very useful information.<br />
Other basic information can be found at [http://www.unil.ch/bienvenue/page9044_en.html this page].<br />
<br />
* '''Swiss residence permit'''<br />
<br />
You will have to request it from the office of your town of residence. The request is made by our admin.<br />
<br />
*''' Medical care insurances'''<br />
<br />
It's mandatory to have a health insurance once you arrive in Switzerland. <br />
Have a look at the official [http://www.priminfo.ch/praemien/index.php?sprache=f federal list of insurances] and compare the offers with [http://fr.comparis.ch/krankenkassen/default.aspx?tid=googleAd-KK_fr&WT.srch=1&extclient=comparis comparis.ch].<br />
Some additional information about the different health systems can be found in [http://www.frc.ch/pages.php?id=1140 this article] from la fédération romande des consommateurs.<br />
<br />
==''' General info ''' ==<br />
<br />
* '''Coffees'''<br />
<br />
Coffee is free. Hurray!<br />
<br />
* '''Supplies'''<br />
<br />
All kinds of pens, notebooks,Post-it, stamps, envelopes, ... can be provided by our admin).<br />
<br />
* '''Google calendar'''<br />
<br />
We share a google calendar where all kind of infos are written (vacations, conferences, lab meeting...). To get the access, ask any member of the CBG.<br />
<br />
* '''DBC meetings/CBG meetings/Journal clubs'''<br />
<br />
We have a number of regular meetings that include the DGM progress report, CBG group meetings and the [[Journal Club]]. Time and places are indicated on the google calendars.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Welcome_info&diff=6701Welcome info2023-05-30T11:11:36Z<p>Sven: </p>
<hr />
<div><br />
This page contains some information you will need to start working at the CBG. Please update it if necessary. In addition, you can read the<br />
'''[[Guidelines for a successful stay at the CBG]]'''<br />
<br />
== '''First steps''' ==<br />
<br />
Once you arrive at the CBG/DBC, here is the list of things you should do first.<br />
<br />
<br />
* '''Building keys and hardware lockers'''<br />
<br />
Ask Stéphanie Scuderi to get your keys to access the building and your office. Once you have setup your desktop, ask for some cables to lock your hardware.<br />
<br />
<br />
* '''UNIL account'''<br />
You will find here some useful informations concerning [http://www.unil.ch/ci/page88358.html your personal access to the UNIL] and [http://www.unil.ch/ci/page34.html the services] provided.<br />
<br />
Open the [https://www.unil.ch/ci/files/live/sites/ci/files/shared/acces/Creation-Id-V1.12-formulaire.pdf pdf], fill it out, get it signed by your supervisor and send it to the Centre Informatique.<br />
<br />
You will receive by post your username and password to will allow you to use all the services and resources at UNIL.<br />
<br />
* '''Wiki Access'''<br />
Ask [[User:Michael|Michael]] to provide you with a login for the wiki. You should then add yourself to the "people" [[People | page]], and update your personal webpage User:Username, where username is your username.<br />
<br />
* ''' Maling list access'''<br />
Ask [[User:Daniel| Daniel]] to put you on the CBG mailing list and ask Michelle N'Cho to add you to the DBC mailing list.<br />
<br />
* '''Calendar Access'''<br />
Ask any member of the lab to give you the credentials to access the our shared google calendars, one for the CBG and one for the DGM. These calendars allow you to be updated on upcoming events and meetings, as well as when people are away from the lab. <br />
<br />
* '''Campus card (student card)'''<br />
<br />
Fill in the following form [http://www.unil.ch/webdav/site/campuscard/shared/pdf/CC_formulaire_etudiant_nov08.pdf Student Campus Card form] and sent it back to the service des immatriculations at UNIL.<br />
<br />
Please see also section "PhD student and Doctoral Programme" to know how to enrol at UNIL.<br />
<br />
== ''' IT access ''' ==<br />
<br />
*''' Printer''' <br />
<br />
Ask Michelle.<br />
<br />
* '''Access to the servers'''<br />
<br />
Ask [[User:Michael|Michael]] to create you an account on the calculation servers we have here. <br />
We also have a server hosted by vital-it. <br />
<br />
* '''Softwares available'''<br />
<br />
To see what sort of softwares are available at UNIL:<br />
<br />
**For PCs: [http://www.vista4beginners.com/Map-Network-Drive Map the following network drive] : \\distripc.unil.ch\soft and connect to it typing ad\username and entering your password (the one from your email account).<br />
<br />
http://www.unil.ch/ci/page33723.html<br />
<br />
**For Macs: Connect to the following server (cmd + k on the Finder window) afp://bigmac.unil.ch using your email username and password.<br />
<br />
* Informatique Service'''<br />
[http://wwwfbm.unil.ch/si/en/ The information technology service of the FBM (SI)] helps to all informatics and computer related problems at the FBM. It's a plate-forme between the departments on the Bugnon-Epalinges site.<br />
<br />
* '''Services au personnel''' <br />
<br />
http://www.unil.ch/ci/page34.html<br />
<br />
* '''UNIL Internal Portal'''<br />
<br />
http://www.unil.ch/interne<br />
<br />
== ''' PhD Student and Doctoral Programme''' ==<br />
<br />
* PhD students have to be registered at UNIL from the beginning until the end of their doctoral studies, meaning until the registration of their thesis at the Bibliothèque Cantonale et Universitaire. All the instructions for the online registration are available [http://www.unil.ch/immat/page83462_en.html here]. Please also note that there are two deadlines for enrollment at the University: Autumn semester (before 31 July) and Spring semester (before 31 January)<br />
<br />
*As a PhD student starting at the CBG, you will then have to complete the PhD Doctoral Programme in Life Science which is about collecting 12 ECTS credits during your PhD by attending courses, conferences, tutorials... Details can be found [http://www.unil.ch/edfbm/page79197.html here].<br />
<br />
* The SIB also provides all along the year [http://www.sib.swiss/training training courses] and once a year a summer shcool is organized by the [http://www.sib.swiss/training/for-sib-phd-students SIB PhD training network] . PhD students can register to those activities and gather credits for the UNIL Doctoral Programme.<br />
<br />
*More info about research and career can be found [https://www.unil.ch/researcher/en/home.html here]<br />
<br />
== ''' SIB affiliation ''' ==<br />
<br />
* As a member of the CBG, you are member of the [http://www.isb-sib.ch/ Swiss Institute of Bioinformatics] . You will have to fill in [http://www2.unil.ch/cbg/images/e/e6/New_arrivals_departures_form.pdf the registration form] according to the instructions. Please note that new arrival or new departure has to be announced by you at the SIB administration.<br />
*Usually at the end of January of each year, the SIB organizes the SIB days (2 days retreat) bringing together all the members of the SIB across Switzerland. Please make sure you register to this event.<br />
<br />
=='''Special foreigners arriving in Switzerland''' ==<br />
<br />
You will find [http://www.unil.ch/bienvenue/page20660_en.html here] the students' handbook, which contains very useful information.<br />
Other basic information can be found at [http://www.unil.ch/bienvenue/page9044_en.html this page].<br />
<br />
* '''Swiss residence permit'''<br />
<br />
You will have to request it from the office of your town of residence. The request is made by our admin.<br />
<br />
*''' Medical care insurances'''<br />
<br />
It's mandatory to have a health insurance once you arrive in Switzerland. <br />
Have a look at the official [http://www.priminfo.ch/praemien/index.php?sprache=f federal list of insurances] and compare the offers with [http://fr.comparis.ch/krankenkassen/default.aspx?tid=googleAd-KK_fr&WT.srch=1&extclient=comparis comparis.ch].<br />
Some additional information about the different health systems can be found in [http://www.frc.ch/pages.php?id=1140 this article] from la fédération romande des consommateurs.<br />
<br />
==''' General info ''' ==<br />
<br />
* '''Coffees'''<br />
<br />
Coffee is free. Hurray!<br />
<br />
* '''Supplies'''<br />
<br />
All kinds of pens, notebooks,Post-it, stamps, envelopes, ... can be provided by our admin).<br />
<br />
* '''Google calendar'''<br />
<br />
We share a google calendar where all kind of infos are written (vacations, conferences, lab meeting...). To get the access, ask any member of the CBG.<br />
<br />
* '''DBC meetings/CBG meetings/Journal clubs'''<br />
<br />
We have a number of regular meetings that include the DGM progress report, CBG group meetings and the [[Journal Club]]. Time and places are indicated on the google calendars.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Welcome_info&diff=6700Welcome info2023-05-30T11:07:40Z<p>Sven: </p>
<hr />
<div><br />
This page contains some information you will need to start working at the CBG. Please update it if necessary. In addition, you can read the<br />
'''[[Guidelines for a successful stay at the CBG]]'''<br />
<br />
== '''First steps''' ==<br />
<br />
Once you arrive at the CBG/DBC, here is the list of things you should do first.<br />
<br />
<br />
* '''Building keys and hardware lockers'''<br />
<br />
Ask Stéphanie Scuderi to get your keys to access the building and your office. Once you have setup your desktop, ask for some cables to lock your hardware.<br />
<br />
<br />
* '''UNIL account'''<br />
You will find here some useful informations concerning [http://www.unil.ch/ci/page88358.html your personal access to the UNIL] and [http://www.unil.ch/ci/page34.html the services] provided.<br />
<br />
Open the [https://www.unil.ch/ci/files/live/sites/ci/files/shared/acces/Creation-Id-V1.12-formulaire.pdf pdf], fill it out, get it signed by your supervisor and send it to the Centre Informatique.<br />
<br />
You will receive by post your username and password to will allow you to use all the services and resources at UNIL.<br />
<br />
* '''Wiki Access'''<br />
Ask [[User:Michael|Michael]] to provide you with a login for the wiki. You should then add yourself to the "people" [[People | page]], and update your personal webpage User:Username, where username is your username.<br />
<br />
* ''' Maling list access'''<br />
Ask [[User:Daniel| Daniel]] to put you on the CBG mailing list and ask Michelle N'Cho to add you to the DBC mailing list.<br />
<br />
* '''Calendar Access'''<br />
Ask any member of the lab to give you the credentials to access the our shared google calendars, one for the CBG and one for the DGM. These calendars allow you to be updated on upcoming events and meetings, as well as when people are away from the lab. <br />
<br />
* '''CHUV card (canteen card)''' <br />
<br />
Get your inscription form from Suzanne. Bring the form with your picture to the 3rd floor (entrance is at the 2nd floor) of Les Allières building (MP20-[[Media:CHUV.png]]).<br />
<br />
* '''Campus card (student card)'''<br />
<br />
Fill in the following form [http://www.unil.ch/webdav/site/campuscard/shared/pdf/CC_formulaire_etudiant_nov08.pdf Student Campus Card form] and sent it back to the service des immatriculations at UNIL.<br />
<br />
Please see also section "PhD student and Doctoral Programme" to know how to enrol at UNIL.<br />
<br />
== ''' IT access ''' ==<br />
<br />
*''' Printer''' <br />
<br />
Connect to OKI MC362 (located in Suzanne's office). Look for the latest drivers on the web: http://www.oki.fr/support/printer-drivers/index.aspx<br />
<br />
IP: 130.223.204.108<br />
<br />
* '''Access to the servers'''<br />
<br />
Ask [[User:Mattia|Mattia]] to create you an account on the calculation servers we have here. <br />
We also have a server hosted by vital-it. <br />
* '''Softwares available'''<br />
<br />
Some softwares are under individual licence for which you will need to fill in a form in Suzanne's office.<br />
<br />
To see what sort of softwares are available at UNIL<br />
<br />
**For PCs: [http://www.vista4beginners.com/Map-Network-Drive Map the following network drive] : \\distripc.unil.ch\soft and connect to it typing ad\username and entering your password (the one from your email account).<br />
<br />
http://www.unil.ch/ci/page33723.html<br />
<br />
**For Macs: Connect to the following server (cmd + k on the Finder window) afp://bigmac.unil.ch using your email username and password.<br />
<br />
* Informatique Service'''<br />
[http://wwwfbm.unil.ch/si/en/ The information technology service of the FBM (SI)] helps to all informatics and computer related problems at the FBM. It's a plate-forme between the departments on the Bugnon-Epalinges site.<br />
<br />
* '''Services au personnel''' <br />
<br />
http://www.unil.ch/ci/page34.html<br />
<br />
* '''UNIL Internal Portal'''<br />
<br />
http://www.unil.ch/interne<br />
<br />
== ''' PhD Student and Doctoral Programme''' ==<br />
<br />
* PhD students have to be registered at UNIL from the beginning until the end of their doctoral studies, meaning until the registration of their thesis at the Bibliothèque Cantonale et Universitaire. All the instructions for the online registration are available [http://www.unil.ch/immat/page83462_en.html here]. Please also note that there are two deadlines for enrollment at the University: Autumn semester (before 31 July) and Spring semester (before 31 January)<br />
<br />
*As a PhD student starting at the CBG, you will then have to complete the PhD Doctoral Programme in Life Science which is about collecting 12 ECTS credits during your PhD by attending courses, conferences, tutorials... Details can be found [http://www.unil.ch/edfbm/page79197.html here].<br />
<br />
* The SIB also provides all along the year [http://www.sib.swiss/training training courses] and once a year a summer shcool is organized by the [http://www.sib.swiss/training/for-sib-phd-students SIB PhD training network] . PhD students can register to those activities and gather credits for the UNIL Doctoral Programme.<br />
<br />
*More info about research and career can be found [https://www.unil.ch/researcher/en/home.html here]<br />
<br />
== ''' SIB affiliation ''' ==<br />
<br />
* As a member of the CBG, you are member of the [http://www.isb-sib.ch/ Swiss Institute of Bioinformatics] . You will have to fill in [http://www2.unil.ch/cbg/images/e/e6/New_arrivals_departures_form.pdf the registration form] according to the instructions. Please note that new arrival or new departure has to be announced by you at the SIB administration.<br />
*Usually at the end of January of each year, the SIB organizes the SIB days (2 days retreat) bringing together all the members of the SIB across Switzerland. Please make sure you register to this event.<br />
<br />
=='''Special foreigners arriving in Switzerland''' ==<br />
<br />
You will find [http://www.unil.ch/bienvenue/page20660_en.html here] the students' handbook, which contains very useful information.<br />
Other basic information can be found at [http://www.unil.ch/bienvenue/page9044_en.html this page].<br />
<br />
* '''Swiss residence permit'''<br />
<br />
You will have to request it from the office of your town of residence. It usually turns out that the request is made by the DGM via Suzanne.<br />
<br />
*''' Medical care insurances'''<br />
<br />
It's mandatory to have a health insurance once you arrive in Switzerland. <br />
Have a look at the official [http://www.priminfo.ch/praemien/index.php?sprache=f federal list of insurances] and compare the offers with [http://fr.comparis.ch/krankenkassen/default.aspx?tid=googleAd-KK_fr&WT.srch=1&extclient=comparis comparis.ch].<br />
Some additional information about the different health systems can be found in [http://www.frc.ch/pages.php?id=1140 this article] from la fédération romande des consommateurs.<br />
<br />
==''' General info ''' ==<br />
<br />
* '''Coffees'''<br />
<br />
You can get Nespresso capsules from Suzanne for CHF 5/box.<br />
<br />
* '''Supplies'''<br />
<br />
All kinds of pens, notebooks,Post-it, stamps, envelopes....can be found in Suzanne's office or at the 3rd floor (room 333).<br />
<br />
* '''Clothes locker'''<br />
<br />
You can get your own locker for clothes. If you are interested, ask Suzane.<br />
<br />
* '''Google calendar'''<br />
<br />
We share a google calendar where all kind of infos are written (vacations, conferences, lab meeting...). To get the access, ask any member of the CBG.<br />
<br />
* '''DBC meetings/CBG meetings/Journal clubs'''<br />
<br />
We have a number of regular meetings that include the DGM progress report, CBG group meetings and the [[Journal Club]]. Time and places are indicated on the google calendars.<br />
<br />
* '''Opportunity to buy a laptop'''<br />
<br />
The UNIL offers 50% of the price of a new laptop (up to 1000 CHF). Ask Sven if interested and then visit the [http://wwwfbm.unil.ch/si/en/ Service Informatique portal] to make your order.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Welcome_info&diff=6699Welcome info2023-05-30T11:05:56Z<p>Sven: </p>
<hr />
<div><br />
This page contains some information you will need to start working at the CBG. Please update it if necessary. In addition, you can read the<br />
'''[[Guidelines for a successful stay at the CBG]]'''<br />
<br />
== '''First steps''' ==<br />
<br />
Once you arrive at the CBG/DBC, here is the list of things you should do first.<br />
<br />
<br />
* '''Building keys and hardware lockers'''<br />
<br />
Ask Stéphanie Scuderi to get your keys to access the building and your office. Once you have setup your desktop, ask for some cables to lock your hardware.<br />
<br />
<br />
* '''UNIL account'''<br />
You will find here some useful informations concerning [http://www.unil.ch/ci/page88358.html your personal access to the UNIL] and [http://www.unil.ch/ci/page34.html the services] provided.<br />
<br />
Open the [https://www.unil.ch/ci/files/live/sites/ci/files/shared/acces/Creation-Id-V1.12-formulaire.pdf pdf], fill it out, get it signed by your supervisor and send it to the Centre Informatique.<br />
<br />
You will receive by post your username and password to will allow you to use all the services and resources at UNIL.<br />
<br />
* '''Wiki Access'''<br />
Ask [[User:Michael|Michael]] to provide you with a login for the wiki. You should then add yourself to the "people" [[People | page]], and update your personal webpage User:Username, where username is your username.<br />
<br />
* ''' Maling list access'''<br />
Ask [[User:Daniel| Daniel]] to put you on the CBG mailing list and email carlo.rivolta@unil.ch and ask him to add you to the DBC mailing list.<br />
<br />
* '''Calendar Access'''<br />
Ask any member of the lab to give you the credentials to access the our shared google calendars, one for the CBG and one for the DGM. These calendars allow you to be updated on upcoming events and meetings, as well as when people are away from the lab. <br />
<br />
* '''CHUV card (canteen card)''' <br />
<br />
Get your inscription form from Suzanne. Bring the form with your picture to the 3rd floor (entrance is at the 2nd floor) of Les Allières building (MP20-[[Media:CHUV.png]]).<br />
<br />
* '''Campus card (student card)'''<br />
<br />
Fill in the following form [http://www.unil.ch/webdav/site/campuscard/shared/pdf/CC_formulaire_etudiant_nov08.pdf Student Campus Card form] and sent it back to the service des immatriculations at UNIL.<br />
<br />
Please see also section "PhD student and Doctoral Programme" to know how to enrol at UNIL.<br />
<br />
== ''' IT access ''' ==<br />
<br />
*''' Printer''' <br />
<br />
Connect to OKI MC362 (located in Suzanne's office). Look for the latest drivers on the web: http://www.oki.fr/support/printer-drivers/index.aspx<br />
<br />
IP: 130.223.204.108<br />
<br />
* '''Access to the servers'''<br />
<br />
Ask [[User:Mattia|Mattia]] to create you an account on the calculation servers we have here. <br />
We also have a server hosted by vital-it. <br />
* '''Softwares available'''<br />
<br />
Some softwares are under individual licence for which you will need to fill in a form in Suzanne's office.<br />
<br />
To see what sort of softwares are available at UNIL<br />
<br />
**For PCs: [http://www.vista4beginners.com/Map-Network-Drive Map the following network drive] : \\distripc.unil.ch\soft and connect to it typing ad\username and entering your password (the one from your email account).<br />
<br />
http://www.unil.ch/ci/page33723.html<br />
<br />
**For Macs: Connect to the following server (cmd + k on the Finder window) afp://bigmac.unil.ch using your email username and password.<br />
<br />
* Informatique Service'''<br />
[http://wwwfbm.unil.ch/si/en/ The information technology service of the FBM (SI)] helps to all informatics and computer related problems at the FBM. It's a plate-forme between the departments on the Bugnon-Epalinges site.<br />
<br />
* '''Services au personnel''' <br />
<br />
http://www.unil.ch/ci/page34.html<br />
<br />
* '''UNIL Internal Portal'''<br />
<br />
http://www.unil.ch/interne<br />
<br />
== ''' PhD Student and Doctoral Programme''' ==<br />
<br />
* PhD students have to be registered at UNIL from the beginning until the end of their doctoral studies, meaning until the registration of their thesis at the Bibliothèque Cantonale et Universitaire. All the instructions for the online registration are available [http://www.unil.ch/immat/page83462_en.html here]. Please also note that there are two deadlines for enrollment at the University: Autumn semester (before 31 July) and Spring semester (before 31 January)<br />
<br />
*As a PhD student starting at the CBG, you will then have to complete the PhD Doctoral Programme in Life Science which is about collecting 12 ECTS credits during your PhD by attending courses, conferences, tutorials... Details can be found [http://www.unil.ch/edfbm/page79197.html here].<br />
<br />
* The SIB also provides all along the year [http://www.sib.swiss/training training courses] and once a year a summer shcool is organized by the [http://www.sib.swiss/training/for-sib-phd-students SIB PhD training network] . PhD students can register to those activities and gather credits for the UNIL Doctoral Programme.<br />
<br />
*More info about research and career can be found [https://www.unil.ch/researcher/en/home.html here]<br />
<br />
== ''' SIB affiliation ''' ==<br />
<br />
* As a member of the CBG, you are member of the [http://www.isb-sib.ch/ Swiss Institute of Bioinformatics] . You will have to fill in [http://www2.unil.ch/cbg/images/e/e6/New_arrivals_departures_form.pdf the registration form] according to the instructions. Please note that new arrival or new departure has to be announced by you at the SIB administration.<br />
*Usually at the end of January of each year, the SIB organizes the SIB days (2 days retreat) bringing together all the members of the SIB across Switzerland. Please make sure you register to this event.<br />
<br />
=='''Special foreigners arriving in Switzerland''' ==<br />
<br />
You will find [http://www.unil.ch/bienvenue/page20660_en.html here] the students' handbook, which contains very useful information.<br />
Other basic information can be found at [http://www.unil.ch/bienvenue/page9044_en.html this page].<br />
<br />
* '''Swiss residence permit'''<br />
<br />
You will have to request it from the office of your town of residence. It usually turns out that the request is made by the DGM via Suzanne.<br />
<br />
*''' Medical care insurances'''<br />
<br />
It's mandatory to have a health insurance once you arrive in Switzerland. <br />
Have a look at the official [http://www.priminfo.ch/praemien/index.php?sprache=f federal list of insurances] and compare the offers with [http://fr.comparis.ch/krankenkassen/default.aspx?tid=googleAd-KK_fr&WT.srch=1&extclient=comparis comparis.ch].<br />
Some additional information about the different health systems can be found in [http://www.frc.ch/pages.php?id=1140 this article] from la fédération romande des consommateurs.<br />
<br />
==''' General info ''' ==<br />
<br />
* '''Coffees'''<br />
<br />
You can get Nespresso capsules from Suzanne for CHF 5/box.<br />
<br />
* '''Supplies'''<br />
<br />
All kinds of pens, notebooks,Post-it, stamps, envelopes....can be found in Suzanne's office or at the 3rd floor (room 333).<br />
<br />
* '''Clothes locker'''<br />
<br />
You can get your own locker for clothes. If you are interested, ask Suzane.<br />
<br />
* '''Google calendar'''<br />
<br />
We share a google calendar where all kind of infos are written (vacations, conferences, lab meeting...). To get the access, ask any member of the CBG.<br />
<br />
* '''DBC meetings/CBG meetings/Journal clubs'''<br />
<br />
We have a number of regular meetings that include the DGM progress report, CBG group meetings and the [[Journal Club]]. Time and places are indicated on the google calendars.<br />
<br />
* '''Opportunity to buy a laptop'''<br />
<br />
The UNIL offers 50% of the price of a new laptop (up to 1000 CHF). Ask Sven if interested and then visit the [http://wwwfbm.unil.ch/si/en/ Service Informatique portal] to make your order.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Welcome_info&diff=6698Welcome info2023-05-30T11:05:29Z<p>Sven: </p>
<hr />
<div><br />
This page contains some information you will need to start working at the CBG. Please update it if necessary. In addition, you can read the<br />
'''[[Guidelines for a successful stay at the CBG]]'''<br />
<br />
== '''First steps''' ==<br />
<br />
Once you arrive at the CBG/DBC, here is the list of things you should do first.<br />
<br />
<br />
* '''Building keys and hardware lockers'''<br />
<br />
Ask Stéphanie Scuderi to get your keys to access the building and your office. Once you have setup your desktop, ask for some cables to lock your hardware.<br />
<br />
<br />
* '''UNIL account'''<br />
You will find here some useful informations concerning [http://www.unil.ch/ci/page88358.html your personal access to the UNIL] and [http://www.unil.ch/ci/page34.html the services] provided.<br />
<br />
Open the [https://www.unil.ch/ci/files/live/sites/ci/files/shared/acces/Creation-Id-V1.12-formulaire.pdf pdf], fill it out, get it signed by your supervisor and send it to the Centre Informatique.<br />
<br />
You will receive by post your username and password to will allow you to use all the services and resources at UNIL.<br />
<br />
* '''Wiki Access'''<br />
Ask [[User:Micha|Micha]] to provide you with a login for the wiki. You should then add yourself to the "people" [[People | page]], and update your personal webpage User:Username, where username is your username.<br />
<br />
* ''' Maling list access'''<br />
Ask [[User:Daniel| Daniel]] to put you on the CBG mailing list and email carlo.rivolta@unil.ch and ask him to add you to the DBC mailing list.<br />
<br />
* '''Calendar Access'''<br />
Ask any member of the lab to give you the credentials to access the our shared google calendars, one for the CBG and one for the DGM. These calendars allow you to be updated on upcoming events and meetings, as well as when people are away from the lab. <br />
<br />
* '''CHUV card (canteen card)''' <br />
<br />
Get your inscription form from Suzanne. Bring the form with your picture to the 3rd floor (entrance is at the 2nd floor) of Les Allières building (MP20-[[Media:CHUV.png]]).<br />
<br />
* '''Campus card (student card)'''<br />
<br />
Fill in the following form [http://www.unil.ch/webdav/site/campuscard/shared/pdf/CC_formulaire_etudiant_nov08.pdf Student Campus Card form] and sent it back to the service des immatriculations at UNIL.<br />
<br />
Please see also section "PhD student and Doctoral Programme" to know how to enrol at UNIL.<br />
<br />
== ''' IT access ''' ==<br />
<br />
*''' Printer''' <br />
<br />
Connect to OKI MC362 (located in Suzanne's office). Look for the latest drivers on the web: http://www.oki.fr/support/printer-drivers/index.aspx<br />
<br />
IP: 130.223.204.108<br />
<br />
* '''Access to the servers'''<br />
<br />
Ask [[User:Mattia|Mattia]] to create you an account on the calculation servers we have here. <br />
We also have a server hosted by vital-it. <br />
* '''Softwares available'''<br />
<br />
Some softwares are under individual licence for which you will need to fill in a form in Suzanne's office.<br />
<br />
To see what sort of softwares are available at UNIL<br />
<br />
**For PCs: [http://www.vista4beginners.com/Map-Network-Drive Map the following network drive] : \\distripc.unil.ch\soft and connect to it typing ad\username and entering your password (the one from your email account).<br />
<br />
http://www.unil.ch/ci/page33723.html<br />
<br />
**For Macs: Connect to the following server (cmd + k on the Finder window) afp://bigmac.unil.ch using your email username and password.<br />
<br />
* Informatique Service'''<br />
[http://wwwfbm.unil.ch/si/en/ The information technology service of the FBM (SI)] helps to all informatics and computer related problems at the FBM. It's a plate-forme between the departments on the Bugnon-Epalinges site.<br />
<br />
* '''Services au personnel''' <br />
<br />
http://www.unil.ch/ci/page34.html<br />
<br />
* '''UNIL Internal Portal'''<br />
<br />
http://www.unil.ch/interne<br />
<br />
== ''' PhD Student and Doctoral Programme''' ==<br />
<br />
* PhD students have to be registered at UNIL from the beginning until the end of their doctoral studies, meaning until the registration of their thesis at the Bibliothèque Cantonale et Universitaire. All the instructions for the online registration are available [http://www.unil.ch/immat/page83462_en.html here]. Please also note that there are two deadlines for enrollment at the University: Autumn semester (before 31 July) and Spring semester (before 31 January)<br />
<br />
*As a PhD student starting at the CBG, you will then have to complete the PhD Doctoral Programme in Life Science which is about collecting 12 ECTS credits during your PhD by attending courses, conferences, tutorials... Details can be found [http://www.unil.ch/edfbm/page79197.html here].<br />
<br />
* The SIB also provides all along the year [http://www.sib.swiss/training training courses] and once a year a summer shcool is organized by the [http://www.sib.swiss/training/for-sib-phd-students SIB PhD training network] . PhD students can register to those activities and gather credits for the UNIL Doctoral Programme.<br />
<br />
*More info about research and career can be found [https://www.unil.ch/researcher/en/home.html here]<br />
<br />
== ''' SIB affiliation ''' ==<br />
<br />
* As a member of the CBG, you are member of the [http://www.isb-sib.ch/ Swiss Institute of Bioinformatics] . You will have to fill in [http://www2.unil.ch/cbg/images/e/e6/New_arrivals_departures_form.pdf the registration form] according to the instructions. Please note that new arrival or new departure has to be announced by you at the SIB administration.<br />
*Usually at the end of January of each year, the SIB organizes the SIB days (2 days retreat) bringing together all the members of the SIB across Switzerland. Please make sure you register to this event.<br />
<br />
=='''Special foreigners arriving in Switzerland''' ==<br />
<br />
You will find [http://www.unil.ch/bienvenue/page20660_en.html here] the students' handbook, which contains very useful information.<br />
Other basic information can be found at [http://www.unil.ch/bienvenue/page9044_en.html this page].<br />
<br />
* '''Swiss residence permit'''<br />
<br />
You will have to request it from the office of your town of residence. It usually turns out that the request is made by the DGM via Suzanne.<br />
<br />
*''' Medical care insurances'''<br />
<br />
It's mandatory to have a health insurance once you arrive in Switzerland. <br />
Have a look at the official [http://www.priminfo.ch/praemien/index.php?sprache=f federal list of insurances] and compare the offers with [http://fr.comparis.ch/krankenkassen/default.aspx?tid=googleAd-KK_fr&WT.srch=1&extclient=comparis comparis.ch].<br />
Some additional information about the different health systems can be found in [http://www.frc.ch/pages.php?id=1140 this article] from la fédération romande des consommateurs.<br />
<br />
==''' General info ''' ==<br />
<br />
* '''Coffees'''<br />
<br />
You can get Nespresso capsules from Suzanne for CHF 5/box.<br />
<br />
* '''Supplies'''<br />
<br />
All kinds of pens, notebooks,Post-it, stamps, envelopes....can be found in Suzanne's office or at the 3rd floor (room 333).<br />
<br />
* '''Clothes locker'''<br />
<br />
You can get your own locker for clothes. If you are interested, ask Suzane.<br />
<br />
* '''Google calendar'''<br />
<br />
We share a google calendar where all kind of infos are written (vacations, conferences, lab meeting...). To get the access, ask any member of the CBG.<br />
<br />
* '''DBC meetings/CBG meetings/Journal clubs'''<br />
<br />
We have a number of regular meetings that include the DGM progress report, CBG group meetings and the [[Journal Club]]. Time and places are indicated on the google calendars.<br />
<br />
* '''Opportunity to buy a laptop'''<br />
<br />
The UNIL offers 50% of the price of a new laptop (up to 1000 CHF). Ask Sven if interested and then visit the [http://wwwfbm.unil.ch/si/en/ Service Informatique portal] to make your order.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Dates_and_Deadlines_2023&diff=6545Dates and Deadlines 20232023-05-22T14:02:06Z<p>Sven: </p>
<hr />
<div>* '''First ''kick-off'' meeting''': Friday, 3. March 2023 at 9:00-12:00 (POL/202, 204.2)<br />
** The concept of the course will be explained (~15 min)<br />
** The projects will be briefly presented by the respective supervisors (~15 min for each supervisor)<br />
** The course wiki will be explained (~15 min)<br />
<br />
* Students need <br />
** to '''confirm their participation''' in this course by: Monday, 6. March 2023 (midnight),<br />
** to '''form study groups''' of 3-4 students and <br />
** to announce by e-mail the '''three projects they are most interested in working on'''<br />
<br />
* Projects will be assigned no later than: Thursday, 9. March 2023<br />
<br />
* The first session with the supervisors will arranged per e-mail<br />
<br />
* ''free working & weekly meetings with supervisors'': until the first feedback meeting<br />
<br />
* '''[[Open office for feedback 2023]]''': Friday 24 March 2023 at 9:00-12:00 (GEN 2025.1)<br />
* Students are invited to see the course coordinator to:<br />
** Report briefly what their project is about and the goals they want to achieve<br />
** Discuss how they want to achieve these goals and what analysis tools they will use<br />
** Highlight any issues or worries about their project that could interfere with their success<br />
<br />
* '''[[Intermediate report meeting 2023]]''': Friday 28 April 2023 at 9:00-12:00 (GEN 2024)<br />
* Students will present their projects highlighting<br />
** reminder of the background of the project<br />
** preliminary results <br />
** the goals they already achieved<br />
<br />
* ''free working & weekly meetings with supervisors'': until end of May 2023<br />
<br />
* '''[[Final report meeting 2023]]''': Friday 26. May 2023 at 9:00-12:00 (GEN 2024)<br />
** Each study group presents their results (Presentations should take 25-30 minutes, including about 5' for questions, and are the basis for the student evaluation)<br />
** Feedback on the course in general<br />
<br />
(Meetings will be arranged freely between students and supervisors.)<br />
<br />
* back to [[UNIL BSc course: Solving Biological Problems that require Math 2022]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=Publications&diff=6544Publications2023-05-15T11:47:08Z<p>Sven: </p>
<hr />
<div>[[Category:Homepage]]<br />
<br />
__NOTOC__<br />
<br />
== 2023 ==<br />
<pubmed><br />
37137228 37131961 36864135<br />
</pubmed><br />
<br />
== 2022 ==<br />
<pubmed><br />
34897509 35459101 36156592 35697829 35228297<br />
</pubmed><br />
<br />
== 2021 ==<br />
<pubmed><br />
34059833 34349265 34520206 34699229 34475573 34900130 32372009<br />
</pubmed><br />
<br />
== 2020 ==<br />
<pubmed><br />
33046691 32271874 32372009<br />
</pubmed><br />
<br />
== 2019 ==<br />
<pubmed> <br />
30643258 30535405 31318216 31578528 31471613 31263163 31152163 30851093 30788345 31048460 30778226<br />
</pubmed><br />
<br />
== 2018 ==<br />
<pubmed><br />
30388399 30275313 30038396 29912962 29491460 29093028 29273807<br />
</pubmed><br />
<br />
== 2017 ==<br />
<pubmed><br />
28118358 28292428 28249171 28272467 28436984 28512139 28821713 29194434 28832619 28642257 28448500 28443625 28436984 28360221 28146470<br />
</pubmed><br />
<br />
== 2016 ==<br />
<pubmed><br />
26631737 26950747 26808494 26751788 27280446 27604219 27798627 27680694 27412012 27225129 27089181 26959991 27915449 27799538 <br />
</pubmed><br />
<br />
== 2015 ==<br />
<pubmed><br />
26414677 25903154 25899854 25493955 26101320 26131930 26150232 26352407 26426971<br />
</pubmed><br />
<br />
= 2014 =<br />
<pubmed><br />
25261457 25078964 24733935 24581740 24586186 25231870 24954895 24578125 24357391 <br />
</pubmed><br />
<br />
= 2013 =<br />
<pubmed><br />
24316795 24068962 24076239 24029420 23966204 23951114 23307926 23637639 23459469 23558354 23307926<br />
</pubmed><br />
<br />
= 2012 =<br />
<pubmed><br />
23152332 23222517 22859963 22781128 22702538 22492992 22479191 22458817 22415877 22374392 22337502 22094361 23022100 21502950 23285067 23062006 23122585 22238593<br />
</pubmed><br />
<br />
= 2011 =<br />
<pubmed><br />
22205949 22184326 22028824 22180014 22139419 22132133 22095909 22069379 22039350 21909115 21909110 22028671 22012392 21814489 21980298 21907016 21881559 21511889 21465548 21355061 21304579 21665994 20543033 22169038 21511889<br />
</pubmed><br />
Hersch M, Billard A, Bergmann S. ''Iterative Estimation of Rigid Body Transformations - Application to robust object tracking and Iterative Closest Point.'' Journal of Mathematical Imaging and Vision. 2011 [[Media:hersch2012iterative.pdf| pdf]] [[ICP software]]<br />
<br />
= 2010 =<br />
<pubmed><br />
21102462 20940178 20935629 20935630 <br />
20881960 20711174 20671149 20661308 <br />
20212523 20543033 20371495 20060832 <br />
20375113 20081857 20081858 20169148<br />
20520806 20430392<br />
</pubmed><br />
<br />
= 2009 =<br />
<pubmed><br />
19672458 19542082 19503597 19139842 <br />
19430483 19079261 19060907<br />
</pubmed><br />
<br />
= 2008 =<br />
<pubmed><br />
18262040 18391952 18454148 18518969<br />
18758442 18940312 18464786 18191212<br />
</pubmed><br />
<br />
= 2007 = <br />
<pubmed><br />
17700364 17298180<br />
</pubmed><br />
<br />
= 2006 and older= <br />
<pubmed><br />
16869982 16628014<br />
15720560 16188942 16081737 16470937<br />
15606968 15044247 14737187 12134151 12689096<br />
</pubmed></div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6531UNIL BSc course: Bioinformatics for Genomics 20232023-04-26T20:03:37Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Ilaria|Ilaria]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Ilaria, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Ilaria, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://colab.research.google.com/drive/1GsazMsMxtEHxWYYMkGXqyb47RJTDsPeR?usp=sharing Tutorial] (Lead: Anneke, Support: Daniel, Ilaria, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://colab.research.google.com/drive/1FDlKl1iuNQYb4wc11Lgdj1s98SzfBDOb?usp=sharing Tutorial] (Lead: Daniel, Support: Sofia, Ilaria, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 [https://docs.google.com/presentation/d/1LpSUx5nQaQCWQXqzWdNfarFA1ha6JMyeC-q5Nf_RfPQ/edit?usp=sharing Lecture] (Sven)<br />
*** 16:00-17:30 [https://colab.research.google.com/drive/1V6iKh0zLhe7Ofxx5aN40MYzNsJ4O3pJk?usp=sharing Tutorial] (Lead: Sofia, Support: Anneke, Ilaria, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6530UNIL BSc course: Bioinformatics for Genomics 20232023-04-25T15:29:06Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Ilaria|Ilaria]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Ilaria, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Ilaria, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://colab.research.google.com/drive/1GsazMsMxtEHxWYYMkGXqyb47RJTDsPeR?usp=sharing Tutorial] (Lead: Anneke, Support: Daniel, Ilaria, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://colab.research.google.com/drive/1FDlKl1iuNQYb4wc11Lgdj1s98SzfBDOb?usp=sharing Tutorial] (Lead: Daniel, Support: Sofia, Ilaria, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 [https://docs.google.com/presentation/d/1LpSUx5nQaQCWQXqzWdNfarFA1ha6JMyeC-q5Nf_RfPQ/edit?usp=sharing Lecture] (Sven)<br />
*** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Ilaria, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6529UNIL BSc course: Bioinformatics for Genomics 20232023-04-25T15:24:30Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Ilaria|Ilaria]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Ilaria, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Ilaria, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://colab.research.google.com/drive/1GsazMsMxtEHxWYYMkGXqyb47RJTDsPeR?usp=sharing Tutorial] (Lead: Anneke, Support: Daniel, Ilaria, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://colab.research.google.com/drive/1FDlKl1iuNQYb4wc11Lgdj1s98SzfBDOb?usp=sharing Tutorial] (Lead: Daniel, Support: Sofia, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 [https://docs.google.com/presentation/d/1LpSUx5nQaQCWQXqzWdNfarFA1ha6JMyeC-q5Nf_RfPQ/edit?usp=sharing Lecture] (Sven)<br />
*** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6528UNIL BSc course: Bioinformatics for Genomics 20232023-04-25T15:22:32Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Ilaria|Ilaria]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Ilaria, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Ilaria, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://colab.research.google.com/drive/1GsazMsMxtEHxWYYMkGXqyb47RJTDsPeR?usp=sharing Tutorial] (Lead: Anneke, Support: Daniel, Ilaria, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://colab.research.google.com/drive/1FDlKl1iuNQYb4wc11Lgdj1s98SzfBDOb?usp=sharing Tutorial] (Lead: Daniel, Support: Sofia, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 Lecture (Sven)<br />
*** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6523UNIL BSc course: Bioinformatics for Genomics 20232023-04-19T07:38:28Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Ilaria|Ilaria]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Ilaria, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Ilaria, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://colab.research.google.com/drive/1GsazMsMxtEHxWYYMkGXqyb47RJTDsPeR?usp=sharing Tutorial] (Lead: Anneke, Support: Daniel, Ilaria, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Daniel, Support: Sofia, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 Lecture (Sven)<br />
*** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6522UNIL BSc course: Bioinformatics for Genomics 20232023-04-19T07:37:48Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Ilaria|Ilaria]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Ilaria, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Ilaria, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://colab.research.google.com/drive/1GsazMsMxtEHxWYYMkGXqyb47RJTDsPeR?usp=sharing Tutorial] (Lead: Anneke, Support: Daniel, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Daniel, Support: Sofia, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 Lecture (Sven)<br />
*** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6521UNIL BSc course: Bioinformatics for Genomics 20232023-04-03T19:50:19Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Ilaria|Ilaria]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Ilaria, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Ilaria, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Anneke, Support: Daniel, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Daniel, Support: Sofia, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 Lecture (Sven)<br />
*** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6520UNIL BSc course: Bioinformatics for Genomics 20232023-04-03T19:49:31Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Anneke, Support: Daniel, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Daniel, Support: Sofia, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 Lecture (Sven)<br />
*** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6516UNIL BSc course: Bioinformatics for Genomics 20232023-03-27T15:04:22Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Michael, Support: Olga, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Anneke, Support: Daniel, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Daniel, Support: Sofia, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 Lecture (Sven)<br />
*** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6515UNIL BSc course: Bioinformatics for Genomics 20232023-03-27T15:03:49Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Michael, Support: Olga, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Anneke, Support: Daniel, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Daniel, Support: Sofia, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 Lecture (Sven)<br />
*** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.<br />
<br />
* Lecture presentations:<br />
** TBA<br />
<br />
* Exercise material:<br />
** TBA</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6514UNIL BSc course: Bioinformatics for Genomics 20232023-03-27T15:00:21Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:305-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Michael, Support: Olga, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Anneke, Support: Daniel, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Daniel, Support: Sofia, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 Lecture (Sven)<br />
*** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.<br />
<br />
* Lecture presentations:<br />
** TBA<br />
<br />
* Exercise material:<br />
** TBA</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6513UNIL BSc course: Bioinformatics for Genomics 20232023-03-27T14:35:44Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:305-12:00 Tutorial (Lead: Olga, Support: Michael, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Michael, Support: Olga, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Anneke, Support: Daniel, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Daniel, Support: Sofia, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 Lecture (Sven)<br />
*** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.<br />
<br />
* Lecture presentations:<br />
** TBA<br />
<br />
* Exercise material:<br />
** TBA</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6512UNIL BSc course: Bioinformatics for Genomics 20232023-03-21T19:11:36Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:305-12:00 Tutorial (Lead: Olga, Support: Michael, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Michael, Support: Olga, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Anneke, Support: Daniel, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 Lecture (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Daniel, Support: Sofia, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 Lecture (Sven)<br />
*** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.<br />
<br />
* Lecture presentations:<br />
** TBA<br />
<br />
* Exercise material:<br />
** TBA</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6511UNIL BSc course: Bioinformatics for Genomics 20232023-03-21T19:07:31Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven)<br />
*** 10:305-12:00 Tutorial (Lead: Olga, Support: Michael, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:30-10:00 Lecture (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Michael, Support: Olga, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:30-10:00 Lecture (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Anneke, Support: Daniel, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:30-10:00 Lecture (Sven)<br />
*** 10:30-12:00 Tutorial (Lead: Daniel, Support: Sofia, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:00-15:30 Lecture (Sven)<br />
*** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.<br />
<br />
* Lecture presentations:<br />
** TBA<br />
<br />
* Exercise material:<br />
** TBA</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2023&diff=6510UNIL BSc course: Bioinformatics for Genomics 20232023-03-21T18:53:55Z<p>Sven: </p>
<hr />
<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
<br />
* Course aims:<br />
** Get to know some key bioinformatics methods necessary for genomic analysis<br />
** Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses) <br />
** Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results<br />
<br />
* Prerequisites:<br />
** Notions of genomics (gene, genome, transcriptome)<br />
** Basic statistics (what is a test, a p-value)<br />
** Basic literacy in R and/or Python.<br />
<br />
* Teacher: [[Sven Bergmann]] <br />
<br />
* Assistants<br />
** [[User:Olga|Olga]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Anneke|Anneke]]<br />
** [[User:Daniel|Daniel]]<br />
** [[User:Sofia|Sofia]]<br />
<br />
* Schedule<br />
** 29 March 2023: "Measuring and visualising genome-wide gene expression"<br />
*** 8:15-10:00 Lecture (Sven)<br />
*** 10:15-12:00 Tutorial (Lead: Olga, Support: Michael, Sven)<br />
** 5 April 2023: "Advanced analysis of genome-wide gene expression"<br />
*** 8:15-10:00 Lecture (Sven)<br />
*** 10:15-12:00 Tutorial (Lead: Michael, Support: Olga, Sven)<br />
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"<br />
*** 8:15-10:00 Lecture (Sven)<br />
*** 10:15-12:00 Tutorial (Lead: Anneke, Support: Daniel, Sven)<br />
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"<br />
*** 8:15-10:00 Lecture (Sven)<br />
*** 10:15-12:00 Tutorial (Lead: Daniel, Support: Sofia, Sven)<br />
** 27 April 2023: "Defining and visualising gene networks"<br />
*** 14:15-16:00 Lecture (Sven)<br />
*** 16:15-18:00 Tutorial (Lead: Sofia, Support: Anneke, Sven)<br />
<br />
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.<br />
<br />
* Lecture presentations:<br />
** TBA<br />
<br />
* Exercise material:<br />
** TBA</div>Sven