http://www2.unil.ch/cbg/index.php?title=Special:NewPages&feed=atom&hideredirs=1&limit=50&offset=&namespace=0&username=&tagfilter=CBG - New pages [en]2024-03-28T08:40:05ZFrom CBGMediaWiki 1.31.12http://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Bioinformatics_for_Genomics_2024UNIL BSc course: Bioinformatics for Genomics 20242024-03-19T09:24:56Z<p>Sven: </p>
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<div>This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.<br />
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* 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 />
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* 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 />
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* Teacher: [[Sven Bergmann]] <br />
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* 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 />
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* 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 />
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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=Dates_and_Deadlines_2024Dates and Deadlines 20242024-03-08T10:14:52Z<p>Sven: </p>
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<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 />
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* 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 />
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* Projects will be assigned no later than: Thursday, 14. March 2024<br />
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* The first session with the supervisors will be arranged per e-mail<br />
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* ''free working & weekly meetings with supervisors'': until the first feedback meeting<br />
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* '''[[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 />
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* '''[[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 />
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* ''free working & weekly meetings with supervisors'': until end of May 2024<br />
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* '''[[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 />
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(Meetings will be arranged freely between students and supervisors.)<br />
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* back to [[UNIL BSc course: Solving Biological Problems that require Math 2024]]</div>Svenhttp://www2.unil.ch/cbg/index.php?title=UNIL_BSc_course:_Solving_Biological_Problems_that_require_Math_2024UNIL BSc course: Solving Biological Problems that require Math 20242024-03-08T10:07:50Z<p>Michael: </p>
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<div>* Coordinator: [[Sven Bergmann]]<br />
* [[Concept]]<br />
* [[Useful tools]]<br />
* [[Dates and Deadlines 2024]]<br />
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* 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) [https://docs.google.com/presentation/d/1OVMC5dTSXAHYHlILYNNPzCkz4tKS9Liv/edit?usp=sharing&ouid=102265589893567928624&rtpof=true&sd=true Introduction slides]<br />
** Vascular properties of plant leaves (Ilaria)<br />
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* Supervisors<br />
** [[User:Sofia|Sofia]]<br />
** [[User:Sacha|Sacha]]<br />
** [[User:Leah|Leah]]<br />
** [[User:Michael|Michael]]<br />
** [[User:Ilaria|Ilaria]]<br />
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* [[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>Sven