Difference between revisions of "Notebook"
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| + | == 2016-07-07 == | ||
| + | *dockers: [https://github.com/rocker-org/rocker/wiki/Sharing-files-with-host-machine storing output in host] | ||
| + | *DREAM dockers: setting up minimal python docker | ||
| + | *configuring lab servers to run docker | ||
| + | |||
| + | == 2016-07-06 == | ||
| + | *DREAM dockers, weekly challenge call: | ||
| + | ** Tufts: what to dockerize, how to run | ||
| + | ** python code running over night | ||
| + | |||
| + | == 2016-07-05 == | ||
| + | *DREAM dockers | ||
| + | ** Read Tufts' write-up, downloaded code | ||
| + | *Gravitating SNPs | ||
| + | ** looked at genotypes/phenotypes data | ||
| + | |||
| + | == 2016-06-28/29 == | ||
| + | * porting Roger's STOCSY code to octave: ongoing | ||
| + | * servers' room | ||
| + | |||
| + | == 2016-06-26/27 == | ||
| + | *Readings: | ||
| + | ** PASCAL paper | ||
| + | ** Sven's grant | ||
| + | |||
| + | == 2016-06-23 == | ||
| + | *dockerization | ||
| + | ** Created a hello world Octave container (from Ubuntu) | ||
| + | **[http://containertutorials.com/alpine/get_started.html Alpine]: bash is not available. | ||
| + | ** [https://docs.docker.com/get-started/ Docker guide] | ||
| + | * porting Roger's STOCSY code to octave: ongoing | ||
| + | |||
| + | == 2016-06-22 == | ||
| + | *dockerization | ||
| + | ** Created a hello world Java container (from Alpine) | ||
| + | *Sven's research proposal: detailed research plan | ||
| + | |||
| + | == 2016-06-21 == | ||
| + | *dockerization | ||
| + | ** images vs containers: create a docker image which runs as a container | ||
| + | ** boot2docker if you work on a mac | ||
| + | ** [https://www.youtube.com/watch?v=hnxI-K10auY creating your first Dockerfile] | ||
| + | *** [https://docs.docker.com/engine/reference/builder/ dockerfile] | ||
| + | *** [https://docs.docker.com/samples/alpine/ Alpine] running a minimal Linux image (5MB) | ||
| + | ***[https://developer.atlassian.com/blog/2015/08/minimal-java-docker-containers/ minimal Java image] | ||
| + | |||
| + | == 2016-06-19/20 == | ||
| + | * Metabomatching: feature ''Import Metabolite Associations'' | ||
| + | ** Added a parameter to out file: "kegg_known_x_1" | ||
| + | **Fixed associated_snips: the tag can be repeated, the keggid must be unique. | ||
| + | **Read loma into matrix in one go rather than iterating over each line of the file. | ||
| + | |||
| + | == 2016-06-12/15 == | ||
| + | [https://www.sib.swiss/training/upcoming-training-events/2017-06-metabolomics Metabolomics: from data to publication] | ||
| + | |||
== 2016-06-07 == | == 2016-06-07 == | ||
* Preparing for SIB's "Metabolomics: from data to publication" | * Preparing for SIB's "Metabolomics: from data to publication" | ||
| − | ** LC-MS raw data | + | ** LC-MS [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518119/ raw data] |
| − | ** Multivariate analysis | + | ** [https://www.quora.com/How-do-univariate-and-multivariate-statistics-differ Multivariate analysis] |
** In Situ Metabolomics | ** In Situ Metabolomics | ||
| − | * bnlearn R package (journal club) | + | * R |
| + | ** [https://cran.r-project.org/doc/manuals/r-release/R-intro.pdf intro] | ||
| + | ** bnlearn R package (journal club) | ||
* Open-ended brainstorming with Rosanna | * Open-ended brainstorming with Rosanna | ||
Latest revision as of 12:41, 7 July 2017
Contents
2016-07-07
- dockers: storing output in host
- DREAM dockers: setting up minimal python docker
- configuring lab servers to run docker
2016-07-06
- DREAM dockers, weekly challenge call:
- Tufts: what to dockerize, how to run
- python code running over night
2016-07-05
- DREAM dockers
- Read Tufts' write-up, downloaded code
- Gravitating SNPs
- looked at genotypes/phenotypes data
2016-06-28/29
- porting Roger's STOCSY code to octave: ongoing
- servers' room
2016-06-26/27
- Readings:
- PASCAL paper
- Sven's grant
2016-06-23
- dockerization
- Created a hello world Octave container (from Ubuntu)
- Alpine: bash is not available.
- Docker guide
- porting Roger's STOCSY code to octave: ongoing
2016-06-22
- dockerization
- Created a hello world Java container (from Alpine)
- Sven's research proposal: detailed research plan
2016-06-21
- dockerization
- images vs containers: create a docker image which runs as a container
- boot2docker if you work on a mac
- creating your first Dockerfile
- dockerfile
- Alpine running a minimal Linux image (5MB)
- minimal Java image
2016-06-19/20
- Metabomatching: feature Import Metabolite Associations
- Added a parameter to out file: "kegg_known_x_1"
- Fixed associated_snips: the tag can be repeated, the keggid must be unique.
- Read loma into matrix in one go rather than iterating over each line of the file.
2016-06-12/15
Metabolomics: from data to publication
2016-06-07
- Preparing for SIB's "Metabolomics: from data to publication"
- LC-MS raw data
- Multivariate analysis
- In Situ Metabolomics
- R
- intro
- bnlearn R package (journal club)
- Open-ended brainstorming with Rosanna
2016-06-06
- Metabomatching: adding feature Import Metabolite Associations
- done: waiting for code review w/ Rico
- Bayesian Networks: background reading for journal club
2016-06-02
setsid [program]to fork a process
- Metabomatching: adding feature Import Metabolite Associations
- creating functions
- looping through structures
2016-06-01
- p-values vs. Bayes factors with Marco and Daniele
- Q-Q plots with Reyhan
- GIT and matlab
- "From Bench to Market" @ EPFL
