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31.1.2014
CBMS paper, miXGENE -- a web tool for integrative gene expression data analysis using prior knowledge
Valentin: 1. workflow automated execution implementation -- the last steps, 2. user's data import -- including phenotypes in external file and platform annotation, 3. SubAgg and SVDAgg implementation.
Matej: 1. 2 pictures that exemplify a particular workflow (2 different ways of CV meta-plugin), share with Valentin, 2. CBMS paper outline, collection of the earlier texts relevant to the topic, 3. a section on workflow management, 4. a section on GE classification with prior knowledge.
Next meeting: Fri 7th of February 10am
6.12.2013
Valentin: 1. ongoing task: XGENE workflow -- implement and show a simple workflow that contains cross-validation, focus on workflow configuration tools (scopes, validity checks, block inputs and outputs, running workflow), 2. thesis draft: workflow management description + ongoing review of workflow management systems and miXGENE x XGENE
Matej: finish plugin overview page (provide links to Python/R libraries or actual implementations relevant to the individual plugins)
Next meeting: Tue 17th of December 1pm
15.11.2013
Valentin: 1. ongoing task: XGENE workflow management -- implementation of workflow system with functionality identical to the original XGENE (the first input block has already been done + infrastructure), 2. review: XGENE x miXGENE comparison (programming tools/platforms, functions) bioinformatics workflow management systems (overview, inspiration)
Matej: 1. specification of future diploma theses that develop current implmentation, 2. plugin overview page
Review draft: Fri 22th of November
Next meeting: Fri 29th of November 10am
20.9.2013
Globalni: migrovat gene set funkcni XGENE workflow s dvema platformami na miXGENE
Valentin: schopnost importovat GEO soft-format (zrejme knihovna BioPythonu), implementace workflow s pouzitim BroadInstitute definice gene sets, workflow: import dat, konverze identifikatoru, vypocet features odpovidajicich gene sets (prumerovani, PCA), analyza novych features pomoci t-testu (seradit features dle kvality), PCA (vizualizace vzorku v novem feature prostoru) a SVM (klasifikace)
Matej: doda BroadInstitute gene sets, nove plugins v R knihovne miXGENE
Do budoucna: import RNA-seq dat, nejlepe zahrnujici soucane mRNA a miRNA, vyuziti targets
Dalsi schuzka: patek 4.10. v 10h
11.9.2013
Matej: summarizes and delivers R packages that form a meaningful XGENE workflow Valentin: implements an import of mRNA GSE from NCBI, implements a miXGENE workflow using packages from Matej Jiri: checks whether we can import mRNA, miRNA and methylation NCBI data that match
checkpoint: Fri 20th 10am
Done:
- We can merge msigdb gene sets with GSE datasets with PROBE ID as units
- Splitting dataset into test and train sets
- User is able to assign samples to user defined classes
- Files fetched from NCBI are now cached
- Update version of the R miXGENE package
Done:
- Parsing SOFT format into probe expression table, probe <-> entrez_gene_id mapping.
- Parsing and generation .gmt format, and basic support for gene sets.
- PCA, SVM, Ttest and global test can be applied to arbitrary GSE (here is problem with sample classes, now we try to infer class from sample title as prefix ended by "_" or "," ). Small and good example GSE25724 used entrez_gene_id units.
- Routine update in UI: now configuration parameters can be grouped.
- [Bugfix:] Context update is now atomic action.
What's next: