Notebook

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

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

  • 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