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

• 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