NBIC Conference 2011: BioAssist Tutorials

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At the 2011 NBIC conference, the BioAssist "TechTrack" session consisted of parallel tutorials that people could attend at their own speed.

Pictures

Pictures of the event by Rob Hooft

General organisation

  • Local Galaxy server. Todo.
    • Router for wireless
  • Local PBS/SVN server. Todo.
  • Wireless: Hotel wireless should be OK?
  • Posters for at the door for each tutorial
  • Big dice for people that want to randomize their participation
  • Electricity supplies on each table --> Hotel

Deadlines

  • March 11th: all tutorials completed
  • March 25th: comments for tutorials
  • April 15th: tutorials updated

Tutorials

Trac & SVN

Organizer: Jan

Teacher(s): Tjeerd

Status: First draft of the Trac-tutorial sent to Jan

Done:

  • Registered "nbictechtrack" project at trac.nbic.nl
  • techtrack.nbiceng.net virtual server created; login details at Tjeerd

Todo:

  • Create dummy-accounts (techtrackuser001@xxxxx...techtrackuser020@xxxxx) which can be assigned to the "nbictechtrack" project
  • Half poster
  • Zip file with prerequisites

Grid/Cluster

Organizer: Jan Bot

Teacher(s): Marcel Kempenaar

Status:

Todo:

  • Exercises to be finished (5 more to add, any ideas can be placed below)
  • Zip file with prerequisites and example scripts
    • Status: incomplete
  • Get access to PBS server for demonstration
    • Temporary accounts can be requested on the Millipede cluster at the RUG
    • Alternatively, create/find VM('s) that, combined, function as a cluster (UI-node, worker-node(s))
  • Create a poster

Galaxy

Organizer: Leon Mei (NBIC)

Teacher(s): Berend (UMCG), Pieter (UU), Freek(NBIC), Jeroen (LUMC/NBIC), David (NBIC), Leon (NBIC)

General Setup

Date/Time: 14:00 - 15:30, April 19

Number of participants: ??

Participants should bring their own laptop.

A local 16 port switch (and ten 5m cables) will be available to connect to the Galaxy server.

Status

  • Proteomics
    1. msCompare pipeline installed at NBIC Galaxy
  • NGS
    1. GAPSS pipeline installed at NBIC Galaxy
    2. A draft manual for SNP calling/annotation is ready
  • Script to generate NBIC Galaxy VM is ready.

Todo

  • Pieter/Freek will prepare some tutorial for Proteomics modules
    1. tutorial, testing dataset (by March 10) Done
    2. send to Jan by March 15 Done
  • Jeroen/Leon will prepare a NGS pipeline
    1. Update GAPSS on NBIC Galaxy, testing dataset, and the manual (by March 10) Done
    2. send to Jan by March 15 Done
  • David/Leon will prepare a Galaxy VM
    1. Test the setup of a local Wifi with Galaxy VM (by March 10) Done
    2. Prepare a Galaxy VM based on a latest NBIC Galaxy server (if possible, also including new chip-seq pipeline, Color space SNP calling pipeline, benchmarking) (by April 15) Done
    3. Bring the Galaxy VM to the NBIC conference (via a spare BET laptop) and make it available through a local wired net.
  • Freek/Leon will prepare a poster for all NBIC Galaxy related tutorials (by April 10) Done

RCytoscape

Organizer: Jan is looking for someone to do this

Teacher(s):

Status:

Todo:

ggPlot

Organizer: Rutger Brouwer

General setup:

Participants should bring their own laptop preferably with R and ggplot2 already installed. ggplot2 can be installed as follows:


Rconsole> install.packages( 'ggplot2' )

Teacher(s):

Status:

  • due to the mid-term review and other projects, the final guide will be available on Monday (Sorry)
  • writing the guide R_ggplot2_tutorial

Todo:

  • writing
  • make assignments

Review: the DATASET is not available, can't be tested.

CytoscapeRPC

Organizer: Jan Bot

Teacher(s): Jan Bot

Status:

Todo:

  • Zip file with prerequisites
  • update cover
  • add list of commonly used functions
  • ...

Review:

  • No comments, tutorial looks good!

Hadoop

Organizer: Evert Lammerts

Teacher(s): Evert Lammerts

Status:

  • Will be given at other locations as well

Todo:

  • Virtual machine images

Grid / Moteur

Organizer: Barbera van Schaik

Teacher(s): Barbera van Schaik, Mark Santcroos, Aldo Jongejan, Antoine van Kampen and Silvia D Olabarriaga

Status:

Todo:

  • Add short intro to tutorial - done
  • Order USB sticks - done
  • Put VM, Virtualbox, Vbrowser, Moteur, wrapper script on USB sticks - done
  • Add one extra section to the tutorial - done
  • Create course grid certificate and add it to the VM (only in the VM on the USB stick) - done
  • Make poster - no poster