Difference between revisions of "NBIC Conference 2011: BioAssist Tutorials"

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Teacher(s): Jan Bot
 
Teacher(s): Jan Bot
  
Status: Detailed tutorial done. [[Media:CytoscapeRPC_tutorial.pdf | Tutorial]]
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* Detailed tutorial done. [[Media:CytoscapeRPC_tutorial.pdf | Tutorial]]
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* [https://wiki.nbic.nl/index.php/CytoscapeRPC_install Installation instructions] done.
  
 
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Revision as of 17:12, 16 March 2011

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

This page collects ideas and organisational details.

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

Todo:

  • Create dummy-accounts (techtrackuser001@gmail.com...techtrackuser020@gmail.com) which can be assigned to the "nbictechtrack" project
  • Half poster
  • Zip file with prerequisites
  • Tjeerd needs admin access to trac to be able to help people with their accounts

Grid/Cluster

Organizer: Jan Bot

Teacher(s): Marcel Kempenaar

Status: Writing tutorial

Todo:

  • Exercises to be finished
  • Zip file with prerequisites

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)
    2. send to Jan by March 15
  • Jeroen/Leon will prepare a NGS pipeline
    1. Update GAPSS on NBIC Galaxy, testing dataset, and the manual (by March 10)
    2. send to Jan by March 15
  • 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)
    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)

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

CytoscapeRPC

Organizer: Jan Bot

Teacher(s): Jan Bot

Status:

Todo:

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

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, Silvia D Olabarriaga

Status:

Todo:

  • Add short intro to tutorial
  • Add one extra section to the tutorial (optional)
  • Create course grid certificate and add it to the VM (only in the VM on the USB stick)
  • Order USB sticks
  • Put VM, Virtualbox, Vbrowser, Moteur, wrapper script on USB sticks
  • Make poster