View source for NBIC Conference 2011: BioAssist Tutorials Installation

=Installation instructions for the software tutorials=

==Port applications to the grid and run them as part of a workflow==

'''Teachers:''' [mailto:b.d.vanschaik@amc.uva.nl Barbera van Schaik], Mark Santcroos, Aldo Jongejan, Silvia Olabarriaga

'''Description:''' The tutorial demonstrates how to port and run applications on the grid with the eBioScience infrastructure. The participant learns how to run an existing grid workflow, wrap an application as a workflow component and link components in a workflow.

'''Material:''' [http://bioinformaticslaboratory.nl/twiki/bin/view/BioLab/NBICTutorial Tutorial and installation instructions]

==CytoscapeRPC==

'''Teachers:''' [mailto:j.j.bot@tudelft.nl Jan Bot]

'''Description:''' This tutorial shows the participants how to control Cytoscape from scripting languages. We'll create networks, add nodes & edges, apply visual properties etc.

'''Material:''' [[CytoscapeRPC_install]]

==PBS Tutorial==

'''Teachers:''' [mailto:marcel.kempenaar@nbic.nl Marcel Kempenaar]

'''Description:''' This tutorial will teach the basics of using a grid through the ''Portable Batch System'' (PBS) software, it shows how to create, submit and monitor jobs. 

'''Material:''' [[Media:TechTrack-PBS-Tutorial_d2.pdf | PBS Tutorial]], [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html PuTTY Download Page] for Windows users (no further requirements)

==Trac/SVN Tutorial==

'''Teachers:''' [mailto:t.w.abma@umcutrecht.nl Tjeerd Abma]

'''Description:''' This tutorial will teach the basics of Trac and SVN.

'''Material:''' SSH-server: techtrack.nbiceng.net, username/password list (nbictechtrack01..30) generated/owned by teacher.

==R visualization tutorial==

'''Teachers:''' [mailto:r.w.w.brouwer@erasmusmc.nl Rutger Brouwer]

'''Description:''' This tutorial will demonstrate the basic use of the ggplot2 library for data visualization. This library allows advanced visualizations to be created from statistical data. During this tutorial, participants can bring their own data.  

'''Material:''' [http://www.r-project.org R] and ggplot2. To install ggplot2 see [[R_ggplot2_tutorial]]. 

'''Hand-outs:''' [[R_ggplot2_tutorial]] and [[File:R_visualization_tutorial.pdf]]

==Galaxy tutorials==

'''Organizers:''' [mailto:nbicgalaxy-admin@trac.nbic.nl NBIC Galaxy admin team]

'''Teachers:''' Berend (UMCG), Pieter (UU), Freek(NBIC), Jeroen (LUMC/NBIC), David (NBIC), Leon (NBIC) 

'''Description:''' These tutorials will introduce you to the functionality of [http://galaxy.psu.edu/ Galaxy] - an open-source, scalable framework for tool and data integration. Galaxy was designed with the motto "Stop wasting time writing interfaces and get your tools used by biologists!"

'''Material:''' You'll need a web browser and internet access... 

'''Hand-outs:''' There are two tutorial topics to choose from: next gen sequencing and [[media:LysX.pdf|protease cleavage site analysis]].