NBIC Conference 2011: BioAssist Tutorials Installation

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BioInformatics on Hadoop

Teachers: Evert Lammerts

Description: The tutorial aims to give the participants a feel for Apache Hadoop, a popular system for data-intensive parallel processing, and its API's, illustrated by CloudBurst, a parallel read-mapping algorithm.

Material: Installation, Images and documents

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

Teachers: Barbera van Schaik, Mark Santcroos, Aldo Jongejan, Antoine van Kampen and 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: Tutorial and installation instructions (pdf)

CytoscapeRPC

Teachers: 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, hand-out

PBS Tutorial

Teachers: 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: PBS Tutorial, PuTTY Download Page for Windows users (no further requirements)

Trac/SVN Tutorial

Teachers: Tjeerd Abma

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

Material:

Tutorial document: Subversion and Trac tutorial (PDF)
SSH-server: techtrack.nbiceng.net
SSH-client: PuTTY for Windows or *nix built-in SSH-client
Username/password list (nbictechtrack01..30) generated/owned by teacher.

R visualization tutorial

Teachers: 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: R and ggplot2. To install ggplot2 see R_ggplot2_tutorial.

Hand-outs: R_ggplot2_tutorial and File:R visualization tutorial.pdf

Galaxy tutorials

Organizers: 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 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 protease cleavage site analysis.