T07 - Scientific Workflows for Analysing, Integrating and Scaling Bioinformatics Data: a Practical Introduction to Galaxy, Taverna and WS-PGRADE

This tutorial will provide an introduction to the use of scientific workflows for bioinformatics data analysis, integration and scaling and will highlight the main differences and similarities between the myriad of systems available. Examples and comparisons will be illustrated based on WS-PGRADE, Taverna and Galaxy as representatives of grid workflows, distributed computing workflows and local tools workflows respectively. Case studies from large-scale transcriptome analysis projects will be used to motivate the technical comparison and demonstrate where the use of workflows can bring large advantages to researchers. Practical exercises will provide basic hands-on experience with those three systems.

At the end of the day the attendees will have gained experience in designing, constructing and executing scientific workflows in order to address bioinformatics research questions. They will be informed about different types of the most widely-used workflow management systems, and have basic information to identify when it is appropriate to use what type of system. This introductory knowledge will allow the attendees to select and apply workflow methods to address their own scientific case.

Date: Sept 6, 2014, starting at 9am at the Forum of the Medecine Campus, 4 rue Kirschleger

Course materials

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Requirements

Participant needs to bring a laptop with wireless connection for the hands-on practice. For the WS-PGRADE part you need a recent version of Chrome or Firefox and enable Java Web Start.

Program 

9:00-10:30 Session 1
Round introduction
Introduction to using scientific workflows in bioinformatics (Katy Wolstencroft)
Introduction to Galaxy with demo (Leon Mei)

Coffee break

10:45-12:00 Session 2
Hands-on practical Galaxy on RNAseq analysis (Leon Mei)

Lunch

13:30-16:00 Session 3

Introduction to Taverna - distributed tools and services for downstream enrichment analysis (Katy Wolstencroft)
Hands-on taverna (Katy Wolstencroft)
Introduction to WS-PGRADE - tapping into Grid and Cloud resources for analyses requiring heavy computation (Silvia Olabarriaga)
Hands-on WS-PGRADE (Silvia Olabarriaga)

Coffee break

16:20-18:00 Session 4
Discussion: comparison between workflow system properties
Recap of system properties for Galaxy, Taverna and WS-PGRADE;
Brief discussions in groups
Wrap-up and conclusions
Q&A: hands-on or bring your own workflow problems

Instructors

Katy Wolstencroft

Dr Katy Wolstencroft is an Assistant Professor in Bioinformatics at the Leiden Institute of Advanced Computer Science, University of Leiden, NL. Previously, she was a Post-Doctoral Research Fellow at the University of Manchester, where she was the bioinformatics team leader and outreach coordinator for the myGrid research group. myGrid produced the Taverna workflow system, the myExperiment workflows repository and the BioCatalogue Web Services repository. Katy has given over 50 tutorials and hands-on workshops world-wide on scientific workflows, Taverna and distributed computing. She designs Taverna workflows for her research in bioinformatics and systems biology.

Leon Mei

Dr Hailiang (Leon) Mei is the head of Sequencing Analysis Support Core at Leiden University Medical Center. The main task of this group is to develop and execute software pipelines to analyze Next Generation Sequencing data. Prior to joining LUMC, Leon worked at the Netherlands Bioinformatics Centre (NBIC) where he was the coordinator of the Next Generation Sequencing taskforce and the co-organizer of the Galaxy Community Conference in 2011. Leon is also the main developer/administrator of the public NBIC Galaxy server and provided lectures and hands-on workshops on Galaxy at a number of NBIC organized courses. 

Sílvia Delgado Olabarriaga

Dr Silvia Olabarriaga is Assistant Professor at the Academic Medical Center of the University of Amsterdam, NL. She leads the e-science research line since 2009, and before that she worked in various academic and industrial organizations in The Netherlands, Brazil, Portugal and the US. Silvia participates in various national and international activities involving research or usage of scientific workflow management systems to perform computationally-demanding experiments with large biomedical data. She regularly teaches about e-science topics for biomedical students, where workflow management is introduced using WS-PGRADE for practical exercises. Silvia has more than 10 years experience in teaching in various countries, and recently obtained a Dutch certificate for Basic Teaching Qualification for high education. 

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