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Workshops - April 24

Four parallel workshops will be organized on April 24th. The workshops are planned from 13:45 - 15:15.

Provenance information in bioinformatics

Provenance is a scientific concept coming from the humanities, where it refers to the chronology of the ownership or location of an object. In e-science provenance assist scientists and programmers with tracking their data through all transformations, analyses, and interpretations. With the current data deluge in bioinformatics a comprehensive provenance framework is essential to reproduce scientific results, assess data quality, validate the scientific process and results.

Bioinformatics workflows lend themselves very well to provide detailed provenance data through a framework that tracks all steps and intermediate data in the workflow. Different workflow engines and tools already offer hooks or even their own framework for provenance tracking. During this workshop we will take a closer look at a couple of these solutions and study the specific provenance challenges in bioinformatics and present some practical solutions to incorporate data provenance in research.

13:45 - 13:50 David van Enckevort (NBIC) - Introduction
13:50 - 14:10 Pieter Neerincx (UMCG) Data modelling Provenance
14:10 - 14:30 Souley Madougou (AMC) Use cases from the PLIER Project
14:30 - 14:50 Radek Szklarczyk (CMBI) Provenance in Galaxy
14:50 - 15:15 Discussion

Workshop Personal Branding & Social Media

What is your BRAND?

Have you ever considered that people around you, near or from a distance, have certain perceptions about you?  What do people think about you, professionally? Does it fit with the things you have to offer? Pinpointed any misconceptions lately?

Personal Branding is the overall perception of you, your knowledge, your skills, the services you have to offer, you as a human being. If your resources are more valuable than people perceive they are, you might not get that promotion, that job, that certain project you were dying to get your hands on.

Join this workshop to explore Personal Branding and how you can use social platforms to communicate your personal brand to the outer world. Your stage is the world, you only need to open the curtains!

Maximum number of participants: 20

Workshop organisor: Mireille Vaal, Radboud University Nijmegen

Workshop Grant acquisition and writing

Where is the money?

In today’s economic climate finding funding for your next job, your new group or even your favourite piece of research can be a long and difficult process; there are a multitude of funders and funding schemes where the rules seem to change every five minutes. However, navigating the funding jungle successfully is a major part of life for the vast majority of modern researchers and that is not going to change for the foreseeable future.

Although daunting, especially for those making their first independent grant applications, there are resources and strategies which can help increase your likelihood of success. This is a chance to explore what funding possibilities exist and learn about (and how to avoid) the most common pitfalls in grant applications.

Phil Irving, EMBL, Heidelberg

Experiences from Dutch bioinformaticians:
- Chris Evelo, Head of dept. of Bioinformatics, Maastricht University
- Morris Swertz, Head of Genomics Coordination Center, Groningen

eBiomics: a Bioinformatics e-Learning Environment for Biologists

Patrick Koks - last year’s BIUP poster prize winner - will give a demonstration of “eBiomics”, an e-learning platform in bioinformatics intended as a support to post-graduate students and scientists involved in omics or systems biology projects. Please bring your own laptop!

With the ever expanding number and size of data sets in life sciences, the challenge of analysing these data is also growing and in need of well-trained researchers. Bioinformatics tools are therefore becoming more and more researchers' tools. In order to educate more people and promote good practices in bioinformatics, we present eBiomics, an e-learning platform in bioinformatics for biologists. eBiomics is a didactic guide for an extensive range of on-line databases and tools commonly referred to in -omics applications. The system is freely available to the public at For this workshop, a workflow for variation detection using short read re-sequencing data has been developed in collaboration with Keygene.

After a general introduction to the website and its navigation scheme, you will be guided through a Conceptual Flow Chart (CFC), eBiomics' graphical representation of a workflow. We will show you an example of a protocol in a Next Generation Sequencing Application, from pre-processing and mapping of raw NGS data through variant detection to variant annotation and functional annotation of structural variants. Such a multi-step protocol is not easily performed and requires local installation of many (command-line) tools. We will use a Galaxy server, that enables us to link a number of these command-line tools together and show, on the limited scale of a test dataset, what can be done using these tools in practice.