Hidden complex beauty of plants

Biel/Bienne, Switzerland, 7-8 June 2016


There are 11 parallel workshops proposed during the SIB Days 2016. They will take place on Wednesday 8 June, from 10:00 to 12:00. Kindly let us know via the registration form which one you would like to attend. Please note that available space is limited for some of them and that priority will be given on a first come, first served basis.

Workshop 1: GO and beyond: gene list enrichment in ontologies   Kongresssaal (1)

Organizers: Frédéric Bastian, Marc Robinson-Rechavi

Summary: GO enrichment is a well-established way to characterize gene lists obtained from various high-throughput analyses. Yet (i) the complexities and pitfalls of GO and of enrichment statistics (GO versions, role of background, decorrelation statistics, etc), as well as the best tools to use it (don’t use DAVID!), are not always mastered by users of GO enrichment. And (ii) despite the development of many ontologies in biology, the bioinformatics community has not proposed many additional tools for “knowledge enrichment” of lists of genes or other biological objects. In this workshop we will present our experience, and open the discussion concerning both (i) the best practices in GO enrichment and (ii) the potential at SIB to develop other ontology enrichment tools. We will notably leverage the experience acquired in developing TopAnat, which allows anatomy enrichment of gene lists through gene expression, based on the Uberon ontology of anatomy.

Target audience: Any SIB members who are interested in better understanding the pitfalls of ontology enrichment tests, or in developing their own, i.e. extending enrichment to other ontologies than GO and Uberon. Participants should bring their laptop.

Workshop 2: Key techniques for a successful bioinformatics training   Galerie

Organizers: Diana Marek, Patricia Palagi

Summary: One of SIB’s missions is to train the next generation of bioinformaticians as well as to ensure that life and health scientists fully benefit from bioinformatics and SIB’s resources. The SIB Training relies on several SIB members with diverse expertise to offer courses and workshops on various bioinformatics and data science-related fields. Delivering excellent training is a challenge in any domain, and bioinformatics is no exception. Excellent training requires good planning and careful thinking, just like a well-formulated research plan. This workshop will be a forum to learn general best practices in how to establish successful bioinformatics courses, with particular emphasis on continuing education. This hands-on workshop is for all SIB members interested in maximizing their training skills and discovering how the SIB Training team can help them to set up and efficiently plan their courses.

Target audience: Any SIB member interested or engaged in teaching

Workshop 3: PhyloSIB4YOU: Phylogenetic & phylogenomic services of broad scientific relevance   WS1

Organizers: Maria Anisimova, Brigitte Boeckmann, Christophe Dessimoz, Ioannis Xenarios

Summary: The PhyloSIB community provides a wide range of services to study experimental findings under an evolutionary perspective. The workshop focuses on phylogenetic and phylogenomic services of broad scientific relevance. After a brief introduction, participants are invited to a bazaar where they can explore software tools, databases and web servers along with investigators and developers.

Target audience: All scientific SIB Days attendees.

Workshop 4: SIB Open Access Training Materials and Copyright   Galerie

Organizers: Marc Filliettaz and Frédéric Schütz

Summary: This workshop is about open access and copyright applied to training material. In particular, we will discuss how you can reuse (or not !) training material created by others for your own course, and how you can redistribute your own course material for others to reuse.

Target audience: Anyone who is interested in open access and copyright and general, and about these issues related to training materials in particular.

Workshop 5: Technology sharing among SIB groups   WS2

Organizers: Heinz Stockinger and SIB Technology group

Summary: Basically all SIB groups develop software for bioinformatics tools and databases. Specific tools and expertise in one group might help another group to improve their resource. Some examples: (1) a visualization tool of one resource might also be applicable to another resource; (2) a new data management technology might help to speed up searches in a database; (3) a group applies an approach to service development or operation (incl. security) to be shared with others, etc.

The main aim of this workshop is to point out technical topics for collaboration between SIB groups that help us learn from each other, share technical approaches, improve our resources and potentially have higher quality resources.

We will also provide a short overview of existing sharing platforms such as SIBlink (SIB's intranet, Confluence), GitLab, rxtx (SIB's OwnCloud) etc.

Target audience:

  • Software developers, analysts and system administrators (to talk about technical aspects and point out areas for collaboration and sharing)
  • Project managers, senior scientists and group leaders (to help set priorities and potentially scope early project/collaboration ideas)

Workshop 6: Facilitating Reproducibility of Computational Research in Bioinformatics   Vereinssaal

Organizers: Philipp Bucher, Eivind Hovig and Geir Kjetil Sandve

Summary:The lack of reproducibility of computational research based on information given in scientific publications is increasingly perceived as a severe impediment to scientific and technological progress. It is argued that reproducible computational work is reusable by others and thus useful to human society whereas unreproducible work is essentially useless.

Topics covered by the workshop will include: 1. Tools to make published research more reproducible (e.g. executable documents, virtual machines, etc); 2. Examples of reproducible and unreproducible computational research; 3. Specific benefits of computational reproducibility to authors, collaborators, peers, the bioinformatics community and society as a whole; 4. Measures stakeholders (journals, universities, funding agencies, etc.) could take to encourage reproducible computational research.

The proposed format consists of 3-4 talks on specific topics followed by a panel discussion mostly focusing on topics 3 and 4.

Target audience: Everybody, from master students to the Director

Workshop 7: Basic principles of Git   Kongresssaal (2)

Organizer: Stefan Bienert

Summary:Git is a very popular tool for versioning of, and collaborating on, software projects. In addition, it's actually useful for any project that undergoes an iterative process. With a couple of free of charge, publicly available servers for git repositories, it also helps to distribute your software. Since Git is easy to use, this session will equip you with the basic principles of “how to Git”. Topics that will be covered are "how to host your own private repository" and "how to collaborate via GitHub or GitLab". In addition to mandatory workflows that allow keeping repositories up to date and sharing your contributions, it will also include a tiny bit of troubleshooting of the most common speed bumps. Some additional tools of Git for daily use will be presented, which go a step further than versioning and sharing projects.

Target audience: Any SIB member interested in learning the basic principles of Git. No particular programming skills needed, experience with command line tools would be an advantage. Laptops are welcome for people who want to try things/get things fixed/set up.

Workshop 8: Would you like to be part of an outreach grant proposal?   WS3

Organizers: Marie-Claude Blatter, Swiss-Prot and SIB Outreach group.

Summary: In the past few years, the SIB outreach group has created a broad range of workshops to describe the world of bioinformatics in an easy and playful way to a wide audience. This kind of project can be funded by different Swiss funding agencies, such as the SNF Agora grant - a grant whose aim is to support researchers who wish to explain what they do to the outside world. SIB's Drug Design workshop, that we designed with the help of Vincent Zoete and Antoine Daina from the Molecular Modelling group in Lausanne, is one of our success stories. The aim of this workshop is to gather scientists who would like to share their knowledge, data, ideas and passion with the public, by suggesting a new project - or several new projects - which could enlarge SIB's current outreach offers as well as establish or strengthen SIB-wide collaborations.

Target audience: All

Workshop 9: Shape the future of Personalized Health in Switzerland   WS4

Organizers: Valérie Barbié and Torsten Schwede

Summary: There is currently a major paradigm shift in health care, with the introduction of big data in medical practices and health monitoring. The buzzword Personalized Health is everywhere, but what does it mean in practice, what are the major needs and hurdles, and how could we address them? Help shaping Personalized Health implementation in Switzerland around a practical case.

Target audience: Anyone willing to get more more familiar with the implementation of Personalized Health and its potential for people’s health in the future.

Workshop 10: Computer-aided drug design with SwissDrugDesign   Galerie

Organizers: Vincent Zoete, Antoine Daina, Ute F Röhrig, Olivier Michielin

Summary: The attendee will be introduced to the latest developments in computer-aided drug design proposed by the Molecular Modeling Group of the SIB Swiss Institute of Bioinformatics. Using their own computer and a simple browser, attendees will predict secondary targets of small molecules in relation with toxicity issues or drug repurposing, estimate ADME properties, perform virtual high-throughput screening, and get proficient ideas about possible compound modifications based on the data mining of the medicinal chemistry literature.

Target audience: Everyone interested in drug design, discovery and development. No pre-requisite. Just bring your computer.

Workshop 11: Genome Beacon projects and the Global Alliance for Genomics and Health   WS5

Organizer: Michael Baudis, Heinz Stockinger

Summary: The Global Alliance for Genomics and Health (GA4GH) was established in 2013, to facilitate the sharing of genomic and related phenotypic data in research and clinical application contexts. While there is ongoing work on the definition of data schemas, in parallel the concept of genome “Beacons” was established to test technical, legal and ethical requirements for sharing of human genome data, and to promote participation by genome data and service providers.

This workshop will provide an introduction to both the GA4GH in general as also specific at Beacon concept. Contributors from the Beacon community will provide both presentations and will engage in discussions about future developments of genome data sharing standards.

Target audience: Everyone interested in genome data sharing and resource development, especially for human health related applications.