About the Bio-IT Project

The Bio-IT Project aims to achieve its objectives through activity in four areas:

Find out more about our activities and the resources available by reading in the sections below.

Bio-IT Mission

To provide EMBL-HD with a platform for information and discussion about bioinformatics and to promote networking amongst its diverse bioinformatics user community.

The computational biology community at EMBL Heidelberg is growing steadily and rapidly. This is a reflection of EMBL’s position at the forefront of cutting-edge data-driven research, but brings with it some challenges. The Bio-IT project is a community initiative, which aims to build, support, and promote computational biology activity at EMBL Heidelberg. The objective is for community members to help each other conduct their research, and to share their skills, experience, and tools with others.


The number of scientists at EMBL Heidelberg who spend >50% of their time on computational work has been increasing steadily since 2009.

The number of scientists at EMBL Heidelberg who spend >50% of their time on computational work has been increasing steadily since 2009.

Training & Consulting

The Bio-IT project provided 8 training courses in 2015, aimed at novice computational biologists and more experienced users. Several project members are qualified Software Carpentry instructors, who annually host SWC workshops at EMBL. You can see a list of upcoming courses here and access existing course materials here.
Command Line Teaching
We’re always looking for new subjects to provide training on. If you are interested in providing training on an area that you have expertise on, we would be delighted to help e.g. by taking care of the organisational burden, helping to develop teaching materials, advertising, covering catering costs etc. Please contact us if you would like to discuss providing a new course or workshop.

In addition to these training efforts, we provide advice & consulting on computational biology, software, and resources at EMBL. Bio-IT Drop-In Sessions run every Tuesday morning in the cafeteria, 10-12, and you can contact Toby Hodges or Malvika Sharan any time.

Community

Bio-IT strategy and operations are discussed bimonthly by the Bio-IT Taskforce, a collection of stakeholders in computational biology from across the research units and core facilities at EMBL Heidelberg. At these meetings, members raise topics for discussion that concern computational biology and the community. Example outcomes include new topics for training courses, consultation on new services and resources, and collaborative development of new tools.

The Group at the 2011 Biocomputing RetreatBio-IT also organises monthly Beer Sessions, with a technical focus. These events are intended to encourage discussion (over refreshments!) of a central theme of general interest to the computational community. The first event of this series took place in June 2016, on the subject of using the features of EMBL’s GitLab system for collaborative projects.

The computational biology community at EMBL Heidelberg has an annual retreat, at Hotel Saigerhöh in recent years. The retreat is an opportunity for community members to better get to know their colleagues and the work that they do, to think beyond the science of their project work, and even to enjoy some winter sports in the nearby hills.

HUB23 PosterSeveral members of the Bio-IT community are also active contributors to the Heidelberg Unseminars in Bioinformatics (HUB) series. HUB events are alternative format meetings of people from Heidelberg and the surrounding area, who share an interest in computational biology. These events are informal, with a strong social focus based around group activities and avoiding the same old “one speaker, silent audience” seminar format. Topics of recent events have included Jupyter notebooks, biocuration, and visualisations of biological data (in association with the VizBi conference 2016).

Tools & Resources

Tux_Git_LogosSeveral tools and resources that improve computational biology capability at EMBL Heidelberg have grown out of the Bio-IT project. These include the (now deprecated) Biocomputing Repository (BCR) of software available on the previous EMBL compute environment, the GitLab version control management system, and, the EMBL Q&A forum, and the internal workplace chat system, chat.mbl.org.

Contact

For any questions relating to the Bio-IT project, please send an email to bio-it@embl.de or contact Toby Hodges and Malvika Sharan.