Minutes: Bio-IT Taskforce Meeting 03-Aug-2016

Bio-IT Taskforce meeting

List of participants

Po-Chia Chen, Holger Dinkel, Toby Gibson, Charles Girardot, Marc Gouw, Jean-Karim Hériché, Toby Hodges, Panagiotis Mantas, Jelle Scholtalbers, Thomas Schwarzl, Malvika Sharan, Artem Tarasov, Grischa Toedt, Michael Wahlers, Georg Zeller

Wednesday 3rd August 2016, 14.00 - 15.00, Biocomputing Seminar Room

Opening Notes

The group welcomed new Taskforce members, Malvika Sharan, Panagiotis Mantas, and Marc Gouw - thanks for joining us!

The meeting began with a quick vote of approval for the idea of requesting a standing desk in the ATC Computer Training Lab. The group approved.

Discussions during the meeting

Bio-IT Course Planning

The group discussed plans for upcoming courses, and agreed that a system for estimating demand for new courses should be developed. JKH has proposed a new course on database design & management, and Bio-IT will advertise this new course with a request that people register their interest. If enough people state an interest, then the course will be developed and run.
If you have an idea for a new course, you are encouraged to contact Toby or Malvika, who will be happy to hear your suggestions.


The EMBL GitLab system has been successfully updated to a newer version, and efforts could now be made to introduce a Continuous Integration server for repositories hosted at git.embl.de. If you would be interested in using CI with your project(s), please let the git admins know.
The server is currently supported and maintained by IT Services, with development of the GitLab instance taken care of by Bio-IT members. Volunteers are being sought to help with the long-term development and maintenance of git.embl.de. Again, if you are interested in this, please contact the git admins.

Cloud Computing

The possibility of connecting with the EMBASSY cloud computing platform at the EBI was discussed. It was acknowledged that information is not readily available regarding the cloud resources that are already available to EMBL members.

Basic Bioinformatics Course

A course aiming to train non-computational scientists on fundamental bioinformatics tools (particularly those with a graphical/web-based interface) will be developed. It was noted that these tools tend to be domain-specific, which may limit the courses appeal.
The possibility of inviting the EBI's Ensembl Outreach Team to do some training in HD will be investigated. It was suggested that a question could be posted on forum.embl.org to assess the demand and take suggestions of tools that people would benefit from training on.

Web of Science & Convaris

The group was informed about recent changes in the ownership of Convaris, which has been bought by a venture capital firm.

Central Software Repositories

The SBGrid software distribution system has been introduced for Structural Biology groups. A question remains over what system might replace the BCR/SEPP system in future across all units at EMBL HD, to minimise duplication of effort. More investigations will be made into Docker/container-based solutions.

Action points

TH & MS to develop new courses, in collaboration with other Bio-IT community members.