Monthly Archives: December 2016

FAIRDOM becomes an Association e.V

Fantastic news and a great end to the year: we are now an Association e.V.!

Core members of the team met in Berlin on 12th December to establish the FAIRDOM Association e.V. as a legal entity.

Founding institutions include: The University of Manchester, Heidelberg Institute for Theoretical Studies, and New Forest Ventures Ltd.

This means that interested parties are now able to join us as contributing members. We are still establishing the finer details of membership, but in the meantime, if you are interested in joining the FAIRDOM Association e.V you can speak with us directly to find out more (community@fair-dom.org).  

We were supported in the process by the expertise of SB ScienceManagement.

Systems Biology Developer’s Foundry workshop

More than 4 years after organising the first such workshop, FAIRDOM in collaboration with de.NBI ran the 3rd Systems Biology Developer’s Foundry Workshop.

Foundry Workshops are an innovative, experimental workshop format that is based on a mixture between a demo session and scientific speed dating („show-and-tell sessions“). In the show-and-tell sessions, people show what they have achieved. Most demos in conferences are run by very many people in parallel, and in very short time, giving the viewers the need to choose the demos they view based on first sight. In contrast, in show-and-tell sessions a number of people present to everyone else participating in the speed dating in a number of small talks.
The first day is devoted to a number of sessions in which 3 presenters each present their work to a 3rd of the audience in parallel, and for 10 minutes. After their first presentations, another third of the audience will visit them to receive the same presentation, and finally the rest of the audience. Like that all the audience receive the talk, but as the public is small and the public changes, each small group of participants receive a presentation tailored to their needs, emphasizing the content that is most interesting to this small group.
This process is repeated with other presenters until all participants have seen all other participants’ work. After these sessions, people tend to know each other pretty well, which fuels the subsequent discussions, and makes them more interesting and effective.

screen-shot-2016-12-12-at-13-10-16
In the 2016 edition of the Foundry Workshop, 16 scientists from Switzerland, Slovenia, the Netherlands, Germany, and UK gave and received talks on topics as diverse as usability of data management systems, modeling tools for systems biologists, and solving concrete systems medicine problems using the workflow engine KNIME and the statistical literate programming language RMarkdown. While this wide variety of topics may appear to be too varied for real discussions, there was much common ground among the participants. We all work in an environment where we try to combine complex tools into powerful, yet simple services for use of a demanding public: Scientists. After an initial introduction of the participants, assigning the talks to sessions, and the sequence of show-and-tell sessions, we spontaneously agreed to have a session about SnakeMake, nextflow, Galaxy, Taverna, KNIME. People with knowledge about the respective systems prepared material in a 30 minute break and then gave small presentations followed by lively discussions. Then we had to break discussions for dinner.
In the evening, we continued the discussions in a Trattoria I Siciliani in Frankfurt, preceded by an involuntary, but fun, traversal of the Frankfurt Christmas market and crossing the Main on a footbridge, enjoying the Frankfurt skyline.

On the second day, we started again with two workflow systems reports and then dived into Bérénice Batut’s introduction to docker, that (with discussions) took up the whole rest of the day. Docker is a system for simplifying the use of containers that currently has enormous traction and an extremely lively community. The level of previous docker exposure of the participant was very diverse, which was not a drawback, but spawned fruitful discussions. Each slide was discussed, leading to new insights for the participants.
In our view, this workshop created the following values for its participants:
(i) Knowing more people outside the previous collaborations who can help with concrete challenges, (ii) adding new, relevant tools to the own toolkit, (iii) clearer insight into use and misuse of docker, and finally (iv) a better view on with whom to integrate, and at which level.
Running such workshops is challenging, and fun. The challenge lies in creating a make-it-up-as-we-go atmosphere while still keeping an eye on the goals of the workshop. If it works, depends very strongly on the participants who have to be open-minded and interested. We wish to thank the participants who very quickly bonded and acted as a team.
In the preparation of the workshop, someone who did not participate expressed interest to run a Foundry Workshop with this structure about another, related topic in Bioinformatics. We are looking forward to this development and will support this where we can.

Sponsors of the workshop
Wolfgang Müller is grateful for the base funding he receives at HITS gGmbH, a private not-for-profit research insitute. This base funding that enables running the group also afforded some support for costs incurred in this workshop.
de.NBI, funded by the German BMBF, is the German Network for Bioinformatics Infrastructure. The de.NBI-SysBio node closely collaborates with FAIRDOM, as HITS is a member of FAIRDOM. Service, training, dissemination, outreach are part of de.NBI’s mission.
FAIRDOM is a transnational project funded by BBSRC, BMBF, SystemsX, NWO that aims at FAIR Data Operations Models management. We are collaborating with many other groups and scientists interested in FAIR Data, Operations and Models. Service, training, dissemination, outreach are part of FAIRDOM’s mission.

Featured Image
The image of Frankfurt Skyline featured in this article is Frankfurt by Barnyz. The original can be found on Flickr, and it is used in accordance with the Creative Commons licence.

New Blog Post: Systems Biology Developer’s Foundry workshop

More than 4 years after organising the first such workshop, FAIRDOM in collaboration with de.NBI ran the 3rd Systems Biology Developer’s Foundry Workshop.

Foundry Workshops are an innovative, experimental workshop format that is based on a mixture between a demo session and scientific speed dating („show-and-tell sessions“). In the show-and-tell sessions, people show what they have achieved. Most demos in conferences are run by very many people in parallel, and in very short time, giving the viewers the need to choose the demos they view based on first sight. In contrast, in show-and-tell sessions a number of people present to everyone else participating in the speed dating in a number of small talks….. To read more please visit our blog

New Paper: “FAIRDOMHub: a repository and collaboration environment for sharing systems biology research”.

We’re excited to announce our latest publication “FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.” can now be accessed from http://nar.oxfordjournals.org/content/early/2016/11/28/nar.gkw1032.full

You can now use this reference to cite FAIRDOM in your papers:

“Wolstencroft K, Krebs O, Snoep JL, Stanford NJ, Bacall F, Golebiewski M, Kuzyakiv R, Nguyen Q, Owen S, Soiland-Reye S, Straszewski J, van Niekerk DD, Williams AR, Malmström L, Rinn B, Müller W, and Goble C (2016). FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. Nucleic Acids Research, doi: 10.1093/nar/gkw1032″