Systems Biology Developers Foundry |4th Systems Biology Developers Foundry (FAIRDOM/de.NBI)
6th-7th December 2018
About the workshop
Data management is generally recognised as a crucially important but challenging part of Systems Biology. Data management systems that are useful, usable and used are difficult to get right. It is not easy to find out about already existing software, or the state of standards that could or should be adopted.
Following the successes of the Systems Biology Software Developers Workshop in 2012, 2014, and 2016 we propose the next meeting in the series that enables practitioners in the field to meet like-minded scientists, show their working and upcoming developments, and give opportunities to team up.
A meeting to socialise, yes. But also a meeting to figure out how we can team up beyond the confines of single work packages, or projects, in the light of ESFRI research infrastructures, national infrastructure projects, as well as the move from systems biology to systems medicine and synthetic biology.
At the same time, the rise of containers creates a new set of software reuse opportunities. This foundry workshop series has already demonstrated its use as a platform creating and intensifying collaborations.
We will provide
- One day of innovative interactive show-and-tell sessions that take the best from scientific speed dating and lightning talks. Let us all get to show our software and drill down on others.
- One day of interfacing tools with the FAIRDOM software stack for storing, annotating, and cataloguing data.
- Time and space to socialise
The workshop is being sponsored by FAIRDOM and de.NBI.
The workshop is organised by
- Björn Grüning, University of Freiburg, de.NBI
- Wolfgang Müller, HITS gGmbH, Heidelberg, de.NBI & FAIRDOM
- Bernd Rinn, ETH Zürich and SIB, FAIRDOM
- Dagmar Waltemath, University of Rostock, de.NBI & FAIRDOM
Who should come?
Participation is limited to 25 people and the intended participants are software developers working in the field of data management in biology.
If you want to participate you should be:
- fluent in at least one programming language
- daily working as either a programmer or as someone concerned with software engineering or code audit.
- willing to participate in discussions about the (technical) future and extensibility of the software project you are involved with.
Participation in the workshop is free. However, participants have to bear travel and accommodation costs by themselves, and we reserve the right to pick participants.
Check out the information at http://www.station-lounge.de . It is literally across the street from Hauptbahnhof Frankfurt.
The first day will focus on interactive demonstration/discussion in 4 parallel sessions, Each session takes 40 minutes. Each demo/talk is about 10 minutes and is given 4 times to varying small groups of people! Each parallel session will see all tables. This way, we get small discussion groups which facilitates true, interactive discussion.
Participants have described the process as fun, exhausting, and rewarding.
Questions to be addressed in each lightning demo:
- What does my tool/data source do?
- What are the (natural interaction/integration partners) of the tool? How would you do it?
- Who are the users of the tool?
The second day will be devoted to a hackathon: Interfacing with the FAIRDOM software stack.
Here we will discuss ways to usefully interface your software with the FAIRDOM software stack, and we will write some code that serves as a starter to integrating your software with FAIR data management.
In more detail:
6th of December
11:00 – 11:30 Welcome and opening
11:30-12:10 Lightning demos 1-4
12:20-13:00 Lightning demos 5-8
13:50-14:30 Lightning demos 8-12
14:40-15:20 Lightning demos 13-16
15:30-16:10 Lighnting demos 17-20
16:30-18:00 Discussion about APIs, workflow engines, and paths to interesting implementations
19:00 – Dinner
7th of December
09:00 Welcome coffee
09:30 – 14:30 hackathon, interrupted by lunch
14:40 – 16:00 Demos + roundup
Please use this Google form to register before 23rd of November, 2018
If you do not like your data to be processed in Google forms and want to register, please write a mail directly to firstname.lastname@example.org, title “4th Foundry registration”, and give your name, e-Mail address, what tool you want to present.