Dates: 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

Carole Goble, University of Manchester, FAIRDOM
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.

The venue
Check out the information at http://www.station-lounge.de . It is literally across the street from Hauptbahnhof Frankfurt.

Preliminary Program
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

13:00-13:50 Lunch

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

Registration

Please use this Google form to register before 23rd of November, 2018

https://docs.google.com/forms/d/e/1FAIpQLSfo0ZKSXq_h5VIwZCrg6b7_OrKAgRRbPqco9cf_qCgC6u8o7w/viewform?usp=sf_link

If you do not like your data to be processed in Google forms and want to register, please write a mail directly to This email address is being protected from spambots. You need JavaScript enabled to view it., title “4th Foundry registration”, and give your name, e-Mail address, what tool you want to present.

Lipidomics

https://lipidomics-forum.isas.de/

gcc2019 logo big

2019 Galaxy Community Conference (GCC2019)
Freiburg, Germany, 1-6 July 2019
#usegalaxy / Chat

We are pleased to announce that GCC2019 will be held in Freiburg, Germany, 1-6 July. Like previous Galaxy Community Conferences, GCC2019 will feature invited keynotes, accepted talks, posters, and demos, birds-of-a-feather gatherings, multiple days of collaborative work, and plenty of opportunities to network with your fellow data-intensive researchers and practitioners. If you are working in data-intensive life science, there is no better place to be.

Location: 
Freiburg is on the edge of the Black Forest, and is famous for its architecture, cobblestone streets and historic districts, and is home to one of Germany's oldest universities (and our host)!. Freiburg is in the Baden wine-growing region and is the sunniest city in Germany.
GCC2019 will be held at Konzerthaus Freiburg in central Freiburg, adjacent to the Freiburg train station.

Hosts:  
GCC2019 is hosted by the Freiburg Galaxy Project, the University of Freiburg, and de.NBI (the German Network for Bioinformatics Infrastructure).

More Information:
https://galaxyproject.org/events/gcc2019/

Big Data in life science is scattered across hundreds of unstructured data sets, biological databases and thousands of scientific journals. Current high-throughput technologies generate large quantities of high-dimensional data. The challenge for Applied Bioinformatics is to capture, model, integrate, analyze, visualize and make these data accessible in a FAIR way to provide new and more profound insights into complex biological systems like crops.

The 15th Gatersleben Research Conference (#GRC2019) on Applied Bioinformatics in Crops takes place 18-20 March 2019 at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben, Germany. This conference will be of interest to Life Scientists, Bioinformaticians, Computer Scientists, Systems Biologists, Synthetic Biologists and others working or interested in the developing area of Applied Bioinformatics for crops. The meeting will provide an excellent environment and a range of opportunities to present and discuss methods, theoretical approaches, and their practical applications.

Topics of interests:
- Image-Based Data Analyses and Data Visualization
- Distributed Computing, Tools and Infrastructures
- Systems Biology and Modeling
- Biodiversity and Information Systems
- Breeding Informatics

The conference is supported by de.NBI. For more information see: http://meetings.ipk-gatersleben.de/grc2019-abc/