Talk in the research seminar of the Systems Biology group at the University of Rostock. The goal was to introduce the two new projects running in SEMS from summer 2015: The de.NBI-SYSBIO German Network for Bioinformatics infrastructure (focus: systems biology data management) and SBGN-ED (support and further development of SBGN-ED and libSBGN).

1. de.NBI-SYSBIO
and
e:Bio SBGN-ED+
Dagmar Waltemath
SBI research seminar, February 2015

2. SEMS: Improving reproducibility of virtual experiments
using tools from database and information sciences
2

3. SEMS: Improving reproducibility of virtual experiments
using tools from database and information sciences
de.NBI-SYSBIO
SBGN-ED+
3

4. SEMS: Improving reproducibility of virtual experiments
using tools from database and information sciences
de.NBI-SYSBIO
4

5. de.NBI – German Network for
Bioinformatics Infrastructure
A German network of (1) specialised service units with outstanding
expertise in research areas within the life sciences, and (2) local
hubs for high-quality databases. [..]
de.NBI bundles these know-hows and secures the technical
equipment of the service units, as well as the continued
development of bioinformatics services and standards.
de.NBI furthermore develops concepts for long-term availability of
these services and resources.
5

6. de.NBI – German Network for
Bioinformatics Infrastructure
Leistungszentren
Lokale Datenressourcen
HD-HuB
DKFZ
BiGi
Bielefeld
Bioinfra Prot
Bochum
RBC
Freiburg
CiBi
Tübingen
GCBN
Gatersleben/
München
PANGAEA
Bremen
Datenbanken
SILVA
Bremen
Brenda
Braun-
schweig
DSMZ
DBs
Braun-
schweig
Koordinationseinheit
N.N.
2. Call
BMBF / Pt Jülich
NBI-
SysBIO
Heidelberg
Daten-Management
• 1 coordination unit, 6 Bioinformatics centers, 2 database nodes
2nd call planned for “late 2014”
Fig. courtesy PTJ Jülich
6

7. de.NBI – German Network for
Bioinformatics Infrastructure
• Project duration: March 2015 – February 2018
• Coordinator: Alfred Pühler, University of Bielefeld
• 18 project partners
Fig. courtesy PTJ Jülich
7

8. • Project partner:
• HITS Heidelberg (W. Müller)
• Initially 6 partners, project to improve software tools for
modeling and simulation in computational biology
• Collaborators:
• M. Golebiewski (SABIO-RK),
• C. Goble (Rightfield),
• U. Klingmüller (Exemplify)
• Tools
• SEEK
• SABIO-RK
de.NBI-SYSBIO: Data and model
management
8

9. de.NBI-SYSBIO: Data and model
management
• Project goals (3 yrs; 3 full time scientific developers, 1 @SBI)
• Data management support for systems biology projects,
with focus on provenance and reproducibility
• To establish the use of standards in the modelling workflow
• To enable experimentalists to submit data to SABIO-RK
• To provide high quality curated biochemical data to modellers
and experimentalists
• Training, training, training...
• Dagmar's motivation:
• To implement algorithms for model management in SEEK
• To promote COMBINE standards in Germany
• To interact more with the people doing in data management
4 life sciences We are hiring:
E13 full-time scientific
developer, possibility to
do a Ph.D.
9

10. SEMS: Improving reproducibility of virtual experiments
using tools from database and information sciences
Tools and concepts for the
management of
simulation experiments
• MVC support (BiVeS)
• Management of simulation
studies (MASYMOS,
MORRE)
• Standards compliance
(COMBINE)
de.NBI-SYSBIO
10

11. SEMS: Improving reproducibility of virtual experiments
using tools from database and information sciences
SBGN-ED+
11

12. SBGN-ED+
SBGN = Systems Biology Graphical Notation
Fig.: Nicolas Le Novère et al:
The Systems Biology Graphical
Notation. Nature Biotech (2009)
12

13. SBGN-ED+
• SBGN-ED = SBGN Editor
• Java based
• Add-on for VANTED
Fig.: Tobias Czauderna
et al: Editing, validating
and translating of SBGN
maps. Bioinformatics
2010;26:2340-2341
13

14. SBGN-ED+
• SBGN-ED+ = better SBGN Editor
• Java based
• Add-on for VANTED
Fig.: Tobias Czauderna
et al: Editing, validating
and translating of SBGN
maps. Bioinformatics
2010;26:2340-2341
14

15. SBGN-ED+
• Coordinator: Falk Schreiber (IPK Gatersleben → Monash
University)
• Project duration: April 2012 – May 2014, plus 1.5yrs at SBI
• Partners:
• H. Hermjakob (EMBL-EBI),
• B. de Bono (UCL)
• Achievements:
• Improved layout algorithms
• Further development of libSBGN
• Improved user interface
• SBML – SBGN-ML transformation
15

16. SBGN-ED+
• Project goals (1 full-time scientific developer)
• Conversion of SBML/BioPAX models in SBGN-ML and vice
versa
• Connecting SBGN-ED with BioModels Database
• Promotion of SBGN & case studies
• Development of libSBGN
• Training, training, training …
• Dagmar's motivation
• Providing a [usable] tool to work with SBGN maps,
specifically to provide maps for COMBINE archives
• Promotion of SBGN with modelers
We are hiring:
One E13 full-time
scientific developer
for 1.5 yrs
16

17. SEMS: Improving reproducibility of virtual experiments
using tools from database and information sciences
Model version control
and provenance
• Visualisation of
differences in model
versions (BiVeS)
• Generation of SBGN
maps for CAT
Courtesy M. Scharm
SBGN-ED+
17

18. Thank you