de.NBI-SYSBIO

and

e:Bio SBGN-ED+

Dagmar Waltemath

SBI research seminar, February 2015

SEMS: Improving reproducibility of virtual experiments

using tools from database and information sciences

2

SEMS: Improving reproducibility of virtual experiments

using tools from database and information sciences

de.NBI-SYSBIO

SBGN-ED+

3

SEMS: Improving reproducibility of virtual experiments

using tools from database and information sciences

de.NBI-SYSBIO

4

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.

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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

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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

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• 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

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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.

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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

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SEMS: Improving reproducibility of virtual experiments

using tools from database and information sciences

SBGN-ED+

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SBGN-ED+

SBGN = Systems Biology Graphical Notation

Fig.: Nicolas Le Novère et al:

The Systems Biology Graphical

Notation. Nature Biotech (2009)

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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

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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

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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

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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

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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+

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Thank you