SYSTEMS BIOLOGY

BIOINFORMATICS

ROSTOCKS E Ssimulation experiment management system

The CombineArchive Toolkitfacilitating the transfer of research results.

MARTIN SCHARM, FLORIAN WENDLANDDepartment of Systems Biology & Bioinformatics, University of Rostock

http://sems.uni-rostock.de

SBI Research SeminarWS 2014/2015

October 20, 2014 CombineArchive Toolkit | Martin Scharm, Florian Wendland 1

How do you share your data?

science sucks - stern i4ever

science sucks - stern i4ever

science sucks - stern i4ever

October 20, 2014 CombineArchive Toolkit | Martin Scharm, Florian Wendland 2

The COMBINE Archiveone file to share them all

TM

October 20, 2014 CombineArchive Toolkit | Martin Scharm, Florian Wendland 3

The COMBINE Archiveone file to share them all

• OMEX: Open Modelling EXchange Format

• Contents:

• manifest.xml – information about files and their formats

• Meta data files – clerical information

• The files – necessary to reproduce a modelling result

• Already convinced

October 20, 2014 CombineArchive Toolkit | Martin Scharm, Florian Wendland 4

CATThe CombineArchive Toolkit

Martin Scharm

Florian Wendland

Martin Peters

Dagmar Waltemath

Tom Theile

Markus Wolfien

October 20, 2014 CombineArchive Toolkit | Martin Scharm, Florian Wendland 5

CATThe CombineArchive Toolkit

• Java library:• Oragnise files

• Attach and retrieve meta data

• Build, validate, and repair archive

• Desktop Application

• Web Interface

Website: sems.uni-rostock.de/cat

Martin Scharm

Florian Wendland

Martin Peters

Dagmar Waltemath

Tom Theile

Markus Wolfien

October 20, 2014 CombineArchive Toolkit | Martin Scharm, Florian Wendland 6

CATThe CombineArchive Toolkit

Desktop WebApplication Interface

CombineArchive Library

CombineArchive Toolkit

create

science sucks - stern i4ever

modifyBioModelsDatabase

explore

CellML ModelRepository

share

science sucks - stern i4ever

science sucks - stern i4ever

science sucks - stern i4ever

science sucks - stern i4ever

Martin Scharm

Florian Wendland

Martin Peters

Dagmar Waltemath

Tom Theile

Markus Wolfienpeerj.com/preprints/514

October 20, 2014 CombineArchive Toolkit | Martin Scharm, Florian Wendland 7

Foundry WorkshopThe CombineArchive Toolkit

What does my tool do? The CombineArchive Toolkit facilitates the transfer ofresearch results.What are the neighbors of the tool? Our library can be integrated inwebsites, databases, and other software projects to add support for COMBINEArchives. The user interfaces provide intuitive access to COMBINE Archives forend users.Who are the users of the tool? Every scientist can use theCombineArchive Toolkit to share reproducible research results. Softwaredevelopers may integrate our library into their tools.What is the current sustainability concept? The format as well as ourtools are open and free to use for everyone interested in reproducibility.How does this fit in with ELIXIR/ISBE/National efforts? Thecombine archive format was co-developed by active members of ELIXIR, ISBE, andthe BMBF. Thus, this format is supposed to become the standard format in thesesocieties.

October 20, 2014 CombineArchive Toolkit | Martin Scharm, Florian Wendland 8

SYSTEMS BIOLOGY

BIOINFORMATICS

ROSTOCKS E Ssimulation experiment management system

Thank you for your attention!

SEMS group

Dagmar WaltemathRon HenkelMartin PetersMarkus WolfienRebekka AlmOlaf Wolkenhauer

@SemsProject

http://sems.uni-rostock.de

October 20, 2014 CombineArchive Toolkit | Martin Scharm, Florian Wendland 9