The CombineArchive Toolkit - facilitating the transfer of research results.

SYSTEMS BIOLOGY

BIOINFORMATICS

ROSTOCKS E Ssimulation experiment management system

The CombineArchive Toolkitfacilitating the transfer of research results.

MARTIN SCHARMDepartment of Systems Biology & Bioinformatics, University of Rostock

http://sems.uni-rostock.de

Foundry Workshop, Heidelberg

October, 2014 CombineArchive Toolkit | Martin Scharm 1

http://www.sbi.uni-rostock.de/team/single/martin-scharm/



SYSTEMS BIOLOGY

BIOINFORMATICS


S E Ssimulation experiment management system

Graph Database

Version Control

∆ ∆

Retrieval

Ranking

retrieve

rank

track development

store

Version 1

Version 2

latest



How do you share your data?

science sucks - stern i4ever





The COMBINE Archiveone file to share them all



The COMBINE Archiveone file to share them all

• ZIP container (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 supported by



CATThe CombineArchive Toolkit

• Java library:

• Extract single files / whole archive

• Browse through the archive

• Add and remove files

• Rename and organise files

• Attach and retrieve meta data

• Desktop Application

• Web Interface

Website: sems.uni-rostock.de/cat

Publication: peerj.com/preprints/514

Martin Scharm

Florian Wendland

Martin Peters


http://sems.uni-rostock.de/cat

https://peerj.com/preprints/514/


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.



SYSTEMS BIOLOGY

BIOINFORMATICS


Thank you for your attention!

SEMS group

Dagmar WaltemathRon HenkelMartin PetersMarkus WolfienRebekka AlmOlaf Wolkenhauer

@SemsProject



https://twitter.com/semsproject



The CombineArchive Toolkit - facilitating the transfer of research results.

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