SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK SE S simulation experiment management system M2CAT Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit MARTIN SCHARM Department of Systems Biology & Bioinformatics, University of Rostock http://sems.uni-rostock.de 9th International CellML Workshop Waiheke Island, New Zealand 2015 April 13, 2015 M2CAT | Martin Scharm 1
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M2CAT: Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit
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SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCKS E Ssimulation experiment management system
M2CATExtracting reproducible simulation studiesfrom model repositories using theCombineArchive Toolkit
MARTIN SCHARMDepartment of Systems Biology & Bioinformatics, University of Rostock
http://sems.uni-rostock.de
9th International CellML WorkshopWaiheke Island, New Zealand 2015
Improving the Management of Simulation Studies in Computational BiologyMartin Scharm, Vivek Garg, Srijana Kayastha, Martin Peters, Dagmar Waltemath
Events
S E Ssimulation experiment management system
https://sems.uni-rostock.de
de.NBI InfrastructureWe will provide data management and support for systems biol-ogy projects, with a focus on provenance and reproducibility ofexperimental and modelling results. de.NBI:SYSBIO is part of alarge German Network for Bioinformatics Infrastructure.WE ARE HIRING!
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SBGN-EDSBGN is a markup language to describe mod-els and exchange information about biological sys-tems graphically. We will further develop meth-ods and tools for SBGN-compliant visualisation ofmodel-related information. WE ARE HIRING!
CombineArchive ToolkitSharing in silico experiments is essential for the advance of researchin computational biology. The COMBINE archive is a digital containerformat to easen the management of numerous files and to enable theexchange of reproducible modelling results. We developed the Combin-eArchive Toolkit, consisting of a library, a web interface and a desktopapplication. It support scientists in creating, exploring, modifying, andsharing COMBINE archives.
2MT2MT is our web based platform todemonstrate the capabilities of SEMS-related tools. It exemplifies how ourmodel management solutions can beused in existing tools.
Models as graphsThe increasing diversity of model-related data that is nec-essary to perform a simulation study leads to new chal-lenges in model storage. We developed a concept forgraph-based storage of models and model-related data.Graphs reflect the models’ structure much better, enablelinking of model-related data on the storage layer, and al-low for an efficient search.
MasymosContaining SBML- and CellML models,linked semantic annotations (e.g., from bio-ontologies), simulation descriptions, graph-ical representations and other availabletypes of model-related data, out graphdatabase Masymos can now be queried forcomplete simulation experiments.
MorreOur retrieval engine for models applies In-formation Retrieval techniques to retrieverelevant models from MASYMOS. The pro-posed ranking and retrieval techniques fo-cus on the processing of model meta-information.
Ontology of DifferencesChanges in model versions are manifoldand appear on different layers. We de-velop an ontology of differences occurring inmodel versions. It will support researchersin analysing differences, discovering typicalchanges, summarising major changes andproviding statistics.
Version Control forComputational Models
With thousands of models available, a framework to track the differencesbetween models and their versions is essential to compare and combinemodels. Focusing on SBML and CellML, we developed an algorithm toaccurately detect and describe differences between versions of a modelwith respect to (i) the models’ encoding, (ii) the structure of biologicalnetworks, and (iii) mathematical expressions.
version x-1 version x version x+1
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G BiVeSArmed with our method for difference detec-tion, BiVeS is able to detect and communicatethe differences in computational models. Thedifferences are exported in several machine-and human-readable formats, ideally suited tobe integrated in other tools.
BudHatBudHat showcases how BiVeS improvesthe understanding of a model’s changes.BudHat calls BiVeS for the comparisontwo versions of a computational model anddisplays the obtained results in the webbrowser.
VW Summer School, March 9-13, 2015During the 2015 Whole Cell summer school we aim todevelop a standard-compliant, open version of the whole-cell model. Eleven tutors and 48 students will hack andcode, model and simulate, layout and annotate the whole-cell model using openly available software and COM-BINE standards. This event is funded by the VolkswagenStiftung.
HARMONY, April 19-23, 2015HARMONY is a hackathon-type meeting of the COMBINE Community,with a focus on development of the standards, interoperability and infras-tructure. Instead of general discussions or oral presentations, the time isdevoted to hands-on hacking and interaction between people focused onpractical development of software and standards. The HARMONY 2015is located at the Leucorea Wittenberg and it is hosted by the groups ofFalk Schreiber and Dagmar Waltemath.
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Workshop on Reproducible and Citable Dataand Models, September 14-16, 2015Computational biologists and experimentalists will learnabout standards, citable data, about how to make scien-tific results sustainable, available through open reposito-ries, and about how to find and reuse other people’s worksin a mixture of lectures and hands-on sessions. The work-shop is funded by the ERASYS-APP program.