MaSyMoS: Finding Hidden Treasures in Model Repositories

Ensuring reproducibility of simulation studies in computational biology poses a challenge to data management solutions. One specific problem is the organisation and linking of all files related to a simulation study at the storage level. Such a study comprises of a number of files, and additional links to third party resources. MaSyMoS is a graph-based approach to representing the links between the files necessary to reproduce a simulation study. It is based on a Neo4J database and designed specifically to handle files in COMBINE standard formats. Availability: https://sems.uni-rostock.de/projects/masymos/

[1]  Chris J. Myers,et al.  Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE) , 2011, Standards in Genomic Sciences.

[2]  Nicolas Le Novère,et al.  COMBINE archive: One File To Share Them All , 2014, ArXiv.

[3]  Ronan M. T. Fleming,et al.  A community-driven global reconstruction of human metabolism , 2013, Nature Biotechnology.

[4]  Jim Webber,et al.  Graph Databases: New Opportunities for Connected Data , 2013 .

[5]  Melanie I. Stefan,et al.  BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models , 2010, BMC Systems Biology.

[6]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[7]  Michel Dumontier,et al.  Controlled vocabularies and semantics in systems biology , 2011, Molecular systems biology.

[8]  Olaf Wolkenhauer,et al.  Annotation-based feature extraction from sets of SBML models , 2014, Journal of Biomedical Semantics.

[9]  Nicolas Le Novère,et al.  BioModels linked dataset , 2014, BMC Systems Biology.

[10]  J. Tyson,et al.  Modeling the control of DNA replication in fission yeast. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Nicolas Le Novère,et al.  Ranked retrieval of Computational Biology models , 2010, BMC Bioinformatics.

[12]  Ron Henkel,et al.  Combining computational models, semantic annotations, and associated simulation experiments in a graph database , 2014 .

[13]  Zoran Nikoloski,et al.  A quantitative comparison of Calvin-Benson cycle models. , 2011, Trends in plant science.

[14]  Peter J. Hunter,et al.  The CellML Model Repository , 2008, Bioinform..

[15]  Michael Darsow,et al.  ChEBI: a database and ontology for chemical entities of biological interest , 2007, Nucleic Acids Res..