One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project

Autor: Bergmann, Frank T., Adams, Richard, Moodie, Stuart, Cooper, Jonathan, Glont, Mihai, Golebiewski, Martin, Hucka, Michael, Laibe, Camille, Miller, Andrew K., Nickerson, David P., Olivier, Brett G., Rodriguez, Nicolas, Sauro, Herbert M., Scharm, Martin, Soiland-Reyes, Stian, Waltemath, Dagmar, Yvon, Florent, Novère, Nicolas Le

Publikováno v: BMC Bioinformatics 15 (2014) 369

Background: With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been p

Externí odkaz: http://arxiv.org/abs/1407.4992

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Data Management in Computational Systems Biology

Autor: Stanford, Natalie J., Scharm, Martin, Dobson, Paul D., Golebiewski, Martin, Hucka, Michael, Kothamachu, Varun B., Nickerson, David, Owen, Stuart, Pahle, Jürgen, Wittig, Ulrike, Waltemath, Dagmar, Goble, Carole, Mendes, Pedro, Snoep, Jacky, Oliver, Stephen G., Castrillo, Juan I.

Publikováno v: Yeast Systems Biology: Methods and Protocols, 285-314
ISSUE=2;STARTPAGE=285;ENDPAGE=314;TITLE=Yeast Systems Biology
Methods in Molecular Biology ISBN: 9781493997350
Stanford, N J, Scharm, M, Dobson, P D, Golebiewski, M, Hucka, M, Kothamachu, V B, Nickerson, D, Owen, S, Pahle, J, Wittig, U, Waltemath, D, Goble, C, Mendes, P & Snoep, J 2019, Data Management in Computational Systems Biology : Exploring Standards, Tools, Databases, and Packaging Best Practices . in S G Oliver & J I Castrillo (eds), Yeast Systems Biology : Methods and Protocols . 2nd edn, Methods in Molecular Biology, vol. 2049, Humana Press Inc, pp. 285-314 . https://doi.org/10.1007/978-1-4939-9736-7_17

Computational systems biology involves integrating heterogeneous datasets in order to generate models. These models can assist with understanding and prediction of biological phenomena. Generating datasets and integrating them into models involves a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fad95249f1b679f40a6a2b3850242b96
https://research.vu.nl/en/publications/0d5dac82-810f-4c91-83e0-226229c98812

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COMODI: COmputational MOdels DIffer - a hands-on-poster

Autor: Scharm, Martin, Waltemath, Dagmar, Wolkenhauer, Olaf

Models are regularly updated, even after publication. The BiVeS library [3, 4, 5] offers comparison of versions of SBML [6] and CellML [7] encoded models. The result of such a comparison is a list of changes, based on the differences in both XML file

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2e79799a883fc41349cbfa555ba639a8