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The evolution of standards and data management practices in systems biology

Stanford, Natalie J.; Wolstencroft, Katherine; Golebiewski, Martin; Kania, Renate; Juty, Nick; Tomlinson, Christopher; Owen, Stuart; Butcher, Sarah; Hermjakob, Henning; Le Novere, Nicolas; Mueller, Wolfgang; Snoep, Jacky; Goble, Carole (EMBO, 2015-12)

Systems biology involves the integration of multiple heterogeneous data sets, in order to model and predict biological processes. The domain's interdisciplinary nature requires data, models and other research assets to be ...

Minimum information about a simulation experiment (MIASE)

Waltemath, Dagmar; Adams, Richard; Beard, Daniel A.; Bergmann, Frank T.; Balla, Upinder S.; Britten, Randall; Chelliah, Vijayalakshmi; Cooling, Michael T.; Cooper, Jonathan; Crampin, Edmund J.; Garny, Alan; Hoops, Stefan; Hucka, Michael; Hunter, Peter; Klipp, Edda; Laibe, Camille; Miller, Andrew K.; Moraru, Ion; Nickerson, David; Nielsen, Poul; Nikolski, Macha; Sahle, Sven; Sauro, Herbert M.; Schmidt, Henning; Snoep, Jacky L.; Tolle, Dominic; Wolkenhauer, Olaf; Le Novere, Nicolas (PLOS, 2011-04)

Reproducibility of experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved a helpful means of enabling reuse of existing work in modern biology. The Minimum Information Required in ...

Reproducible computational biology experiments with SED-ML -The Simulation Experiment Description Markup Language

Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T.; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K.; Moraru, Ion I.; Nickerson, David; Sahle, Sven; Snoep, Jacky L.; Le Novere, Nicolas (BioMed Central, 2011-12)

Background: The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum ...

Identifiers for the 21st century : how to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

McMurry, Julie A.; Juty, Nick; Blomberg, Niklas; Burdett, Tony; Conlin, Tom; Conte, Nathalie; Courtot, Melanie; Deck, John; Dumontier, Michel; Fellows, Donal K.; Gonzalez-Beltran, Alejandra; Gormanns, Philipp; Grethe, Jeffrey; Hastings, Janna; Heriche, Jean-Karim; Hermjakob, Henning; Ison, Jon C.; Jimenez, Rafael C.; Jupp, Simon; Kunze, John; Laibe, Camille; Le Novere, Nicolas; Malone, James; Martin, Maria Jesus; McEntyre, Johanna R.; Morris, Chris; Muilu, Juha; Muller, Wolfgang; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Sariyar, Murat; Snoep, Jacky L.; Soiland-Reyes, Stian; Stanford, Natalie J.; Swainston, Neil; Washington, Nicole; Williams, Alan R.; Wimalaratne, Sarala M.; Winfree, Lilly M.; Wolstencroft, Katherine; Goble, Carole; Mungall, Christopher J.; Haende, Melissa A.; Parkinson, Helen (Public Library of Science, 2017-06-29)

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on ...