A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos

Martin Scharm, Dagmar Waltemath
2016 F1000Research  
COMBINE archives are standardised containers for data files related to a simulation study in computational biology. This manuscript describes a fully featured archive of a previously published simulation study, including (i) the original publication, (ii) the model, (iii) the analyses, and (iv) metadata describing the files and their origin. With the archived data at hand, it is possible to reproduce the results of the original work. The archive can be used for both, educational and research
more » ... poses. Anyone may reuse, extend and update the archive to make it a valuable resource for the scientific community. Martin Scharm ( ), Dagmar Waltemath ( ) Corresponding authors: martin.scharm@uni-rostock.de dagmar.waltemath@uni-rostock.de Scharm M and Waltemath D. How to cite this article: A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles 2016, :2421 (doi: in embryos [version 1; referees: 1 approved, 2 approved with reservations] Drosophila F1000Research 5 ) PubMed Abstract | Publisher Full Text 2. Prinz F, Schlange T, Asadullah K: Believe it or not: how much can we rely on published data on potential drug targets? Nat Rev Drug Discov. 2011; 10(9): 712. PubMed Abstract | Publisher Full Text 3. Ioannidis JP, Allison DB, Ball CA, et al.: Repeatability of published microarray gene expression analyses. Nat Genet. 2009; 41(2): 149-155. PubMed Abstract | Publisher Full Text 4. Begley CG, Ellis LM: Drug development: Raise standards for preclinical cancer research. Nature. 2012; 483(7391): 531-533. PubMed Abstract | Publisher Full Text 5. Sandve GK, Nekrutenko A, Taylor J, et al.: Ten simple rules for reproducible computational research. PLoS Comput Biol. 2013; 9(10): e1003285. PubMed Abstract | Publisher Full Text | Free Full Text 6. Corcho Ó, Garijo Verdejo D, Belhajjame K, et al.: Workflow-centric research objects: First class citizens in scholarly discourse. In 2nd Workshop on Semantic Publishing. Informatica, 2012. Reference Source 7. Bechhofer S, De Roure D, Gamble M, et al.: Research objects: Towards exchange and reuse of digital knowledge. The Future of the Web for Collaborative Science. 2010. Publisher Full Text 8. Bergmann FT, Adams R, Moodie S, et al.: COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics. 2014; 15(1): 369. PubMed Abstract | Publisher Full Text | Free Full Text 9. Scharm M, Wendland F, Peters M, et al.: The CombineArchiveWeb application -A web-based tool to handle files associated with modelling results. In
doi:10.12688/f1000research.9379.1 pmid:27830063 pmcid:PMC5082596 fatcat:mrrmaxj7w5fqtp3hwneheihynq