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The SONATA data format for efficient description of large-scale network models.
Dai K, Hernando J, Billeh YN, Gratiy SL, Planas J, Davison AP, Dura-Bernal S, Gleeson P, Devresse A, Dichter BK, Gevaert M, King JG, Van Geit WAH, Povolotsky AV, Muller E, Courcol JD, Arkhipov A. Dai K, et al. PLoS Comput Biol. 2020 Feb 24;16(2):e1007696. doi: 10.1371/journal.pcbi.1007696. eCollection 2020 Feb. PLoS Comput Biol. 2020. PMID: 32092054 Free PMC article.
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits.
Gleeson P, Cantarelli M, Marin B, Quintana A, Earnshaw M, Sadeh S, Piasini E, Birgiolas J, Cannon RC, Cayco-Gajic NA, Crook S, Davison AP, Dura-Bernal S, Ecker A, Hines ML, Idili G, Lanore F, Larson SD, Lytton WW, Majumdar A, McDougal RA, Sivagnanam S, Solinas S, Stanislovas R, van Albada SJ, van Geit W, Silver RA. Gleeson P, et al. Neuron. 2019 Aug 7;103(3):395-411.e5. doi: 10.1016/j.neuron.2019.05.019. Epub 2019 Jun 11. Neuron. 2019. PMID: 31201122 Free PMC article.
NetPyNE, a tool for data-driven multiscale modeling of brain circuits.
Dura-Bernal S, Suter BA, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GM, Lytton WW. Dura-Bernal S, et al. Elife. 2019 Apr 26;8:e44494. doi: 10.7554/eLife.44494. Elife. 2019. PMID: 31025934 Free PMC article.
Harmonizing semantic annotations for computational models in biology.
Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D. Neal ML, et al. Brief Bioinform. 2019 Mar 22;20(2):540-550. doi: 10.1093/bib/bby087. Brief Bioinform. 2019. PMID: 30462164 Free PMC article. Review.
OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans.
Sarma GP, Lee CW, Portegys T, Ghayoomie V, Jacobs T, Alicea B, Cantarelli M, Currie M, Gerkin RC, Gingell S, Gleeson P, Gordon R, Hasani RM, Idili G, Khayrulin S, Lung D, Palyanov A, Watts M, Larson SD. Sarma GP, et al. Philos Trans R Soc Lond B Biol Sci. 2018 Sep 10;373(1758):20170382. doi: 10.1098/rstb.2017.0382. Philos Trans R Soc Lond B Biol Sci. 2018. PMID: 30201845 Free PMC article. Review.
12 results