These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
3. 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 Elife; 2019 Apr; 8():. PubMed ID: 31025934 [TBL] [Abstract][Full Text] [Related]
4. The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology. Hucka M; Finney A; Sauro HM; Bolouri H; Doyle J; Kitano H Pac Symp Biocomput; 2002; ():450-61. PubMed ID: 11928498 [TBL] [Abstract][Full Text] [Related]
5. Computational neuroscience and neuroinformatics: Recent progress and resources. Nayak L; Dasgupta A; Das R; Ghosh K; De RK J Biosci; 2018 Dec; 43(5):1037-1054. PubMed ID: 30541962 [TBL] [Abstract][Full Text] [Related]
6. Towards reproducible descriptions of neuronal network models. Nordlie E; Gewaltig MO; Plesser HE PLoS Comput Biol; 2009 Aug; 5(8):e1000456. PubMed ID: 19662159 [TBL] [Abstract][Full Text] [Related]
7. Accessing and distributing EMBL data using CORBA (common object request broker architecture). Wang L; Rodriguez-Tomé P; Redaschi N; McNeil P; Robinson A; Lijnzaad P Genome Biol; 2000; 1(5):RESEARCH0010. PubMed ID: 11178259 [TBL] [Abstract][Full Text] [Related]
8. OSS-DBS: Open-source simulation platform for deep brain stimulation with a comprehensive automated modeling. Butenko K; Bahls C; Schröder M; Köhling R; van Rienen U PLoS Comput Biol; 2020 Jul; 16(7):e1008023. PubMed ID: 32628719 [TBL] [Abstract][Full Text] [Related]
9. Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data. Kyoda K; Tohsato Y; Ho KH; Onami S Bioinformatics; 2015 Apr; 31(7):1044-52. PubMed ID: 25414366 [TBL] [Abstract][Full Text] [Related]
10. KInNeSS: a modular framework for computational neuroscience. Versace M; Ames H; Léveillé J; Fortenberry B; Gorchetchnikov A Neuroinformatics; 2008; 6(4):291-309. PubMed ID: 18695948 [TBL] [Abstract][Full Text] [Related]
11. 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 Neuron; 2019 Aug; 103(3):395-411.e5. PubMed ID: 31201122 [TBL] [Abstract][Full Text] [Related]
12. Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits. Dai K; Gratiy SL; Billeh YN; Xu R; Cai B; Cain N; Rimehaug AE; Stasik AJ; Einevoll GT; Mihalas S; Koch C; Arkhipov A PLoS Comput Biol; 2020 Nov; 16(11):e1008386. PubMed ID: 33253147 [TBL] [Abstract][Full Text] [Related]
14. Reproducibility in Computational Neuroscience Models and Simulations. McDougal RA; Bulanova AS; Lytton WW IEEE Trans Biomed Eng; 2016 Oct; 63(10):2021-35. PubMed ID: 27046845 [TBL] [Abstract][Full Text] [Related]
15. NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. Gleeson P; Crook S; Cannon RC; Hines ML; Billings GO; Farinella M; Morse TM; Davison AP; Ray S; Bhalla US; Barnes SR; Dimitrova YD; Silver RA PLoS Comput Biol; 2010 Jun; 6(6):e1000815. PubMed ID: 20585541 [TBL] [Abstract][Full Text] [Related]