The NeuroML ecosystem for standardized multi-scale modeling in neuroscience
Sinha A*, Gleeson P*, Marin B, Dura-Bernal S, Panagiotou S, Crook S, Cantarelli M, Cannon RC, Davison AP, Gurnani H, Silver RA
eLife 13:RP95135 (2024)
Preprint wth PDF on bioRxiv
NeuroML-DB: Sharing and characterizing data-driven neuroscience models described in NeuroML.
Birgiolas J, Haynes V, Gleeson P, Gerkin RC, Dietrich SW and Crook S
PLoS Computational Biology 19 (3), e1010941 (2023)
Integrating model development across computational neuroscience, cognitive science, and machine learning.
Gleeson P, Crook S, Turner D, Mantel K, Raunak M, Willke T, and Cohen JD
Neuron 111 (10):1526-1530 (2023)
Editorial: Neuroinformatics of large-scale brain modelling.
Griffiths JD, Shen K and Gleeson P
Frontiers in Neuroinformatics, 16, 1043732 (2022)
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, … (17 authors), Arkhipov A
PLOS Computational Biology 16(2):e1007696 (2020)
NetPyNE, a tool for data-driven multiscale modeling of brain circuits.
Dura-Bernal S, Suter BA, Gleeson P, Cantarelli M, Quintana A, … (14 authors), Lytton WW
eLife 8, e44494 (2019)
The Importance of Standards for Sharing of Computational Models and Data.
Poldrack RA, Feingold F, Frank MJ, Gleeson P, … (15 authors), Cohen JD
Computational Brain & Behavior 2, 229–232 (2019)
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, … (27 authors), Silver RA
Neuron 103 (3):395–411 (2019)
Code Generation in Computational Neuroscience: A Review of Tools and Techniques.
Blundell I, Brette R, Cleland TA, Close TG, Coca D, Davison AP, Diaz-Pier S, Fernandez Musoles C, Gleeson P, … (29 authors), Eppler JM
Frontiers in Neuroinformatics 12:68 (2018)
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 and Larson SD
Phil. Trans. R. Soc. B 373 20170382 (2018)
Geppetto: a reusable modular open platform for exploring neuroscience data and models.
Cantarelli M, Marin B, Quintana A, Earnshaw M, Court R, Gleeson P, Dura-Bernal S, Silver RA, and Idili G
Phil. Trans. R. Soc. B 373 20170380 (2018)
c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans.
Gleeson P, Lung D, Grosu R, Hasani R and Larson SD
Phil. Trans. R. Soc. B 373 20170379 (2018)
Toward standard practices for sharing computer code and programs in neuroscience.
Eglen SJ, Marwick B., Halchenko YO, Hanke M, Sufi S, Gleeson P, … (14 authors), Poline JB
Nature Neuroscience 20, 770–773 (2017)
A Commitment to Open Source in Neuroscience.
Gleeson P, Davison AP, Silver RA, and Ascoli GA
Neuron 96, 964–965 (2017)
libNeuroML and PyLEMS: Using Python to combine procedural and declarative modeling approaches in computational neuroscience.
Vella M, Robinson HPC, Cannon RC, Ganapathy G, Crook S, Davison AP, Silver RA, Gleeson P
Frontiers in Neuroinformatics 8:38 (2014)
Glutamate-bound NMDARs arising from in vivo-like network activity extend spatio-temporal integration in a L5 cortical pyramidal cell model.
Farinella M, Ruedt DT, Gleeson P, Lanore F, Silver RA
PLOS Computational Biology 10(4):e1003590 (2014)
OpenWorm: an open-science approach to modeling Caenorhabditis elegans.
Szigeti B, Gleeson P, Vella M, Khayrulin S, Palyanov A, Hokanson J, Currie M, Cantarelli M, Idili G and Larson S
Frontiers in Computational Neuroscience 8:137 (2014)
LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2.
Cannon RC*, Gleeson P*, Crook S, Ganapathy G, Marin B, Piasini E and Silver RA
Frontiers in Neuroinformatics 8:79 (2014)
Updated energy budgets for neural computation in the neocortex and cerebellum
Howarth C, Gleeson P and Attwell D
J Cereb Blood Flow Metab. 32(7):1222-32 (2012)
Rapid desynchronization of an electrically coupled interneuron network with sparse excitatory synaptic input.
Vervaeke K, Lorincz A, Gleeson P, Farinella M, Nusser Z, Silver RA
Neuron 67(3):435451 (2010)
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 Computational Biology 6(6):e1000, 815 (2010)
MorphML: Level 1 of the NeuroML Standards for Neuronal Morphology Data and Model Specification
Crook S, Gleeson P, Howell F, Svitak J and Silver RA
Neuroinformatics 5, 96–104 (2007)
neuroConstruct: a tool for modeling networks of neurons in 3D space.
Gleeson P, Steuber V, Silver RA
Neuron 54(2):219-235 (2007)