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Items: 16

1.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.

Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D.

J Integr Bioinform. 2018 Mar 29;15(1). pii: /j/jib.2018.15.issue-1/jib-2018-0013/jib-2018-0013.xml. doi: 10.1515/jib-2018-0013.

PMID:
29596055
2.

A Commitment to Open Source in Neuroscience.

Gleeson P, Davison AP, Silver RA, Ascoli GA.

Neuron. 2017 Dec 6;96(5):964-965. doi: 10.1016/j.neuron.2017.10.013.

3.

Toward standard practices for sharing computer code and programs in neuroscience.

Eglen SJ, Marwick B, Halchenko YO, Hanke M, Sufi S, Gleeson P, Silver RA, Davison AP, Lanyon L, Abrams M, Wachtler T, Willshaw DJ, Pouzat C, Poline JB.

Nat Neurosci. 2017 May 25;20(6):770-773. doi: 10.1038/nn.4550. No abstract available.

PMID:
28542156
4.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Myers C, Nickerson D, Sommer B, Walthemath D.

J Integr Bioinform. 2016 Dec 18;13(3):289. doi: 10.2390/biecoll-jib-2016-289.

5.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D.

J Integr Bioinform. 2016 Sep 1;13(3):1-7. doi: 10.1515/jib-2016-289.

PMID:
29215991
6.

The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex.

Ramaswamy S, Courcol JD, Abdellah M, Adaszewski SR, Antille N, Arsever S, Atenekeng G, Bilgili A, Brukau Y, Chalimourda A, Chindemi G, Delalondre F, Dumusc R, Eilemann S, Gevaert ME, Gleeson P, Graham JW, Hernando JB, Kanari L, Katkov Y, Keller D, King JG, Ranjan R, Reimann MW, Rössert C, Shi Y, Shillcock JC, Telefont M, Van Geit W, Diaz JV, Walker R, Wang Y, Zaninetta SM, DeFelipe J, Hill SL, Muller J, Segev I, Schürmann F, Muller EB, Markram H.

Front Neural Circuits. 2015 Oct 8;9:44. doi: 10.3389/fncir.2015.00044. eCollection 2015. No abstract available.

7.

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, Larson S.

Front Comput Neurosci. 2014 Nov 3;8:137. doi: 10.3389/fncom.2014.00137. eCollection 2014.

8.

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, Silver RA.

Front Neuroinform. 2014 Sep 25;8:79. doi: 10.3389/fninf.2014.00079. eCollection 2014.

9.

libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.

Vella M, Cannon RC, Crook S, Davison AP, Ganapathy G, Robinson HP, Silver RA, Gleeson P.

Front Neuroinform. 2014 Apr 23;8:38. doi: 10.3389/fninf.2014.00038. eCollection 2014.

10.

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 Comput Biol. 2014 Apr 24;10(4):e1003590. doi: 10.1371/journal.pcbi.1003590. eCollection 2014 Apr.

11.

Updated energy budgets for neural computation in the neocortex and cerebellum.

Howarth C, Gleeson P, Attwell D.

J Cereb Blood Flow Metab. 2012 Jul;32(7):1222-32. doi: 10.1038/jcbfm.2012.35. Epub 2012 Mar 21. Review.

12.

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. 2010 Aug 12;67(3):435-51. doi: 10.1016/j.neuron.2010.06.028.

13.

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 17;6(6):e1000815. doi: 10.1371/journal.pcbi.1000815.

14.

Interoperability of neuroscience modeling software: current status and future directions.

Cannon RC, Gewaltig MO, Gleeson P, Bhalla US, Cornelis H, Hines ML, Howell FW, Muller E, Stiles JR, Wils S, De Schutter E.

Neuroinformatics. 2007 Summer;5(2):127-38. Review.

15.

MorphML: level 1 of the NeuroML standards for neuronal morphology data and model specification.

Crook S, Gleeson P, Howell F, Svitak J, Silver RA.

Neuroinformatics. 2007 Summer;5(2):96-104. Review.

PMID:
17873371
16.

neuroConstruct: a tool for modeling networks of neurons in 3D space.

Gleeson P, Steuber V, Silver RA.

Neuron. 2007 Apr 19;54(2):219-35.

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