Topographica protocols

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Topographica specifications

Information


Unique identifier OMICS_17193
Name Topographica
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Source code URL http://ioam.github.io/topographica/Downloads/index.html
Maintained Yes

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Documentation


Maintainer


  • person_outline James Bednar <>

Publications for Topographica

Topographica in pipeline

2015
PMCID: 4396193
PMID: 25926788
DOI: 10.3389/fninf.2015.00011

[…] and networks (neuron, moose), highly-efficient large-scale networks of spiking point neurons (nest, pcsim, ncs, brian) to population coding or point-neuron models of large brain regions (nengo, topographica). note that although we have categorized each simulator by its main area of application, most of these tools support modeling at a range of scales and levels of detail: bednar (), […]


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Topographica in publications

 (13)
PMCID: 5442232
PMID: 28596730
DOI: 10.3389/fninf.2017.00034

[…] ; o'reilly et al., ), the neural simulation language (weitzenfeld et al., ), emergent (o'reilly et al., ), the simulation platform dana (rougier and fix, ), thevirtualbrain (sanz leon et al., ), topographica (bednar, ) and the neural field simulator (nichols and hutt, ). similarly, efficient simulators for population-density approaches (miind: de kamps et al., , dipde: cain et al., ) as well […]

PMCID: 5374876
PMID: 28408869
DOI: 10.3389/fncir.2017.00021

[…] sections in our previous work (antolík and bednar, ; stevens et al., ). the architecture of the 3 gcal variants presented in this paper is depicted in figures , . the models are implemented in the topographica simulator, freely available at www.topographica.org. each of the gcal models consists of a set of sheets of model neural units, corresponding to: (1) the photo-receptors, (2) […]

PMCID: 4889583
PMID: 27313528
DOI: 10.3389/fncom.2016.00052

[…] their contributions to presaccadic remapping. the results yielded comparisons with prior in vivo inactivation data and predictions for future in vivo experiments., we used a software package called topographica (http://www.topographica.org), designed originally for modeling visual cortex (bednar, ), to create large scale, hierarchical, connected neural network maps. in topographica, […]

PMCID: 4609756
PMID: 26539076
DOI: 10.3389/fnins.2015.00380

[…] et al., ), nengo is unique in focusing on large-scale functional simulations, rather than attempting to support detailed single-neuron models (though this capability is still possible in nengo). topographica (bednar, ) plays a similar role, in that it can interact with multiple neural simulators with a high-level api, but its api focuses specifically on models of topographic maps […]

PMCID: 4396193
PMID: 25926788
DOI: 10.3389/fninf.2015.00011

[…] (stewart et al., ), moose (ray and bhalla, ), steps (wils and de schutter, ) and ncs (drewes et al., ). however, as the articles by goodman and brette () on the brian simulator and bednar () on the topographica simulator demonstrate, it is also possible to develop new simulation environments purely in python, making use of the vectorization techniques available in the underlying numpy package […]


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Topographica institution(s)
Institute for Adaptive and Neural Computation, University of Edinburgh, Edinburgh, UK
Topographica funding source(s)
Supported in part by the National Institutes of Mental Health under Human Brain Project grant 1R01-MH66991, by the National Science Foundation under grant IIS-9811478, and by the EPSRC/MRC Doctoral Training Centre in Neuroinformatics at the University of Edinburgh.

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