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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

Versioning


No version available

Documentation


Maintainer


  • person_outline James Bednar

Publications for Topographica

Topographica citations

 (6)
library_books

Integration of Continuous Time Dynamics in a Spiking Neural Network Simulator

2017
Front Neuroinform
PMCID: 5442232
PMID: 28596730
DOI: 10.3389/fninf.2017.00034

[…] art, ; 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 […]

library_books

Benchmarking neuromorphic systems with Nengo

2015
Front Neurosci
PMCID: 4609756
PMID: 26539076
DOI: 10.3389/fnins.2015.00380

[…] ison 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 and other se […]

library_books

Current Practice in Software Development for Computational Neuroscience and How to Improve It

2014
PLoS Comput Biol
PMCID: 3900372
PMID: 24465191
DOI: 10.1371/journal.pcbi.1003376

[…] rely within the group.The biggest challenge with the Heroic Model is that such tools rarely reach the maturity and completeness required to constitute a public tool. Notable exceptions are Brian and Topographica , which have gained momentum and partially transitioned into other development models. However, many of the Heroic tools we examined have a single developer and no apparent ongoing activi […]

library_books

An automated and reproducible workflow for running and analyzing neural simulations using Lancet and IPython Notebook

2013
Front Neuroinform
PMCID: 3874632
PMID: 24416014
DOI: 10.3389/fninf.2013.00044

[…] dividual problems as they appear is likely to become unreadable over time, and is unlikely to be reused between projects. To illustrate, the RunBatchCommand and associated classes implemented for the Topographica simulator now offer significantly more functionality for batch simulations than was initially available with the simulator. Although the latest Topographica Lancet extension is still unde […]

library_books

Increasing quality and managing complexity in neuroinformatics software development with continuous integration

2013
Front Neuroinform
PMCID: 3539731
PMID: 23316158
DOI: 10.3389/fninf.2012.00031

[…] of the INCF Software Center (http://software.incf.org) revealed that out of more than 300 projects, less than 10 explicitly mention that they are using some form of CI, e.g., Slicer (CDash), NiPy and Topographica (buildbot). This suggests that either the awareness of CI is low in the neuroinformatics community, or that the hurdles to implement it have been too high.Therefore, as an experiment, we […]

library_books

Trends in Programming Languages for Neuroscience Simulations

2009
Front Neurosci
PMCID: 2796921
PMID: 20198154
DOI: 10.3389/neuro.01.036.2009

[…] ion of Python interfaces to several existing simulators, including NEURON (Hines et al., ), NEST (Eppler et al., ), Nengo (Stewart et al., ), MOOSE (Ray and Bhalla, ), STEPS (Wils and De Schutter, ), Topographica (Bednar, ) and NCS (Drewes et al., ), and in the choice of Python as the sole or principal interface language for new simulators such as Brian (Goodman and Brette, ) and PCSIM (Pecevski e […]

Citations

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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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