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pyLEMS specifications

Information


Unique identifier OMICS_34209
Name pyLEMS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Padraig Gleeson

Publication for pyLEMS

pyLEMS citations

 (3)
library_books

Modeling Behavioral Experiment Interaction and Environmental Stimuli for a Synthetic C. elegans

2017
Front Neuroinform
PMCID: 5727351
PMID: 29276485
DOI: 10.3389/fninf.2017.00071

[…] li modeling approach and its implementation presented in this paper may provide stimuli input for C. elegans behavioral experiments for various neuronal simulation systems, such as jLems (jLEMS, ) or pyLEMS (Vella et al., ).The work has been focused only on the natural input that the neurons will receive during the simulation and not in the processes that convert such input into neural activation. […]

library_books

Improving Collaboration by Standardization Efforts in Systems Biology

2014
Front Bioeng Biotechnol
PMCID: 4259112
PMID: 25538939
DOI: 10.3389/fbioe.2014.00061

[…] n et al., ), which hierarchically defines structure and dynamics of a large variety of biological models. For parsing, writing, and manipulating NeuroML and LEMS files, the Python APIs libNeuroML and PyLEMS as well as the Java™ APIs jNeuroML and jLEMS are available (Vella et al., ). The original idea to link sub-modules of processes in NeuroML to models encoded in SBML or CellML (Gleeson et al., ) […]

call_split

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

2014
Front Neuroinform
PMCID: 4005938
PMID: 24795618
DOI: 10.3389/fninf.2014.00038
call_split See protocol

[…] are passed every time a change is applied to the software and pushed to GitHub. Test coverage is 91% [measured with the Python Coverage module version 3.7.1 (https://pypi.python.org/pypi/coverage)]. PyLEMS is also developed on GitHub and released as part of NeuroML release cycle. Basic unit testing and continuous integration on Travis-CI have been added to PyLEMS and will be expanded in the futur […]

Citations

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pyLEMS institution(s)
Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK, Textensor Limited, Edinburgh, UK, School of Mathematical and Statistical Sciences and School of Life Sciences, Arizona State University, Tempe, AZ, USA; Unité de Neurosciences, Information et Complexité, CNRS, Gif sur Yvette, France; Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
pyLEMS funding source(s)
Supported by a Medical Research Council (MRC) Capacity Building Studentship, the Google Summer of Code Program 2012, with the INCF as mentoring organization, in part by the US National Institute of Mental Health under grant R01MH061905, in part by grant R01EB014640 from the US National Institute of Biomedical Imaging and Bioengineering, the Wellcome Trust (086699/101445), a Wellcome Trust Principal Research Fellowship (095667), an ERC Advanced Grant (294667) and in part by European Union grant FP7-269921 (BrainScaleS).

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