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WholeCellViz specifications

Information


Unique identifier OMICS_08805
Name WholeCellViz
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline WholeCellSimDB
  • person_outline Markus Covert

Information


Unique identifier OMICS_08805
Name WholeCellViz
Interface Web user interface
Restrictions to use None
Programming languages Javascript, PHP
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline WholeCellSimDB
  • person_outline Markus Covert

Publication for WholeCellViz

WholeCellViz citations

 (3)
library_books

Toward community standards and software for whole cell modeling

2016
IEEE Trans Biomed Eng
PMCID: 5451320
PMID: 27305665
DOI: 10.1109/TBME.2016.2560762

[…] d to estimate parameters and test models. (4) A multi-algorithm simulator will be used to conduct in silico experiments. (5) Simulation databases and visualization software such as WholeCellSimDB and WholeCellViz will be used to discover new biology by visualizing and analyzing in silico experiments.Together, this pipeline will enable more researchers to more easily build, manage, simulate, and re […]

library_books

Open source libraries and frameworks for biological data visualisation: A guide for developers

2015
Proteomics
PMCID: 4409855
PMID: 25475079
DOI: 10.1002/pmic.201400377

[…] ractive looks and interactive features. It works in all web browsers that support HTML5 canvas (which means most of the popular ones). Flot is supporting chart generation in a number of tools such as WholeCellViz [], which can perform data visualisation for whole-cell models, and HapMap-CN [] a CouchDB-based database which allows automated gene-centric annotations, and provides a web interface to […]

library_books

3D molecular models of whole HIV 1 virions generated with cellPACK

2014
Faraday Discuss
PMCID: 4569901
PMID: 25253262
DOI: 10.1039/c4fd00017j

[…] e driving biological project of modeling HIV-1, it becomes a relatively short step to model a slightly larger and more complex organism such as Mycoplasma genitalium. A systems biology project called WholeCellViz has provided a computational recipe of the hypothetical quantities, localizations, and interactions of every gene product of M. genitalium, dynamically over a full life cycle. The WholeCe […]

Citations

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WholeCellViz institution(s)
Department of Bioengineering, Stanford University, Stanford, CA, USA; Graduate Program in Biophysics, Stanford University, Stanford, CA, USA
WholeCellViz funding source(s)
Supported by a NIH Director’s Pioneer Award (5DP1LM01150-05), an Allen Distinguished Investigator Award, an Hellman Faculty Scholarship; a Stanford Bioengineering REU scholarship; NDSEG, NSF, and Stanford Graduate Fellowships.

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