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SloppyCell specifications

Information


Unique identifier OMICS_20248
Name SloppyCell
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Alpha
Maintained Yes

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Additional information


http://sloppycell.sourceforge.net/api/

Publication for SloppyCell

SloppyCell in publications

 (10)
PMCID: 4933380
PMID: 27380265
DOI: 10.1371/journal.pgen.1006132

[…] systems biology markup language (sbml) format [] from the feb. 8, 2012 release of biomodels []. we calculated dynamical influence for all protein-related biological parameters in each model, using sloppycell [] and simulating under the conditions considered in each model’s original paper (). these parameters represent a variety of biological phenomena, such as binding and catalytic constants […]

PMCID: 4807028
PMID: 27010978
DOI: 10.1371/journal.pone.0152316

[…] in pbs, and stored at -80c., model fitting, simulation, and other computational analyses were done using the python programming language. the system of differential equations was integrated using sloppycell []. model fitting was done by solving a weighted nonlinear least squares problem. let xijlt represent the data collected for species i at interferon level j, in replicate l at time point […]

PMCID: 4636272
PMID: 26545295
DOI: 10.1371/journal.pcbi.1004562

[…] impossible with increasingly complex models, so computational biologists have turned to the use of monte carlo techniques to explore the viable parameter space efficiently (e.g., hyperspace [] and sloppycell []). here, we used a previously developed mcmc method [] to explore the parameter space, initiating a random walk away from each of the 40 acceptable parameter sets and keeping 100 viable […]

PMCID: 4625875
PMID: 26511837
DOI: 10.1186/s12862-015-0515-x

[…] chemostat experiment with which we compare metabolite concentrations []. the complete set of equations is reproduced in additional file . all computations with the kinetic model were performed in sloppycell []., the model contains 22 parameters for the biochemistry of the enzymes, 4 parameters for input metabolite concentrations, and 2 parameters for cellular utilization of pyrimidines. […]

PMCID: 4238958
PMID: 25412287
DOI: 10.1371/journal.pcbi.1003958

[…] for serine utilization in the condition of low glucose availability., individual steps of the computation in this study are listed and explained below using kfp as the example (many of them use sloppycell, a python package originally developed for analyzing biochemical networks ). relevant python codes are deposited at http://github.com/leihuang/rkfp., encoding models: models are encoded […]


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SloppyCell institution(s)
Cornell Theory Center, Cornell University, Ithaca, NY, USA; Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA
SloppyCell funding source(s)
Supported by NSF grant DMR-0218475, USDA-ARS project 1907-21000-017-05 , and an NIH Molecular Biophysics Training grant (No. T32-GM-08267).

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