StochKit statistics

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StochKit specifications

Information


Unique identifier OMICS_21679
Name StochKit
Alternative name StochKit2
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Linda Petzold <>

Publication for StochKit

StochKit in publications

 (14)
PMCID: 5833289
PMID: 29451894
DOI: 10.1371/journal.pcbi.1006004

[…] representing the degradation of the entities involved are also included., we performed stochastic simulations of the above system of events using the gillespie algorithm implemented in the tool stochkit []. the rate constants were obtained from the literature (). the production rate of nf-κb, knfκb, and the basal transcription rate of hiv-1, kbasal, remained uncertain. we fixed […]

PMCID: 5870780
PMID: 28881987
DOI: 10.1093/bioinformatics/btx253

[…] pt(x)↦pt+δt(x), whereas hssa maps from ℝnx+nθ→ℝnx i.e. (xt,θ)↦xt+δt. to overcome the ssa’s huge computational load we used an approximate version, which is the τ-leaping algorithm implementation of stochkit2 (). note that by combining intrinsic and extrinsic noise we have to deal with a distributed cme. as for real valued stochastic variables, the corresponding ensemble of probability functions […]

PMCID: 5507631
PMID: 28706991
DOI: 10.1126/sciadv.1700006

[…] and degraded, with rate constant kdec. the value of kdec is taken from either the mgc or the cdta experiments., distributions were generated with gillespie’s stochastic simulation algorithm, using stochkit (), from 10,000 runs of 1000 min for each combination of random parameter values. random values were generated for kon, koff, and ktr so that the predicted fano factor () approximates […]

PMCID: 5294885
PMID: 28166778
DOI: 10.1186/s12918-017-0394-4

[…] which we calculate using the finite state projection method [] (additional file : figure s1)., stochastic simulations were performed according to the ssa method, implemented by the software package stochkit2 []., the steady-state probability π(x) over n microstates is obtained from k as the normalized eigenvector corresponding to the zero-eigenvalue, satisfying k π(x) = 0 []. quasipotential […]

PMCID: 4895904
PMID: 27266276
DOI: 10.1186/s12918-016-0279-y

[…] for rnap binding to a tetr-regulated promoter determined by meier et al. (1988), we found ktb2=5.7×10−6μm3 and ktb3=8.6×10−6μm3 []., the stochastic simulations were performed using the software stochkit2 []. this provided us with a fast way of simulating large sets of stochastic equations for extended simulation periods. the stability and switching rate calculations were performed using […]


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StochKit institution(s)
Department of Computer Science, University of California Santa Barbara, Santa Barbara, CA, USA
StochKit funding source(s)
Supported by the National Institute of Biomedical Imaging and Bioengineering (Grant No. R01EB007511); Institute for Collaborative Biotechnologies from the US Army Research Office (Grant No. DFR3A-8-447850-23002); DOE Contract No. DE-FG02-04ER25621; NSF Contract No. IGERT DG02-21715 and DMS-1001012; National Science Foundation Graduate Research Fellowships.

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