optGpSampler statistics

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optGpSampler specifications

Information


Unique identifier OMICS_24203
Name optGpSampler
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C++, MATLAB, Python
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Wout Megchelenbrink <>

Publication for optGpSampler

optGpSampler in publications

 (6)
PMCID: 5838312
PMID: 29545779
DOI: 10.3389/fmicb.2018.00291

[…] of minutes to hours for large metabolic network resulting in a valuable tool to explore the solution space without requiring the use of a reduced model., flux distributions were calculated using optgpsampler (). for each condition, the network was first constrained using uptake and production rates as well as sink reactions associated with metabolites accumulation. then, 100.000 flux […]

PMCID: 5691038
PMID: 29147021
DOI: 10.1038/s41598-017-16026-9

[…] ch was used to identify the transcriptionally, post-transcriptionally and metabolically regulated reactions. first, the flux solution space of l. mesenteroides growing on s or g was sampled using the optgpsampler implemented in cobra toolbox. the significance of change between the expression and flux of each reaction was then z-scored using the formula below:5\documentclass[12pt]{minimal} \use […]

PMCID: 5384209
PMID: 28382977
DOI: 10.1038/ncomms14915

[…] hr iteratively chooses a random direction and collects new samples in that direction such that they also reside in the solution space. in this work, we use an optimized implementation of hr, called optgpsampler. regarding the hr simulations, we set the number of sampled points to be equal to 104 for an increasing number of explored configurations t from 104 to 107 in most of the cases; […]

PMCID: 5372704
PMID: 28424673
DOI: 10.3389/fmicb.2017.00534

[…] a sink (minimizing the flux) reaction for each metabolite. metabolites were considered dead-ends if the model was unable to produce, nor consume them., we conducted a random sampling analysis using optgpsampler (megchelenbrink et al., ), an efficient algorithm based on the monte carlo procedure hit and run (smith, ). for each experimental condition, we set the algorithm parameters in order […]

PMCID: 5309336
PMID: 28217746
DOI: 10.1128/mSystems.00142-16

[…] of co2 uptake. exchange reactions not shown here are blocked., lb, lower bound., ub, upper bound., to uniformly sample the solution space of the p.┬átricornutum metabolic network ilb1027_lipid (), optgpsampler () for matlab (the mathworks inc., natick, ma) with gurobi optimizer version 6.5.0 (gurobi optimization inc., houston, tx) was used. two different carbon conditions were sampled, low […]


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optGpSampler institution(s)
Institute for Computing and Information Sciences (ICIS), Radboud University Nijmegen, Nijmegen, The Netherlands; Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands; Centre for Systems Biology and Bioenergetics (CSBB), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
optGpSampler funding source(s)
Supported by The Netherlands Organisation for Scientific Research (NWO) and The Netherlands Organisation for Health Research and Development (ZonMW).

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