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RegrEx specifications

Information


Unique identifier OMICS_18750
Name RegrEx
Alternative name Regularized context-specific model Extraction method
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some RNAseq human expression profiles.
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Zoran Nikoloski

Additional information


RegrEx was implemented in MATLAB, and the code is provided in Supplementary file.

Publication for Regularized context-specific model Extraction method

RegrEx citations

 (4)
library_books

Resolving the central metabolism of Arabidopsis guard cells

2017
Sci Rep
PMCID: 5559522
PMID: 28814793
DOI: 10.1038/s41598-017-07132-9

[…] A flux distribution leading to an optimal value for the RegrEx objective is likely not unique since typically not all reactions in a genome-scale model are endowed with reaction associated data. Therefore, there are reactions whose flux value can vary with […]

call_split

On the effects of alternative optima in context specific metabolic model predictions

2017
PLoS Comput Biol
PMCID: 5469500
PMID: 28557990
DOI: 10.1371/journal.pcbi.1005568
call_split See protocol

[…] e an overview of the approach, which is followed by a description of the method to explore its alternative optima space. We start by a representative of a flux-centered approach—a modified version of RegrEx []—and the method that we propose to explore its alternative optima, termed RegrEx Alternative Optima Sampling (RegrExAOS). We then focus on Core Expansion (CorEx), also developed in this study […]

library_books

Benchmarking Procedures for High Throughput Context Specific Reconstruction Algorithms

2016
Front Physiol
PMCID: 4722106
PMID: 26834640
DOI: 10.3389/fphys.2015.00410

[…] The RegrEx implementation in the supplementary files of Robaina Estévez and Nikoloski () was used. This algorithm has previously only been used with RNA-seq data and therefore no established discretizatio […]

library_books

w REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations

2012
J Chem Theory Comput
PMCID: 3541756
PMID: 23316122
DOI: 10.1021/ct300896h

[…] ng simply from multiple independent simulations and the limitation of increased computational cost, we compare w-REXAMD to conventional MD in the same replica exchange framework, which we refer to as REGREX. In a REGREX simulation, multiple independent conventional MD replicas exchange their configurations at the same frequency at which exchanges are attempted in a w-REXAMD simulation. The states […]

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RegrEx institution(s)
Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology (MPIMP), Potsdam-Golm, Germany

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