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GenYsis specifications

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Unique identifier OMICS_20012
Name GenYsis
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 3.0
Stability No
Maintained No

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Publications for GenYsis

GenYsis citations

 (4)
library_books

A Clb/Cdk1 mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle

2017
NPJ Syst Biol Appl
PMCID: 5460246
PMID: 28649434
DOI: 10.1038/s41540-017-0008-1

[…] modifications as described in ., kinetic modeling and global sensitivity analysis were performed as previously described with modifications as described in . boolean simulations were performed with genysis, which uses efficient, reduced ordered binary decision diagrams based algorithms to efficiently compute cyclic attractors. all simulations were performed using the synchronous mode. […]

library_books

Approximating Attractors of Boolean Networks by Iterative CTL Model Checking

2015
Front Bioeng Biotechnol
PMCID: 4562258
PMID: 26442247
DOI: 10.3389/fbioe.2015.00130

[…] of the attractors of (s, ↪). the time needed to confirm faithfulness, univocality and completeness is given in table . we confirmed the number of steady states and cyclic attractors with ginsim and genysis. the execution of ginsim is, like the computation of minimal trap spaces, instantaneous. the running times of genysis are comparable to that of our algorithm for networks with |v| < 40 […]

library_books

Predicting missing expression values in gene regulatory networks using a discrete logic modeling optimization guided by network stable states

2012
Nucleic Acids Res
PMCID: 3592407
PMID: 22941654
DOI: 10.1093/nar/gks785

[…] a gene becomes active; otherwise the gene is inactive. this result is consistent with the results obtained using previously published software to compute attractors in boolean systems [boolnet (), genysis (), ginsim ()]. in other words, this network is clearly not suitable to describe this two steady states system with the known gene states. figure 2., but let us introduce in our small network […]

library_books

Scalable Steady State Analysis of Boolean Biological Regulatory Networks

2009
PLoS One
PMCID: 2779454
PMID: 19956604
DOI: 10.1371/journal.pone.0007992

[…] brns as well as for randomly generated networks. we compiled the real brns from the pathway database pid and other published work , , , . reports the running times for garg et al.'s method named genysis and our algorithm with different parameter settings., we used a cut-off time of 24-hours and “-” indicates that the method could not find all steady states within this time. denotes seconds […]


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GenYsis institution(s)
Vital-IT Systems Biology Division, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; Electrical and Computer Engineering, University of Pittsburgh, Pittsburgh, PA, USA; Quartz Bio, Plan-Les-Ouates, Switzerland; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
GenYsis funding source(s)
Supported by European Commission FP6 project ENFIN (Experimental Network for Functional INtegration -LSHG-CT-2005-518254), Swiss Federal Government through the Federal Office of Education Science and Innovation (SERI), Postdoc Fellowship (RPF) Program.

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