GSR: Simulator - GeneSPIDER

Basic Package Attributes
AttributeValue
Title GeneSPIDER
Short Description Gene regulatory network inference benchmarking with controlled network and data properties
Long Description Inference of gene regulatory networks (GRNs) is a central goal in systems biology. It is therefore important to evaluate the accuracy of GRN inference methods in the light of network and data properties. Although several packages are available for modelling, simulate, and analyse GRN inference, they offer limited control of network topology together with system dynamics, experimental design, data properties, and noise characteristics. Independent control of these properties in simulations is key to drawing conclusions about which inference method to use in a given condition and what performance to expect from it, as well as to obtain properties representative of real biological systems.
Keywords Gene regulatory network inference and analysis
Version 1.11
Project Started 2015
Last Release 4 years, 5 months ago
Homepagehttps://bitbucket.org/sonnhammergrni/genespider/src/master/
Citations Tjärnberg A, Morgan DC, Studham M, Nordling TEM, Sonnhammer ELL, GeneSPIDER - gene regulatory network inference benchmarking with controlled network and data properties., Mol Biosyst, 06-27-2017 [ Abstract, cited in PMC ]
GSR CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluated04-07-2021 (165 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataRNA,
Variations
Simulation MethodOther,
Input
Data TypeOther,
File formatProgram Specific,
Output
Data Type
Sequencing ReadsOther,
File FormatProgram Specific,
Sample TypeRandom or Independent,
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation Models
Events Allowed
Other
InterfaceCommand-line, Script-based,
Development
Tested PlatformsLinux and Unix,
LanguageOther,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Application, Support,

The following 5 publications are selected examples of applications that used GeneSPIDER.

2020

Magnusson R, Gustafsson M, LiPLike: towards gene regulatory network predictions of high certainty., Bioinformatics, 04-15-2020 [Abstract]

Morgan D, Studham M, Tjärnberg A, Weishaupt H, Swartling FJ, Nordling TEM, Sonnhammer ELL, Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms., Sci Rep, 08-25-2020 [Abstract]

Seçilmiş D, Hillerton T, Morgan D, Tjärnberg A, Nelander S, Nordling TEM, Sonnhammer ELL, Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data., NPJ Syst Biol Appl, 11-09-2020 [Abstract]

2019

Jurman G, Filosi M, Visintainer R, Riccadonna S, Furlanello C, Stability in GRN Inference., Methods Mol Biol, 01-01-2019 [Abstract]

Muldoon JJ, Yu JS, Fassia MK, Bagheri N, Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants., Bioinformatics, 09-15-2019 [Abstract]


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