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.
Version 1.11
Project Started 2015
Last Release 3 years, 9 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 ]
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Author verificationThe basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated Data
Variations
Simulation Method
Input
Data Type
File format
Output
Data Type
Sequencing Reads
File Format
Sample Type
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
Interface
Development
Tested Platforms
Language
License
GSR Certification

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