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GSR: Simulator - GeneSPIDER
| Attribute | Value |
|---|---|
| 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 | 7 years ago |
| Homepage | https://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 Certification |  ✔ Accessibility |
| Last evaluated | 04-07-2021 (1102 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | RNA, |
| Variations | |
| Simulation Method | Other, |
| Input | |
| Data Type | Other, |
| File format | Program Specific, |
| Output | |
| Data Type | |
| Sequencing Reads | Other, |
| File Format | Program Specific, |
| Sample Type | Random 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 | |
| Interface | Command-line, Script-based, |
| Development | |
| Tested Platforms | Linux and Unix, |
| Language | Other, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 5
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]