A community-maintained standard library of population genetic models
| Autor: | Christopher C. Kyriazis, Bernard Y. Kim, Adam Siepel, Graham Gower, Franz Baumdicker, Patrick F. McKenzie, Christopher B. Cole, Jeffrey R. Adrion, Noah Dukler, Jedidiah Carlson, Arun Durvasula, Peter L. Ralph, Georgia Tsambos, Travis J. Struck, Fernando Racimo, Kirk E. Lohmueller, Diego Ortega-Del Vecchyo, Jerome Kelleher, Reed A. Cartwright, Philipp W. Messer, Simon Gravel, Daniel R. Schrider, Ryan N. Gutenkunst, Ilan Gronau, Ariella L. Gladstein, Jared Galloway, Andrew D. Kern, Ekaterina Noskova, Aaron P. Ragsdale |
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| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Computer science ROBUST Arabidopsis Population genetics Inference Field (computer science) Task (project management) Resource (project management) 0302 clinical medicine open source HISTORY Biology (General) computer.programming_language 0303 health sciences education.field_of_study Genomic Library Genome General Neuroscience General Medicine simulation Tools and Resources GENOME Drosophila melanogaster Medicine Computational and Systems Biology Human Pongo abelii QH301-705.5 Systems biology Science Population General Biochemistry Genetics and Molecular Biology 03 medical and health sciences Dogs Genetic model Escherichia coli Animals Humans education reproducibility 030304 developmental biology Gene Library Evolutionary Biology General Immunology and Microbiology Models Genetic MUTATIONS Genome Human Simulation modeling Computational genomics Python (programming language) Data science EVOLUTION 030104 developmental biology Open source SIZE Genetics Population INFERENCE computer 030217 neurology & neurosurgery Software |
| Zdroj: | Adrion, J R, Cole, C B, Dukler, N, Galloway, J G, Gladstein, A L, Gower, G, Kyriazis, C C, Ragsdale, A P, Tsambos, G, Baumdicker, F, Carlson, J, Cartwright, R A, Durvasula, A, Gronau, I, Kim, B Y, McKenzie, P, Messer, P W, Noskova, E, Ortega-Del Vecchyo, D, Racimo, F, Struck, T J, Gravel, S, Gutenkunst, R N, Lohmueller, K E, Ralph, P L, Schrider, D R, Siepel, A, Kelleher, J & Kern, A D 2020, ' A community-maintained standard library of population genetic models ', eLife, vol. 9, 54967 . https://doi.org/10.7554/eLife.54967 eLife, Vol 9 (2020) eLife |
| DOI: | 10.1101/2019.12.20.885129 |
| Popis: | The explosion in population genomic data demands ever more complex modes of analysis, and increasingly these analyses depend on sophisticated simulations. Recent advances in population genetic simulation have made it possible to simulate large and complex models, but specifying such models for a particular simulation engine remains a difficult and error-prone task. Computational genetics researchers currently re-implement simulation models independently, leading to inconsistency and duplication of effort. This situation presents a major barrier to empirical researchers seeking to use simulations for power analyses of upcoming studies or sanity checks on existing genomic data. Population genetics, as a field, also lacks standard benchmarks by which new tools for inference might be measured. Here we describe a new resource,stdpopsim, that attempts to rectify this situation.Stdpopsimis a community-driven open source project, which provides easy access to a growing catalog of published simulation models from a range of organisms and supports multiple simulation engine backends. This resource is available as a well-documented python library with a simple command-line interface. We share some examples demonstrating howstdpopsimcan be used to systematically compare demographic inference methods, and we encourage a broader community of developers to contribute to this growing resource. |
| Databáze: | OpenAIRE |
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