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127 lines
5.5 KiB
YAML
127 lines
5.5 KiB
YAML
cff-version: 1.2.0
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message: "If you use Allelica or derived population-genetics visualizations from this repository, please cite this software, the upstream source, and the listed source references."
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title: "Allelica: Hardy-Weinberg Population Genetics Visualizer"
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type: software
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authors:
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- alias: "khandelwalsumo-oss"
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- alias: "allaunthefox"
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repository-code: "https://github.com/allaunthefox/Allelica"
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url: "https://github.com/allaunthefox/Allelica"
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abstract: >-
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Allelica is a Python-based Hardy-Weinberg population genetics visualizer for
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allele-frequency data, Hardy-Weinberg expected genotype-frequency estimates,
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and population-level comparisons across selected genes and traits. It is
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currently a bounded, educational and exploratory tool, not a clinical genetics
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system or evidence of causation for traits, adaptation, disease risk, or
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evolutionary mechanisms.
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keywords:
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- Allelica
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- allele frequency
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- Hardy-Weinberg equilibrium
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- population genetics
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- genotype frequency
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- genetic variation
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- biological addressability
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- gnomAD
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license: MIT
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references:
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- type: software
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title: "Allelica upstream repository"
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authors:
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- alias: "khandelwalsumo-oss"
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repository-code: "https://github.com/khandelwalsumo-oss/Allelica"
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url: "https://github.com/khandelwalsumo-oss/Allelica"
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notes: >-
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Upstream source repository named by GitHub as the fork origin for this
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repository. Preserve this attribution when using or extending the fork.
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- type: webpage
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title: "Built a Hardy-Weinberg population genetics visualizer with real gnomAD data — looking for honest feedback (17 y/o, self taught)"
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authors:
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- alias: "Puzzled_Maximum7018"
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url: "https://www.reddit.com/r/bioinformatics/"
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notes: >-
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Reddit r/bioinformatics provenance page supplied by the fork maintainer as
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context for the original project goals, feedback, and limitations. The page
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frames Allelica as a first GitHub / high-school informatics project using
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Hardy-Weinberg expected genotype frequencies from allele-frequency data and
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asks for critique on biological validity. Treat this as provenance and
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review context, not as a scientific source or validation of the method.
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A canonical Reddit post permalink was not captured in the pasted source.
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- type: dataset
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title: "Genome Aggregation Database (gnomAD)"
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url: "https://gnomad.broadinstitute.org/"
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notes: >-
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Source database named in the project README for allele-frequency data.
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Users should cite the relevant gnomAD release and any underlying studies
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directly when performing scientific analyses. This entry records repository
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provenance only and is not a substitute for release-specific gnomAD citation.
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- type: article
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title: "A global reference for human genetic variation"
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authors:
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- family-names: "Karczewski"
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given-names: "Konrad J."
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- family-names: "Francioli"
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given-names: "Laurent C."
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- family-names: "Tiao"
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given-names: "Grace"
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- family-names: "Cummings"
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given-names: "Beryl B."
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- family-names: "Alföldi"
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given-names: "Jessica"
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- family-names: "Wang"
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given-names: "Qingbo"
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- family-names: "Collins"
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given-names: "Ryan L."
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- family-names: "Laricchia"
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given-names: "Kristen M."
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- family-names: "Ganna"
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given-names: "Andrea"
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- family-names: "Birnbaum"
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given-names: "Daniel P."
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journal: "Nature"
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year: 2020
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volume: 581
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pages: "434-443"
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doi: "10.1038/s41586-020-2308-7"
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url: "https://doi.org/10.1038/s41586-020-2308-7"
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notes: >-
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Canonical gnomAD reference for human genetic variation. Listed as a bounded
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data-source reference for Allelica's population-genetics visualizations.
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- type: article
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title: "Mendelian proportions in a mixed population"
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authors:
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- family-names: "Hardy"
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given-names: "G. H."
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journal: "Science"
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year: 1908
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volume: 28
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issue: 706
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pages: "49-50"
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doi: "10.1126/science.28.706.49"
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url: "https://doi.org/10.1126/science.28.706.49"
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notes: >-
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Original short note associated with the Hardy-Weinberg equilibrium baseline.
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Allelica uses this equilibrium as a baseline comparator, not as proof that
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real populations satisfy all equilibrium assumptions.
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- type: article
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title: "On the law of inheritance in man"
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authors:
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- family-names: "Weinberg"
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given-names: "Wilhelm"
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journal: "Jahreshefte des Vereins für vaterländische Naturkunde in Württemberg"
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year: 1908
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volume: 64
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pages: "368-382"
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notes: >-
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Historical source associated with the Hardy-Weinberg equilibrium principle.
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Included to document the mathematical baseline underlying Allelica.
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notes: >-
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Project guardrail: VariantExists does not imply VariantMatters. Allele and
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Hardy-Weinberg expected genotype-frequency visualizations require population
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context, phenotype context, environmental assumptions, database provenance,
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sample size, uncertainty estimates, and evidence receipts before supporting
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biological interpretation. Hardy-Weinberg output should be treated as a baseline
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comparator when equilibrium assumptions may be violated. Reddit feedback in the
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supplied provenance page specifically flags hardcoded values, unclear extraction,
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ancestry/environment grouping ambiguity, lack of observed genotype comparison,
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and the need for sample sizes, uncertainty, and equilibrium/selection tests.
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