From ec42debefc17d03d9ef126db2234c73f0c012c21 Mon Sep 17 00:00:00 2001 From: Kevin Rue-Albrecht Date: Fri, 5 Jul 2024 13:01:30 +0100 Subject: [PATCH] start editing --- paper.md | 69 ++++++++++++++++++++++++++------------------------------ 1 file changed, 32 insertions(+), 37 deletions(-) diff --git a/paper.md b/paper.md index 99c554f..2641188 100644 --- a/paper.md +++ b/paper.md @@ -1,56 +1,51 @@ --- -title: 'Gala: A Python package for galactic dynamics' +title: 'TVTB: The VCF Tool Box' tags: - - Python - - astronomy - - dynamics - - galactic dynamics - - milky way + - Bioconductor + - Bioinformatics authors: - - name: Adrian M. Price-Whelan - orcid: 0000-0000-0000-0000 - equal-contrib: true - affiliation: "1, 2" # (Multiple affiliations must be quoted) - - name: Author Without ORCID - equal-contrib: true # (This is how you can denote equal contributions between multiple authors) - affiliation: 2 - - name: Author with no affiliation - corresponding: true # (This is how to denote the corresponding author) - affiliation: 3 - - given-names: Ludwig - dropping-particle: van - surname: Beethoven - affiliation: 3 + - name: Kevin Rue-Albrecht + orcid: 0000-0003-3899-3872 + affiliation: "1" affiliations: - - name: Lyman Spitzer, Jr. Fellow, Princeton University, USA + - name: MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK index: 1 - - name: Institution Name, Country - index: 2 - - name: Independent Researcher, Country - index: 3 -date: 13 August 2017 +date: 05 July 2024 bibliography: paper.bib # Optional fields if submitting to a AAS journal too, see this blog post: # https://blog.joss.theoj.org/2018/12/a-new-collaboration-with-aas-publishing -aas-doi: 10.3847/xxxxx <- update this with the DOI from AAS once you know it. -aas-journal: Astrophysical Journal <- The name of the AAS journal. +#aas-doi: 10.3847/xxxxx <- update this with the DOI from AAS once you know it. +#aas-journal: Astrophysical Journal <- The name of the AAS journal. --- # Summary -The forces on stars, galaxies, and dark matter under external gravitational -fields lead to the dynamical evolution of structures in the universe. The orbits -of these bodies are therefore key to understanding the formation, history, and -future state of galaxies. The field of "galactic dynamics," which aims to model -the gravitating components of galaxies to study their structure and evolution, -is now well-established, commonly taught, and frequently used in astronomy. -Aside from toy problems and demonstrations, the majority of problems require -efficient numerical tools, many of which require the same base code (e.g., for -performing numerical orbit integration). +`TVTB` is an R/Bioconductor package that offers a toolkit for the filtering, +summarisation, and visualisation of genetic variation data stored in +Variant Call Format (VCF) files pre-processed by the Ensembl Variant Effect +Predictor (VEP). +In particular, `TVTB` extends core Bioconductor infrastructure in the +`VariantAnnotation` and `S4Vectors` packages to define classes of filtering +rules applicable to the diverse fields of information recorded in the VCF +format. +An interactive web-application, the Shiny Variant Explorer, provides an +interface to demonstrate the package functionality in a programming-free +environment. # Statement of need +The Variant Call Format (VCF) provides infrastructure for storing a plethora of +raw and processed information related to the analysis of genetic variation data. + +Computational analysis ... exploration ... visualisation ... + + + +The plethora of information stored in Variant Call Format (VCF) files + +Analyses of genetic variation data produce a plethora of information + `Gala` is an Astropy-affiliated Python package for galactic dynamics. Python enables wrapping low-level languages (e.g., C) for speed without losing flexibility or ease-of-use in the user-interface. The API for `Gala` was