1. OpenMendel: a cooperative programming project for statistical genetics
- Author
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Zhou, Hua, Sinsheimer, Janet S, Bates, Douglas M, Chu, Benjamin B, German, Christopher A, Ji, Sarah S, Keys, Kevin L, Kim, Juhyun, Ko, Seyoon, Mosher, Gordon D, Papp, Jeanette C, Sobel, Eric M, Zhai, Jing, Zhou, Jin J, and Lange, Kenneth
- Subjects
Biological Sciences ,Genetics ,Human Genome ,Networking and Information Technology R&D (NITRD) ,Algorithms ,Computational Biology ,Genome ,Human ,Genome-Wide Association Study ,Humans ,Models ,Statistical ,Polymorphism ,Single Nucleotide ,Programming Languages ,Software ,Statistical genomics ,GWAS ,Computational statistics ,Open source ,Collaborative programming ,stat.AP ,q-bio.GN ,Complementary and Alternative Medicine ,Paediatrics and Reproductive Medicine ,Genetics & Heredity ,Reproductive medicine - Abstract
Statistical methods for genome-wide association studies (GWAS) continue to improve. However, the increasing volume and variety of genetic and genomic data make computational speed and ease of data manipulation mandatory in future software. In our view, a collaborative effort of statistical geneticists is required to develop open source software targeted to genetic epidemiology. Our attempt to meet this need is called the OPENMENDEL project (https://openmendel.github.io). It aims to (1) enable interactive and reproducible analyses with informative intermediate results, (2) scale to big data analytics, (3) embrace parallel and distributed computing, (4) adapt to rapid hardware evolution, (5) allow cloud computing, (6) allow integration of varied genetic data types, and (7) foster easy communication between clinicians, geneticists, statisticians, and computer scientists. This article reviews and makes recommendations to the genetic epidemiology community in the context of the OPENMENDEL project.
- Published
- 2020