Chemoinformatics and structural bioinformatics in OCaml

BACKGROUND: OCaml is a functional programming language with strong static types, Hindley–Milner type inference and garbage collection. In this article, we share our experience in prototyping chemoinformatics and structural bioinformatics software in OCaml. RESULTS: First, we introduce the language,...

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Detalles Bibliográficos
Autores principales: Berenger, Francois, Zhang, Kam Y. J., Yamanishi, Yoshihiro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2019
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6689879/
https://www.ncbi.nlm.nih.gov/pubmed/30719579
http://dx.doi.org/10.1186/s13321-019-0332-0
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author Berenger, Francois
Zhang, Kam Y. J.
Yamanishi, Yoshihiro
author_facet Berenger, Francois
Zhang, Kam Y. J.
Yamanishi, Yoshihiro
author_sort Berenger, Francois
collection PubMed
description BACKGROUND: OCaml is a functional programming language with strong static types, Hindley–Milner type inference and garbage collection. In this article, we share our experience in prototyping chemoinformatics and structural bioinformatics software in OCaml. RESULTS: First, we introduce the language, list entry points for chemoinformaticians who would be interested in OCaml and give code examples. Then, we list some scientific open source software written in OCaml. We also present recent open source libraries useful in chemoinformatics. The parallelization of OCaml programs and their performance is also shown. Finally, tools and methods useful when prototyping scientific software in OCaml are given. CONCLUSIONS: In our experience, OCaml is a programming language of choice for method development in chemoinformatics and structural bioinformatics.
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spelling pubmed-66898792019-08-15 Chemoinformatics and structural bioinformatics in OCaml Berenger, Francois Zhang, Kam Y. J. Yamanishi, Yoshihiro J Cheminform Research Article BACKGROUND: OCaml is a functional programming language with strong static types, Hindley–Milner type inference and garbage collection. In this article, we share our experience in prototyping chemoinformatics and structural bioinformatics software in OCaml. RESULTS: First, we introduce the language, list entry points for chemoinformaticians who would be interested in OCaml and give code examples. Then, we list some scientific open source software written in OCaml. We also present recent open source libraries useful in chemoinformatics. The parallelization of OCaml programs and their performance is also shown. Finally, tools and methods useful when prototyping scientific software in OCaml are given. CONCLUSIONS: In our experience, OCaml is a programming language of choice for method development in chemoinformatics and structural bioinformatics. Springer International Publishing 2019-02-05 /pmc/articles/PMC6689879/ /pubmed/30719579 http://dx.doi.org/10.1186/s13321-019-0332-0 Text en © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Berenger, Francois
Zhang, Kam Y. J.
Yamanishi, Yoshihiro
Chemoinformatics and structural bioinformatics in OCaml
title Chemoinformatics and structural bioinformatics in OCaml
title_full Chemoinformatics and structural bioinformatics in OCaml
title_fullStr Chemoinformatics and structural bioinformatics in OCaml
title_full_unstemmed Chemoinformatics and structural bioinformatics in OCaml
title_short Chemoinformatics and structural bioinformatics in OCaml
title_sort chemoinformatics and structural bioinformatics in ocaml
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6689879/
https://www.ncbi.nlm.nih.gov/pubmed/30719579
http://dx.doi.org/10.1186/s13321-019-0332-0
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