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Chemoinformatics and structural bioinformatics in OCaml

2019; BioMed Central; Volume: 11; Issue: 1 Linguagem: Inglês

10.1186/s13321-019-0332-0

ISSN

1758-2946

Autores

Francois Berenger, Kam Y. J. Zhang, Yoshihiro Yamanishi,

Tópico(s)

Bioinformatics and Genomic Networks

Resumo

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.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.In our experience, OCaml is a programming language of choice for method development in chemoinformatics and structural bioinformatics.

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