Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story.

IF 6.8 2区生物学 Q1 BIOCHEMICAL RESEARCH METHODS Briefings in bioinformatics Pub Date : 2024-07-25 DOI:10.1093/bib/bbae367

Yann Spöri, Jean-François Flot

{"title":"Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story.","authors":"Yann Spöri, Jean-François Flot","doi":"10.1093/bib/bbae367","DOIUrl":null,"url":null,"abstract":"<p><p>Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript, and Python. Although Haxe is more and more used for a variety of purposes, including games, it has not yet attracted much attention from bioinformaticians. This is surprising, as Haxe allows generating different versions of the same program (e.g. a graphical user interface version in JavaScript running in a web browser for beginners and a command-line version in C++ or Python for increased performance) while maintaining a single code, a feature that should be of interest for many bioinformatic applications. To demonstrate the usefulness of Haxe in bioinformatics, we present here the case story of the program SeqPHASE, written originally in Perl (with a CGI version running on a server) and published in 2010. As Perl+CGI is not desirable anymore for security purposes, we decided to rewrite the SeqPHASE program in Haxe and to host it at Github Pages (https://eeg-ebe.github.io/SeqPHASE), thereby alleviating the need to configure and maintain a dedicated server. Using SeqPHASE as an example, we discuss the advantages and disadvantages of Haxe's source code conversion functionality when it comes to implementing bioinformatic software.</p>","PeriodicalId":9209,"journal":{"name":"Briefings in bioinformatics","volume":null,"pages":null},"PeriodicalIF":6.8000,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11350380/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Briefings in bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/bib/bbae367","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}

引用次数: 0

Abstract

Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript, and Python. Although Haxe is more and more used for a variety of purposes, including games, it has not yet attracted much attention from bioinformaticians. This is surprising, as Haxe allows generating different versions of the same program (e.g. a graphical user interface version in JavaScript running in a web browser for beginners and a command-line version in C++ or Python for increased performance) while maintaining a single code, a feature that should be of interest for many bioinformatic applications. To demonstrate the usefulness of Haxe in bioinformatics, we present here the case story of the program SeqPHASE, written originally in Perl (with a CGI version running on a server) and published in 2010. As Perl+CGI is not desirable anymore for security purposes, we decided to rewrite the SeqPHASE program in Haxe and to host it at Github Pages (https://eeg-ebe.github.io/SeqPHASE), thereby alleviating the need to configure and maintain a dedicated server. Using SeqPHASE as an example, we discuss the advantages and disadvantages of Haxe's source code conversion functionality when it comes to implementing bioinformatic software.

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

Haxe 作为生物信息学应用的瑞士刀：SeqPHASE 案例故事。

Haxe 是一种通用的面向对象编程语言，支持语法宏。Haxe 编译器因其能够将 Haxe 程序的源代码翻译成包括 Java、C++、JavaScript 和 Python 在内的多种其他编程语言的源代码而闻名。尽管 Haxe 越来越多地被用于包括游戏在内的各种用途，但它尚未引起生物信息学家的广泛关注。这很令人吃惊，因为 Haxe 允许生成同一程序的不同版本（例如，为初学者生成在网络浏览器中运行的 JavaScript 图形用户界面版本，以及为提高性能生成的 C++ 或 Python 命令行版本），同时保持单一代码。为了证明 Haxe 在生物信息学中的实用性，我们在此介绍 SeqPHASE 程序的案例，该程序最初用 Perl 编写（CGI 版本在服务器上运行），于 2010 年发布。出于安全考虑，Perl+CGI 不再可取，因此我们决定用 Haxe 重写 SeqPHASE 程序，并将其托管在 Github Pages (https://eeg-ebe.github.io/SeqPHASE)，从而减少了配置和维护专用服务器的需要。我们以 SeqPHASE 为例，讨论了 Haxe 源代码转换功能在实施生物信息软件方面的优缺点。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文去求助

来源期刊

Briefings in bioinformatics 生物-生化研究方法

CiteScore

13.20

自引率

13.70%

发文量

549

审稿时长

6 months

期刊介绍： Briefings in Bioinformatics is an international journal serving as a platform for researchers and educators in the life sciences. It also appeals to mathematicians, statisticians, and computer scientists applying their expertise to biological challenges. The journal focuses on reviews tailored for users of databases and analytical tools in contemporary genetics, molecular and systems biology. It stands out by offering practical assistance and guidance to non-specialists in computerized methodologies. Covering a wide range from introductory concepts to specific protocols and analyses, the papers address bacterial, plant, fungal, animal, and human data. The journal's detailed subject areas include genetic studies of phenotypes and genotypes, mapping, DNA sequencing, expression profiling, gene expression studies, microarrays, alignment methods, protein profiles and HMMs, lipids, metabolic and signaling pathways, structure determination and function prediction, phylogenetic studies, and education and training.