@article{15fdfb34a14e41a4a9769ef664a0a24e,
title = "A Practical Guide to Metabolomics Software Development",
abstract = "A growing number of software tools have been developed for metabolomics data processing and analysis. Many new tools are contributed by metabolomics practitioners who have limited prior experience with software development, and the tools are subsequently implemented by users with expertise that ranges from basic point-and-click data analysis to advanced coding. This Perspective is intended to introduce metabolomics software users and developers to important considerations that determine the overall impact of a publicly available tool within the scientific community. The recommendations reflect the collective experience of an NIH-sponsored Metabolomics Consortium working group that was formed with the goal of researching guidelines and best practices for metabolomics tool development. The recommendations are aimed at metabolomics researchers with little formal background in programming and are organized into three stages: (i) preparation, (ii) tool development, and (iii) distribution and maintenance.",
author = "Chang, {Hui Yin} and Colby, {Sean M.} and Xiuxia Du and Gomez, {Javier D.} and Helf, {Maximilian J.} and Katerina Kechris and Kirkpatrick, {Christine R.} and Shuzhao Li and Patti, {Gary J.} and Renslow, {Ryan S.} and Shankar Subramaniam and Mukesh Verma and Jianguo Xia and Young, {Jamey D.}",
note = "Funding Information: This work was supported by NIH grants U2C ES030164 (H.-Y.C.), U2C ES030170 (S.M.C., R.S.R.), U01 CA235507 (X.D.), U01 CA235488 (K.K.), U2C DK119886 (C.R.K., SS), U01 CA235493 (S.L., J.X.), U01 CA235482 (G.J.P.), and U01 CA235508 (J.D.G., J.D.Y.). M.J.H. was supported by a Research Fellowship from the Deutsche Forschungsgemeinschaft (DFG), Project Number 386228702. The authors thank the Metabolomics Consortium Steering Committee for useful discussions and feedback. Funding Information: Many bioinformatics software tools are developed by one or a handful of people, consisting mainly of graduate students or postdoctoral fellows. This can often cause issues when the main developer(s) relocates (i.e., due to graduation or because funding for the project ends). Therefore, it is critical to create a maintenance plan, such as choosing a programming language and framework that are familiar within the team at the development stage, strategically training next-generation developers during the transition period, or transferring the program into an open-source community project when the software grows beyond the maintenance capacity of the original development team (e.g., Cytoscape or Galaxy). To address the needs and concerns related to software development and maintenance, the US National Science Foundation (NSF) has recently funded the conceptualization of a U.S. Research Software Sustainability Institute (URSSI) to serve as a community hub and support scientists to create improved, more sustainable software. Publisher Copyright: {\textcopyright} ",
year = "2021",
month = feb,
day = "2",
doi = "10.1021/acs.analchem.0c03581",
language = "English (US)",
volume = "93",
pages = "1912--1923",
journal = "Analytical Chemistry",
issn = "0003-2700",
number = "4",
}