Answering research questions or making new discoveries in this day and age is often dependent on software tools as Luis Bastiao Silva from BMD Software recently highlighted. In publishing the details of your software tool and making it open source you can make a real difference to the research of others. Plus, publishing a software tool article is an excellent way to get credit for what you have created; and the F1000Research platform, with its article versioning system, support for LaTeX submissions and proper syntax highlighting, is particularly well-suited to publishing software articles.
A good researcher names (and publishes) their tools
Not only does software facilitate research, it is also a first class research output as evidenced by our latest software tool articles. Recently, a group of researchers from the Keck School of Medicine, University of Southern California, published a software tool article describing Arkas – a novel RNA-Seq analysis pipeline combining data preparation, quality control, data analysis and secondary analysis tools. As noted by Harold Pimentel, Stanford University, in his peer review report, the pipeline usefully documents software versions and enforces consistency allowing users to easily identify any potential differences among versions.
Software tools are also essential to the field of agriculture, as demonstrated by web repository for Brassica phenotype data named the Brassica Information Portal (BIP). The portal, developed by Annemarie Eckes and colleagues from the Earlham Institute and published in our GODAN gateway, serves as a centralised source of trait data which is both open access and open source. Christoper J. Rawlings of Rothamsted Research applauds BIP’s greater use of ontologies in his peer review report.
Last week, in a paper published on F1000Research, Rafael Jimenez from the ELIXIR Hub and colleagues outlined recommendations to improve the quality and sustainability of research software. The paper passed peer review in only 12 days following publication. Unlike similar initiatives, the suggestions were drafted with more than just software developers in mind; the recommendations are directed at funders, institutions, journals, group leaders, and project managers. The authors stress the importance of making source code publically accessible from the start in order to increase reuse and collaboration, or as Linus Torvalds once put it: “Talk is cheap. Show me the code.”
Show us your code
To date, F1000Research has published over 160 software tool articles and we’re looking for more! Our current call for software tool papers, entitled ‘Show me the code’, intends to raise the profile of research software while highlighting its diversity. This means we’re looking for a wide range of papers spanning the life sciences and medicine, including but not limited to: Bioconductor vignettes, Cytoscape apps, Docker containers, Galaxy workflows, and R packages.
Interested? Submit your software tool article by 30 November 2017 to be part of the buzz. Be sure to mention ‘show me the code’ at submission stage to receive 50% off your next software tool article.