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In June, we asked researchers to show us their code and send us their latest Software Tool Articles. We will now share with you highlights from some of the 16 new articles published since then. And as a testament to the diversity of software used in research, these articles span the life sciences and medicine; include R packages, Bioconductor vignettes, and Docker containers, and have been written in a wide range of programming languages such Perl, Java, and Python.

Compiling

Despite publishing over 170 software tool articles since we were established nearly five years ago, this call for papers saw a first for F1000Research: a software tool written in OCaml! Fragger is a new protein fragment picker, developed by Francois Berenger from Kyushu University and colleagues, which can quickly search a large collection of proteins to identify fragments regardless of length.

By contrast to Fragger, three software tools found common company in our Bioconductor gateway: PPInfer, EGSEA, and bcbioRNASeq. The PPInfer package, developed by Dongmin Jung and Xijin Ge, leverages the STRING database to help identify functionally related proteins from protein-protein interaction networks. As noted by peer reviewer Charlotte Soneson at University of Zurich, this tool is likely to be useful for users of bcbio (a tool for sequencing analysis). What’s more, the paper moves beyond the constraints of the traditional PDF and includes three interactive figures.

Perhaps as cool as interactive figures, if not cooler, NastyBugs was developed as part of a hackathon hosted by the NCBI. The program, which is available as a Docker image, can be used by clinicians and researchers as a fast and reliable way to extract antimicrobial resistance genomic signatures from human metagenomes.

Similarly, TicTimer developed by Jonathan K. Black, Brigham Young University, and colleagues also has clinical applications. The java program logs tics and reward delivery for research on Tourette Syndrome and related disorders. While the article does not aim to describe clinical outcomes, as noted in the peer review report by Patrick Haggard, University College London, TicTimer may be useful in behavioural analysis and clinical training.

A continuous loop

Our current call for software tool articles ends shortly on 30 November 2017. Submitting an article by this date will ensure a 50% discount on your next submission by mentioning ‘show me the code’ at submission. Still, we would like to encourage you to continue to submit your software well beyond this date.

After all, 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.