{"id":13219,"date":"2017-04-04T18:00:55","date_gmt":"2017-04-04T17:00:55","guid":{"rendered":"https:\/\/blogs.nature.com\/naturejobs\/?p=13219"},"modified":"2017-07-12T20:34:44","modified_gmt":"2017-07-12T19:34:44","slug":"joss-gives-computational-scientists-their-academic-due","status":"publish","type":"post","link":"https:\/\/blogs.nature.com\/naturejobs\/2017\/04\/04\/joss-gives-computational-scientists-their-academic-due\/","title":{"rendered":"TechBlog: JOSS<\/i> gives computational scientists their academic due"},"content":{"rendered":"
\"JOSS_banner\"<\/a>

{credit}JOSS{\/credit}<\/p><\/div>\n

The currency of science is\u2013duh!<\/em>\u2013publication. You do the work, you write a paper. Acceptance advances a researcher\u2019s career in every way that counts: tenure, promotion, reputation, and funding.<\/p>\n

But what if your research output isn\u2019t a research publication? For programmers who labor in the trenches to advance their and their colleagues\u2019 science, that\u2019s not a hypothetical question. The output of their research is code. And hard as it is to solve problems computationally, it\u2019s even harder to it well, requiring considerable testing, debugging, and documentation.<\/p>\n

In the world of computational science, says Arfon Smith<\/a>, who heads the Data Science Mission Office at the Space Telescope Science Institute in Baltimore, Maryland, creating, documenting, and releasing a polished bit of code effectively is<\/em> a publication. But unless that software is described in a traditional research publication and cited, its authors will rarely receive their due academic credit.<\/p>\n

As it turns out, few journals actually publish papers that document software on their own. Usually, they require that the software be bundled into a larger package that uses the software to drive some scientific advance.<\/p>\n

That situation struck Smith, who used to head scientific efforts at GitHub, as inherently absurd. So, he decided to do something about it. In May 2016, he launched the Journal of Open Source Software<\/a><\/em>. On 27 March, the journal was designated an affiliate<\/a> of the Open Source Initiative, an open-source software advocacy group.<\/p>\n

As described in a blog post<\/a> announcing its formation, JOSS<\/em> is a \u201cdeveloper-friendly journal for research software packages.\u201d Article preparation should take no more than an hour, Smith says, with articles amounting effectively to abstracts and pointers to the online homes of the software they describe.<\/p>\n

The journal is a \u201chack,\u201d Smith writes (meaning, in programmer lingo, a hasty workaround). But it\u2019s also legit. The journal has an ISSN number; articles are assigned citable DOIs; there is a formal (and open) peer-review process<\/a>; and a top-flight editorial board<\/a>.<\/p>\n

\u201cThey pass the \u2018sniff test\u2019,\u201d he says, of JOSS<\/em> articles, \u201cbut they are deliberately short. Because we think if you have gone through the effort of producing high-quality software, you shouldn\u2019t have to go through the effort of creating the paper to announce it.\u201d<\/p>\n

The requirements for publication are few: Software must serve a research application, be available on a public repository such as GitHub or Bitbucket, have an open-source license, and include a short file containing the article title, summary, authors, affiliations, and references. Accepted packages must be archived on sites such as Zenodo or Figshare.<\/p>\n

Once submitted, peer reviewers verify the software is freely available, that it installs correctly, and that it functions as advertised. They ask that the software abide by the open-source ethos \u2013 that there be mechanisms for researchers to comment, post queries, and suggest improvements, for instance. And they ensure the software is well documented.\u00a0(Researchers can also\u00a0cross-submit articles that have already been accepted at rOpenSci<\/a>; four or five authors have done so, says Smith.)<\/p>\n

Because the publishing team is all-voluntary, considerable effort was put into automating the editorial process, Smith says. For instance, paper submissions through the JOSS<\/em> web site automagically produce an \u201cissue\u201d in the journal\u2019s GitHub page, where the review process occurs in plain view (see\u00a0an example thread here<\/a>). The team produced a GitHub bot called \u201c@whedon\u201d (named for screenwriter\/director\u00a0Joss Whedon<\/a>) that performs tasks such as assigning editors and reviewers, and updating article status.<\/p>\n

JOSS<\/em>\u00a0has received 126 submissions since mid-May 2016, 87 of which have been accepted; 38 manuscripts are under review. No papers have yet been rejected, Smith\u00a0says, though a few have been withdrawn because they did not describe research applications. Others were so under-developed they were not yet ready for publication, but they too were not rejected outright, he says, but rather put on hold.<\/p>\n

\u201cSoftware is a living entity, it should be enhanced and improved. So, it\u2019s not a problem to keep things open a long time.\u201d<\/p>\n

Smith admits JOSS<\/em> is not a long-term solution but a temporary workaround to a system that really doesn\u2019t work for computational scientists. In his blog, he calls it \u201ca necessary hack for a crappy metrics system.\u201d Ultimately, science must evolve beyond citation metrics and other traditional measures of academic success, he writes, but \u201cthat\u2019s the long-term fix.\u201d In the meantime, there\u2019s JOSS<\/em>.<\/p>\n

 <\/p>\n

Jeffrey Perkel is Technology Editor at\u00a0<\/em>Nature.\u00a0<\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"

The currency of science is\u2013duh!\u2013publication. You do the work, you write a paper. Acceptance advances a researcher\u2019s career in every way that counts: tenure, promotion, reputation, and funding.  Read more<\/a> Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":104777,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[190,192,359,200],"tags":[6322191,5945961,6322193,407,116,6677357],"class_list":["post-13219","post","type-post","status-publish","format-standard","hentry","category-academia-2","category-blog-2","category-publishing-2","category-technology-2","tag-arfon-smith","tag-jeffrey-perkel","tag-journal-of-open-source-software","tag-open-source","tag-publishing","tag-techblog"],"_links":{"self":[{"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/posts\/13219","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/users\/104777"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/comments?post=13219"}],"version-history":[{"count":0,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/posts\/13219\/revisions"}],"wp:attachment":[{"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/media?parent=13219"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/categories?post=13219"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.nature.com\/naturejobs\/wp-json\/wp\/v2\/tags?post=13219"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}