JABBA vs Jabba: when is software not really software?

It was only a matter of time I guess. Today I was alerted to a new publication by Simon Cockell (@sjcockell), it's a book chapter titled:

From the abstract:

Recently, a new hybrid error correcting method has been proposed, where the second generation data is first assembled into a de Bruijn graph, on which the long reads are then aligned. In this context we present Jabba, a hybrid method to correct long third generation reads by mapping them on a corrected de Bruijn graph that was constructed from second generation data

Now as far as I can tell, this Jabba is not an acronym, so we safely avoid the issue of presenting a JABBA award for Jabba. However, one might argue that naming any bioinformatics software 'Jabba' is going to present some problems because this is what happens when you search Google for 'Jabba bioinformatics'.

There is a bigger issue with this paper that I'd like to address though. It is extremely disappointing to read a software bioinformatics paper in the year 2015 and not find any explicit link to the software. The publication includes a link to http://www.ibcn.intec.ugent.be, but only as part of the author details. This web page is for the Internet Based Communication Networks and Services research group at the University of Gent. The page contains no mention of Jabba, nor does their 'Facilities and Tools' page, nor does searching their site for Jabba.

Initially I wondered if this is paper is more about the algorithm behind Jabba (equations are provided) and not about an actual software implementation. However, the paper includes results from their Jabba tool in comparison to another piece of software (LoRDEC) and includes details of CPU time and memory requirements. This suggests that the Jabba software exists somewhere.

To me this is an example of 'closed science' and represents a failure of whoever reviewed this article. I will email the authors to find out if the software exists anywhere…it's a crazy idea but maybe they might be interested if people could, you know, use their software.

Update 2015-11-20: I heard back from the authors…the Jabba software is on GitHub.

ACGT is now AFCW (Approved for Free Cultural Works): thoughts on switching to a CC-BY license

This website, as well as my personal website and Rescued by Code, licenses material under a Creative Commons license. Specifically, I've been using the Attribution Non-Commerical license, popularly known as CC BY-NC. My joint venture with Abby Yu, The Take-Home Message web comic, has been even more restrictive and has been licensing content under the Attribution Non-Commercial Share-Alike license (CC BY-NC-SA).

These choice of licenses is something that's been on my mind for a while. I've known that I'm not being as open as I could be and maybe this has stemmed from an unwarranted (not to mention unlikely) fear that someone would take all my blog posts and somehow seek to profit from them.

Today I saw a tweet by Rogier Kievit (@rogierK) that has helped me change my mind:

I found the third link — something that is now over a decade old — particularly persuasive and accordingly I have switched all of my website licenses to CC-BY. Apparently this means that all of my writings now fall into the category of Free Cultural Works. I am grateful to Abby Yu to agreeing to this change for The Take-Home Message.

This change also means that someone can now use my blog posts to write the definitive book on JABBA-awards…just as long as they give me appropriate attribution.

10 years of Open Access at the Wellcome Trust in 10 numbers [Link] →

A great summary of how the Wellcome Trust has helped drive big changes in open access publishing. Of the ten numbers that the post uses to summarise the last decade, this one surprised me the most:

20% – the volume of UK-funded research which is freely available at the time of publication
A recent study commissioned by Universities UK found that 20% of articles authored by UK researchers and published in the last two years were freely accessible upon publication. This figure increases to 24% within six months of publication, and 32% within 12 months.

If you had asked me to guess what this number would be, I think I would have been far too optimistic. Even the figure of 32% of articles being free within 12 months seems lower than I would imagine. Lots of progress still to be made!