Sunday, November 04, 2018

Programming in the Life Sciences #23: research output for the future

A random public domain
picture with 10 in it.
Ensuring that you and others can understand you research output five years from now requires effort. This is why scholars tend to keep lab notebooks. The computational age has perhaps made us a bit lazy here, but we still make an effort. A series of Ten Simple Rules articles outline some of the things to think about:
  1. Goodman A, Pepe A, Blocker AW, Borgman CL, Cranmer K, Crosas M, et al. Ten Simple Rules for the Care and Feeding of Scientific Data. Bourne PE, editor. PLoS Computational Biology. 2014 Apr 24;10(4):e1003542.
  2. List M, Ebert P, Albrecht F. Ten Simple Rules for Developing Usable Software in Computational Biology. Markel S, editor. PLOS Computational Biology. 2017 Jan 5;13(1):e1005265.
  3. Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost F da V, et al. Ten Simple Rules for Taking Advantage of Git and GitHub. Markel S, editor. PLOS Computational Biology. 2016 Jul 14;12(7):e1004947.
  4. Prlić A, Procter JB. Ten Simple Rules for the Open Development of Scientific Software. PLoS Computational Biology. 2012 Dec 6;8(12):e1002802.
  5. Sandve GK, Nekrutenko A, Taylor J, Hovig E. Ten Simple Rules for Reproducible Computational Research. Bourne PE, editor. PLoS Computational Biology. 2013 Oct 24;9(10):e1003285.
Regarding licensing, I can highly recommend reading this book:
  1. Rosen L. Open Source Licensing [Internet]. 2004. Available from:
Regarding Git, I recommend these two resources:
  1. Wiegley J. Git From the Bottom Up [Internet]. 2017. Available from:
  2. Task 1: How to set up a repository on GitHub [Internet]. 2018. Available from:

Saturday, November 03, 2018

Fwd: "We challenge you to reuse Additional Files (a.k.a. Supplementary Information)"

Download statistics of J. Cheminform.
Additional Files show a clear growth.
Posted on the BMC (formerly BioMedCentral) Research in progress blog our challenge to you to reuse additional files:
    Since our open-access portfolio in BMC and SpringerOpen started collaborating with Figshare, Additional Files and Supplementary Information have been deposited in journal-specific Figshare repositories, and files available for the Journal of Cheminformatics alone have been viewed more than ten thousand times. Yet what is the best way to make the most of this data and reuse the files? Journal of Cheminformatics challenges you to think about just that with their new upcoming special issue.
We already know you are downloading the data frequently and more every year, so let us know what you're doing with that data!

For example, I would love to see more data from these additional files end up in databases, such as Wikidata, but any reuse in RDF form would interest me.

Tuesday, October 30, 2018

Some steps needed in knowledge dissemination

Last week I had holiday from my BiGCaT position and visited Samuel Winthrop at the SpringerNature offices to discuss our Journal of Cheminformatics. It was a great meeting (1.5 days) and we discussed a lot of things we could do (or are in the process of doing) to improve using the journal format for knowledge dissemination. We have some interesting things lined up ... </suspense>

For now, check out my personal views in these slides I presented last week:

Thursday, October 11, 2018

Two presentations at WikiPathways 2018 Summit #WP18Summit

Found my way back to my room a few kilometers from the San Francisco city center, after a third day at the WikiPathways 2018 Summit at the Gladstone Institutes in Mission Bay, celebrating 10 years of the project, which I only joined some six and a half years ago.

The Summit was awesome and the whole trip was awesome. The flight was long, with a stop in Seattle. I always get a bit nervous of lay-overs (having missed my plane twice before...), but a stop in Seattle is interesting, with a great view of Mt. Rainier, which is also from an airplane quite a sight. Alex picked us up from the airport and the Airbnb is great (HT to Annie for being a great host), from which we can even see the Golden Gate Bridge.

The Sunday was surreal. With some 27 degrees Celsius the choice to visit the beach and stand, for the first time, in the Pacific was great. I had the great pleasure to meet Dario and his family and played volleyball at a beach for the first time in some 28 years. Apparently, there was an airshow nearby and several shows were visible from our site, including a very long show by the Blue Angels.
Thanks for a great afternoon!

Sunday evening Adam hosted us for an WikiPathways team dinner. His place gave a great view on San Francisco, the Bay Bridge, etc. Because Chris was paying attention, we actually got to see the SpaceX rocket launch (no, my photo is not so impressive :). Well, I cannot express in words how cool that is, to see a rocket escape the earth gravity with your own eyes.

And the Summit had not even started yet.

I will have quite a lot to write up about the meeting itself. It was a great line up of speakers, great workshops, awesome discussions, and a high density of very knowledgeable people. I think we need 5M to implement just the ideas that came up in the past three days. And it would be well invested. Anyway, more about that later. Make sure to keep an eye on the GitHub repo for WikiPathways.

That leave me only, right now, to return to the title of this post. And below they are, my two contributions to this summit:

Saturday, September 29, 2018

Two presentations of last week: NanoTox 2018 and the BeNeLuX Metabolomics Days

Slide from the BeNeLux Metabolomics Days
presentation (see below).
The other week I gave a two presentations, one at the BeNeLux Metabolomics Days in Rotterdam and the next day one at NanoTox 2018 in Neuss, Germany. During the first I spoke about research ongoing in our research group and in Neuss about the eNanoMapper project and some of the ongoing eNanoMapper projects I am involved in.

Here are the slides of both talks.