June 17, 2009

Nettab 2009 Day Two: Wikis ‘n’ Workflows

Alex Bateman on the RNA WikiprojectThis is a  brief report and some links from the second day of Network Applications and Tools in Biology (NETTAB 2009) in Catania, Sicily. There were two keynotes on the RNA WikiProject [1] by Alex Bateman and myExperiment [2] (by me) as as well as presentations by (I think but I wasn’t concentrating enough) Dietlind Gerloff, Guiliano Armano, Frédéric Cadier and Leandro Ciuffo.

Alex Bateman (wikipedia user:Alexbateman) did an entertaining talk on the RNA wikiproject: Community annotation of RNA families where they have taken data from the Rfam database [3], and put it all into regular wikipedia. This project got quite a lot of media attention back in February. In this case, the primary advantages of “letting go of data” by giving it to wikipedia are that it is read by everyone who uses Google (where pages are frequently the top search result) and wikipedia gets lots more traffic than biological databases like rfam.sanger.ac.uk do. Thanks to wikirank which tells you what is popular on wikipedia, it is also possible to quickly compare the popularity of pages, see RNA vs. Ribosomal RNA vs Micro RNA vs SnoRNA for an example. The Rfam project have some interesting stats on who makes the most edits to the Rfam pages, it isn’t always the scientists who make important contributions, but anonymous users and machines (e.g. like Rfambot, Smackbot and Citation bot) who are often doing most of the hard work. There is a very long tail of contributors who make small contributions – which supports the 90% of users in on-line communities are lurkers who never contribute rule and is reminiscent of Citizen Science and Muggles. I wanted to put the slides from this talk on slideshare, but they contain some unpublished data. You can, however, subscribe to the feed of the Rfam and Pfam blog at xfam.wordpress.com, if you’d like to keep up to date on developments in this area.

After the keynote there were presentations by Dietlind Gerloff on Open Knowledge (a new agent-based infrastructure for bioinformatics experimentation – nice pictorial intro using lego here) and Guiliano Armano? on ProDaMa-C – a collaborative web application to generate specialised protein structure datasets.

The next keynote was on myexperiment.org, “Where Experimental Work Flows” – my slides on Who are you, Managing collaborative digital identities in bioinformatics with myexperiment are embedded below.

I followed this presentation with a live 30 minute demonstration and discussion of myexperiment. The most interesting question people asked was Why use OpenID instead of full blown Public Key Infrastructure? (answer: OpenID is currently a lot easier and provides good-enough security). The rest of the day is a bit of a blur, I’m with Tim Bray in enjoying the monster adrenaline high of public speaking, but with all that ChEBI:28918 coursing through my veins it can be difficult to think straight (immediately before, during or after a talk)… so you’ll have to take a look at the proceedings for the full details of what happened in the afternoon – but they included Make Histri (great name!), SBMM: Systems Biology Metabolic Modeling Assistant [4] by Ismael Navas-Delgado and Biomedical Applications of the EELA-2 project.

By the evening time, there was some Opera dei Pupi (traditional sicilian puppet theatre), a trip to Acireale and a delicious italian feast in a ristorante (the name of which I can’t remember) to round off an enjoyable day.


  1. Daub, J., Gardner, P., Tate, J., Ramskold, D., Manske, M., Scott, W., Weinberg, Z., Griffiths-Jones, S., & Bateman, A. (2008). The RNA WikiProject: Community annotation of RNA families RNA, 14 (12), 2462-2464 DOI: 10.1261/rna.1200508
  2. De Roure, D., & Goble, C. (2009). Software Design for Empowering Scientists IEEE Software, 26 (1), 88-95 DOI: 10.1109/MS.2009.22
  3. Gardner, P., Daub, J., Tate, J., Nawrocki, E., Kolbe, D., Lindgreen, S., Wilkinson, A., Finn, R., Griffiths-Jones, S., Eddy, S., & Bateman, A. (2009). Rfam: updates to the RNA families database Nucleic Acids Research, 37 (Database) DOI: 10.1093/nar/gkn766
  4. Reyes-Palomares, A., Montanez, R., Real-Chicharro, A., Chniber, O., Kerzazi, A., Navas-Delgado, I., Medina, M., Aldana-Montes, J., & Sanchez-Jimenez, F. (2009). Systems biology metabolic modeling assistant: an ontology-based tool for the integration of metabolic data in kinetic modeling Bioinformatics, 25 (6), 834-835 DOI: 10.1093/bioinformatics/btp061

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