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 I wanted to put the slides from this talk on slideshare, but they contain some unpublished data.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

November 24, 2008

Embracing Registries of Web Services

Filed under: informatics,web of science — Duncan Hull @ 2:00 pm
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Embracing by tanakwhoIf you travel back in time, to around 2002, it isn’t difficult to find people claiming that Web services were going to be the new silver bullet technology to create world peace, eradicate global poverty and finally make some sense of all the data produced by the human genome project. Over hyped? Just a bit. One of the many reasons none of these things happened, is it turned out to be much harder than anticipated to build centralised registries, where people could go to find Web services to perform a given task. Can service registries ever be built? Critics like Tim Bray at Sun Microsystems for example, have suggested that (quote) “registries are a fantasy”, but some already exist and there are more in the pipeline. This article briefly introduces some of them: Seekda, BioMOBY, the Embrace service registry and the Biocatalogue project. (more…)

November 6, 2007

What’s The Point of Blogging?

I am a hard bloggin' scientist. Read the Manifesto.
Sometimes I wonder what what the point of blogging is and just how much time people (myself included) waste reading and writing them. Let’s face it, most leading scientists are too damn busy to pay much attention to the blogosphere, especially when it descends (as it frequently does) into “uncontrollable verbal discharge”. This unfortunate medical condition is also known as Blogorrhoea. A free-flowing blog is unlikely to directly increase a scientists productivity (as approximated by the infamous h-index), and might even decrease it. Now, we all know that powerpoint can be PowerPointless, so is blogging also a pointless activity? Or to put it another way: Nodalpoint or Nodalpointless?

If you’ve ever wondered what the point of scientific blogging is, you should read the following, (if you haven’t already):

So what the heck, if blogging is fun and helps you communicate ideas with people, why get all uptight about questionable metrics for measuring scientific productivity? Wherever you blog, blog hard, blog fast and enjoy it. At the very least, it will fill the gaping void left on the Web by traditional scientific publishing. Who knows what the other benefits might be?


  1. Jorge Hirsch An index to quantify an individual’s scientific research output Proceedings of the National Academy of Sciences. 2005 November;102(46):16569-16572 DOI:10.1073/pnas.0507655102
  2. this post originally on nodalpoint with comments

May 26, 2006

BioGrids: From Tim Bray to Jim Gray (via Seymour Cray)

Filed under: biotech — Duncan Hull @ 11:30 pm
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Recycle or Globus Toolkit?Grid Computing already plays an important role in the life sciences, and will probably continue doing so for the forseeable future. BioGrid (Japan), myGrid (UK) and CoreGrid (Europe) are just three current examples, there are many more Grid and Super Duper Computer projects in the life sciences. So, is there an accessible Hitch Hikers Guide to the Grid for newbies, especially bioinformaticians?

Unfortunately much of the literature of Grid Computing is esoteric and inaccessible, liberally sprinkled with abstract and wooly concepts like “Virtual Organisations” with a large side-order of acronym soup. This makes it difficult or impossible for the everyday bioinformatican to understand or care about. Thankfully, Tim Bray from Sun Microsystems has a written an accessible review of the area, “Grids for dummies”, if you like. Its worth a read if you’re a bioinformatician with a need for more heavyweight distributed computing than the web currently provides, but you find Grid-speak is usually impenetrable nonsense.

One of the things Tims discusses in his review is Microsoftie Jim Gray, who is partly responsible for the 2020 computing initiative mentioned on nodalpoint earlier. Tim describes Jim’s article Distributed Computing Economics. In this, Jim uses wide variety of examples to illustrate the current economics of grids, from “Megaservices” like Google, Yahoo! and Hotmail to the bioinformaticians favourites, BLAST and FASTA. So how might Grids affect the average bioinformatician? There are many different applications of Grid computing, but two areas spring to mind:

  1. Running your in silico experiments (genome annotation, sequence analysis, protein interactions etc), using someone elses memory, disk space, processors on the Grid. This could mean you will be able to do your experiments more quickly and reliably than you can using the plain ol’ Web.
  2. Executing high-throughput and long-running experiments, e.g. you’ve got a ton of microarray data and it takes hours or possibly days to analyse computationally.

So if you deal with microarray data daily, you probably know all this stuff already, but Tims overview and Jims commentary are both accessible pieces to pass on to your colleagues in the lab. If this kind of stuff pushes your button, you might also be interested in the eProtein Scientific Meeting and Workshop Proceedings.

[This post was originally published on nodalpoint with comments.]

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