May 21, 2010

myExperiment: The Videos

myExperiment is a research project that is exploring models, techniques and infrastructure for sharing digital items associated with  research , especially scientific workflows. The project is funded by the Joint Information Standards Committee (JISC) as part of a series of projects building Virtual Research Environments (VRE’s) and is run by Dave De Roure and Carole Goble at the Universities of Southampton and Manchester in the UK.

Last year, JISC made some professional videos describing the project. Needless to say, the videos were much more fun to make than the accompanying papers [1,2,3] and a probably more informative too. The best way of linking the research papers to the videos on youtube is to blog about them, so here they are. The first video (below) talks about the project generally:

The second video (below) discusses the data used in tackling African trypanosomiasis (sleeping sickness) in cattle.

The videos include interviews with Carole Goble, Dave De Roure, Paul Fisher, Andy Brass and yours truly.


  1. David De Roure, Carole Goble, & Robert Stevens (2007). Designing the myExperiment Virtual Research Environment for the Social Sharing of Workflows IEEE International Conference on e-Science and Grid Computing, 603-610 DOI: 10.1109/E-SCIENCE.2007.29
  2. David De Roure, Carole Goble, Jiten Bhagat, Don Cruickshank, Antoon Goderis, Danius Michaelides, & David Newman (2008). myExperiment: Defining the Social Virtual Research Environment IEEE Fourth International Conference on eScience, 2008. eScience ’08., 182-189 DOI: 10.1109/eScience.2008.86
  3. Goble, C., Bhagat, J., Aleksejevs, S., Cruickshank, D., Michaelides, D., Newman, D., Borkum, M., Bechhofer, S., Roos, M., Li, P., & De Roure, D. (2010). myExperiment: a repository and social network for the sharing of bioinformatics workflows Nucleic Acids Research DOI: 10.1093/nar/gkq429

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

June 15, 2009

Andrea Wiggins on little e-Science

Andrea WigginsAndrea Wiggins [1,2] from Syracuse University, New York is visiting Manchester this week and will be doing a seminar on “Little e-Science“, the details of which are below.

Date, time: 12 – 2pm on Thursday 18th June

Location: Atlas 1&2, Kilburn building

Title: Little eScience

Abstract: An interdisciplinary community of researchers has started to coalesce around the study of free/libre open source software (FLOSS) development. The research community is in many ways a reflection of the phenomenon of FLOSS practices in both social and technological respects, as many share the open source community’s values that support transparency and democratic participation. As community ties develop, new collaborations have spurred the creation of shared research resources: several repositories provide access to curated research-ready data, working paper repositories provide a means for disseminating early results, and a variety of analysis scripts and workflows connecting the data sets and literature are freely available. Despite these apparently favorable conditions for research collaboration, adoption of the tools and practices associated with eResearch has been slow as yet.

The key issues observed to date seem to stem from the challenges of pre-paradigmatic little science research. Researchers from software engineering, information systems, and even anthropology may examine the same construct, such as FLOSS project success, but will likely proceed from different epistemologies, utilize different data sources, identify different independent variables with varying operationalizations, and employ different research methodologies. In the decentralized and phenomenologically-driven FLOSS research community, creating and maintaining cyberinfrastructure [3] is a substantial effort for a small number of participants. In the little sciences, achieving critical mass of participation may be the most significant factor in creating a viable community of practice around eScience methods.

Update Slides are embedded below:


  1. Andrea Wiggins (2009) Social Life of Information: We Are Who We Link Andrea’s blog
  2. Andrea Wiggins, James Howison, & Kevin Crowston (2008). Social dynamics of FLOSS team communication across channels Open Source Development, Communities and Quality
  3. Lincoln Stein (2008). Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges Nature Reviews Genetics, 9 (9), 678-688 DOI: 10.1038/nrg2414

June 1, 2009

Scott Marshall on Interoperability

M. Scott MarshallScott Marshall is visiting Manchester this week, he will be doing a seminar on Friday 5th June, here are some details for anyone who is interested in attending:

Speaker: Dr. M. Scott Marshall, The University of Amsterdam

Date/Time: 5th June 2009, 11:00

Location: Room MLG.001 (Lecture Theatre), MIB building, (number 16 on campus map)

Title: Standards Enabled Interoperability: W3C Semantic Web for Health Care and Life Sciences Interest Group

Abstract: The W3C Semantic Web for Health Care and Life Sciences Interest Group (HCLS) has the mission of developing, advocating for, and supporting the use of Semantic Web technologies for biological science, translational medicine and health care. HCLS covers hot topics including data integration and federation, bridging commonly used domain standards such as CDISC and HL7, and the applications of medical terminologies. This talk will introduce the HCLS, as well as provide an overview of the activities that are currently ongoing within the task forces, as well as new developments and the recent Face2Face meeting. The role of information extraction and the current interest in Shared Identifiers will also be discussed.


  1. Ruttenberg, A., Rees, J., Samwald, M., & Marshall, M. (2009). Life sciences on the Semantic Web: the Neurocommons and beyond Briefings in Bioinformatics, 10 (2), 193-204 DOI: 10.1093/bib/bbp004

April 9, 2009

Upcoming Gig: The Scholarly Communication Landscape

The Scholarly Communication LandscapeDetails of an upcoming gig, The Scholarly Communication Landscape in Manchester on the 23rd of April 2009. If you are interested in coming, you need to register by Monday the 13th April at the official symposium pages.

Why? To help University staff and researchers understand some of the more complex issues embedded in the developments in digital scholarly communication, and to launch Manchester eScholar, the University of Manchester’s new Institutional Repository.

How? Information will be presented by invited speakers, and views and experience exchanged via plenary sessions.

Who For? University researchers (staff and students), research support staff, librarians, research managers, and anyone with an active interest in the field will find this symposium helpful to their developing use and provision of research digital formats. The programme for the symposium currently looks like this:

Welcome and Introduction by Jan Wilkinson, University Librarian and Director of The John Rylands Library.

Session I Chaired by Jan Wilkinson

  • Is the Knowledge Society a ‘social’ Network? Robin Hunt, CIBER, University College London
  • National Perspectives, Costs and Benefits Michael Jubb, Director, Research Information Network
  • The Economics of Scholarly Communication – how open access is changing the landscape Deborah Kahn, Acting Editorial Director Biology, BioMed Central

Session II Chaired by Dr Stella Butler

  • Information wants to be free. So … ? Dr David Booton, School of Law, University of Manchester
  • Putting Repositories in Their Place – the changing landscape of scholarly communication Bill Hubbard, SHERPA, University of Nottingham
  • The Year of Blogging Dangerously – lessons from the blogosphere, by Dr Duncan Hull (errr, thats me!), mib.ac.uk. This talk will describe how to build an institutional repository using free (or cheap) web-based and blogging tools including flickr.com, slideshare.net, citeulike.org, wordpress.com, myexperiment.org and friendfeed.com. We will discuss some strengths and limitations of these tools and what Institutional Repositories can learn from them.

Session III Chaired by Professor Simon Gaskell

Sumary and close by Professor Simon Gaskell, Vice-President for Research

September 4, 2008

Famous for fifteen people

Marilyn Monroe by Andy Warhol (and oddsock)The artist Andy Warhol once said:

“In the future everybody will be world famous for fifteen minutes”.

This well worn saying has been quoted and misquoted in hundreds of different ways in the forty years since Warhol first coined it [1].

Bad Scientist Ben Goldacre, in his keynote speech* at Science Blogging (sciblog) 2008, highlighted one of these deliberate misquotes, which he attributed to NTK.net (Need To Know: Britain’s most sarcastic high-tech weekly newsletter). It goes a little something like this:

“On the internet everybody can be world famous for fifteen people“.

This wonderful expression captures the nature and scale of science blogging on the internet today in a nutshell. Personally, I think it also sums up much of the spirit of the Science Blogging 2008 conference as well. In total, around eight groups of fifteen people, attended the conference. It was physically impossible to talk to all of them in one day, especially since I had to slink off early at 7pm, but I did manage to meet the following people: (more…)

August 26, 2008

Open Notebook Science in Manchester

Jean-Claude (Horace Moody)Organic chemist Jean-Claude Bradley is currently touring the UK. He is doing various talks up and down the country, including one in Manchester on Friday September 5th 2008 at the Manchester Interdisciplinary Biocentre (MIB). So, if you’re interested in novel uses of web technology, including Open Notebook Science to facilitate drug discovery, come along and join the fun. The abstract for his talk on Open Notebook Science using free and hosted tools can be found over at myexperiment.org which is sponsoring this event.

Creative Commons licensed picture of Jean-Claude Bradley (aka Horace Moody) in Second Life by Hiro Sheridan.

update see Jean-Claude Bradley’s presentation on slideshare:

April 25, 2008

WWW2008: The Great Firewall of China

Passage [The Great Wall / Beijing] by d'n'cThe seventeenth international World Wide Web conference (WWW2008.org) is currently finishing in Beijing, China. There are some interesting papers this year. Thankfully, the Great Firewall of China doesn’t prevent these papers reaching the rest of the world. It’s One World, One Web (allegedly). Here are some brief highlights from the conference. (more…)

April 4, 2008

myScience: “social software” for scientists

myExperimentWith apologies to Jonathan Swift:

“Great sites have little sites upon their back to bite ‘em
And little sites have lesser sites, and so ad infinitum…”

So what happened was, Carole Goble asked on the myExperiment mailing list, “is there a list of scientist social networking sites”? Here is first attempt at such a list (not comprehensive), you’ll have to decide for yourself which are the great, greater, little and lesser sites.

March 5, 2008

Science 2.0

Filed under: web of science — Duncan Hull @ 5:43 pm
Tags: , , , , , ,

I’ve often wondered how all the ridiculous fluffy Web 2.0 marketing hype (see Tim O’Reilly’s principles of Web 2.0) maps into the world of Science. In a talk yesterday, Dave DeRoure argued there is a massive gap between scientists and infrastructure on the Web of Science, most people would agree with this. He points out that there is nothing in the middle to bridge between the two disparate worlds of people and technology. He also claims that Web 2.0 can bridge the gap, and also explains how Web 2.0 “design patterns” maps onto Science. You can see the original slides for yourself, here is my summary. (more…)

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