O'Really?

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.

References

  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

February 5, 2010

Classic paper: Montagues and Capulets in Science

Romeo and Juliet by HappyHippoSnacksIn preparation for a joint seminar I’ll be doing with Midori Harris here at the EBI, here’s a classic paper [1,2] on the social problems of building biomedical ontologies. This paper is worth reading (or re-reading) because it makes lots of relevant points about the use and abuse of research and how people misunderstand each other [3]. It’s funny (and available Open Access too) plus how many papers do you read with an abstract written in the style of Big Bard Bill Shakespeare?

ABSTRACT: Two households, both alike in dignity, In fair Genomics, where we lay our scene, (One, comforted by its logic’s rigour, Claims ontology for the realm of pure, The other, with blessed scientist’s vigour, Acts hastily on models that endure), From ancient grudge break to new mutiny, When ‘being’ drives a fly-man to blaspheme. From forth the fatal loins of these two foes, Researchers to unlock the book of life; Whole misadventured piteous overthrows, Can with their work bury their clans’ strife. The fruitful passage of their GO-mark’d love, And the continuance of their studies sage, Which, united, yield ontologies undreamed-of, Is now the hour’s traffic of our stage; The which if you with patient ears attend, What here shall miss, our toil shall strive to mend.

So if you read the paper, you have to ask yourself, are you a Montague or a Capulet?

References

  1. Carole Goble and Chris Wroe (2004). The Montagues and the Capulets Comparative and Functional Genomics, 5 (8), 623-632 DOI: 10.1002/cfg.442
  2. Carole Goble (2004) The Capulets and Montagues: A plague on both your houses?, SOFG: Standards and Ontologies for Functional Genomics
  3. William Shakespeare (1596) Romeo and Juliet

[Romeo and Juliet picture via Happy Hippo Snacks]

May 21, 2009

Upcoming Gig: The Italian Job at NETTAB

NETTAB: Network Tools and Applications in BiologyNetwork Tools and Applications in Biology (NETTAB) is a series of workshops in Bioinformatics. It focuses on the most promising and innovative ICT tools and their utility in Bioinformatics. These workshops aim to introduce participants to the evolving network standards and technologies that are being applied to the field of biology.

Since 2001, the NETTAB workshops have being doing a Giro d’Italia or  Grand Tour of Italy; Genova, Bologna, Naples, Sardinia, Lake Como and Pisa have all played host to the workshop. This year, NETTAB 2009 is in Catania at the Università degli Studi di Catania in Sicily close to Mount Etna.

There is special theme for this years workshop, held on June 10-13, on Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development. So I’m very pleased that Paolo Romano asked me to do a keynote presentation (w00t!) on the work we have been doing in the REFINE project and myExperiment. Grazie Paolo, grazie. And thanks Carole Goble too for the recommendation.

If you’re going to NETTAB this year, see you there. If you’d like to come, today is the last day for the early bird discount, sign up at the registration page. The scientific programme looks interesting, it will be good to meet Alex Bateman and Tim Clark and the rest of this years speakers.

Now, if my keynote presentation is going to (as Michael Caine once famously said [1]) “blow the bl**dy doors off” [2], it needs loads more work. So I’d better get back to it. Ciao!

[Update: See reports from day one, day two and day three of NETTAB 2009.]

References

  1. Peter Collinson and Troy Kennedy-Martin (1969) The Italian Job
  2. Michael Caine (1969) “You’re only supposed to blow the bl**dy doors off!”
  3. Cannata, N., Schröder, M., Marangoni, R., & Romano, P. (2008). A Semantic Web for bioinformatics: goals, tools, systems, applications BMC Bioinformatics, 9 (Suppl 4) DOI: 10.1186/1471-2105-9-S4-S1

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

December 10, 2008

Congratulations Carole Goble, e-Scientist

Carole Goble wins first Jim Gray e-Science awardAt the Microsoft e-Science workshop in Indianapolis, earlier this week Carole Goble was awarded with the first Jim Gray 2008 e-Science award, pictured here collecting the prize from Tony Hey of Microsoft Research. You can read all about it in the Seattle Tech Report which says:

“As director of the U.K.’s myGrid project, Goble helped create Taverna, open source software that allows scientists to analyse complex data sets with a standard computer.”

It is very inspiring when colleagues win prizes and awards. Personally, I would not be here doing what I’m doing if it wasn’t for Carole and myGrid, and neither would many other people who work on (or have worked on) myGrid and related projects.

Carole, you are an inspiration to us all, congratulations! To celebrate your success, I’m off to commit some more of the seven deadly sins of bioinformatics [1]…

References

  1. Carole Goble The Seven Deadly Sins of Bioinformatics
  2. e-Science in Indianapolis: Carole Goble wins the 1st Jim Gray eScience Award
  3. Joseph Tartakoff British professor given first Jim Gray Award, Seattle Post-Intelligencer, Tech Report
  4. Todd Bishop UK prof receives Jim Gray award Tech Flash
  5. Savas Parastatidis Carole Goble as the first recipient of the “Jim Gray eScience Award”
  6. Microsoft Recognise Manchester e-Science Contribution
  7. Deborah Gage Microsoft creates award in the name of Jim Gray San Francisco Chronicle, The Tech Chronicles
  8. Microsoft New tools for Discovery on Display at e-Science workshop

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.
(more…)

November 30, 2007

Burn semantic Web, Burn!

Taking down A.I. town?

Danger! Religious Wars!The Semantic Web is (quote) “a new form of Web content that is meaningful to computers”. It will “unleash a revolution of new possibilities” using a magical “new” artificially intelligent technology called ontology. So says a much-cited article in Scientific American published back in May 2001. Most people who have read this article, fall into two camps: “believers” and “non-believers”. Let me tell you a short story about a religious war between these two groups…

An Old War Story: Chapter 1

This is a work of fiction, though as they say in Hollywood it is “based on a true story”. Characters names are real.

A crusade of semantic web believers, is started by three people called Jim Hendler, Ora Lassila and Tim Berners-Lee. At the heart of their faith is a holy scripture and a suite of sacred technology called the semantic web stack. If people use this technology, the crusaders believe, the Web would be a better place. Search engines like Google, for example, would be even smarter than they already are, because they would intelligently “know what you mean“, when you type your keywords. All this new magic comes from using good old fashioned logic, metadata and reasoning. Better Search Engines is one of the mantras of the semantic web troops as they pour onto the battlefield towards the promised land. Viva la Webolution! Charge!

A counter-attack is launched by the non-believers of this vision of the future. They rally behind a man called Clay Shirky who roars “the semantic web is doomed” at the top of his voice. Many others echo Shirky’s sentiment, including Peter Norvig, Rob McCool, Cory Doctorow and Tim O’Reilly. General Shirky makes powerful allies in battle, and he has a two-pronged attack. “Ontology is over-rated” he jeers. Led by Shirky, the non-believers capture the sacred technology, add their own firewood and put the torch to it in a very public place. The flames leap into the sky, visible for miles around.

“Burn semantic web, burn!” the non-believers cry as they gleefully dance around the fire.

The battle rages, the believers will not take this heresy lying down. They regroup and surge forward again. Death to the blasphemers! With the help of some biologists, they seek revenge using the Gene Ontology as deadly ammunition. The non-believers are confused by this tactic, they don’t know what genes are and neither do the biologists. Unfortunately, the biologists unwittingly find themselves in the middle of an epic battle they didn’t start. There are ugly skirmishes involving logic and graph theory. Dormant and hideous A.I. monsters are resurrected from their caves, where they spent the A.I. winter. These gruesome monsters make the Balrog beast from Lord of the Rings look like a childrens cuddly toy.

From the relative safety of their command centres, the leaders orchestrating the war look on. Many foot soldiers and PhD students have been slayed on the field of battle, tragic young victims of the holy war. Understandably the crusaders are unhappy. Jim Hendler isn’t pleased as he surveys the carnage and devasation. Ora Lassila is also disappointed.

“We never said that, you completely minsunderstood. You are all burning the wrong thing, using fuel we never gave you. You lied, you cheated, you faked, you changed the stakes!”

There is a lull in battle. But confusion reigns, especially among the innocent civilians and bewildered biologists.

(End of chapter 1)

Epilogue

As of the winter of 2007, the semantic web fire is still burning. While I warm myself next to it, using all the juicy metadata as material for my PhD, it is still too early to predict just how useful the technology is going to be. It doesn’t really matter if you’re a “believer”, a “non-believer” or completely agnostic about the semantic web. The religious war beween the two sides tells you more about human behaviour, than it does about the utility of the technology. Optimists profit from making bold claims to get noticed on the battlefield. Critics are more cynical, furthering their own careers by countering the optimists claims. Other people interpret the interpretations of the cynics second-hand. Thanks to cumulative error, or the Chinese whispers effect, everyone gets really upset. The original optimists vision has been changed in ways they didn’t expect.

It’s a very natural and human story amidst all the “artificial” machine intelligence.

Ora, Jim and Tim have done quite well out of the fighting. Google Scholar reckons their original article has been cited nearly 5000 times. That is a lot of attention, in scientific circles, a veritable blockbuster hit. At the time of writing, not even Albert Einstein can match that, and his ideas are much more important than the semantic web probably ever will be. Many good scientists with important ideas can only dream of publishing a paper that is as heavily cited as that infamous Scientific American article. So which do you think would most scientists prefer:

  • Being internationally known and talked about, but misunderstood by large groups of people?
  • Being relatively unknown, ignored but well understood by a small and obscure group of people?

Neither is ideal but I think in most cases, there is only one thing in the world worse than being talked about, and that is not being talked about.

We have reached the end of chapter 1 of this little story. Wouldn’t it be nice if Chapter 2 was less bloody? Perhaps the two sides could focus more on facts and evidence, rather than the beliefs, opinions, marketing, hype and “visions” that have dominated the battle so far. As the winter solstice approaches and the new year beckons, can we give peace, diplomacy and above all SCIENCE a chance?

The Moral of the Story (so far)

The moral of this old war story is simple. Religions of various kinds have been known to make people commit horrendous and completely unreasonable war crimes. Nobody is innocent. So if you don’t like a fight, steer well clear of religious wars.

Acknowledgements

  1. The “burn” idea comes from Leftfield with John Lydon (1995) Open Up “Burn Hollywood, Burn! Taking down Tinseltown
  2. Thanks to Carole for the idea of using fiction to illustrate science see Carole Goble and Chris Wroe (2005) The Montagues and the Capulets: In fair Genomics, where we lay our scene… Comparative and Functional Genomics 5(8):623-632 DOI:10.1002/cfg.442 seeAlso Shakespearean Genomics: a plague on both your houses)
  3. This post, originally published on nodalpoint

October 8, 2006

Bio-Ignorance: Communicating Biology to Computer Scientists

The Human GenomeMany computer scientists and software engineers are not familiar with basic biology or bioinformatics. Many biologists and bioinformaticians are not familiar with basic computer science or software engineering. This article points to some resources that can help with the former, and asks, what can be done about the latter?

Progress in both computer science and biology is closely linked and dependent on people understanding each others strange language, cross-pollinating ideas and creating technology which hopefully has hybrid vigour. So for example, biologists and bioinformaticians have a healthy apetite for all kinds of better, cheaper, faster and sometimes novel computation. This requires they understand basic computer science and software enginnering. In the other direction, computer scientists often need realistic scenarios to motivate the invention, development and testing of genuinely novel technology. As for the software engineers, more on them later…

It sounds great, but before you can even say the words “inter-discplinary”, there are considerable barriers to communication. The various camps speak different languages, and have radically different cultures. To illustrate this communication breakdown, here is a story from the lab where I work. A while ago, I was discussing the Gene Ontology with a colleague, who shall remain anonymous. This colleague was educated, doing PhD level research and what I’d consider a fairly typical computer scientist. Soon the conversation turned to chromosomes, and they asked me:

“What is a Chromosome?”

Initially I was shocked. How could somebody not know what a chromosome was? Had they never read a newspaper? Never watched the television? Surely, most people have at least a vague idea what a chromosome is? After recovering from the shock, I told this person that according to the Gene Ontology a chromosome is “a very long molecule of DNA and associated proteins that carries hereditary information.” Perhaps this bio-ignorance is an extreme case, but unfortunately, it is all too common. Many computer scientists and software engineers I know stopped studying biology as soon as they possibly could, opting for the so-called “harder” sciences: physics, chemistry and mathematics. Consequently, many (but not all) computer scientists are bio-ignorant. What can we do about it? We really need to understand each other if we are going to make any progress. How can we improve communication between biologists and computer scientists?

Part of the solution to this problem is well-written literature that explains basic concepts quickly and clearly without getting bogged down in jargon or stuck on esoteric details, see the references below for some examples. One of my personal favourites is a little book called The Human Genome: a beginner’s guide to the chemical code of life authored by Jeremy Cherfas. This book is lavishly illustrated and beautifully written, but most importantly of all at 72 pages it is blisteringly concise, so stands a chance of being read by computer geeks and nerds. It is even funny in places, the Nobel laureate and geneticist Thomas Hunt Morgan is amusingly depicted as a red-eyed wild type, just like the fruit flies he studied. Anyway, I lent my copy of said book to my computer science buddy, and they learnt not just what chromosomes are, but also a little bit about why Biology and Genetics are such fascinating subjects.

The literature listed below can help one-way understanding of biology by outsiders, but communication is a two-way street. What about the other direction? Is there any literature that explains computer science and software engineering specifically to biologists and bioinformaticians? I don’t know of any particularly good examples, that are concise, well written and illustrated, but perhaps you do. I’ve frequently found bioinformaticians and biologists misunderstand what computer science is about, and confuse it with software engineering, but that is another story. The moral of this story is, don’t be surprised if people working in different fields to you lack a basic understanding of what you consider fundamental concepts that everybody knows. If they are bio-ignorant computer scientists, you should patiently and tirelessly explain yourself and maybe point to some of the resources below. Maybe we can understand each other just a little better.

References

  1. Anonymous GO:0005694 Chromosome: A very long molecule of DNA AmiGO! Your friend in the Gene Ontology
  2. Alvis Brazma, Helen Parkinson, Thomas Schlitt and Mohammadreza Shojatalab (2001) All you need to know about biology in twenty pages European Bioinformatics Institute (EMBL-EBI) (A technical introduction, written for EBI employees, but useful elsewhere)
  3. Jeremy Cherfas (2002) The Human Genome: a beginner’s guide to the chemical code of life (isbn:0751337161) Dorling Kindersley (A quick but informative introduction that your granny could understand)
  4. Jeremy Cherfas (2006) International Plant Genetic Resources Institute (IPGRI) public awareness blog IPGRI, Rome, Italy. (Some deserved nodalpoint Google Juice for these news and press releasess)
  5. Carole Goble and Chris Wroe (2005) The Montagues and the Capulets: In fair Genomics, where we lay our scene… Comparative and Functional Genomics 5(8):623-632 (A paper describing communication breakdown between two different research “houses”, very possibly the only paper on genomics that will make you laugh. seeAlso Shakespearean Genomics: a plague on both your houses)
  6. John Gribbin Dorling Kindersley’s Essential Science: Human Genome, Global warming, Expanding universe, Food for the future, Digital revolution and How the brain works http://www.dk.com (Some interesting books here)
  7. John W. Kimball Chromosomes Kimball’s Biology Pages (How does John Kimball manage to write so much good introductory material sabout Biology?)
  8. John Bonham, John Paul Jones and Jimmy Page (1969) Communication Breakdown Led Zeppelin (Communication breakdown, it’s always the same, I’m having a nervous breakdown, drive me insane!)
  9. This post was originally published on nodalpoint with comments.

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