O'Really?

August 24, 2009

I bet you think this blog is about you, don’t you?

Filed under: communication,conferences — Duncan Hull @ 5:07 pm
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Science Online London 2009Last Saturday, The Royal Institution of Great Britain (R.I.) hosted a conference called Science Online London (#solo09) co-organised by mendeley.com and network.nature.com. The event centred around the fantastic Faraday Theatre which according to the R.I. is a “beautiful, historic theatre [which] has deeply raked seating that creates an intimate atmosphere, even when full to capacity”. Absolutely. Just like last year, this event attracted delegates and speakers from a wide range of backgrounds in science, publishing and communication from around the world. This post is an approximately alphabetically ordered link-fest of some of the people involved. People are, after all, the most interesting thing about any conference. If you’re not listed here it’s not because I don’t like you (honest!) it’s because we didn’t speak or I didn’t listen or (unlike many people) you’re not vain enough [1] to have a have a blog (yet) 🙂

Now I’m told the presentations mentioned above will be on Nature Precedings in due course, which will be good. Thanks to all the organisers, speakers and participants this year that made Science Online London 2009 well worth attending. Hopefully see some more of you again next year!

References

  1. Carly Simon (1972) You’re So Vain
  2. Geoffrey Bilder (2006). In Google We Trust? Journal of Electronic Publishing, 9 (1) DOI: 10.3998/3336451.0009.101
  3. Matt Brown (2008). Venerable institute gets a refit Nature, 453 (7195), 568-569 DOI: 10.1038/453568a
  4. Matt Brown (2008). Reimagining the Royal Institution Nature, 453 (7195), 595-595 DOI: 10.1038/453595a
  5. Duncan Hull (2009). Slides from the author identity session: Authenticating Scientists with OpenID
  6. Jennifer Rohn and Richard P. Grant (2009). Pre-conference video: Live Roof Surfing at Mendeley Fringe Frivolous

July 24, 2009

Escape from the impact factor: The Great Escape?

Filed under: communication,publishing,Science — Duncan Hull @ 11:40 am
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The Great Escape with Steve McQueenQuite by chance, I stumbled on this interesting paper [1] yesterday by Philip Campbell who is the Editor-in-Chief of the scientific ĂĽber-journal Nature [2]. Here is the abstract:

As Editor-in-Chief of the journal Nature, I am concerned by the tendency within academic administrations to focus on a journal’s impact factor when judging the worth of scientific contributions by researchers, affecting promotions, recruitment and, in some countries, financial bonuses for each paper. Our own internal research demonstrates how a high journal impact factor can be the skewed result of many citations of a few papers rather than the average level of the majority, reducing its value as an objective measure of an individual paper. Proposed alternative indices have their own drawbacks. Many researchers say that their important work has been published in low-impact journals. Focusing on the citations of individual papers is a more reliable indicator of an individual’s impact. A positive development is the increasing ability to track the contributions of individuals by means of author-contribution statements and perhaps, in the future, citability of components of papers rather than the whole. There are attempts to escape the hierarchy of high-impact-factor journals by means of undifferentiated databases of peer-reviewed papers such as PLoS One. It remains to be seen whether that model will help outstanding work to rise to due recognition regardless of editorial selectivity. Although the current system may be effective at measuring merit on national and institutional scales, the most effective and fair analysis of a person’s contribution derives from a direct assessment of individual papers, regardless of where they were published.

It’s well worth reading the views of the editor of an important closed-access journal like Nature, a world champion heavyweight of Impact Factor Boxing. So their view on article-level bibliometrics and novel models of scientific publishing on the Web like PLoS ONE is enlightening. There are some interesting papers in the same issue, which has a special theme on the use and misuse of bibliometric indices in evaluating scholarly performance. Oh, and the article is published in an Open Access Journal too. Is it just me, or is there a strong smell of irony in here?

References

  1. Philip Campbell (2008). Escape from the impact factor Ethics in Science and Environmental Politics, 8, 5-7 DOI: 10.3354/esep00078
  2. Philip Campbell (1995). Postscript from a new hand Nature, 378 (6558), 649-649 DOI: 10.1038/378649b0
  3. John Sturges (1963) The Great Escape

July 23, 2009

Josh the Java Junkie

Filed under: programming — Duncan Hull @ 12:18 pm
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Joshua Bloch at scifooOne of the people I enjoyed seeing at Science Foo Camp this year was Joshua Bloch. Josh is a Java Junkie [1,2,3] and software engineer at Google. When he wasn’t playing harmonica around the foo camp fire (see picture right), he was giving interesting talks about optical illusions, some of which can be found in his book Java Puzzlers. So I bought the book, and have been doing a puzzle a day to keep the doctor away. Most of the puzzles in this book are short Java programs that behave in ways you would not expect. The one below is a nice example:

public class Indecisive {
    public static void main(String[] args) {
        System.out.println(decision());
    }

    static boolean decision() {
        try {
            return true;
        } finally {
            return false;
        }
    }
}

What does this program do? Return true or false? Perhaps it does both or something else completely? Does it even compile? Can’t decide? Welcome to public class Indecisive…

References

  1. Joshua Bloch and Neal Gafter (2005). Java Puzzlers: Traps, Pitfalls, and Corner Cases (isbn:032133678X) Addison-Wesley
  2. Joshua Bloch (2006). How to design a good API and why it matters OOPSLA ’06: Companion to the 21st ACM SIGPLAN symposium on Object-oriented programming systems, languages, and applications, 506-507 DOI: 10.1145/1176617.1176622
  3. Neal Gafter (2008). Is the Java Language Dying? Neal Gafter’s blog: Thoughts about the future of the Java Programming Language.

July 20, 2009

How to be a Rocket Scientist

Filed under: Big Questions — Duncan Hull @ 10:40 pm
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Today, the 20th July 2009, is the 40th anniversary of the first lunar landing. There has been plenty of global coverage, stargazing, astronautical analysis and heavenly commentary recently. But for me personally, the Apollo 11 anniversary brings back fond memories of rocket science lessons [1] – specifically, the things I learned in Chemistry at school. Our teacher used to launch water rockets during classes and these hands-on demonstrations were followed with more down-to-earth calculations back in the laboratory. This was an entertaining way to learn about fundamental concepts like pressure, acceleration, gravity, turbulence and energy. But there were also three very important rules that apply generally to all kinds of science and engineering:

  1. Reach for the stars. A clichĂ©, but it’s true. John F. Kennedy said America continued to pursue the ambitious space race goals, not because they are easy, but because they are hard. Because it is hard, 90% of science and engineering doesn’t even make it off the launchpad (let alone into orbit) and it often goes horribly, horribly wrong. That’s the deal – but it shouldn’t stop you reaching high. Sometimes you make giant leaps.
  2. It’s not rocket science. Another tired clichĂ©. This one has become so well worn that there is a saying amongst NASA rocket scientists at the famous Jet Propulsion Laboratory (JPL) in California :

    “It doesn’t take a rocket scientist to be a rocket scientist.” [2]

    So despite appearances to the contrary, many kinds of science (and engineering) aren’t rocket science. You don’t always need big, complicated, expensive and state-of-the-art technology accompanied by armies of highly qualified experts. Sometimes you do, but not always. All that water rocketry requires is an empty drinks carton, a bicycle pump and some water – it really isn’t rocket science [3].

  3. It should be fun. As you probably already know (or can imagine) water rocketry is great fun. Science and engineering are fun too – it’s all too easy to get bogged down in the inevitable politics, bureaucracy and other sideshows – but at the end of the day the net effect should be fun with a fantastic big capital F. If you’re not having fun then Houston, we’ve had a problem. Something, somewhere needs fixing.

The thing about these rules is that they apply to all kinds of science, technology and business [4]. So if you’re a scientist or an engineer of some kind, or even a budding rocket scientist or entrepreneur, it’s worth stopping to ask yourself three simple questions: 1) Are you aiming high and charting unknown territory? 2) How much do you really need all that complicated technology? 3) Are you having fun?

[CC-licensed picture Reflexology via propellerhead and rocket enthusiast Steve Jurvetson]

References

  1. Tony Hull (1986) Rocket Science for Secondary and High School students (ages ~14-18) This teacher also happens to be my Dad, but that’s another story. Hey Dad, if you’re reading this, there’s a bloke from NASA who wants to get in contact with you about your “environmentally friendly” technique for rocket propulsion 🙂 I gave him your email address.
  2. Jim Longuski (2004) Advice to Rocket Scientists: A Career Survival Guide for Scientists and Engineers (isbn:156347655x)
  3. Clive Whichelow and Hugh Murray (2007) It’s Not Rocket Science: And Other Irritating Modern ClichĂ©s (isbn:0749951591)
  4. Paul Smaglik (2008). Beyond rocket science: Huntsville, Alabama, the original home of NASA and military weapons development, makes a move into biology Nature, 453 (7196), 818-820 DOI: 10.1038/nj7196-818a

July 13, 2009

Science Foo Camp 2009: Scifoo Day Two

Filed under: conferences — Duncan Hull @ 6:30 pm
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Theodore Gray (of Wolfram Research) with super-soluble sodium acetateThe fourth International Science Foo Camp (scifoo) 2009 has just concluded. Here are some very brief and incomplete notes and links from some of the sessions on the second day (Saturday), see the scholarly kitchen for a report on the first day. With seven parallel sessions, most people at this event miss most (six sevenths) of the sessions, but here is a summary of the (one seventh) sessions I managed to get to:

  • Larry Page ran a session on Making Artificial Intelligence happen. In brief, Larry argued that not enough people are working on this problem. Marvin Minsky joined in talked about his book The Emotion Machine. I’d write more about this, but Larry asked for what he said to be off-the-record so he could speak more freely.
  • Following on from this Harry Collins and Lee Smolin ran a session titled: The Social Nature of Knowledge, Science and Artificial Intelligence. As David Colquhoun pointed out in the session, you “need to be something of a sado-masochist” to attend a session on the sociology of Science but there was some interesting discussion on the Science (truth?) vs. Belief (religion) debate. Henry Thomspson pointed out: some argue that “Knowledge is true belief” which can make it hard to distinguish between Science and Religion. Jamie Heywood described his simple “truth formula” where truth = cost to make a claim divided by the cost to disprove claim.
  • Next up Douglas Kell did a session on Data-driven Science. This discussed the relationship and balance between hypothesis driven science (hypothetico-deductive) and data driven science (via inductive reasoning and machine learning for example) [1]. Attendees in this session included Tony Tyson (Director of the Large Synoptic Survey Telescope), Craig Rowell (BioRad), George Poste, Julia Lane (NSF), James Wilsdon (Royal Society), David Colquhoun, Nat Torkington, the six-minute-genome guy from Halcyon Molecular whose name I can’t remember and Annalee Newitz. Much of the discussion was about the over-reliance on hypothesis driven science (e.g. 92% of NIH R01 grants have to be hypothesis-driven) which can make the “fishing-trip” or “data-driven” science difficult to do. One conclusion from this presentation was that both types of science are required and complementary.

Then it’s time for lunch, not just any old food, but some yummy Google Food.

  • In the afternoon, I ran a session on The Invisible Scientist: Personal Digital Identity on the Web, Problems and Solutions. After a short set of introductory slides we discussed some solutions to identifying scientists digital contributions, not just electronic journal publications but wiki edits, blog posts, software development, ontology and database curation etc. Participants in this session included Cameron Neylon, Julie Lant (NSF) who will reuse some of my data in a report she is writing (Yay!), Nicola McCarthy (Senior editor of Nature Reviews Cancer), Shirley Wu, Michael Rogan, Mackenzie Cowell and Chris Holmes. The last time I was at Science Foo Camp (back in 2007) I felt slightly phased by the stellar company (nobel prize winners, billionaires, entrepreneurs, silicon valley A-listers, venture capitalists, artists, policy makers, movers and shakers) that I didn’t present anything. I’m very glad I made the effort this year, it forced me to think harder about the problem of digital identity (and solutions), which included a useful chat with Googler Ben Laurie (a cryptography person) who gave me the lowdown on OpenID, PKI and the like. Very useful stuff – thanks Ben and thanks to everyone who turned up at my session.
  • The second session of the afternoon was on Google Wave with Cameron Neylon. I won’t say too much about this, because it will probably be blogged by Cameron and others – but it was an interesting peek into some of the current strengths and weakness of this software – especially from the point of view of scientists.
  • The last two sessions of the day, I stayed in the Lightning Talks organised by Nat Torkington (see blog). These were great, probably my favourite part of scifoo this year. Each speaker got a very strict five minutes, including Natahan Wolfe, Ben Fry on visualisation, George Dyson on Darwin, Christopher Stumm on astronomical metadata, Adam Summers on fish, Linda Stone on unhealthy computing, Ed Lu, Brian Uzzi and Fiorenzo, Shelley Batts, Larry Weiss, Saul Griffith, Chris DiBona on telemedicine, Joshua Bloch on Java puzzlers, Christian Bok on poetry and Gregory Benford.

In the evening there were further demonstrations and talks, including sodium acetate crystals (ChEBI:32594) (with Theodore Gray – see picture above) and a talk by Bob Metcalfe (of Metcalfe law fame) on the “Enernet: Internet Lessons for Solving Energy”. One of the take home messages from this is that the energy industry should be much more decentralised (like the internet is). Bob argued that the huge centralised powerplants we have today are beginning to look as dated and obsolete as mainframe computers.

So in summary, saturday at scifoo was a fantastic action-packed day, started early in the morning and went on late into the night. It’s almost impossible to capture it all in a blog post, so if you’re interested my scifoo 2009 photo set on flickr has more details. My mind has been blown into lots of little pieces again – thanks to all the organisers and participants for another great day.

References

  1. Kell, D., & Oliver, S. (2004). Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era BioEssays, 26 (1), 99-105 DOI: 10.1002/bies.10385

July 8, 2009

California Googlin’

Filed under: lyrical — Duncan Hull @ 3:27 pm
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The Googlin' Gate BridgeSo, I’m going to San Francisco and on to the Googleplex in the heart of Silly Valley, California for Science Foo Camp (scifoo) 2009. As I put the Flowers In My Hair (what’s left of it) and confirm my booking at the Hotel California I’m not just California Dreamin’ but California Googlin’. Just how many American and Californian musical clichĂ©s it is possible to cram into one blog post and accompanying iPod playlist? Now there’s no shortage of lyrics to choose from, which is handy because it is a long journey from the UK to California and I’m extremely bored waiting for a flight westwards. So with a little help from a well known search engine and just like in the novel High Fidelity by Nick Hornby here is a (personal) top twenty-ish all time greatest hits:

    • Let’s start with The Beatles since they played their last ever gig in San Francisco (at Candlestick Park), so it seems appropriate. On Get Back Paul McCartney sings

      Jojo was a man who thought he was a loner

      But he knew it couldn’t last

      Jojo left his home in Tucson, Arizona

      For some California grass

      Get back, get back, back to where you once belonged

    • And what better to follow with than some Beatles-inspired rivalry in the shape of The Beach Boys who when they’re not Surfin’ USA they are singing about California Girls

      I wish they all could be California

      Girls, girls, girls yeah I dig the…

      I wish they all could be California Girls

      Are The Beach Boys possibly the band with the most cliches-per-album in the history of mankind?

      (more…)

July 6, 2009

Ship-shape and Banksy Fashion

Filed under: web — Duncan Hull @ 9:07 am
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Britannia Rules the CCTV

Graffiti artist or blogger?

So I was passing through Bristol the other day, a fine city that has given the world many things. Perhaps one of the best known (apart from the trip-hop and slavery) is the renegade graffiti artist called Banksy who during July and August has an exhibition of work on at the Bristol City Museum and Art Gallery. This show is well worth a visit – take a look at banksy.co.uk and the links below for a taster. A book of Banksy’s work also has plenty of thought provoking content in it, not least, a quote from the artist on where to publish:

“A wall has always been the best place to publish your work.“

To my mind the worlds of graffiti and blogging have much in common. As art forms, they both have a low barrier to entry – all you need is a can of spray paint – or an internet connection. Both blogging and graffiti are often frowned on by The Establishment™. Some of this is probably due to the highly variable quality of blogs and “street art” but when they are done well, they are both worth paying attention too. Last but not least, the Web is like a big public wall where pretty much anyone can scribble, spray and scrawl anything they like, which can be powerful stuff. As one graffiti artist once put it – the can is mightier than the sword – and the Web is mightier than the sword too.

The mighty exhibition Banksy vs. The Museum has been incredibly popular and a huge success, with large queues every day especially at weekends. So if you’re interested in going, get there ship-shape, Bristol fashion and early before it opens at 10am each day and finishes on 31st August 2009.

[Britannia Rules the CCTV above – one of the works from the exhibition by Banksy]

References

  1. Banksy (2006) Wall and Piece (isbn:1884137872)
  2. Miranda Sawyer (2009) Review of Banksy at Bristol City Museum (The Guardian)
  3. Serena Davies (2009) Review of Banksy versus The Museum (The Daily Telegraph)
  4. BBC News (2009) In pictures: Banksy’s Bristol Show
  5. Ship-shape and Bristol Fashion means “in first class order” according to phrases.org.uk

Fabio Rinaldi on OntoGene

Filed under: Uncategorized — Duncan Hull @ 8:26 am
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Fabio RinaldiFabio Rinaldi is currently visiting Manchester from the University of Zurich, he will be doing a seminar on Monday 6th July, the details of which are below.

Title : OntoGene in the BioNLP shared task and in BioCreative II.5

Speaker: Dr Fabio Rinaldi, University of Zurich

Date: Monday 6th July 2009

Time: 14:00

Location: Lecture Theatre – MLG.001, MIB building

Abstract In this talk I will describe our participation to the BioNLP shared task and the BioCreative II.5 competitions [1]. Our approach is based on a common core: a pipeline of NLP tools and a dependency parser. The adaptation for the BioNLP shared task consisted of suitable input filters and a transformation-based approach which maps syntactic dependencies to event structures. Despite the very simple approach, results were satisfactory (34.78 F-score). The adaptation for BioCreative requires the detection and disambiguation of domain entities, while candidate interactions are proposed on the basis of a simple learning approach.

If time allows I will then describe our approach to finding the ‘focus organisms’ i.e. the organisms in which the experiments have been conducted or which are the source of the interacting proteins. This information is of crucial importance for the correct disambiguation of other entities mentioned in the article.

References

  1. Rinaldi, F., Kappeler, T., Kaljurand, K., Schneider, G., Klenner, M., Clematide, S., Hess, M., von Allmen, J., Parisot, P., Romacker, M., & Vachon, T. (2008). OntoGene in BioCreative II Genome Biology, 9 (Suppl 2) DOI: 10.1186/gb-2008-9-s2-s13

June 23, 2009

Impact Factor Boxing 2009

Filed under: data mining,informatics,publishing — Duncan Hull @ 12:59 pm
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Fight Night Punch Test by djclear904[This post is part of an ongoing series about impact factors]

The latest results from the annual impact factor boxing world championship contest are out. This is a combat sport where scientific journals are scored according to their supposed influence and impact in Science. This years competition rankings include the first-ever update to the newly introduced Five Year Impact Factor and Eigenfactor™ Metrics [1,2] in Journal Citation Reports (JCR) on the Web (see www.isiknowledge.com/JCR warning: clunky website requires subscription*), presumably in response to widespread criticism of impact factors. The Eigenfactor™ seems to correlate quite closely with the impact factor scores, both of which work at the level of the journal, although they use different methods for measuring a given journals impact. However, what many authors are often more interested in is the impact of an individual article, not the journal where it was published. So it would be interesting to see how the figures below tally with Google Scholar, see also comments by Abhishek Tiwari. I’ve included a table below of bioinformatics impact factors, updated for June 2009. Of course, when I say 2009 (today), I mean 2008 (these are the latest figures available based on data from 2007) – so this shiny new information published this week is already out of date [3] and flawed [4,5] but here is a selection of the data anyway: [update: see figures published in June 2010.]

Journal Title 2008 data from isiknowledge.com/JCR Eigenfactor™ Metrics
Total Cites Impact Factor 5-Year Impact Factor Immediacy Index Articles Cited Half-life Eigenfactor™ Score Article Influence™ Score
BMC Bionformatics 8141 3.781 4.246 0.664 607 2.8 0.06649 1.730
OUP Bioinformatics 30344 4.328 6.481 0.566 643 4.8 0.18204 2.593
Briefings in Bioinformatics 2908 4.627 1.273 44 4.5 0.02188
PLoS Computational Biology 2730 5.895 6.144 0.826 253 2.1 0.03063 3.370
Genome Biology 9875 6.153 7.812 0.961 229 4.4 0.07930 3.858
Nucleic Acids Research 86787 6.878 6.968 1.635 1070 6.5 0.37108 2.963
PNAS 416018 9.380 10.228 1.635 3508 7.4 1.69893 4.847
Science 409290 28.103 30.268 6.261 862 8.4 1.58344 16.283
Nature 443967 31.434 31.210 8.194 899 8.5 1.76407 17.278

The internet is radically changing the way we communicate and this includes scientific publishing, as media mogul Rupert Murdoch once pointed out big will not beat small any more – it will be the fast beating the slow.  An interesting question for publishers and scientists is, how can the Web help the faster flyweight and featherweight boxers (smaller journals) compete and punch-above-their-weight with the reigning world champion heavyweights (Nature, Science and PNAS)? Will the heavyweight publishers always have the killer knockout punches? If you’ve got access to the internet, then you already have a ringside seat from which to watch all the action. This fight should be entertaining viewing and there is an awful lot of money riding on the outcome [6-11].

Seconds away, round two…

References

  1. Fersht, A. (2009). The most influential journals: Impact Factor and Eigenfactor Proceedings of the National Academy of Sciences, 106 (17), 6883-6884 DOI: 10.1073/pnas.0903307106
  2. Bergstrom, C., & West, J. (2008). Assessing citations with the Eigenfactor Metrics Neurology, 71 (23), 1850-1851 DOI: 10.1212/01.wnl.0000338904.37585.66
  3. Cockerill, M. (2004). Delayed impact: ISI’s citation tracking choices are keeping scientists in the dark. BMC Bioinformatics, 5 (1) DOI: 10.1186/1471-2105-5-93
  4. Allen, L., Jones, C., Dolby, K., Lynn, D., & Walport, M. (2009). Looking for Landmarks: The Role of Expert Review and Bibliometric Analysis in Evaluating Scientific Publication Outputs PLoS ONE, 4 (6) DOI: 10.1371/journal.pone.0005910
  5. Grant, R.P. (2009) On article-level metrics and other animals Nature Network
  6. Corbyn, Z. (2009) Do academic journals pose a threat to the advancement of Science? Times Higher Education
  7. Fenner, M. (2009) PLoS ONE: Interview with Peter Binfield Gobbledygook blog at Nature Network
  8. Hoyt, J. (2009) Who is killing science on the Web? Publishers or Scientists? Mendeley Blog
  9. Hull, D. (2009) Escape from the Impact Factor: The Great Escape? O’Really? blog
  10. Murray-Rust, P. (2009) THE article: Do academic journals pose a threat to the advancement of science? Peter Murray-Rust’s blog: A Scientist and the Web
  11. Wu, S. (2009) The evolution of Scientific Impact shirleywho.wordpress.com

* This important data should be freely available (e.g. no subscription), since crucial decisions about the allocation of public money depend on it, but that’s another story.

[More commentary on this post over at friendfeed. CC-licensed Fight Night Punch Test by djclear904]

June 19, 2009

Nettab 2009 Day Three: Semantic Integration

Filed under: conferences — Duncan Hull @ 11:26 am
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Catania ElephantA brief report (well just some scribbled notes, bullet points and links really) on the third and final day of Network Applications and Tools in Biology (NETTAB) 2009 in Catania, Sicily. There was a special section on Methods and Tools for RNA Structure and Functional Analysis. Disclaimer: RNA mania isn’t really my thing – so the RNA presentations and papers are grossly under-represented in this mini-report (sorry).

  • Keynote: Semantically Integrated eCommunities in Biomedicine: Next-Generation Models of Biomedical Communication, Tim Clark Massachusetts General Hospital and Harvard Medical School, Boston. His presentation opened by asking: What do the following have in common?

    1. Alzheimer’s Disease
    2. Huntington’s Disease
    3. Nicotine Addiction
    4. Schizophrenia
    5. Bipolar Disorder
    6. Autism
    7. Parkinson’s Disease
    8. ALS (Amyotrophic lateral sclerosis)
    9. Neuropathic Pain
    10. Major Depressive Disorder
    11. Cancer (multiple forms)

    Answer:

    1. Highly complex disorders
    2. Much information, incomplete understanding
    3. Inadequate treatment options
    4. Huge cost in human suffering
    5. Multi-factorial causality
    6. Require multi-disciplinary collaboration for progress to understanding and cure

    Tim discussed using The Science Collaboration Framework (SCF) a reusable, semantically-aware toolkit for building on-line communities. These make heavy use of Open Linked Data, controlled vocabularies and  Drupal to build websites to tackle the above disorders. For example pdonlineresearch.org (Parkinson’s Disease), StemBook.org (Harvard Stem Cell Institute) and alzforum.org (Alzheimers) [1]. The controlled vocabulary and ontology approach works well for understood stuff (where named entities are known) but not so good at the outer boundaries of our knowledge. Reusable framework for building web communities, Uses shared ontologies/vocabularies, Open source, freely available.

  • Michaela Guendel (Leaf Bioscience) presented DC-THERA Directory: A Knowledge Management System to Support Collaboration on Dendritic Cell and Immunology Research,  using cell type ontology, dendritic cell ontology, chebi, obi. Project involves Andrea Splendiani, Ciro Scognamiglio and Marco Brandizi
  • GePh-CARD: an information exchange application for an Hub & Spoke Network for Skeletal Dysplasias was presented by M. Mordenti & L. Sangiorgi
  • Panel Discussion: Collaborative and Social Bioinformatics Research and Development: Why, When, Who and How? Alex Bateman, Tim Clark, Duncan Hull and all participants. This panel discussion concentrated on Who? (experts vs. non experts, crowds vs. individuals, how to motivate and reward people to contribute to online communities. community annotation of data only possible when curators cede control of data) and then Where? (open wikis vs. closed ones, private vs. public data, wikis often not suitable for highly structured data, centralised vs. distributed systems)
  • Keynote: Bacterial Phylogeny and Taxonomy in the High-Throughput Sequencing World, Gabriel Valiente
  • Magdalena Musielak (has worked with Piotr Byzia) presented RNA tertiary structure prediction with ModeRNA,
  • Olivier Perriquet presented Improved heuristic for pairwise RNA secondary structure prediction,
  • Giampaolo Bella talked about Analysing microRNA by Theorem Proving. qualitative logic proving before quantitative experimental measures e.g. “shall we go to restaurant” before “how much does it cost”?
  • Mapping miRNA genes on human fragile sites and translocation breakpoints Alfredo Ferro et al.
  • Keynote: Computational challenages in the study of small RNAs Doron Betel, memorial sloan-kettering cancer center
  • microrna.gr. a suite of web based tools for elucidating microrna function was presented by Giorgo L. Papadopoulous, DIANA bioinformatics lab, biomedical Science research center, Alexander Fleming, Vari, Athens, Greece
  • Last but not least there was miRScape: a cytoscape plugin to annotate biological networks with microRNAs

The Tenth NETTAB (2010) Workshop will be in Rome, where the theme will be Oncology Bioinformatics and will be held at the end of  May or beginning of  June 2010.

References

  1. Das, S., Girard, L., Green, T., Weitzman, L., Lewis-Bowen, A., & Clark, T. (2009). Building biomedical web communities using a semantically aware content management system Briefings in Bioinformatics, 10 (2), 129-138 DOI: 10.1093/bib/bbn052
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