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Informatics

Duncan Hull
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  • April 1, 2010
  • 06:24 AM
  • 2,384 views

Καλό Πάσχα: Happy Easter: Frohe Ostern

by Duncan Hull in O'Really?

Whatever your inclination, it’s difficult to ignore that sandwiched between the Vernal equinox and Beltane, it’s Easter time already. So Happy Easter, Frohe Ostern or Καλό Πάσχα, as they say down south, to all readers of this O’Really? blog.
If you’re gorging yourself on chocolate (see picture right), you might like to consider the food science [...]... Read more »

Stephen T. Beckett. (2000) The Science Of Chocolate. Royal Society of Chemistry Publihshing. DOI: 10.1039/9781847552143  

  • June 18, 2009
  • 01:12 PM
  • 2,288 views

Ooh aah Cantona! Welcome back Eric…

by Duncan Hull in O'Really?

It is great to see the eminent french football philosopher and scientist Eric Cantona back in his adopted hometown of Manchester. As well as visiting in person during production of the latest Ken Loach film (on the famous Keppel Road, Chorlton) and appearing at the premiere, Eric is currently gracing silver screens in cinemas all [...]... Read more »

Hopkin, M. (2006) Goal fever at the World Cup. Nature, 441(7095), 793-793. DOI: 10.1038/441793a  

  • July 20, 2009
  • 06:40 PM
  • 2,111 views

How to be a Rocket Scientist

by Duncan Hull in O'Really?

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. [...]... Read more »

  • April 8, 2010
  • 06:04 AM
  • 2,026 views

8-OHdG: Entity of the Month

by Duncan Hull in O'Really?

Chemical Entities of Biological Interest (ChEBI) release 67 is now available, containing 548,850 total entities, of which 20,565 are annotated entities and 720 were submitted via the ChEBI submission tool. New in this release, the ChEBI ontology is now available in Web Ontology Language (OWL), which is part of an ongoing research project to automate [...]... Read more »

Wishart, D., Knox, C., Guo, A., Eisner, R., Young, N., Gautam, B., Hau, D., Psychogios, N., Dong, E., Bouatra, S.... (2009) HMDB: a knowledgebase for the human metabolome. Nucleic Acids Research, 37(Database). DOI: 10.1093/nar/gkn810  

Tarng DC, Huang TP, Wei YH, Liu TY, Chen HW, Wen Chen T, & Yang WC. (2000) 8-hydroxy-2'-deoxyguanosine of leukocyte DNA as a marker of oxidative stress in chronic hemodialysis patients. American journal of kidney diseases : the official journal of the National Kidney Foundation, 36(5), 934-44. PMID: 11054349  

  • March 4, 2010
  • 06:29 AM
  • 2,010 views

Sildenafil citrate: Entity of the Month

by Duncan Hull in O'Really?

Release 66 of Chemical Entities of Biological Interest (ChEBI) is now available, containing 534,521 total entities, of which 20,151 are annotated entities and 698 were submitted via the ChEBI submission tool. This months entity of the month is Viagra, also known as Sildenafil citrate: (Text below reproduced from ChEBI website)
Few chemical compounds are better known [...]... Read more »

  • June 15, 2009
  • 12:19 PM
  • 1,848 views

Nettab 2009 Day One: Bio-wikis (and football)

by Duncan Hull in O'Really?

A brief wiki-report and some wiki-links from the first short and introductory day of Network Applications and Tools in Biology (NETTAB 2009) in Sicily where there was a tutorial on Technologies of wiki resources and bio-wikis delivered by Paolo Romano and Elda Rossi. This covered Gene Wiki, Wikiproteins, Wikigenes and Wikipathways [1-4].

There is already a [...]... Read more »

Mons, B., Ashburner, M., Chichester, C., van Mulligen, E., Weeber, M., den Dunnen, J., van Ommen, G., Musen, M., Cockerill, M., Hermjakob, H.... (2008) Calling on a million minds for community annotation in WikiProteins. Genome Biology, 9(5). DOI: 10.1186/gb-2008-9-5-r89  

Huss, J., Orozco, C., Goodale, J., Wu, C., Batalov, S., Vickers, T., Valafar, F., & Su, A. (2008) A Gene Wiki for Community Annotation of Gene Function. PLoS Biology, 6(7). DOI: 10.1371/journal.pbio.0060175  

Pico, A., Kelder, T., van Iersel, M., Hanspers, K., Conklin, B., & Evelo, C. (2008) WikiPathways: Pathway Editing for the People. PLoS Biology, 6(7). DOI: 10.1371/journal.pbio.0060184  

  • April 28, 2011
  • 04:36 PM
  • 1,786 views

Are machines taking over the planet?

by Duncan Hull in O'Really?

Talk of machines taking over the planet is the stuff of science fiction but if world domination was just a simple numbers game, some machines have already “taken over” from their human masters. One machine, the particular brand of computer processor found inside all iPhones and lots of other electronic devices, has been quietly spreading [...]... Read more »

  • July 24, 2009
  • 07:40 AM
  • 1,747 views

Escape from the impact factor

by Duncan Hull in O'Really?

Quite by chance, I stumbled on this interesting paper [1] yesterday by Philip Campbell who is the Editor-in-Chief of 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, [...]... Read more »

Philip Campbell. (2008) Escape from the impact factor. Ethics in Science and Environmental Politics, 5-7. DOI: 10.3354/esep00078  

Philip Campbell. (1995) Postscript from a new hand. Nature, 378(6558), 649-649. DOI: 10.1038/378649b0  

  • September 18, 2009
  • 06:50 AM
  • 1,731 views

Popular, personal and public data at PLoS

by Duncan Hull in O'Really?

The Public Library of Science (PLoS) is a non-profit organisation committed to making the world’s scientific and medical literature freely accessible to everyone via open access publishing. As recently announced they have just published the first article-level metrics (e.g. web server logs and related information) for all articles in their library. This is novel, interesting [...]... Read more »

Levy, S., Sutton, G., Ng, P., Feuk, L., Halpern, A., Walenz, B., Axelrod, N., Huang, J., Kirkness, E., Denisov, G.... (2007) The Diploid Genome Sequence of an Individual Human. PLoS Biology, 5(10). DOI: 10.1371/journal.pbio.0050254  

Holy, T., & Guo, Z. (2005) Ultrasonic Songs of Male Mice. PLoS Biology, 3(12). DOI: 10.1371/journal.pbio.0030386  

The PLoS Medicine Editors. (2006) The Impact Factor Game. PLoS Medicine, 3(6). DOI: 10.1371/journal.pmed.0030291  

Voight, B., Kudaravalli, S., Wen, X., & Pritchard, J. (2006) A Map of Recent Positive Selection in the Human Genome. PLoS Biology, 4(3). DOI: 10.1371/journal.pbio.0040072  

Hagmann, P., Cammoun, L., Gigandet, X., Meuli, R., Honey, C., Wedeen, V., & Sporns, O. (2008) Mapping the Structural Core of Human Cerebral Cortex. PLoS Biology, 6(7). DOI: 10.1371/journal.pbio.0060159  

Saunders, N., Beltrão, P., Jensen, L., Jurczak, D., Krause, R., Kuhn, M., & Wu, S. (2009) Microblogging the ISMB: A New Approach to Conference Reporting. PLoS Computational Biology, 5(1). DOI: 10.1371/journal.pcbi.1000263  

  • January 15, 2010
  • 08:11 AM
  • 1,710 views

Bio2RDF: Large Scale, Distributed Biological Knowledge Discovery

by Duncan Hull in O'Really?

Michel Dumontier was visiting the EBI this week, here’s the details of his seminar Bio2RDF and Beyond! Large Scale, Distributed Biological Knowledge Discovery (slides embedded below) for anyone interested who missed it:
Abstract: The Bio2RDF.org [1] project aims to transform silos of bioinformatics data into a distributed platform for biological knowledge discovery. Initial work focused on [...]... Read more »

BELLEAU, F., NOLIN, M., TOURIGNY, N., RIGAULT, P., & MORISSETTE, J. (2008) Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. Journal of Biomedical Informatics, 41(5), 706-716. DOI: 10.1016/j.jbi.2008.03.004  

  • December 10, 2009
  • 06:18 PM
  • 1,686 views

The Semantic Biochemical Journal experiment

by Duncan Hull in O'Really?

There is an interesting review [1] (and special issue) in the Biochemical Journal today, published by Portland Press Ltd. It provides (quote) “a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment”. Here is a quick outline of the publishing projects the review describes and [...]... Read more »

Attwood, T., Kell, D., McDermott, P., Marsh, J., Pettifer, S., & Thorne, D. (2009) Calling International Rescue: knowledge lost in literature and data landslide!. Biochemical Journal, 424(3), 317-333. DOI: 10.1042/BJ20091474  

Fink, J., Kushch, S., Williams, P., & Bourne, P. (2008) BioLit: integrating biological literature with databases. Nucleic Acids Research, 36(Web Server). DOI: 10.1093/nar/gkn317  

Pafilis, E., O'Donoghue, S., Jensen, L., Horn, H., Kuhn, M., Brown, N., & Schneider, R. (2009) Reflect: augmented browsing for the life scientist. Nature Biotechnology, 27(6), 508-510. DOI: 10.1038/nbt0609-508  

Pettifer, S., Thorne, D., McDermott, P., Marsh, J., Villéger, A., Kell, D., & Attwood, T. (2009) Visualising biological data: a semantic approach to tool and database integration. BMC Bioinformatics, 10(Suppl 6). DOI: 10.1186/1471-2105-10-S6-S19  

  • February 12, 2010
  • 10:12 AM
  • 1,642 views

The 3rd OBO Foundry Workshop 2010, Cambridge, UK

by Duncan Hull in O'Really?

The Open Biomedical Ontologies (OBO) [1] are a set of reference ontologies for describing all kinds of biomedical data shared in a centralised OBO Foundry. Every year, users and developers of these ontologies gather from around the globe for a workshop at the EBI near Cambridge, UK. Following on from the first workshop two years [...]... Read more »

Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L., Eilbeck, K., Ireland, A., Mungall, C.... (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology, 25(11), 1251-1255. DOI: 10.1038/nbt1346  

  • July 7, 2010
  • 03:30 AM
  • 1,622 views

Top Ten Excuses for World Cup Football Failures (with citations)

by Duncan Hull in O'Really?

Football fever grips the globe as we reach the final stages of the 2010 FIFA World Cup in South Africa. Alongside the traditional game where one winning team takes all, leaving 31 losing teams to go home earlier than expected, there is another competition running in parallel. Which losing team can come up with the [...]... Read more »

Lucifora, C., & Simmons, R. (2003) Superstar Effects in Sport: Evidence From Italian Soccer. Journal Of Sports Economics, 4(1), 35-55. DOI: 10.1177/1527002502239657  

Zak, P., Kurzban, R., Ahmadi, S., Swerdloff, R., Park, J., Efremidze, L., Redwine, K., Morgan, K., & Matzner, W. (2009) Testosterone Administration Decreases Generosity in the Ultimatum Game. PLoS ONE, 4(12). DOI: 10.1371/journal.pone.0008330  

Elmar Bittner, Andreas Nussbaumer, Wolfhard Janke, & Martin Weigel. (2006) Football fever: goal distributions and non-Gaussian statistics. Eur. Phys. J. B 67, 459 (2009). arXiv: physics/0606016v1

Goff, J., & Carré, M. (2010) Soccer ball lift coefficients via trajectory analysis. European Journal of Physics, 31(4), 775-784. DOI: 10.1088/0143-0807/31/4/007  

Kranjec, A., Lehet, M., Bromberger, B., & Chatterjee, A. (2010) A Sinister Bias for Calling Fouls in Soccer. PLoS ONE, 5(7). DOI: 10.1371/journal.pone.0011667  

Wayne C. Naidoo, & Jules R. Tapamo. (2006) Soccer video analysis by ball, player and referee tracking. SAICSIT '06: Proceedings of the 2006 annual research conference of the South African institute of computer scientists and information technologists on IT research in developing countries. DOI: 10.1145/1216262.1216268  

  • June 10, 2009
  • 03:24 AM
  • 1,614 views

Kenjiro Taura on Parallel Workflows

by Duncan Hull in O'Really?

Kenjiro Taura is visting Manchester next week from the Department of Information and Communication Engineering at the University of Tokyo. He will be doing a seminar, the details of which are below:

Title: Large scale text processing made simple by GXP make: A Unixish way to parallel workflow processing

Date-time: Monday, 15 June 2009 at 11:00 AM

Location: [...]... Read more »

  • April 28, 2010
  • 01:28 AM
  • 1,600 views

Philip Campbell on Science Facts and Frictions

by Duncan Hull in O'Really?

As part of the Gates Distinguished Lecture Series editor Philip Campbell is giving a public lecture at 6.30pm tonight titled Science – facts and frictions at Emmanuel College, Cambridge. The abstract and text below reproduced from talks.cam.ac.uk: ‘Climategate’, MMR vaccine, GM crops, stem cells – these are examples of public debates in which science and [...]... Read more »

Philip Campbell. (1995) Postscript from a new hand. Nature, 378(6558), 649-649. DOI: 10.1038/378649b0  

  • December 3, 2009
  • 04:28 AM
  • 1,570 views

It’s Snowing (JavaScript)!

by Duncan Hull in O'Really?

You know it’s December when it starts snowing in your web browser.
Let it snow, let it snow, let it snow!
Or programmatically:
snowStorm = new SnowStorm();
There was a time, not so very long ago when JavaScript snow would have been “best viewed in browser x”. Thankfully now its much more reliable, JBrowse [1] is a nice example [...]... Read more »

Skinner, M., Uzilov, A., Stein, L., Mungall, C., & Holmes, I. (2009) JBrowse: A next-generation genome browser. Genome Research, 19(9), 1630-1638. DOI: 10.1101/gr.094607.109  

  • February 5, 2010
  • 06:53 AM
  • 1,543 views

Classic paper: Montagues and Capulets in Science

by Duncan Hull in O'Really?

In 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 [...]... Read more »

Goble, C., & Wroe, C. (2004) The Montagues and the Capulets. Comparative and Functional Genomics, 5(8), 623-632. DOI: 10.1002/cfg.442  

  • September 10, 2009
  • 09:28 AM
  • 1,535 views

Why don’t scientists share data?

by Duncan Hull in O'Really?

As Vince Smith once put it [1] data are the fuel of Science:
“The fabric of science is changing, driven by a revolution in digital technologies that facilitate the acquisition and communication of massive amounts of data. This is changing the nature of collaboration and expanding opportunities to participate in science. If digital technologies are the [...]... Read more »

Schofield, P., Bubela, T., Weaver, T., Portilla, L., Brown, S., Hancock, J., Einhorn, D., Tocchini-Valentini, G., Hrabe de Angelis, M., & Rosenthal, N. (2009) Post-publication sharing of data and tools. Nature, 461(7261), 171-173. DOI: 10.1038/461171a  

Toronto International Data Release Workshop Authors. (2009) Prepublication data sharing. Nature, 461(7261), 168-170. DOI: 10.1038/461168a  

Bryn Nelson. (2009) Data sharing: Empty archives. Nature, 461(7261), 160-163. DOI: 10.1038/461160a  

  • February 25, 2010
  • 05:00 AM
  • 1,525 views

Apache Maven: A Misbehavin’ Build Tool?

by Duncan Hull in O'Really?

One of the many tools we use in our team to manage the development of ChEBI software is an automated build tool called Apache Maven. Opinions are often divided on whether Maven is a good or a bad thing. Most of them are very subjective, argumentative and often very extended. See why does maven have [...]... Read more »

Bjarne Stroustrup. (2007) Evolving a language in and for the real world: C 1991-2006. Proceedings of the third ACM SIGPLAN conference on History of programming languages. DOI: 10.1145/1238844.1238848  

Bjarne Stroustrup. (1993) A history of C : 1979–1991. The second ACM SIGPLAN conference on History of programming languages. DOI: 10.1145/154766.155375  

  • June 28, 2011
  • 03:31 PM
  • 1,488 views

Impact Factor Boxing 2011

by Duncan Hull in O'Really?

[This post is part of an ongoing series about impact factors] Well it’s that time again. The annual sweaty fist-fight for supremacy between the scientific journals, as measured by impact factors, is upon us. Much ink (virtual and actual) has been spilt on the subject of impact factors, which we won’t add to here, other [...]... Read more »

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