O'Really?

November 5, 2009

Artemether: Entity of the Month

Filed under: biocuration — Duncan @ 1:27 pm
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ArtemetherNovember’s entity of the month at ChEBI is the antimalarial drug Artemether. This accompanies release 62 of ChEBI, not just yet another incremental release but an increase of more than twentyfold in the number of entities in ChEBI, thanks to merging of data between an updated ChEBI [1] and ChEMBL [2]. ChEBI now (as of release 62) has over 455,000 total entities, compared to just under 19,000 in the previous version (release 61), see ChEBI news for details. The text below on Artemether is reproduced from the ChEBI website, where content is available under a Creative Commons license:

Artemether (CHEBI:195280) is a lipid-soluble antimalarial for the treatment of multi-drug resistant strains of Plasmodium falciparum malaria. First prepared in 1979 [3], it is a methyl ether of the naturally occurring sesquiterpene lactone (+)-artemisinin, which is isolated from the leaves of Artemisia annua L. (sweet wormwood), the traditional Chinese medicinal herb known as Qinghao. However, because of artemether’s extremely rapid mode of action (it has an elimination half-life of only 2 hours, being metabolized to dihydroartemisinin which then undergoes rapid clearance), it is used in combination with other, longer-acting, drugs. One such combination, licensed in April of this year by the WHO, is Coartem in which the artemether is mixed with lumefantrine – a racemic mixture of a synthetic fluorene derivative known formerly as benflumetol – which has a much longer and pharmacologically complementary terminal half-life of 3–6 days, allowing the two drugs to act synergistically against Plasmodium.

The molecule of artemether is interesting because of its extreme rigidity, with very few rotational bonds. Unlike quinine class antimalarial drugs, it has no nitrogen atom in its skeleton. However, an important chemical feature (and unique in drugs) is the presence of an O–O endoperoxide bridge which is essential for its antimalarial activity, as it is this bridge which is split in an interaction with heme, blocking the conversion into hemozoin and thus releasing into the parasite heme and a host of free radicals which attack the cell membrane.

Artemether is fully Rule-of-Five compliant and has recently also been under investigation as a possible candidate for cancer treatment [4,5].

GO ChEBI!

References

  1. de Matos, P., Alcantara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S., & Steinbeck, C. (2009). Chemical Entities of Biological Interest: an update Nucleic Acids Research DOI: 10.1093/nar/gkp886
  2. Warr, W. (2009). ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI) Journal of Computer-Aided Molecular Design, 23 (4), 195-198 DOI: 10.1007/s10822-009-9260-9
  3. Li, Y. et al. (1979) K’o Hsueh T’ung Pao, 24, 667 [Chem. Abstr., 91, 211376u].
  4. Singh, N., & Panwar, V. (2006). Case Report of a Pituitary Macroadenoma Treated With Artemether Integrative Cancer Therapies, 5 (4), 391-394 DOI: 10.1177/1534735406295311
  5. Wu, Z., Gao, C., Wu, Y., Zhu, Q., Yan Chen, ., Xin Liu, ., & Chuen Liu, . (2009). Inhibitive Effect of Artemether on Tumor Growth and Angiogenesis in the Rat C6 Orthotopic Brain Gliomas Model Integrative Cancer Therapies, 8 (1), 88-92 DOI: 10.1177/1534735408330714

October 23, 2009

Wellcome to the Genome Campus

Filed under: funding, informatics — Duncan @ 7:31 am
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Henry Wellcome, Mr. PharmacistSo, I’ve just started a new job and moved home. There is loads to blog about but little time to do it. Before it’s too late, here are some first week impressions from a newbie starter at the European Bioinformatics Institute (EBI) on the Wellcome Trust Genome Campus.

The Genome Campus owes its existence to the pharmacist Henry Wellcome, pictured over on the left. When he died in 1936, his legacy founded the Wellcome Trust, set up with money from his success as a pharmaceutical manufacturer and salesman. Today, the trust is the largest charity in the UK, funding innovative biomedical research and spending over £600 million each year. A large part of this legacy is being (and has been) spent on the Wellcome Trust Genome Campus, home to the Wellcome Trust Sanger Institute (WTSI) (aka “The Sanger”) and the European Bioinformatics Institute (EBI) an outstation of the European Molecular Biology Laboratory (EMBL) based in Hinxton, twelve miles south of Cambridge in Cambridgeshire.

Cambridgeshire life: Good and Bad

It’s a bit of shock moving “Down South” from Manchester. Although still in the UK, sometimes it feels like a different country and culture to “Up North”. So I’ll have to resort to bullet points to cover the good and bad of life down here so far.

  • Bad: Middle of nowhere Hinxton, Cambridgeshire is the middle of nowhere - there is nothing else here apart from the Red Lion. There is not much choice of shops, pubs, eateries, curry houses and restaurants to visit at lunchtime. The nearest train stations are miles away although there is an excellent bus service. However, there is no escaping the fact that Hinxton is a pretty inaccessible compared to being in the centre of a city. Still, at least London is a short train ride away from Cambridge.
  • Bad: It’s Grim Down South Southern English prejudice often states that It’s Grim Up North, but this a topic of much contention. Northerners often think the converse is true, and have frequently pointed out that actually It’s Grim Down South, because life costs more but you get a lot less for your money. It all depends on what you mean by those weasel words less, more and grim of course, but that’s another story.
  • Bad: Norman-no-mates Being the newboy-with-shiny-shoes, I can’t help wondering where all my friends, colleagues and frolleagues went. I knew I’d forgotten to pack something in the move. I feel all lost without my pals from the Information Management Group (IMG), dbkgroup and the MCISB back “home” in Manchester. But I wouldn’t have got this job without them, especially the opportunities provided by Carole Goble, Robert Stevens and Douglas Kell. The only consolation is while we are no longer colleagues at the University of Manchester, we’re still colleagues at the Invisible College.
  • Good: Big, world class and international There’s something like ~300 people employed at the EBI and another ~800 or so at The Sanger. They come from all around the world, the ChEBI group for example currently has German, South African, Norwegian, Portugese, Chilean, Dutch and English nationalities amongst its number. So there is a lot to learn from the people around you, a high quality series of seminars to choose from and excellent support networks for various things, both technical and social.
  • Good: High profile and expert When it comes to bioinformatics this place obviously has a high profile and there is no shortage of expertise to draw on locally, both on campus and in the surrounding Silicon Fen.
  • Good: Canteen, gym, library etc There are some impressive facilities here, a well stocked library, extensive gym, sports facilities and huge canteen. They look after their employees too, little things like paying for removals when you relocate can make a big difference. There’s also tax benefits of working for a European organisation.
  • Good: Beautiful countryside and campus The south cambridgeshire countryside is quite beautiful with its rolling Gog Magog Downs. It’s looking good at this time of year, with hundreds of colourful autumn trees populating the 55 acres of landscaped parkland on campus.
  • Good: Best of both worlds The EBI is an academic institution (ebi.ac.uk) but it feels more industrial than academia in many ways. So you can (I hope) get the best of both worlds, academic and industrial.

Anyway, the Chemical Entities of Biological Interest (ChEBI) team of which I am now part are making me feel very wellcome here and I’m enjoying working on research and development of the ChEBI ontology [1]. It is interesting to wonder what a pharmacist like Henry would make of a freely available open source chemical ontology (describing many drugs) and the Genome Campus which bears his name.

Contemplating this question may require growing a long silken moustache which Henry Wellcome clearly excelled at, see picture top left.

References

  1. Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcantara, R., Darsow, M., Guedj, M., & Ashburner, M. (2007). ChEBI: a database and ontology for chemical entities of biological interest Nucleic Acids Research, 36 (Database) DOI: 10.1093/nar/gkm791
  2. The Justified Ancients of Mu Mu, JAMS (1991) It’s Grim Up North
  3. More commetary on this post over at friendfeed.

September 18, 2009

Popular, personal and public data: Article-level metrics at PLoS

Filed under: publishing — Duncan @ 11:50 am
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PLoS: The Public Library of ScienceThe 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 and potentially useful data, not currently made publicly available by other publishers. Here is a  selection of some of the data, taken from the full dataset here (large file), which includes the “top ten” papers by viewing statistics.

Article level metrics for some papers published in PLoS (August 2009)

Rank* Article Journal Views Citations**
1 Why Most Published Research Findings Are False (including this one?) [1] PLoS Medicine 232847 52
2 Initial Severity and Antidepressant Benefits: A Meta-Analysis of Data Submitted to the Food and Drug Administration [2] PLoS Medicine 182305 15
3 Serotonin and Depression: A Disconnect between the Advertisements and the Scientific Literature [3] PLoS Medicine 105498 16
4 The Diploid Genome Sequence of an Individual Human [4] PLoS Biology 88271 54
5 Ultrasonic Songs of Male Mice [5] PLoS Biology 81331 8
6 Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology [6] PLoS ONE 62449 0
7 The Impact Factor Game: It is time to find a better way to assess the scientific literature [7] PLoS Medicine 61353 13
8 A Map of Recent Positive Selection in the Human Genome [8] PLoS Biology 59512 94
9 Mapping the Structural Core of Human Cerebral Cortex [9] PLoS Biology 58151 8
10 Ten Simple Rules for Getting Published [10] PLoS Computational Biology 57312 1
11 Men, Women, and Ghosts in Science [11] PLoS Biology 56982 0
120 Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web [12] (w00t!) PLoS Computational Biology 16295 3
1500 Specificity and evolvability in eukaryotic protein interaction networks [13] PLoS Computational Biology 4270 7
1632 Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions [14] PLoS Computational Biology 4063 10
1755 Folding Very Short Peptides Using Molecular Dynamics [15] PLoS Computational Biology 3876 2
2535 Microblogging the ISMB: A New Approach to Conference Reporting [16] PLoS Computational Biology 3055 1
7521 Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations [17] PLoS Computational Biology 1024 0
12549 Deciphering Proteomic Signatures of Early Diapause in Nasonia [18] PLoS ONE 0 0

*The rank is based on the 12,549 papers for which viewing data (combined usage of HTML + PDF + XML) are available.

**Citation counts are via PubMedCentral (data from CrossRef and Scopus is also provided, see Bora’s comments and commentary at Blue Lab Coats.)

Science is not a popularity contest but…

Analysing this data is not straightforward. Some highly-viewed articles are never cited (reviews, editorial, essays, opinion, etc). Likewise, popularity and importance are not the same thing. Some articles get lots of citations but few views, which suggests that people are not actually reading the papers them before citing them. As described on the PLoS website article-level-metrics.plos.org:

“When looking at Article-Level Metrics for the first time bear the following points in mind:

  • Online usage is dependent on the article type, the age of the article, and the subject area(s) it is in. Therefore you should be aware of these effects when considering the performance of any given article.
  • Older articles normally have higher usage than younger ones simply because the usage has had longer to accumulate. Articles typically have a peak in their usage in the first 3 months and usage then levels off after that.
  • Spikes of usage can be caused by media coverage, usage by large numbers of people, out of control download scripts or any number of other reasons. Without a detailed look at the raw usage logs it is often impossible to tell what the reason is and so we encourage you to regard usage data as indicative of trends, rather than as an absolute measure for any given article.
  • We currently have missing usage data for some of our articles, but we are working to fill the gaps. Primarily this affects those articles published before June 17th, 2005.
  • Newly published articles do not accumulate usage data instantaneously but require a day or two before data are shown.
  • Article citations as recorded by the Scopus database are sometimes undercounted because there are two records in the database for the same article. We’re working with Scopus to correct this issue.
  • All metrics will accrue over time (and some, such as citations, will take several years to accrue). Therefore, recent articles may not show many metrics (other than online usage, which accrues from day one). ”

So all the usual caveats apply when using this bibliometric data. Despite the limitations, it is more revealing than the useful (but simplistic) “highly accesssed” papers at BioMedCentral, which doesn’t always give full information on what “highly” actually means next to each published article. It will be interesting to see if other publishers now follow the lead of PLoS and BioMed Central and also publish their usage data combined with other bibliometric indicators such as blog coverage. For authors publishing with PLoS, this data has an added personal dimension too, it is handy to see how many views your paper has.

As paying customers of the services that commercial publishers provide, should scientists and their funders be demanding more of this kind of information in the future? I reckon they should. You have to wonder, why these kind of innovations have taken so long to happen, but they are a welcome addition.

[More commentary on this post over at friendfeed.]

References

  1. Ioannidis, J. (2005). Why Most Published Research Findings Are False PLoS Medicine, 2 (8) DOI: 10.1371/journal.pmed.0020124
  2. Kirsch, I., Deacon, B., Huedo-Medina, T., Scoboria, A., Moore, T., & Johnson, B. (2008). Initial Severity and Antidepressant Benefits: A Meta-Analysis of Data Submitted to the Food and Drug Administration PLoS Medicine, 5 (2) DOI: 10.1371/journal.pmed.0050045
  3. Lacasse, J., & Leo, J. (2005). Serotonin and Depression: A Disconnect between the Advertisements and the Scientific Literature PLoS Medicine, 2 (12) DOI: 10.1371/journal.pmed.0020392
  4. Levy, S., Sutton, G., Ng, P., Feuk, L., Halpern, A., Walenz, B., Axelrod, N., Huang, J., Kirkness, E., Denisov, G., Lin, Y., MacDonald, J., Pang, A., Shago, M., Stockwell, T., Tsiamouri, A., Bafna, V., Bansal, V., Kravitz, S., Busam, D., Beeson, K., McIntosh, T., Remington, K., Abril, J., Gill, J., Borman, J., Rogers, Y., Frazier, M., Scherer, S., Strausberg, R., & Venter, J. (2007). The Diploid Genome Sequence of an Individual Human PLoS Biology, 5 (10) DOI: 10.1371/journal.pbio.0050254
  5. Holy, T., & Guo, Z. (2005). Ultrasonic Songs of Male Mice PLoS Biology, 3 (12) DOI: 10.1371/journal.pbio.0030386
  6. Franzen, J., Gingerich, P., Habersetzer, J., Hurum, J., von Koenigswald, W., & Smith, B. (2009). Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005723
  7. The PLoS Medicine Editors (2006). The Impact Factor Game PLoS Medicine, 3 (6) DOI: 10.1371/journal.pmed.0030291
  8. 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
  9. 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
  10. Bourne, P. (2005). Ten Simple Rules for Getting Published PLoS Computational Biology, 1 (5) DOI: 10.1371/journal.pcbi.0010057
  11. Lawrence, P. (2006). Men, Women, and Ghosts in Science PLoS Biology, 4 (1) DOI: 10.1371/journal.pbio.0040019
  12. Hull, D., Pettifer, S., & Kell, D. (2008). Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web PLoS Computational Biology, 4 (10) DOI: 10.1371/journal.pcbi.1000204
  13. Beltrao, P., & Serrano, L. (2007). Specificity and Evolvability in Eukaryotic Protein Interaction Networks PLoS Computational Biology, 3 (2) DOI: 10.1371/journal.pcbi.0030025
  14. Beltrao, P., & Serrano, L. (2005). Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions PLoS Computational Biology, 1 (3) DOI: 10.1371/journal.pcbi.0010026
  15. Ho, B., & Dill, K. (2006). Folding Very Short Peptides Using Molecular Dynamics PLoS Computational Biology, 2 (4) DOI: 10.1371/journal.pcbi.0020027
  16. 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
  17. Ho, B., & Agard, D. (2009). Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations PLoS Computational Biology, 5 (4) DOI: 10.1371/journal.pcbi.1000343
  18. Wolschin, F., & Gadau, J. (2009). Deciphering Proteomic Signatures of Early Diapause in Nasonia PLoS ONE, 4 (7) DOI: 10.1371/journal.pone.0006394

September 10, 2009

Why don’t scientists share data?

Filed under: Science, communication, publishing, web of science — Duncan @ 2:28 pm
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Sharing Ice Cream by ClappstarAs 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 engine of this revolution, digital data are its fuel. But for many scientific disciplines, this fuel is in short supply.”

Despite the importance of data, some scientists are often really bad at sharing it properly. So why don’t scientists share data?

Nature has a special issue dedicated to this topic published today at nature.com/news/specials/datasharing [2,3,4,5] which isn’t behind a pay wall (at the moment). It describes some of the technical and cultural barriers to data sharing. You should go and read it yourself if you’re interested, but here is a very brief and incomplete summary, with some extra points thrown in for good measure:

  • Some funding bodies do not adequately support the research projects they sponsor in sharing data properly, both before and after publication.
  • Many scientists lack awareness, incentives and knowledge of data sharing which can be compounded by a fear of being “scooped”.
  • Public databases, often a more natural home for data than traditional publications, are frequently undervalued by a publish or perish culture [6].
  • Traditional scientific publishing is frequently (and ironically) a really inadequate method for sharing data. Important data and metadata routinely gets damaged or destroyed in the process of publishing [7].
  • The technical infrastructure for long term data sharing either does not exist or is not understood by those who should be providing and using it. This can lead to empty archive syndrome.

These are some of the reasons that scientists don’t share data. Which raises the question, how do we get out of this mess? The special issue offers some solutions [3,4] to these cultural and technical problems, including the use of Creative Commons licenses. It’s good to see these important issues given a higher profile but we will probably be striving for better data sharing for many years to come.

References

  1. Vince Smith (2009). Data publication: towards a database of everything BMC Research Notes, 2 (1) DOI: 10.1186/1756-0500-2-113
  2. Anonymous (2009). Data’s shameful neglect: Research cannot flourish if data are not preserved and made accessible. Nature, 461 (7261), 145-145 DOI: 10.1038/461145a
  3. 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
  4. Toronto International Data Release Workshop Authors (2009). Prepublication data sharing Nature, 461 (7261), 168-170 DOI: 10.1038/461168a
  5. Bryn Nelson (2009). Data sharing: Empty archives Nature, 461 (7261), 160-163 DOI: 10.1038/461160a
  6. Michael Seringhaus, & Mark Gerstein (2007). Publishing perishing? Towards tomorrow’s information architecture BMC Bioinformatics, 8 (1) DOI: 10.1186/1471-2105-8-17
  7. Duncan Hull, Steve Pettifer, & Douglas Kell (2008). Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web PLoS Computational Biology, 4 (10) DOI: 10.1371/journal.pcbi.1000204

[CC-licensed picture of Sharing by ryancr, more commentary on this post over at friendfeed.]

September 4, 2009

XML training in Oxford

Filed under: conferences, informatics, publishing — Duncan @ 3:13 pm
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XML Summer School 2009The XML Summer School returns this year at St. Edmund Hall, Oxford from 20th-25th September 2009. As always, it’s packed with high quality technical training for every level of expertise, from the Hands-on Introduction for beginners through to special classes devoted to XQuery and XSLT, Semantic Technologies, Open Source Applications, Web 2.0, Web Services and Identity. The Summer School is also a rare opportunity to experience what life is like as a student in one of the world’s oldest university cities while enjoying a range of social events that are a part of the unique summer school experience.

This year, classes and sessions are taught and chaired by:

W3C XML 10th anniversaryThe Extensible Markup Language (XML) has been around for just over ten years, quickly and quietly finding its niche in many different areas of science and technology. It has been used in everything from modelling biochemical networks in systems biology [1], to electronic health records [2], scientific publishing, the provision of the PubMed service (which talks XML) [3] and many other areas. As a crude measure of its importance in biomedical science, PubMed currently has no fewer than 800 peer-reviewed publications on XML. It’s hard to imagine life without it. So whether you’re a complete novice looking to learn more about XML or a seasoned veteran wanting to improve your knowledge, register your place and find out more by visiting xmlsummerschool.com. I hope to see you there…

References

  1. Hucka, M. (2003). The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models Bioinformatics, 19 (4), 524-531 DOI: 10.1093/bioinformatics/btg015
  2. Bunduchi R, Williams R, Graham I, & Smart A (2006). XML-based clinical data standardisation in the National Health Service Scotland. Informatics in primary care, 14 (4) PMID: 17504574
  3. Sayers, E., Barrett, T., Benson, D., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Edgar, R., Federhen, S., Feolo, M., Geer, L., Helmberg, W., Kapustin, Y., Landsman, D., Lipman, D., Madden, T., Maglott, D., Miller, V., Mizrachi, I., Ostell, J., Pruitt, K., Schuler, G., Sequeira, E., Sherry, S., Shumway, M., Sirotkin, K., Souvorov, A., Starchenko, G., Tatusova, T., Wagner, L., Yaschenko, E., & Ye, J. (2009). Database resources of the National Center for Biotechnology Information Nucleic Acids Research, 37 (Database) DOI: 10.1093/nar/gkn741

August 24, 2009

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

Filed under: communication, conferences — Duncan @ 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: Science, communication, publishing — Duncan @ 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 über-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 see more commentary on this paper over at friendfeed
  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 @ 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 @ 10:40 pm
Tags: , , , , , , , , , , ,

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 cliché, 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 cliché. 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 Clichés (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 @ 6:30 pm
Tags: , , , , , , , , , , , , , , , , , , , , ,

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
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