O'Really?

November 17, 2008

Science blog meme: Why do we blog?

Keep Calm and Carry On via AJC1I have been virally infected by Martin Fenner’s “why do we blog” meme.

1. What is your blog about?

Science and technology, especially bioinformatics, systems biology and the Web. It is a personal laboratory notebook-cum-diary, with a few facts and many opinions that would be difficult to publish conventionally [1].

2. What will you never write about?

Banal personal trivia (“I went shopping today”), confidential work, collaborative projects before they have been published. If in doubt, I try to ask people, “is it OK if I blog this?”

3. Have you ever considered leaving science?

Already did, I left science after my undergraduate degree to work in industry, but came back after six years to do a PhD. I don’t think Science ever really leaves you, once a scientist, always a scientist. Can’t see myself “leaving” again, but you never know.

4. What would you do instead?

Tend olive trees in Greece. Sequence 10,000 + Olive tree genomes, do some olive tree systems biology [2]. Subsidise scientific research with money from olive oil export business.

5. What do you think will science blogging be like in 5 years?

Pretty much the same as it is now I reckon, maybe more senior scientists will start blogging, see big boffins with blogs.

6. What is the most extraordinary thing that happened to you because of blogging?

I’m pretty sure blogging was a significant factor in being invited to Science Foo Camp (scifoo)

7. Did you write a blog post or comment you later regretted?

Non, rien de rien. Non, je ne regrette rien. Some of the posts about semantic web and molecular biology I might come to regret in the future though, but life is too short. There is an ever present temptation to write controversial blog posts (that might be regretted later) to get more visitors to your blog. Sometimes I can’t resist. Also, there is no safety net of peer-review, so you can make mistakes very quickly, even faster than by drinking tequila. I often wonder what prospective employers and/or funding bodies would make of it all – by the time I find out, it might be too late 🙂

8. When did you first learn about science blogging?

Via nodalpoint which is run by Greg Tyrelle.

9. What do your colleagues at work say about your blogging?

So far, there have been five basic responses to my blog among colleagues.

a) Great idea, carry on (see picture, top right). Can you blog this for me?

b) Bad idea, why do you waste so much time blogging? When are you going to do some “real” work?

c) Teasing: “I’m drinking a coffee, are you blogging this?”

d) Head-in-the-sand, no acknowledgment, denial, look the other way.

e) Ignorance is bliss. What is a blog? Do you have one of those interweb things on your computer?

References

  1. Michael R. Seringhaus and Mark B. Gerstein (2007). Publishing perishing? towards tomorrow’s information architecture. BMC Bioinformatics 8, 17+. DOI:10.1186/1471-2105-8-17, pmid:17239245
  2. Royston Goodacre, Douglas B Kell, Giorgio Bianchi (1992). Neural networks and olive oil. Nature 359 (6396), 594. DOI:10.1038/359594a0

[Keep Calm and Carry On via AJC1]

October 27, 2008

OWL Experiences and Directions (OWLED) 2008

Great Grey Owl by Brian ScottThe Web Ontology Language (OWL) is a language for creating ontologies on the Web. It does exactly what it says on the tin. But what is an ontology? One way to think of it is as a better way of storing data and knowledge. Instead of just capturing and describing data in a databases, ontology languages like OWL provide ways to capture and describe knowledge in a knowledge base. Ontologies can allow more intelligent querying, integration and understanding of data than is possible using a plain old relational database.

Since 2003 developers and users of the Web Ontology Language, abbreviated to OWL (not WOL), have been gathering at a two-day workshop called OWLED (OWL Experiences and Directions). This year the workshop is in Karlsruhe in Germany. The full list of accepted papers is available, as with previous years, this years workshop has a distinctly biological flavour to the proceedings: (more…)

October 10, 2008

PhD studentships at EMBL-EBI, UK

EMBL-EBIAny budding biomedical scientists out there, interested in doing a PhD, take note: The European Molecular Biology Laboratory (EMBL) – European Bioinformatics Institute (EBI) is having an open day on Monday 3rd November 2008. According to their website the EBI is “happy to welcome all Master students to this day”. Some talks at this open day include:

The EMBL-EBI lies in the 55 acres of landscaped parkland in rural Cambridgeshire that make up the Wellcome Trust Genome Campus. The Campus also houses the Wellcome Trust Sanger Institute, making it one of the world’s largest concentrations of expertise in genomics and bioinformatics. See also PhD Studies in Bioinformatics at the EBI. If you are interested in attending, sign up at the registration page before the 20th October.

See also PhD Opportunities at the Wellcome Trust Sanger Institute, Cambridge.

August 26, 2008

Open Notebook Science in Manchester

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

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

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

July 15, 2008

ChEBI, Oh ChEBI, Oh Baby!

Filed under: informatics — Duncan Hull @ 2:30 pm
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cherry oh baby With sincere apologies to Jamaican reggae singer-songwriter Eric Donaldson, “ChEBI, Oh ChEBI, Oh Baby, don’t you know I’m in need of thee”?

Chemical Entities of Biological Interest (ChEBI) is a dictionary, controlled vocabulary, database, ontology of small (low molecular-weight) chemical entities that are considered to be biologically interesting, (like amphetamine (CHEBI:2679) for example). After a couple of recent meetings, ChEBI is going through some serious revision, to make it more efficient to maintain and use. Here are some brief notes on the changes, for my own benefit mostly and to collate links, but perhaps others are interested too.

Janna Hastings has created a wiki for the New ChEBI Ontology project which includes links to the ChEBI ontology remediation notes and meeting notes from 9th July 2008.
(more…)

July 6, 2008

You Know OBO? Let’s GO!

Oboe mechanics by starriseAccording to their website “The Open Biomedical Ontologies (OBO) Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain”. This week they are having a workshop in Cambridge, to bring myself up to speed, here is a quick name check of some of the people involved.

June 20, 2008

A Brief Review of RefWorks

Philosophiæ Naturalis Principia MathematicaThere is no shortage of bibliographic management tools out there, which ultimately aim to save your time managing the papers and books in your personal library. I’ve just been to a demo and sales pitch for one of them, a tool called RefWorks. Refworks claims to be “an online research management, writing and collaboration tool — designed to help researchers easily gather, manage, store and share all types of information, as well as generate citations and bibliographies”. It looks like a pretty good tool, similar to the likes of EndNote but with more web-based features that are common with Citeulike and Connotea. Here are some ultra-brief notes. RefWorks in five minutes, the good, the bad and the ugly.

The Good…

Refworks finer features

  • Refworks is web based, you can use it from any computer with an internet connection, without having to install any software. Platform independent, Mac, Windows, Linux, Blackberry, iPhone, Woteva. This feature is becoming increasingly common, see Martin Fenner’s Online reference managers, not quite there yet article at Nature Network.
  • Share selected references and bibliographies on the Web via RefShare
  • It imports and exports all the things you would expect, Endnote (definitely), XML, Feeds (RSS), flat files, BibTeX (check?), RIS (check?) and several others via the screenscraping tool RefGrab-It
  • Interfaces with PubMed and Scopus (and many other databases) closely, e.g. you can search these directly from your RefWorks library. You can also export from Scopus to Refworks…
  • Not part of the Reed-Elsevier global empire (yet), currently part of ProQuest, based in California.
  • Free 30 day trial is available
  • Just like EndNote, it can be closely integrated with Microsoft Word, to cite-while-you-write

(more…)

June 12, 2008

The drugs don’t work, they just make you worse

Filed under: informatics — Duncan Hull @ 3:45 pm
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StampsWhat exactly is a drug? A project I’m currently working on requires a good solid definition, at the very least comprehensible to humans, and preferably understandable by more intelligent, semantically aware computers too. I would like to be able to take some scientific model and ask questions like, “show (or hide) all the drugs in this model”. Trouble is, the word “drug” is such a heavily overloaded term, with many alternative meanings, that it is practically meaningless. Just when you think you have a definition, you can find a case that breaks it. I’m not just being an anally-retentive pedant, well no more than usual anyway. It turns out to be much harder than you might think to define what a drug is. The term drug depends on all kinds of contextual information, dosage, species, legality, intent, social conventions and so on. Here are some broken definitions, warts and all. As you’ll see, the various definitions of drugs don’t work, they just make you worse. (more…)

May 22, 2008

First ChEBI workshop, Day Two

Filed under: informatics — Duncan Hull @ 2:49 pm
Tags: , , , , , , , , ,


Chemist Margaret Thatcher stays at the Crowne House Hotel, Great Chesterford, England
Some rough and ready notes from day two of the first ChEBI workshop, 20th May 2008. There were two talks, one from Kirill Degtyarenko (European Patent Office) and the other from Janna Hastings (EBI), followed by a discussion.

Kirill Degtyarenko: Good annotation practice for chemical data, ChEBI experience

Kirill’s talk described how to give the most appropriate names, especially since “biologists don’t name things properly, if at all” (!). Systematic (IUPAC) names are usually better than common names except for “the unprounounceables” for example, an antibiotic called (E)-roxithromycin (ChEBI:48935) has the IUPAC name:

(3R,4S,5S,6R,7R,9R,10E,11S,12R,13S,14R)-4-(2,6-dideoxy-3-C-methyl-3-O-methyl-α-L-ribo-hexopyranosyloxy)-14-ethyl-7,12,13-trihydroxy-10-{[(2-methoxyethoxy)methoxy]imino}-6-[3,4,6-trideoxy-3-(dimethylamino)-β-D-xylo-hexopyranosyloxy]-3,5,7,9,11,13-hexamethyloxacyclotetradecan-2-one

…which just trips of the tongue (and fits beautifully, without line breaks onto regular computer screens). Fortunately, the curator can draw the chemical (note the wavy bond, unknown stereochemistry), using the curator tools, then the inchi and smiles strings are generated from the drawing. Currently they use something called ACD/Name which can generate PubChem links automatically. As of May 2008 14,000 chebi ids translates to around 11,000 CIDs in PubChem, which is structures only.
(more…)

May 21, 2008

First ChEBI workshop, Day one



Great Chesterford
Some notes from day one of the first ChEBI workshop, 19th May 2008. There were four talks from Colin Batchelor (Royal Society of Chemistry), Ulrike Witting (EML Research GmbH Hiedelberg), Giles Weaver (Unilever) and Paula de Matos (EBI). Christoph Steinbeck has already written some ChEBI notes, these just add a little more detail. (more…)

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