O'Really?

July 31, 2015

Wikipedia Science Conference @WellcomeTrust in London, September 2nd & 3rd 2015 #wikisci

Filed under: conferences,education,engineering,mathematics,open access,Science,technology — Duncan Hull @ 4:18 pm
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There is growing interest in Wikipedia, Wikidata, Commons, and other Wikimedia projects as platforms for opening up the scientific process [1]. The first Wikipedia Science Conference will discuss activities in this area at the Wellcome Collection Conference Centre in London on the 2nd & 3rd September 2015. There will be keynote talks from Wendy Hall (@DameWendyDBE) and Peter Murray-Rust (@petermurrayrust) and many other presentations including:

  • Daniel Mietchen (@EvoMRI), National Institutes of Health: wikipedia and scholarly communication
  • Alex Bateman (@AlexBateman1), European Bioinformatics Institute: Using wikipedia to annotate scientific databases
  • Geoffrey Bilder (@GBilder), CrossRef, Using DOIs in wikipedia
  • Richard Pinch (@IMAMaths), Institute of Mathematics and its Applications. Wikimedia versus academia: a clash of cultures
  • Andy Mabbett (@PigsOnTheWing), Royal Society of Chemistry / ORCID. Wikipedia, Wikidata and more – How Can Scientists Help?
  • Darren Logan (@DarrenLogan), Wellcome Trust Sanger Institute, Using scientific databases to annotate wikipedia
  • Dario Taraborelli (@ReaderMeter), Wikimedia & Altmetrics, Citing as a public service
  • … and many more

I’ll be doing a talk on “Improving the troubled relationship between Scientists and Wikipedia” (see slides below) with help from John Byrne who has been a Wikipedian in Residence at the Royal Society and Cancer Research UK.

How much does finding out more about all this wiki-goodness cost? An absolute bargain at just £29 for two days – what’s not to like? Tickets are available on eventbrite, register now, while tickets are still available. 

References

  1. Misha Teplitskiy, Grace Lu, & Eamon Duede (2015). Amplifying the Impact of Open Access: Wikipedia and the Diffusion of
    Science Wikipedia Workshop at 9th International Conference on Web and Social Media (ICWSM), Oxford, UK arXiv: 1506.07608v1

March 16, 2010

DNA, Diversity and You at Cambridge Science Festival

Filed under: communication,data mining — Duncan Hull @ 8:40 am
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Sequence BraceletsAs part of Cambridge Science festival last weekend, I joined a group of about 40 volunteers from The Sanger and EBI at an event “DNA, diversity and you”. This was a series of education and outreach events designed to explore how differences in your genetic code make you different from other individuals, and what makes the humans different from other living things –  with a bit of computational biology thrown in for good measure.  Here are some notes on a selection of the activities, in case you ever find yourself trying to explain biology, computer science or bioinformatics to anyone aged 4-18 and beyond. These resources are all tried, tested and fun to work with, for students and teachers alike:

  1. DNA origami create your own origami DNA molecule, and hands on way of learning abou tthe double helix structure of DNA
  2. DNA sequence bracelets (see picture right). Thread coloured beads according to sequence sections from a range of organisms including trout, chimpanzee, butterfly, a flesh-eating microbe and rotting corpse flower.
  3. Yummy gummy DNA (under 5’s) build your own DNA helix out of sweets and cocktail sticks. Then scoff it all afterwards.
  4. What’s my name in DNA? find out what your name is in DNA, and what the corresponding (hypothetical) protein is using software from deCODE.
  5. Function Finders translate DNA into a sequence of amino acids using wooden translator blocks, then find out which organism the amino acid sequence is from.
  6. Genome sizes (with seatbelts) Rank organisms (inc. human, zebrafish, mosquito, sugar cane and yeast) and find out if they are in the right order. Results are often not what you would expect.
  7. Play your genes right. A card-based guessing game which compares the number of genes in the human genome with the number of genes from a range of different organisms include the flu virus, E. coli bacteria, armadillo, rice plant and others.
  8. Genome Jigsaws for illustrating the process of finishing supposedly “finished” genomes, by putting together a square sequence jigsaw following base pairing rules to end up with a complete finished square.
  9. DNA Time Team examines of aspects ancestry and evolution. The activity encourages people to work out the sequence of a common ancestor by filling in the gaps on a simple evolutionary tree.
  10. Spot the difference with proteins. Comparing Heat Shock Protein (HSP) in human and other organisms to illustrate how different regions of the protein vary between different organisms and how this affects function.
  11. Ready, steady sort: a sorting network that demonstrates one technique that computers use to sort through large amounts of information like sequence data. This comes straight from Computer Science Unplugged by Tim Bell, Mike Fellows and Ian Witten. This activity can be done either as a smaller board game, or as a larger floor game. Either way, it’s a lot of fun, especially if you time people for an added competitive element (see video below)

There were a whole bunch of new activities at the festival this year, maybe these will appear on the your genome website in the future. Anyway, it was great fun to get involved, there is nothing quite like the challenge of explaining parallel computing to young kids, teenagers and their parents – actually much easier than you’d think if you’ve got access to great teaching materials.

Thanks to Francesca Gale and Louisa Wright for all the hard work that went into organising this fun and successful event.

November 5, 2009

Artemether: Entity of the Month

Filed under: biocuration — Duncan Hull @ 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

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