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Paul Ylioja
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Paul Ylioja

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It's worth exploring the new ChEMBL malaria data portal. It combines compounds with malaria data but retains other activity data.

272,523 compounds with 5,522 targets.

+OSDD Malaria 
The European Bioinformatics Institute
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Open Data and Content Mining
=======================
Talk at Sydney University by
Peter Murray-Rust
University of Cambridge and Open Knowledge Foundation

Seminar Room, Level 2 Fisher Library, 2 pm, Wednesday October 31st, 2012

The publicly funded research in the Scientific Technical Medical (STM) literature contains multibillion dollars of unused value. Most scientific articles contain names, numbers, places, chemicals, organisms, graphs, tables, etc. which can be extracted and re-used. This leads to better science, new information products, startup companies, better information for policy makers and much more which I have estimated  at "low billions" for chemistry alone. For STM, especially medicine, the figure is much higher. Yet this is currently unavailable for the reasons: (a) publishing uses PDF which is a very poor way of conveying the information (b) publishers active prevent mining of the content to preserve their revenues.

We must change this, and soon, though (a) evangelism of the opportunity (b) lobbying for our rights (c) building the next generation of tools. I shall cover all these, including our Manifesto on Open Content Mining and demonstrations of AMI2 - a weakly intelligent amanuensis for the scientist (based initially on understanding PDFs). This offers great opportunities for citizenry in general to liberate this vast resource of valuable information.

All welcome, no RSVP needed
Host: +Matthew Todd  School of Chemistry
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The definitive utensil diagram

First off, I want multiples of all of these (especially a Knork). Secondly, this will be one of the first things I teach my children.

#GeekHumor  
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so...we use a fork or a spork for mash? I'm going to try using a spife next time
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Chemists: Fancy making any of these? Have them already?
 
Start of a short (10-day) consultation on what's needed for round 3 of the project. Will end up with list of 10 Most Wanted synthetic compounds and 10 Most Wanted commercial/lit compounds. We'll only be making a few in Sydney, and putting the others out to tender.
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Not as impressive as last nights crystallisation but still interesting to watch.
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This is where we're at.
 
New human-readable project summary page is up - this page will be updated continuously as new things come in. The arylpyrroles are spectacular compounds, clearing the hERG assay and having astonishing potency against stages of the malaria parasite that are difficult to kill, and low metabolic clearance rates (but low solubility) ... but we've just learned that they showed no oral efficacy in mice. That's a pain. Raw data not up yet - should be in a day or two. We'll need to assess all data together to see whether the series is worth continuing with, hence the need to view all the data together, hence the project status page to give that overview. It's at times like these we need dispassionate opinions of people far removed from the day-to-day of the project.
The story so far in the open source drug discovery for malaria project. History. Last year the Todd lab at The University of Sydney received funding for a pilot project in open source drug discovery f...
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Paul Ylioja

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Talk by Peter Murray-Rust  on open data tomorrow +The University of Sydney  Lvl 2 Fisher Library, 2 pm, then #sydopenres beers at Cooper's, Newtown from 5:30
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Fancy a job anyone? An enthusiastic organic chemist required.
 
Postdoc position available in organic chemical synthesis in the open source drug discovery for malaria team. Details: http://bit.ly/R3oPrD
Postdoctoral Position Available in Open Source Drug Discovery for Malaria. The University of Sydney, Australia. Salary approx $70K. Available immediately, initially for 12 months, with the possibility...
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OpenScience malaria project being streamed at the Open Knowledge Festival right now.
 
OSDDmalaria presentation by +Matthew Todd  being streamed right now at #OKFest  in Helsinki.
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About to trial a hangout in preparation for our  open antimalaria compounds consultation (http://www.thesynapticleap.org/node/412)
The evaluation of the arylpyrroles has gone well, in that we've identified promising new antimalarial compounds. Besides their high potency, they exhibit high levels of activity in a late-stage gameto...
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await +Matthew Todd
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Just booted up on our old CRT tv so far. Next mini-job is to install a vnc server connect it up to the web.
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Just found http://ipadeln.com/ Their use of "iPad" predates iPad release date by several years. Wonder how they/apple feel(s)?
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Have him in circles
1,433 people
Stacey Folds's profile photo
Kumar Han's profile photo
Frank Merchant's profile photo
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Muhammed Madni's profile photo
Mohamed hosny's profile photo
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Chemist, hungry quite a lot of the time.
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