Home » Blog

Linking up open science online

31 August 2008 4 Comments

I am currently sitting at the dining table of Peter Murray-Rust with Egon Willighagen opposite me talking to Jean-Claude Bradley. We pulling together sets of data from Jean-Claude’s UsefulChem project into CML to make it more semantically rich and do a bunch of cool stuff. Jean-Claude has a recently published preprint on Nature Precedings of a paper that has been submitted to JoVE. Egon was able to grab the InChiKeys from the relevant UsefulChem pages and passing those to CDK via a script that he wrote on the spot (which he has also just blogged) generated CML react for those molecules.

Peter at the same time has cut and pasted an existing example of a CML react XML document into a GoogleDoc which we will then modify to represent one example of the Ugi reactions that Jean-Claude reported in the precedings paper. You will be able to see all of these documents. The only way we would be able to do this is with four laptops all online – and for all the relevant documents and services to be available from where we are sitting. I’ve never been involved in a hackfest like this before but actually the ability to handle different aspects of the same document via GoogleDocs is a very powerful way of handling multiple processes at the same time.


  • Hi Cameron. I was going to email you but I rarely use email these days. Sorry we didn’t really get a chance to talk the other day. Since PM-R and I were so busy writing our Manu. in the pub, we never got a chance to brainstorm the other one as planned.

    As ever, great post from you. Full 2.0 steam ahead for all things Open Science.

    You might be interested in reading the following which I posted a couple of weeks ago:- http://mcblawg.blogspot.com/2008/08/international-gang-of-four-igf.html

    We too are collaborating using Google Docs and it’s a very effective way to work collectively.

    I don’t recall OA being mentioned at all at sciblog although ONS as you know was mentioned many times which was great. I was quite taken aback when PMR singled me out to make a comment during the wrap up Panel Discussion. That said, as soon as he mentioned “Patient Advocates”, I did wonder whether he was indeed referring to me ;-)

    Nice to meet you and I’m sure we’ll do so again at some point in the future.

    Cheers,

    Graham

  • Hi Cameron. I was going to email you but I rarely use email these days. Sorry we didn’t really get a chance to talk the other day. Since PM-R and I were so busy writing our Manu. in the pub, we never got a chance to brainstorm the other one as planned.

    As ever, great post from you. Full 2.0 steam ahead for all things Open Science.

    You might be interested in reading the following which I posted a couple of weeks ago:- http://mcblawg.blogspot.com/2008/08/international-gang-of-four-igf.html

    We too are collaborating using Google Docs and it’s a very effective way to work collectively.

    I don’t recall OA being mentioned at all at sciblog although ONS as you know was mentioned many times which was great. I was quite taken aback when PMR singled me out to make a comment during the wrap up Panel Discussion. That said, as soon as he mentioned “Patient Advocates”, I did wonder whether he was indeed referring to me ;-)

    Nice to meet you and I’m sure we’ll do so again at some point in the future.

    Cheers,

    Graham

  • Hey Graham, if you don’t use email, how am I supposed to reply? Great to meet you and another mind blowing weekend really. Struggling to assimilate everything really. We do need to get something down on the whole Web2-4-science thing and I’ve been absolutely hopeless pulling anything together over the last month. Some deadlines are required!

    Cheers

  • Hey Graham, if you don’t use email, how am I supposed to reply? Great to meet you and another mind blowing weekend really. Struggling to assimilate everything really. We do need to get something down on the whole Web2-4-science thing and I’ve been absolutely hopeless pulling anything together over the last month. Some deadlines are required!

    Cheers