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Matthew Todd

Matthew Todd

Senior Lecturer in Chemistry at The University of Sydney
Open Source Competitions and Prizes #1 -
An Example of Open Source Drug Discovery -
Reinventing Discovery on the way to the Sage Congress -
Wikipedia vs. Academic Papers – a Middle Ground -
Goodbye Elsevier, Goodbye Tet Lett etc -
Good luck! (Organic) Chemistry is not particularly know for caring about any of this (nor semantics, nor computing)... but I second Rich' pointer to the Beilstein Journal of Organic Chemistry. And there is Chemistry Central too. What other gold OA options are there for chemists? There is Molecules as ChemComm replacement... others? - Egon Willighagen
I have an idea for a project that might be a good fit with a friendly OA journal near you and could also bring down the costs of peer review in the longer term. It might be a way of shifting at least synthetic org chem into a new space. - Cameron Neylon
Something like Molecules is nice, but the journal has/had no editorial standards, making text mining impossible. Of course, a new journal would not just standardize on format, but also require semantics, which for a ChemComm-like journal is very feasible... - Egon Willighagen
Egon, that's what I'm thinking. A synth org chem process similar to that for Acta Cryst E. basically a defined input format with specified allowed data formats that would then be automatically tested tossed if they're consistent with the supposed structure. - Cameron Neylon
Let me know if you seek someone for an editorial board... (btw, taking about edit boards, I was thinking of a ORC write up of this R package ... would that fit the journal? I would need to write proper testing, which I have not getting around to... eta would probably be summer) - Egon Willighagen
Would like to use a wiki to write papers with students, but papers on the closed projects in my lab (we still have some of these going). i.e. a wiki shared only between me and one or two others, and inaccessible to outside world. For open wiki writing, Openwetware is working very well. Assume closed costs $, so does anyone have any recommendations?
Google Docs works reasonably well for me. Or is there some particular functionality of wikis that you need? - Andrew Su
We use Google docs too. - Andrew Lang
If you're open to hosting it yourself, WorkingWiki ( is an option (also, we could probably just give you one on our server at mcmaster) - Lee Worden
Open Science Funding – Government Grants and Cash Incentives -
Open science, funded. This is beyond awesome. Well done Mat and all involved! - Bill Hooker
What I'd like to see rather than separate groups, is a super group that collaborates openly. In addition to posting things we do openly online, I'd like to see all of us ask more from each other to make stronger links, so we become cells of a larger organism. - Andrew Lang
Sure, yes - whatever works, and gets us to desirable goals within the context of openly sharing what we're doing. We're currently interested in these compounds from the GSK dataset because they are amazing hits, and GSK want to work with people. If anyone wants to come along and be part of that, that would be great. You're right - a proliferation of groups could ultimately be bad. It's... more... - Matthew Todd
One of the points that I fought for in the Submeta ONS Challenge was to base the awards on "good scientific work" as judged by experts instead of deliverables. I have seen human nature at work within a motivational framework made up almost entirely of quantifiable objectives and it does not favor those who share. Under such a system people get good at technically meeting numbers sometimes in ways that don't address the bigger picture intent of the prize. - Jean-Claude Bradley
Our commentary on open science is out in Nature Chem
Thanx for citing the Blue Obelisk paper! - Egon Willighagen
Of course! - Matthew Todd
Our first #openscience paper. Going open made the research faster. And hence more fun.
Like like like like like. :-) - Bill Hooker
Thank you to everyone here for your help, support, encouragement on this project, which has made an enormous difference. The project is still going, but this paper represents a milestone in what we set out to do. We have a commentary coming out on Friday about open science more generally which I hope people will find interesting. - Matthew Todd
Did you ask to post the spectra as .jdx too - only pdf available - are the jdx versions available on your open notebook? - Andrew Lang
Yep, should be, e.g., which is ref 43 in the paper - Matthew Todd
...but I think we're going to start an experiment with posting the raw NMR data rather than .dx and see how that goes. - Matthew Todd
We should look at pulling that raw data down and converting to JCAMP/AniML for you in automated fashion. Having just this discussion around some other data at a meeting with JGF and co at the moment. - Cameron Neylon
Would be v nice. We can post raw data on a sample post as a sandbox if you like - just say the word. - Matthew Todd
I will see whether sufficient of the pieces are in place but does the following appeal in principle? Directory exists on some computer. When new raw NMR file is dropped in that directory a local GUI pops up to ask some q about metadata. When questions answered raw data gets pushed to LabTrove instance. Service monitors a specific feed for new raw data. When it sees some it processes to... more... - Cameron Neylon
Congratulations! And that commentary has one of the coolest titles ever. - Daniel Mietchen
I am in for playing a bit with the MR spectra, though I am more of an imaging guy. - Daniel Mietchen
OK, here's a sample, but maybe we should take this into a new thread/post: - Matthew Todd
OK, NMR thread forked here: - Matthew Todd
The Broader Chemical Community’s View of Uploading Data -
Raw Data in Organic Chemistry Papers/Open Science -
The supplementary information as pdf is always a pain when I want to copy and paste data. My life would be so much easier if these things were posted as .csv. With spectra files, chemdoodle webcomponents is my choice now - not jspecview. Browser based chemistry is the way forward - not Java applets. This way, in online journals, spectra could be interactive. Graphics could be interactive too - using something like Tableau Public, and of course TwirlyMol for 3D images, etc. - Andrew Lang
For instructions on sharing and viewing JCAMP-DX spectra without software see link #4 - Jean-Claude Bradley
‪TEDxBoston - Dr Jay Bradner - Opensource Drug Discovery‬‏ - YouTube -
‪TEDxBoston - Dr Jay Bradner - Opensource Drug Discovery‬‏ - YouTube
Bradner appealing for open source style help with drug optimization. - Matthew Todd from Bookmarklet
Alerted to this by a talk last week from Harry Gray. Crowdsourced project to get kids combining elements in an effort to discover new materials for solar cell applications. Hardware shipped out to participants. Doesn't appear to be open deposition of data. They patent stuff, so I guess not. - Matthew Todd from Bookmarklet
Innovative partnership advances novel drug candidate to combat sleeping sickness -
"SCYX-7158" Cool structures - there's a boron! - Matthew Todd from Bookmarklet
where is the structure given? what's the IUPAC name? - Egon Willighagen
Nice collection of syntheses, arranged in sequence, by step - Matthew Todd from Bookmarklet
Pharmaceutical Sales 2010 - Top U.S. Drugs by Sales | -
Pharmaceutical Sales 2010 - Top U.S. Drugs by Sales |
Nexium-Lipitor-Plavix - Matthew Todd from Bookmarklet
Anyone good at maths want to work out the pressure at the centre of the earth if you dug a super-strong tunnel that kept the rock and heat back? i.e. the pressure from the column of air, 6000 km long, through a rocky sphere? Link:...
Crowdsourcing: The Art and Science of Open Innovation - Description | NIH meeting. via @mikegretes -
Mob rule: Iceland crowdsources its next constitution | World news | The Guardian -
Mob rule: Iceland crowdsources its next constitution | World news | The Guardian
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