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Nature Biotech paper out today

MatTodd — Wed, 08 Apr 2009 08:28:14 -0500

TDI/TSL's paper entitled "A kernel for the Tropical Disease Initiative" is published today in Nature Biotech. We're very pleased an open source project has been published in such a high-ranking journal, and we hope this stimulates the interest of the scientific community in what's possible. Naturally, we want people to contribute to the science!
This paper will shortly be followed by a full article in PLoS Neglected Tropical Diseases.
The kernel may be explored at TDI, with discussion/project planning happening here at TSL.

Open Assembly of Paper on the Impact of Friendfeed on Collaborations

MatTodd — Wed, 08 Apr 2009 08:22:41 -0500

Cameron Neylon has initiated an experiment in the open assembly of a paper on how the aggregator site FriendFeed is impacting the way we collaborate/do science. The background to the call can be found here, and the abstract is being assembled here. This is an open paper-writing project, so please feel free to chime in.

Journal Policies on the Publication of Previously-Released Data

MatTodd — Mon, 23 Mar 2009 08:04:01 -0500

Can we publish papers based on data that have previously been made public? Is a conference presentation prior disclosure? If we worked together to write a review article on a wiki, can we submit it for publication? If we conduct an open source research project with a number of collaborators on a website, where can we send the resulting articles for peer-review?

These issues are important. It is difficult to recommend conducting open research to students if they cannot be sure to get peer-reviewed papers out of their research.

The policies of many journals are out of date on these issues, owing to the enormous advances in web technologies over the last few years. To clarify such policies, a few of us have assembled a draft letter we intend to send to publishers.

2-Boc-1,2,3,4-tetrahydroisoquinoline

MatTodd — Thu, 12 Feb 2009 04:19:36 -0600

2-Boc-1,2,3,4-tetrahydroisoquinoline

Submitted by Althea Tsang and Matthew H. Todd, School of Chemistry, University of Sydney, NSW 2006, Australia. Checked by Victor Sun, Lakshmi Raj Baratha, Soo-Jean Park, same address.

Open data from Merck?

MatTodd — Sat, 28 Feb 2009 17:39:22 -0600

Following on from last week's news from GSK comes a potentially very important announcement from Merck about Sage, a large deposition of biological data and software to the commons. Links and discussion here.

Distributed Drug Discovery Papers

MatTodd — Sat, 31 Jan 2009 17:16:28 -0600

The Scott and O'Donnell labs at IUPUI have published an interesting set of articles in the latest issue (vol 11, issue 1) of the Journal of Combinatorial Chemistry on Distributed Drug Discovery. They're open access articles. The idea is to show that chemical synthesis can be done by multiple labs for the creation of drug-like compounds, and that there is reproducibility between the different sites (from the US to Poland). This is obviously an important requirement for any distributed research effort. Jean-Claude's Open Notebook concept is of course aiming at exactly that.

GSK moves to help generate cheaper drugs for NTDs

MatTodd — Sat, 14 Feb 2009 17:05:20 -0600

Potentially very interesting news that GSK are looking to provide/find cheaper drugs for underdeveloped countries. From the article:

"[Witty] said that GSK will:
• Cut its prices for all drugs in the 50 least developed countries to no more than 25% of the levels in the UK and US – and less if possible – and make drugs more affordable in middle- income countries such as Brazil and India.

• Put any chemicals or processes over which it has intellectual property rights that are relevant to finding drugs for neglected diseases into a "patent pool", so they can be explored by other researchers.

Trial Synthetic Procedure for Chemspider to Find...

MatTodd — Thu, 12 Feb 2009 03:56:30 -0600

There has been an interesting conversation over at Friendfeed about the value of centralised vs. decentralised synthetic procedures for chemistry. i.e. should we try to create a store of chemical reactions, or ought we to be expecting decent search tools to be able to find these for us, wherever they are. From my perspective, both have value. Naturally what we need are tools that understand descriptions of reactions that are semantic (plain English), and which can understand various forms of data that go along with compounds.