The Synaptic Leap

Dear All,
I am a PI at the Stanford University School of Medicine (med.stanford.edu/labs/michael-hsieh) who's seeking a postdoctoral fellow to help develop novel models of urinary schistosomiasis, which, as many of you know, is a "doubly neglected" tropical disease, in part because of difficulties with existing models. Interested candidates may contact me at: mhhsieh@stanford.edu. Please feel free to share this announcement with others who may be potentially interested. Looking forward to working with everyone on collaborative projects in the near future.
Sincerely,
Mike Hsieh

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.

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.

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The policies of many journals are out of date on these issues, owing to the enormous advances in web technologies over the last few years.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.

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.

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.

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.

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.