The Synaptic Leap

I recently gave a talk on open science at Ignite Sydney. These talks are a real challenge in that you have 5 minutes to get across an idea, with the slides rotating every 15 seconds behind you. The event was in a cool club/gallery in the middle of Sydney, and is the first talk I've ever given where I was preceded by a beatbox act. Apparently I was the first scientist to go to Ignite Sydney.
 

To host the raw data from the Pictet-Spengler approach to the enantioselective synthesis of PZQ Michael has started an Electronic Lab Notebook. We're using the open source Southampton Lab Blog interface for this, since we're collaborating with them on a couple of things related to this site.
 
Given that it's open source, the lab blog system can be changed and enhanced by anyone. This is a great chance to make the lab blog perfect for experimental organic chemistry, e.g:
 
1. How do we best report TLC data - at the moment we're taking photos, but this is cumbersome.

It's been a great week for the PZQ project, since we've had an injection of real help from the people we most need - process chemists. Much of this has arisen from a discussion I started on LinkedIn, which then became emails, but all participants have either actively participated on this site, or granted permission for the posting of information here. Nick Tyrell from Almac Sciences has already provided a huge amount of great advice for several aspects of the synthesis, mostly for the resolution of PZQamine.

There is often talk of whether (or when) resistance to praziquantel will develop, and how catastrophic this would be for the treatment of schisto. There have been some important studies on this over the years, but a recent paper in PLoS NTD provides some new evidence for the development of resistance in Kenya. Thanks to Marc for the heads up.

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.

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.