The Synaptic Leap

 
I've now reached the end of my second week in the lab working on the Pictet-Spengler route to praziquantel.
 
It's been quite a steep learning curve so far, particularly in terms of analysis and familiarizing myself with the lab.  I've had experience (if you can call it that) with NMR and MS before, but that was only in the sense that I prepared my sample in the tube/bottle and a week later, I got a spectrum on my bench.  Now I'm preparing NMR and LCMS samples on a daily basis.  I'm finding it much easier to use the LCMS (however, interpreting data is another matter), and I've been introduced to the procedure for recording NMR spectra.
 

 I have just packaged up TCMDC-123794 (PMY 11-2) and -123812 (PMY 10-2) along with the parent acid (PMY 8-2), ester (PMY 6-1), aldehyde (PMY 2-4), near neighbour analogue (PMY 14-1) and also the acylurea by-product (PMY 12-1-A). These have been sent to GSK Tres Cantos where the original study was carried out for further testing.

Saw this very interesting article/development. Intel sponsoring research at top universities, but heavily encouraging the projects to be open source and the universities not to take out patents. A bold step, very counter to the philosophy that is so familiar to any current academic. From the website:
 

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.
 

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.