MatTodd's blog

25 May

New ELN for Pictet-Spengler Approach

Published by MatTodd

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.
 

06 May

Help from the Process Sector

Published by MatTodd

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.

02 Sep

Resistance to Praziquantel

Published by MatTodd

Subject 

External News

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.

08 Apr

Nature Biotech paper out today

Published by MatTodd

Community 

general open research

Subject 

Miscellaneous

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.

08 Apr

Open Assembly of Paper on the Impact of Friendfeed on Collaborations

Published by MatTodd

Community 

general open research

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.

23 Mar

Journal Policies on the Publication of Previously-Released Data

Published by MatTodd

Community 

general open research

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.

28 Feb

Open data from Merck?

Published by MatTodd

Community 

general open research

Subject 

Miscellaneous

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.

14 Feb

GSK moves to help generate cheaper drugs for NTDs

Published by MatTodd

Community 

general open research

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.

31 Jan

Distributed Drug Discovery Papers

Published by MatTodd

Community 

general open research

Subject 

Miscellaneous

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.

31 Jan

Quick status update

Published by MatTodd

Subject 

Miscellaneous

A quick status update. While we were successful in getting our grant with the Australian Research Council and the World Health Organisation, we have so far been unable to formulate a contract that is mutually acceptable to all parties. Negotiations are continuing, but this explains the lack of recent activity coming from our lab on the schisto projects - we don't have the money yet! Fingers crossed this situation will resolve itself positively in the near future.

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