The Synaptic Leap

Dear all,

As of today, a place has been created over at FriendFeed (FF). dedicated to Open Notebook Science.

LINK

Since this of relevance to TSL, I thought folks here might be interested to know this.

As such, this is the first link between TSL and FF that I am aware of.

Kind regards,

Graham 

The National Institute for Allergy and Infectious Diseases (NIAID) has funded two centers for conducting structural gemomics studies on Infectious disease organisms.

There are two centers, one called SSGCID (Seattle Structurals Genomics Center for Infectious Diseases) run by Seattle Biomedical Research Institue (SBRI). Another is CSGID (Center for Structural Genomics of Infectious Diseases).

Both centers are seeking target suggestions from the worldwide community. Make target requests at:

http://www.ssgcid.org/home/Community.asp

-Bartrum

Deepak Singh has very recently started:-

Hello,

I'm quite new to the Synaptic Leap so apologies if this is already covered somewhere that I have missed.

I'm curious if any molecular entities, vaccines or biologics have already been licensed as open source through the FDA or alternative organization?

Kind regards,

Christine

I am a statistician interested in analyzing gene expression data from neglected diseases, especially periodic data (several genes measured at different time points), or a similar data format. If anyone has processed data they are willing to share, please let me know.
Thanks

Hello,

 I'm going to attend XXVI Midwest Enzyme Chemistry Conference
(September 30, 2006, Northwestern U., Chicago; http://www.midwestenzyme.org). If somebody will be there and feels like talking, please drop me a line.

Cheers,

Anatoly

Not sure where this should go - I have v. limited experience here and it is not in my profile, so I say this and nip off. Anyway - hats off for a fine concept and the best of luck

The idea I want to pass on here is one I try on commercial research but they are cautious due to deniability and litigation.

I propose that you set up mechanisms to recieve actual structural files when you discuss  chemical or biological structure related questions. The point being that you can forever associate the comments or threads or blog entries (whatever) with that structure file. In this way you can later perform all manner of searches and comparisons with the stored structural data and also serve up human comments related to those structure entry appearances. Actually what you are doing is storing human information which is difficult to search massively (so far) with a well constrained concept which can very easily be power searched (structure graphs). Structural files in information speak are very highly specific and even with very large collections of files the power of the query launguage (structure query) can allow you to produce query results with very little junk - at least on the structural side (human related comments can of course be junk). Downstream - with more data there are manifold possibilities to mine the structure files to generate knowledge and if all goes well the power of the text handling side shows much promise to multiply the value of the human comments

On the discussion enhancing side I am sure having, at least, images of structures and possibly 3D binding pocket views would be cool - especially if you can save the view and publish it (say as a gif) and attach it to your posts/blog to support your comments, of course as a structure file opponents are at liberty to open it, re-evaluate and suggest alternatives - especially if they can open the file from your wewbsite and be looking exactly at the view and trimmings. If we factor virtual discovery surfaces in here then we could multiply the power of the forum massively

The article on open source written by members of TSL is now online, and may be accessed here. The article is published in the Australian Journal of Chemistry, and the publishers (CSIRO, Australia) have agreed to provide the article as open access, so no subscription is required to download it.

We'd all be very interested in feedback and ideas on the very general points mentioned.

Cheers,

Mat

The WHO world congress has wound up, and of the resolutions an important one with regards access to essential medicines is:

"In order to address the need for people in developing countries to access necessary medicines, vaccines and diagnostics, the Assembly also agreed to an intergovernmental working group open to all interested Member States to draw up a global strategy and plan of action in order to provide a medium-term framework based on the recommendations of the Commission on Intellectual Property Rights, Innovation and Public Health. The working group shall report to the Sixtieth World Health Assembly on the progress made, giving particular attention to needs-driven research and other potential areas for early implementation action. The working group shall submit the final global strategy and plan of action to the Sixty-first World Health Assembly."

This follows a major report on the issue of access to medicines (such as praziquantel, featured in a TSL project) from the Commission on Intellectual Property Rights, Innovation and Public Health. I'm not clear on the legal recommendations (anyone like to distil the report?) but it is good to see movement at the highest levels.

The XML feed from the left-hand block was just providing a feed for the front-page story.  This was confusing to me and at least one other person who emailed me. 

XML feeds for the more dynamic pages e.g. malaria posts, schisto posts is still available at the bottom of those pages.  As well as at the bottom of the discussion forum topics page.