general open research

general content regarding open source biomedical research

21 Jul

Chikungunya in Mauritius

Published by vishwadev

Community 

general open research

Subject 

Request for Help
Sir/Madam,
 
i recently came across this wonderful site and i am pleased that it is doing a very noble work of doing open source research for non-profit motives.
 
I have a request if you don't mind. I am from a tropical island called Mauritius found in the indian ocean. A few months back our island and our neighbour island reunion got badly struck with the chikungunya disease and it has affected our economy and people very much.
 
No drugs are available apart from pain killers and some of the patients (including my mother) are having ever lasting pain. maybe you could please place chikungunya in your research calendar as no labs are coming with drugs or enough research on this project. Maybe because it is a problem not affecting big european countries...
 
here in Mauritius, for the time being it is under control because it is winter and the insects/vectors are having difficulty to reproduce. But we are dreading the return of summer in November. I wish there were enough reseach in this field but there are not many promising ones at present. Therefore i am very humbly requesting you to put your expertise together and come forward with a research programme on this disease so that it can be controlled or cured.
 
Thank you.
Regards
 
 -prakash
Mauritius 
 

Intellectual Property Guidelines

Published by Arti Rai on 13 July 2006 - 7:29pm

DRAFT READY FOR COMMENT

The Synaptic Leap is not responsible for, nor do we lay claim to, any scientific discoveries made or discussed on our site.

In general scientific discoveries placed in the public domain, i.e. this web site, can not subsequently be the subject of a patent.  You can of course work around this by posting only pieces of the science here and holding back sufficient information for a patent. However, the aim of The Synaptic Leap is to encourage open and collaborative science. The more open the better. We hope that you will openly discuss and pursue collaborative scientific discoveries using our site.  
 
Any discussions, blogs or other content authored by you is presumed to be copyright protected according to the Creative Commons Attribution 2.5 License. If you wish to have a different copyright policy for something you post, we recommend that you describe your specific copyright limitations e.g. "All rights reserved."


Creative Commons

Community 

general open research
14 Jun

Site Level Email Subscriptions

Published by gtaylor

Configuring Your Subscription

You may choose to have daily email notifications sent to you from The Synaptic Leap. You must have a registered account first. Once you have have registered and are logged in, you can go to your personal user profile and hit the "my notify settings" tab. From there, you just enable the various buttons.

I configured my settings so that I get a headline, teaser and link for all new comments and articles posted on the site.

click the image to see a full size screen shot of

If no new posts are made, no email is sent. If multiple posts are made, you only receive one email summarizing the posts with links to each post. The email that is generated also includes a link back to your personal notification settings so that you can easily disable it anytime should you ever wish to.

14 Jun

Recommended Browsers for The Synaptic Leap

Published by gtaylor

Community 

general open research

Recommendation

If you're using a mac, we recommend using Firefox (1.5.0.1+).

If you're using a PC, we recommend either Internet Explorer 6.0+ or Firefox (1.5.0.1+).

Using one of these browsers will allow you to easily create compelling posts on The Synaptic Leap using an editor that is quite similar to a word processor.

screen shot of TinyMCE editor

More Background and a Little Off Subject Rant

Neither Apple's Safari nor older versions of Microsoft's Internet Explorer (IE) can support our editor, TinyMCE. And unfortunately Microsoft doesn't provide IE 6 for macs. Therefore if you're a mac user, Firefox is your best bet.

Open Source Article Now Online

Published by MatTodd on 13 June 2006 - 1:20pm

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

 

Subject 

Miscellaneous

Forums 

Q&A and Feedback
09 Jun

Flyer for The Synaptic Leap

Published by gtaylor

Community 

general open research

Subject 

Miscellaneous

The attached document is a 2 page flyer for The Synaptic Leap. It looks best when printed double-sided and in color. I encourage you all to print and distribute it at your research facility. Of course you can always email it too.

And by all means if you have suggestions/edits, post comments below. 

Cheers!

Ginger 

WHO Congress and Access to Drugs for Neglected Diseases

Published by MatTodd on 29 May 2006 - 12:39pm

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.

Community 

general open research

Forums 

Q&A and Feedback
09 May

TSL Status May 12, 2006

Published by gtaylor

Community 

general open research

I hesitated to write this status note. Although we have done a lot, it's mostly behind the scenes work and you aren't likely to feel the love if you know what I mean. However, I want to continue my open communications with you and I don't want you to think nothing is happening. I'll try to acknowledge all contributions and keep the admin information brief.

Accomplishments

Switched Hosting Sites

Doug Chasman, our latest volunteer for The Synaptic Leap, has worked hard to move our site to a different hosting provider.  We wanted to switch hosting providers so that we could consolidate our full set of development tools along with our production environment. This will make it easier for us to build an extensible development environment whereby scientific tools can be added to our site. The great news is that Doug was able to move us without shutting down the site. There is more still to do to build our development site.

Conflicts of Interest Policy

The board and I decided that we needed an official Conflicts of Interest policy to ensure that we make decisions that are truly in the best interest of The Synaptic Leap. With the help of our attorney, we have agreed to a solid policy that will guide us to behave responsibly. 

Operational Review With Our Board of Directors

It's no longer me calling all the shots. With a fully functioning board who will be making decisions, I felt it important to catch them up on the operational details. We met on April 11 for more than three hours covering projected budgets, actual expenses, software and hardware  environments and site adoption and usage trends.  It took me quite a bit of time to pull the information together. The great news is that with more eyeballs on the subject, fresh points were brought up and we are evolving our plan of action together.

27 Apr

Marc's presentation now on Google Tech Talks

Published by gtaylor

Community 

general open research

Marc A. Marti Renom gave a talk at Google on April 7 regarding his open source research within Tropical Disease Initiative and The Synaptic Leap. It's a great introduction describing TDI's goals to provide open source bioinformatic tools to assist with the drug discovery process for tropical diseases. He gives an overview of projects past and future including the Gene Cards and Gene Basket projects that we plan to collaborate together on to deploy on The Synaptic Leap.

Open Source Drug Discovery for Neglected Diseases.  

29 Mar

Advance Purchase Commitment

Published by gtaylor

Community 

general open research

According to The Economist Push and Pull article published this week, the finance ministries of the G8 next month are to decide on proposals for "Advance Purchase Commitment" for developing world countries for diseases such as AIDS, malaria and TB.

Michael Kremer, an economist at Harvard, is for the proposal and believes that by guaranteeing a market it will provide incentive for the big pharmaceutical companies to invest.

Andrew Farlow, an economist at Oxford University, is a huge critic of the idea. He points out that the G8 would have to specify how good is good enough for a guarantee purchase. What happens when the first drug is only slightly effective and the next drug is much better. Lots to consider here and Andrew doesn't think they will get it all right.

At one point in the article, the question is asked - what happens if this promise still isn't enough to inspire sufficient research to discover a cure. Kremer effectively responds we're no worse off than we are today and the G8 will have spent nothing.

Working within TSL, this is where I disagree.  This could be just the kind of policy to keep people from openly collaborating and sharing. Don't get me wrong, if this is the panacea that will inspire significant research in tropical diseases, then I'm all for it. But I'm frankly quite suspicious that it's possible to write a global policy with enough foresight to actually be effective. I have more faith in the powers of collective science.

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