gtaylor's blog

08 Aug

TSL Status August 8, 2006

Published by gtaylor

Community 

general open research

Its been a long, hot, fun summer for me. Due to budgetary constraints, I chose not to send my kids to weekly day camps. This was the first summer I didnt officially work since I was 15 and its been great to spend it with my kids. I still managed to work mornings, a few evenings and Mondays when my mom took the kids. Did I say I wasnt working?? See below for our accomplishments this summer.

06 Aug

Chagas Community Leader Needed

Published by gtaylor

Community 

general open research

Subject 

Request for Help

We'd like to open a research community for Chagas. We have at least one scientist looking to start an open project for Chagas and we're looking for somebody to be the online champion and leader. General responsibilities include:

  • Writing a research cummunity introduction page, something that will inspire others to pitch in.
  • Identify online news sources for Chagas
  • Identify online tools and resource links for Chagas
  • Evangilize open, collaborative research for Chagas spreading the word helping to get more people participating
  • Monitor the site content people and aiding the community by connecting resources to needs
  • Be generally proactive and vocal, giving The Synaptic Leap constructive criticism helping us to evolve The Synaptic Leap processes and tools

Other volunteers at The Synaptic Leap will set up the menu links and other core research community pages.

Email Ginger if you're interested.

21 Jul

On Gates' New Funding Approach for Aids

Published by gtaylor

Community 

general open research

Subject 

External News

The Wall Street Journal recently ran an interesting article, Gates Won't Fund Aids Research Unless They Pool Data. My summary and commentary on that aricle:

The Gates Foundation is awarding $287M over 5 years to 165 researchers from 19 countries and they are requiring the recipients to share their data. A few very important quotes from the article:

  • "Through such data sharing, Dr. Hellmann says, rival teams can build on successes, avoid pitfalls and eliminate redundancy." Dr. Hellmann is the interim HIV projects director at the Gates Foundation.
  • "Enforced data sharing, Dr. Self predicted, "increases the pace of discovery enormously rather than waiting for the process of writing formal journal articles, waiting for them to be published, and [confirmed] by other labs." Steve Self is a a biostatistician at the Fred Hutchinson Cancer Research Center in Seattle.

What is particiularly significant about this is that the Gates Foundation is doing this with Aids, a disease that is not exclusive to tropical regions. There is a profit to be made here. Regardless, this aliance demonstrates that ...' the large enterprise is more important than the position I keep by holding my data close,' (another quote from Steve Self). It appears that the data will be shared across grant recipients and not necessarily wide open on the web. Regardless it's a big step.

They weren't very clear on how they will allow these organizations to profit from their discoveries. However Gates is clearly on the record of respecting intellectual property and the rights to profits.

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.

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 

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.

17 Mar

TDI & TSL mentioned in The Economist article on Open Source

Published by gtaylor

Community 

general open research

Subject 

External News

Open, but not as usual mentions both Tropical Disease Initiative and The Synaptic Leap.

...Other projects, such as the Tropical Disease Initiative and the Synaptic Leap, are forming along similar lines. Synaptic Leap points out that because it is not motivated by profit, it has no motive to keep secret any fruits derived from collaboration in research on, for example, malaria....

It's nice to see us in the news of such a credible magazine. I've long been a fan of The Economist as the best way to get news with a minimum US bias. Both Stephen Maurer and Arti Rai, our advisors and founding members of Tropical Disease Initiatve, have contacts at The Economist. I assume that is how they have heard of us. 

Anyway, nice to see our name in print. I must admit I did a little dance. 

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