general open research

general content regarding open source biomedical research

24 Nov

Give Your Gift

Published by gtaylor

Community 

general open research

Subject 

Rants

In the U.S. we just celebrated Thanksgiving. It's a day we spend with family, eat too much (what's new?), and reflect on all the things we're thankful for. I have a lot to be thankful for. I have a wonderful family, we're generally healthy, and I've been relatively successful in my career in software.

A little more than a year ago, while feeling fortunate and thankful, I was reflecting on what I could do to give back to the world. I thought about it for quite a while, asking myself, with my experience with corporate portals (I was the R&D leader at PeopleSoft for their portal application), how could I best leverage my skills to give something back to the world. Founding The Synaptic Leap was and still is my answer.

It has become a calling for me. I believe passionately that this should be done; I know emphatically that it is technically possible. The question is simply a cultural one. Are biomedical scientists willing to do it? I think so. I believe in the human race. I believe that most of us will give a bit if we think it will make a difference. I hope, that providing The Synaptic Leap, we're giving you a place to connect with other scientists, a place to check your egos at the door and give your ideas freely, and a place to encourage and nurture the ideas of others. I hope we're giving you the perfect place to leverage your talents to give back to the world.

Sample ideas: 

  • Volunteer. Help with an existing project.
  • Take a project you're writing a grant for and make some of it open source. Granting agencies are increasingly favoring this.

Gene Wiki Overview

Published by gtaylor on 12 September 2006 - 11:44am

Community 

general open research

See the attached document for an overall concept of our Gene Wiki idea.

Please login and add comments on your thoughts on this project. Type of feedback we're looking for:

  1. Would this feature be useful to you for in-silico drug design? E.g. If you're a malaria scientist, is this useful for malaria drug target identification or should we focus our efforts on another genome?
  2. Are you interested in reaching out to world-wide resources such as India to help with this work?
  3. Would you use this feature openly if it were deployed on The Synaptic Leap? Please explain if you think it should be deployed somewhere else.
  4. What is your specialty and how would you use this feature? E.g. what contributions would you make to a community driven drug development?
  5. Which feature do you think is most useful?
  6. Are there important other features that you want added in the first or second version of the tool?

The more comments the better - even if they're negative. I want some online brainstorming.

Cheers!

Will you collaborate with somebody you've never met?

Published by gtaylor on 10 September 2006 - 2:26pm

Community 

general open research
09 Sep

Can open-source R&D reinvigorate drug research - Nature

Published by gtaylor

Community 

general open research

Subject 

External News

Bernard Munos, from Eli Lilly, wrote a very thorough article on open and collaborative research for neglected diseases and it was just published at Nature: Can open-source R&D reinvigorate drug research. What I particularly like about the article are the details he provides in describing how he thinks pharmaceutical companies can and should participate in the process.

Let's face it; we're in uncharted territory. We don't really KNOW how it's going to work. We're in the midst of a big evolving experimental process.

My vision for how it will work tends to be a bit more grass roots, less centralized group driving the process. Collaborative process tools like a Gene Wiki will enable dedicated experts to suggest work for less involved volunteers to contribute. People will collaborate with the people they trust and trust must be earned.Â

20 Aug

The Synaptic Leap at Science Foo Camp 2006

Published by gtaylor

Community 

general open research

Subject 

Miscellaneous

I had the honor and privilige of attending Science Foo Camp at Google last weekend. O'Reilly and Associates, Nature and Google sponsored the event and brought together roughly 200 cross-discipline scientists and open source software geeks from around the world. There was definitely a theme of those invited - open, collaboration, biomedical science, global warming, semantic web...

It was fantastic. I met a lot of interesting people and learned a lot. I of course was there talking about The Synaptic Leap. The attached presenentation was my super deck I created before the conference. I didn't present it in whole. I did however talk to people on every topic - on the bus, at the cafe, by the tents... The presentation has comments I made before the conference as well as notes on feedback I gathered - both positive and negative.

tslfoo.pdf 

I encourage you to post additional feedback below.

Cheers! 

 

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.

Storing structures and views for search later

Published by alex_a on 3 August 2006 - 2:04am

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

Community 

general open research

Subject 

Miscellaneous

Forums 

Q&A and Feedback

Vitiligo

Published by Anatoly Chernyshev on 31 July 2006 - 8:09am

Community 

general open research

The project is temporarily suspended.

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.

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