Ginger Taylor - The Synaptic Leap


Notes from PPT Presentation

Viewed September 1, 2006

Ginger Taylor is the founder of the Synaptic Leap - a non profit seeking to open source scientific information:

Slide 4: She distinguishes this project as focusing on the "collaboration AS the science is happening." This means that she supports the idea that scientists shouldn't wait until the end of the experiment/s' they should publish data as they go. This allows for "getting input and advice on the experiments and theories one is working on." She says that some scientists think the process is too slow to allow for joint collaboration, while another advocate says that the problem of OSS is one of patenting. I have come by this argument in both OSS and OA....the idea of ownership. She recommends these links:have read include: Leaf, Clifton. “The Law of Unintended Consequences.” Fortune September 2005. http://money.cnn.com/magazines/fortune/fortune_archive/
2005/09/19/8272884/index.htm
Rai, Arti K. (2005) Proprietary Rights and Collective Action: The Case of Biotechnology Research With Low Commercial Value, in Maskus, Keith E. and Reichman, Jerome H., Eds. International Public Goods and Technology Transfer in a Globalized Intellectual Property Regime, pages 288-306.
http://eprints.law.duke.edu/archive/00001201/

Slide 5: She shows examples of open source projects and writes that it is interesting that some places are requiring collaboration. While not on this slide or in the presentation, the NIH is STRONGLY requesting OA publication of journal articles, and there is a sense by Peter Suber's materials that this will be the NIH standard because legislation will require access to tax payer funded research. Ginger isn't mentioning the final products, here, because this presentation is about the science as it happens.

Slide 6: Discusses the Gates Foundation commitment to collaborative projects. As she states Gates is interested in speeding up the process of scientific discovery that is, at present, upheld by closed labs. He is putting his money behind the ideology. Some good sources mentioned: Chase, Marilyn. “Gates Won’t Fund AIDS Researchers Unless They Pool Data.” The Wall Street Journal, 20
July 2006, B1 http://online.wsj.com/article/SB115335816005811923.html

Slide 8: This slide details the mission and scope of SL. It is meant to "connect the dots" by "provid[ing] a network of online research communities that connect and enable open source biomedical research." This will help produce new ideas, reduce duplication, and, as a result, will speed up the research process.

Slide 9: This slide discusses the necessity of OSS. People suffer daily because of diesease that could be addressed if research was more efficient. In this case, she is talking about "biomedical
diseases that aren’t served well by a naturally profit-driven pharmaceutical industry. A lot of
suffering takes place here. However, open source tends to succeed where profit-driven solutions
fall short. This is the sweet spot for open source biomedical research."

Slide 11: Ginger does not oppose for-profit pharma; however, as she notes in the presentation, " there is a severely under-researched set of diseases where the for-profit incentives are falling short. For these, in the tail of the profit curve, I believe we need to develop new collaborative processes to connect and empower the distributed few who are working on them. We are fortunate, that scientists are already working on many of these diseases even without a profit incentive. We are fortunate that the Web 2.0 is here and in the rapid innovation cycle."

Slide 12: This is an excellent graph that demonstrates the need for research on tropical dieases; malaria, the target of Drexel's lab, is the one of the top diseases; "Tropical diseases represent both the greatest need and opportunity for open collaborative research."

Slide 14: Ginger discusses some of her partners. The Tropical Disease Initiative, Stephen Maurer and Andrej Sali are the groundbreakers in OSS biomedical research and are listed as 2 of the top 50 people to make a difference in this world. Resources: S. M. Maurer, A. Rai and A. Sali. “Finding Cures for Tropical Diseases: Is Open Source the Answer?” PLoS Med December 2004.
http://medicine.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pmed.0010056 and
pioneers. “The 50 People Who Matter”: http://money.cnn.com/popups/2006/biz2/peoplewhomatter/frameset.41.exclude.html

Slide 15 is very useful; it shows how OSS works and targets malaria: This is an intersting slide because it talks about how OSS works on SL. She talks about RSS, and the part that has the most impact is that she hopes attitudes change as a result of this work. I have pasted the text below:

"Each research community is organized by disease. Our goal is to foster cross-discipline scientific collaboration connecting the dots to develop new therapies.
Dr. Marc A. Marti-Renom, then part of the Andrej Sali lab, worked with me to deploy our pilot research community for malaria. We chose malaria as the first tropical disease for our pilot because Marc felt that plasmodium falciparum would be an ideal pilot for his gene wiki idea, his open projects. More on the gene wiki later. Within a research community, we provide several tools to assist scientists working on open collaborative research for malaria. Menu Items for the Malaria Research Community:
•current projects: provides a hierarchy of project books and pages that allow people to organize, attach files and discuss a given open project. The projects shown in this illustration are the various features and functions of a “Gene Wiki” a concept originated by Marc and to be discussed later in this presentation. The Gene Wiki is aid in drug target identification for in-silico (computer-based) drug design.
•research tools: is a simple page of malaria resource links. Our current implementation doesn’t make it easy for anybody to edit the page (e.g. a Wiki). Therefore, other malaria community members are encouraged to add “comment” for other tools they want to see added to the page. Thus far nobody has done so. We’re still in the early adopter stages and I’m sensing more “looky-loo” activity
then a sense of “this is my community and I’m responsible for making it better.” Over time, I hope the attitude changes.
•RSS news feeds: one of the services we provide for our researchers is an aggregation of RSS feeds on Malaria. Many scientists don’t bother with RSS and we’ve gotten good feedback that this is valuable to our users. Two of our best feeds are from Connotea and CiteULike which offer tag specific RSS feeds. This allows the broader scientific community to surface important malaria articles for our users. A side benefit I wasn’t expecting is that the search engines that crawl our site also crawl the headlines of the feeds. Many users researching malaria often find us looking for a specific article on malaria research. They are probably surprised to be taken to our intermediate site first. But, I hope it’s a pleasant surprise.
•community posts: this is a chronological listing of trimmed posts by community users that have been tagged as being appropriate for the malaria community. We offer RSS subscriptions for this view for those scientists who want it.
•image gallery: Many posts published on The Synaptic Leap need an image to effectively illustrate the point. Users can go to the image gallery to upload their images they want to use in a post. Our editor also offers on-the-fly uploading of images, but it’s clunky at best. But, really so is this approach. Over time, I hope we can improve the process of adding images. Drupal The collaborative software we use for our site is Drupal http://www.drupal.org. It’s an open source high-end content management, blogging and collaboration tool. We’ve been very pleased with the usability, the feature depth, reliability and extensibility of the product. Big thanks goes to the open source developers at Drupal.

Why Not a Wiki?
Wikis have gotten very popular. They are terrific at allowing a community to evolve a body of work. Wikipedia and Open WetWare are perfect deployment examples of a wiki. However, in my opinion, they are not the best tool for collaborative debate where one idea is owned and posted by one user and other thoughts are owned and posted by other users. For this, blogs are great. Therefore we chose to go with a high-end blog and publishing application, Drupal."

Slide 18: This slide mentions Jean-Claude Bradley's work at Drexel and shows the spirit of collaboration as it has been delivered through SL.

Slide 19: This discusses the work Jean-Claude is doing in his lab and compares it to their work; "They are taking a research field focus for open collaboration. The Synaptic Leap is taking a disease focus." Essentiall, the difference is that "Presumably Useful Chemistry offers deeper chemistry
collaboration. The Synaptic Leap offers more potential for translational science." I like this idea of translational science because this is where rhetoricians play a role...helping to translate. These are both OSS projects as defined by the fact that they are free and open, but the question becomes how open is open?

Slide 21: I was a little surprised to see my email address on this slide, but I work with Jean-Claude. Basically, this student asked for collaboration, and, because of the ability to collaborate through SL, "Leveraging The Synaptic Leap and Useful Chemistry, Guido (Venezuela) now has resources helping
from Drexel University (Philadelphia US) and University of Sydney"

Slide 22: This is a call for volunteers.

Slide 31: This slide proves that OS scientists don't work for free. OS computer people don't work for free. She says that funders should support OSS because it is a "better investment." I agree.

Slide 32: This talks a bit about ownsership of cietific discovery. Basically, she points out that most scholars care about publishing more than profits. I have no idea if that is true. She uses Mat Todd as an example of publish over profit; "Mat Todd is a great example of how an open project was able to publish because of the openness. It was the special sauce that made the article interesting. And in publishing Mat has now brought more eyes to bear on his project. It’s a win-win scenario." She also mentioned a caution; "The editor of a significant science magazine (there were more than one at the event, so don’t make
assumptions), said that this recommended approach for collaborating and publishing should work.
He cautioned though that the scientist shouldn’t “announce” a discovery on the web site though. I
have his card and plan to follow up with him more on this. If given permission, I will write a blog on
our site to address this issue more deeply."

Slide 37: This is a last slide in a series that discusses how funders will view the process of OSS. The final product is an article in a Peer Reviewed journal. I was surprised that she didn't mention OA journals and repositories for pre and post prints.

Slides 41 and 43 offer further reading; I am including her references here so that i can explore them, as well:

Open Source Research
Sarah Everts. “Open Source Science” Chemical & Engineering News July
24, 2006. http://pubs.acs.org/cen/science/84/8430sci1.html
Thomas B. Kepler, Marc A. Marti-Renom, Stephen M. Maurer, Arti Rai,
Ginger Taylor, and Matthew H. Todd. “Open Source Research - the Power
of Us” Australian Journal of Chemistry June 13, 2006. http://www.publish.csiro.au/
nid/51/paper/CH06095.htm
Arti K. Rai. “Open and Collaborative Research: A New Model for
Biomedics” http://eprints.law.duke.edu/archive/00000882/
“An open source shot in the arm?” The Economist June 10, 2004. http:
www.economist.com/displaystory.cfm?story_id=S%27%2980%2EQQ%2B%21%21%40%20T%
0A&CFID=65254372&CFTOKEN=1976873-7ceee081-6d6a-4df2-9a80-52b144055e75
S. M. Maurer, A. Rai and A. Sali. “Finding Cures for Tropical Diseases: Is
Open Source the Answer?” PLoS Med December 2004.
http://medicine.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pmed.0010056
Marilyn Chase. “Gates Won’t Fund AIDS Researchers Unless They Pool
Data”. Wall Street Journal July 20, 2006 B1
http://online.wsj.com/article/SB115335816005811923.html
Scott Johnson. “Researchers striving for good of humanity, not just own
gain”. San Jose Mercury News July 17, 2006.
Scott is head of Myelin Repair Foundation:
http://www.mercurynews.com/mld/mercurynews/news/opinion/15055872.htm
Cora Daniels. “The Man Who Changed Medicine.” Fortune November 29,
2004.
The Mike Milken story about collaborative research for prostate cancer:
http://money.cnn.com/magazines/fortune/fortune_archive/2004/11/29/8192713/index.htm
Clifton Leaf. “The Law of Unintended Consequences”. Fortune 19
September 2005.
Discussion on how Bayh-Dole Act is hurting our collaborative discovery
process in biomedical research:
http://money.cnn.com/magazines/fortune/fortune_archive/2005/09/19/8272884/index.htm
Important Web 2.0 Concepts
Metcalf’s Law: http://en.wikipedia.org/wiki/Metcalf%27s_law
Social Networks: http://en.wikipedia.org/wiki/Social_networks
Collective Intelligence: http://en.wikipedia.org/wiki/Collective_intelligence
Long Tail: http://www.wired.com/wired/archive/12.10/tail.html
http://en.wikipedia.org/wiki/Long_tail
http://bnoopy.typepad.com/bnoopy/2005/03/index.html//