Let's say you're an eager young bioscientist, ready to use open source models for your biomedical research and development. How do you do it? Well, you could put some of your work up on Bioforge, or try to hook up with a group like BIOS... but where are the enabling systems to make open source, collaborative development straightforward for researchers who don't want to be computer techs in their off-hours?
The Synaptic Leap wants to be that enabling system.
The Synaptic Leap is a start-up nonprofit led by Ginger Taylor of PeopleSoft (most of the group's employees, in fact, come from PeopleSoft). The Synaptic Leap describes itself as "dedicated towards providing a network of online communities that connect and empower scientific and medical researchers to conduct open-source style research." What that means in practice is the provision of online tools to allow researchers to coordinating efforts and exchange knowledge.
Their first project is a big one: Malaria, in coordination with the Tropical Disease Initiative (TDI). (We wrote about the TDI back in January of 2005.) Sometimes considered an "orphan disease" because of the lack of major pharmaceutical projects, much of the current effort to fight malaria focuses on blocking or eliminating the carrier, mosquitos. The TDI intends to find medical treatments to prevent and cure malarial infection; there is still much work to do, and much of what Synaptic Leap intends to accomplish is the efficient organization of the work among the international collaborators:
The Malaria genome is largely unexplored (~65% of ORF are annotated as hypothetical proteins). We intend to provide the Malaria community with tools to use, analyze and annotate the known data about all proteins in the Malaria genome. We believe that collective knowledge can contribute to a large efforts which could not be accomplished by the individuals alone. The use of open source methods and the tools to initiate research collaborations within the Malaria community of TDI, will help towards identifying the most promising targets and compounds for drug discovery against Malaria.
The Synaptic Leap is very much a Tech Bloom-era organization. It uses Drupal and WordPress as content management systems, and project members can participate in online discussions, author blogs, even provide RSS feeds for a site aggregator. In short, The Synaptic Leap is the open source biology version of the "networked politics" movement, or the biomedical corps of the "second superpower." Can smart bio-mobs be far behind?
The Synaptic Leap is still in its earliest days -- the site only went live in the last week or so, and there is still much work ahead for the project. No matter. This is an extremely exciting development, the step that could give open source biomedical research a model for a persistent structure and a toolkit for collaboration beyond a single focus. It is, from what I've found, the first viable example of an open source bioscience effort modeled not on the computer industry, but on the open political network movement. It's an early indicator that open source bio may now be ready to move from the fringes to become an important voice in the future of medical science.
Comments (5)
Interesting. I say this as I'm about to release some software (open source) to do something similar. However, I think that excessive openness causes issues as it prevents people who don't want to, can't or are unsure about openness from participating. I've described this as "the need for openness, control and secrecy" elsewhere.
Also this looks like a centralised service - all hosting etc. done by TSL. Which again excludes some groups from using this kind of thing. What I've done is perfectly capable of being hosted by a shared server in a datacentre somewhere, or using an old machine fished out of a skip sitting in the corner of the lab. Particularly when it all gets wrapped up and put onto a bootable cd thus making installation trivial.
The copyright/IP issues associated with using the web for collaboration are also pretty big, and poorly understood by researchers brought up in a paper-and-reprints world. Us youngsters can be quite gung-ho about copyright which is the flip side of the coin. I think the open source model can help ameliorate some of these issues - particularly with making sure that things like this are not strangled at birth.
So yeah, this kind of shared centralised service is only a small part of the story. Press release for my software to follow in a few days :)
Posted by kd | December 17, 2005 12:44 PM
Posted on December 17, 2005 12:44
I think that excessive openness causes issues as it prevents people who don't want to, can't or are unsure about openness from participating
I hear you. Oh man do I hear you. I am still recovering from trying to get some colleagues to start using BioRoot, a free online database for reagent sharing. Oh, the reluctance! Oh, the suspicion! Oh, the fucking whining!
Sorry. Sore point. But kd is bang-on, there's a lot of resistance to this kind of thing in the scientific community -- which is exactly where I'd expect to find enthusiastic adoption instead. I frankly do not understand it. But, witness BioRoot -- a great idea (some background here, may be of particular use to non-scientists, scuse the self-link), has been live since mid-2005, has about ten labs signed up (including the one I work in, natch). Ten. Out of how many tens of thousands in the US alone? The database has the potential to streamline laboratory information management, save enormous amounts of money and open up undreamed-of collaboration -- and it's being more or less ignored. I do not get it.
So I'll be watching Synaptic Leap with great interest, but some trepidation as well.
(Worldchanging Team -- how about featuring BioRoot? The guy who built it, David Nix, is a nice guy and very responsive in case you wanted an interview.)
Posted by sennoma | December 20, 2005 2:34 PM
Posted on December 20, 2005 14:34
It's a brilliant idea and has that ring of the blindingly obvious that marks true brilliance, IMHO.
One sign of hope is that many members of the scientific community have embraced open source publishing and might see this as a logical extension.
The big question, as everybody's said so far, is whether it will be embraced as a general model by the scientific community. If it isn't, I suspect and hope (as a second-best scenario) that it's an idea that is still just a bit ahead of its time and will emerge again when the community is a bit more ready.
So far, they seem to be going about the beta step just the right way, working with a specific project and an existing and engaged partner.
It would be wonderful if they could work with powerful funding partners that would make participation a requirement for funding.
Posted by Ann Feeney | December 21, 2005 10:22 AM
Posted on December 21, 2005 10:22
Regarding Bioroot:
There is a similar LIMS-like software suite fo laboratory stock.inventory management, LabStoRe which one might also want to have a look at. It is more customizable, but unlike Bioroot, you have to install it on your machine. On a different note, OrderSys is a reagent/supply ordering system which, like LabStoRe, many labs use.
Posted by A Visitor | December 22, 2005 6:52 PM
Posted on December 22, 2005 18:52
I find it really interesting that the Synaptic Leap is starting on malaria. This is exactly where we ended up in our open science initiative UsefulChem. So far the content has been mainly on organic synthesis details because that is our bottleneck step right now.
Concerning the issue of IP, I don't see that doing science in the open on a blog or wiki is any different from giving a talk at a conference. To be clear, I have put up a warning on our blog that anything posted there becomes public domain. The bottom line is that if you want to protect your ideas or results, don't talk about them anywhere until you at least get a provisional patent (US).
Concerning the issue of the reluctance of scientists to collaborate openly, I also agree that the vast majority will not want to do it that way. So what? All it takes is a few intelligent and motivated researchers aroud the world to really get things going. What is interesting here is that if several scientists are competing, the one willing to share openly will have a significant advantage in terms of priority.
Posted by Jean-Claude Bradley | December 29, 2005 2:37 AM
Posted on December 29, 2005 02:37