Among the BioInformaticians

Last Tuesday and Wednesday I attended the Bio-IT World Conference & Expo, at the World Trade Center in Boston. I was a booth babe for Bioinformatics.org, (“The open access institute”) and also was pimping my books. I discovered the BioInformatics organization about a decade ago while pimping my books (what else) at the O’Reilly BioInformatics conference in Tucson. They started out as basically a sourceforge for bioinformatic software, kind of a reaction to corportization of all things genomic, and have grown from there. I wrote about them a little in my famous Salon article How I Decoded the Human Genome.

Because I’m a total dummy and didn’t look at a map, it took me forever to get there from the place I was staying, one mile away, so I only caught the last twenty minutes of the talk given by Philip Bourne on the occasion of his being named 2009’s Franklin Laureate, by the Bioinformatics Organization — an award named in honor of Ben Franklin, who refused to patent his inventions. I saw virtually none of the show. I attended no sessions, and I didn’t even cruise the exhibit hall. Instead, along with Bioinformtics Organization colleagues Jeff Bizarro and Shailender Nagpal, I staffed our organization’s tiny booth and fielded whatever questions came my way– sometimes fielding them lamely, at which times I was glad to be backstopped by Jeff and Shailender.

Some impressions follow. Because my exposure to the show was so limited, they’re kind of like an image taken by a pinhole camera, so take them for whatever they’re worth. The most interesting part of the whole show, for me, was the discussion with Melina Fan, PhD, founder and executive director of the group Addgene, about which more below.

Philip Bourne’s Talk

When I joined the proceedings, Bourne was talking about the emerging trend to uniquely identify individual scientists in order to: disambiguate people who share the same name, unify bibliographic sources and databases, and generally improve information access and reliability. He listed various (competing? complementary?) approaches, and voiced his conclusion that some kind of biometric-based system was inevitable. He acknowledged that people have privacy concerns about such models, but said such a convergence was inevitable, so we should just embrace the idea and try to shape it to address our concerns. On the screen behind him was a poster from The Bourne Identity, with Matt Damon as Jason Bourne in full flight from a vast conspiracy that follows his every movement. Funny, that. I think. . .

In his introductory remarks, Jeff Bizzaro cited this bit from an article of Bourne’s a few years ago:


“My vision is that a traditional biological journal will become just one part of various biological data resources as the scientific knowledge in published papers is stored and used more like a database. Conversely, the scientific literature will seamlessly provide annotation of records in the biological databases. Imagine reading a description of an active site of a biological molecule in a paper, being able to access immediately the atomic coordinates specifically for that active site, and then using a tool to explore the intricate set of hydrogen-bonding interactions described in the paper. Not only are the data generated by the experiment immediately available within the context of what you are reading, but specific tools for interpreting these data are provided by the journal. Alternatively, if you are starting with the data, for example, viewing the chromosome location of a human single-nucleotide polymorphism associated with a neurological disorder, you can immediately access a variety of papers ranked in order of relevance to your profile, not just through links to abstracts but also by pinpointing the reference to the single-nucleotide polymorphism in the full-text article. The type and order of articles displayed could be different, depending on whether you are, for example, a molecular biologist or a neurosurgeon. At this point, whatever your user profile, the distinction between a database and a journal article disappears.”

More about this a little later.

BioInformatics.org fan club

It was nice when people came up and said how much the appreciated the organization. Several people mentioned how much they had learned from articles and citations on the site, or had used software from the site, and more than one person said they had gotten a job through the career center. We met fans of the site from a few continents. Very gratifying to hear that.

The Economy

Bio-IT world is a commercial show, not an academic gathering, but nevertheless I was somewhat taken aback by how much the subject of the lousy state of the economy came up. From time to time personnel from other booths would come by. They generally were not very upbeat. A few people came by our booth trying to sell us stuff. Even after we made clear that we’re a tiny non-profit with a miniscule budget and currently not in the market for anything that was on sale at the show–for example, the BioInformatics Organization is not going to buy a $50,000 computing cluster, even if it can match the throughput of a system that costs ten times as much–there were a couple of guys who kept up with the hard-sell. There was a bit of desperation in the air.

Preventing the Apocalypse

One fellow (whose name I’ve forgotten and who didn’t have a business card on him) stopped by to chat. His nametag listed his affiliation as “DOD”. I enquired what DOD did, and was reminded that that’s the Department of Defense. The fellow had some impressive-sounding title, and it turns out that he’s a top guy in bioterrorism research whose job is to anticipate what terrorists might try to do, and figure out how to counter them. “It’s my job to prevent the apocalypse,” he said.

“Damn,” I said, “You’ve got to read my book!” By a remarkable coincidence, I just happened to have on hand a copy of my own bioinformatic novel Acts of the Apostles, which is a thriller about nanomachines, Gulf War Syndrome, the Iraqi bioweapons program, and an impending apocalypse.

He bought a copy. Maybe it will help him prevent our borgification into the overmind.

Melina Fan and Addgene

Towards the end of the last day of the show, Melina Fan, PhD, founder and executive director of the group Addgenestopped by. Addgene is, according to their website,

Addgene is a non-profit organization dedicated to making it easier for scientists to share plasmids.

Addgene is reaching this goal by operating a plasmid repository for the research community. We are working with hundreds of laboratories to assemble a high-quality library of published plasmids for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request.

Melina explained that she started the organization as a way to share information about plasmids–and the physical plasmids themselves; Addgene has a full wet lab– that would otherwise have been permanently lost. She mentioned that often plasmids were the focus of a graduate student’s research, but after the completion of the degree, the plasmids were discarded. With Addgene, the plasmids and the information about them can be archived for future use. This is similar to what BioInformatics.org does with software, which also often has its origins in academic research projects. There are now more than 400 such projects hosted on our servers.

Thus Addgene is, in many ways, a philosophical cousin of BioInformatics Organization. They’re both about preserving and sharing hard-won information in the spirit of old-school, pre-corporate science.

Not only that, but both organizations are based in eastern Massachusetts.

Addgene also seems to be philosophically aligned with Philip Bourne. Here’s an image from their website, showing the role of Addgene in relation to published literature:

The idea is to not only keep the plasmid samples, but to archive them in a way that makes it easy to associate any plasmid with published research about it. This is reminiscent of the Bourne citation, above.

It seems to me that, at the least, Addgene and Bioinformatis.org should become more aware or each other’s work, and, as appropriate, cross-promote each other. Perhaps there might be opportunities for closer collaboration in the future on projects of mutual interest.

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