Monday, January 28, 2008

First draft of PSB proposal

[Edit: I will move this to Google Docs later today when I get a chance, but feel free to post comments until then and I will do my best to incorporate them in the draft I put up there.]

(Note: This first attempt is probably way too flowery and expansive, and I am probably missing a lot of good material. The proposal can be up to 6 pages long, and what I've written is about 1, maybe 2 pages at most. Please help augment/modify it to be more meat and less air!)

In 1-6 pages,
  1. Identify a coherent topic that can be addressed by 3 to 12 papers (define a specific technical area)
  2. Justify why the proposed area is appropriate for PSB (discuss why the topic is timely and important, and how the topic has been addressed in other conferences or recent publications)
  3. Argue that there is likely to be sufficient high quality, unpublished material to fill the session, e.g. a list of researchers you intend to solicit for papers
  4. Provide a short autobiographical sketch and an explicit statement that your organization endorses your involvement



“Open Science: tools, approaches, and implications”


The practice of science undergoes constant evolution. As discoveries are made, technologies developed, and data generated, new paradigms in the way science is conducted arise and flourish. We are currently witnessing an unprecedented period of scientific and technological advancement, due mostly to the ubiquity and power of computing at multiple levels. Not only has computing drastically changed our ability to produce and analyze data, it is also changing the ways in which we store knowledge and communicate about science. A common theme emerges from these changes: openness.

Openness in science manifests itself in many ways. Open source tools and open access publishing are, by now, familiar concepts. Research would stall without the many public scientific databases and repositories available. The proliferation of such databases, in turn, has spurred the development of open standards and terminologies for data and information exchange ranging from experimental protocols [flow cytometry ref] and biological pathway descriptions [SBML and BioPAX ref] to biomedical text categorization [UMLS, MeSH refs]. Perhaps most notably, the last few years have witnessed an increased interest in what is being termed Open Notebook Science - the practice of disclosing publicly all or part of one's research or laboratory activities, usually through the use of blogs and wikis [ref on ONS].

This session would address the development and practice of Open Science with an emphasis on the following areas:
  • tools and resources for facilitating Open Science (open standards for exchange, tools for conducting Open Science, databases, ontologies),
  • approaches towards Open Science (implementations and investigations of standards, licensing, open access publishing, open notebook science)
  • socio-cultural studies of aspects of Open Science (case studies and investigations)
  • (potentially: Open Science approaches towards science education?)


Without openness, science, and especially the biomedical sciences, would suffer. This is most evident with regards to open data. Many fields rely on open data from public databases such as GenBank, Swiss-prot, and the Protein Data Bank, in addition to countless other resources. The availability of scientific literature also influences the rate at which research advances. Open data, open access, and open source have all become indispensable to research in the biomedical sciences, and their success suggests that even greater benefit would result from increased openness. Governments all over the world are throwing their weight behind Open efforts, the most recent example of which is the NIH mandate in the U.S. that all publicly-funded investigators make their publications open access, which was signed into law in early January.

It is evident that we are on the cusp of embracing Open Science, and yet rigorous forums for presenting methods and discussing issues have been rare, lost among special interest groups and fringe sessions convened for some related, but other purpose. Examples are the Bioinformatics Open Source Conference, held annually as a Special Interest Group (SIG) at Intelligent Systems for Molecular Biology (ISMB), the BioOntologies and BioLINK SIGs at ISMB the past few years, and a Birds of a Feather session at ISMB 2007. In addition to ISMB, the American Medical Informatics Association(AMIA) held sessions on health data exchange and communication in 2007 and 2008, and PSB itself regularly features sessions on data integration, Semantic Web, ontologies, and BioNLP, all of which are related to Open Science as either applications, beneficiaries, or technologies. None of these previous meetings were expressly focused on Open Science as a general concept, however. The best example of an Open Science-themed meeting may be the 2008 Science Blogging Conference held in mid-January in North Carolina, where several of the sessions concentrated on Open Science, public scientific data, and Open Science in the developing world.

There is clearly interest in Open Science in the science community, and the fact that so many areas of research - including a significant proportion of those highlighted at PSB - depend on Open Science principles suggests that it is a fruitful topic for investigation. It is time for the biomedical sciences and biocomputing - which arguably have the most to gain - to begin exploring the challenges and potential within Open Science as they would any other new technology or development. In particular, systematic studies of the current scientific climate and challenges of Open Science - behavioral, cultural, technological - are needed. This session on Open Science would highlight research, tools, and issues relevant to Open Science both to those active in the Open Science community and those interested in learning about Open Science. As Open Science is a relatively novel concept, few scientific publications or conferences have addressed it specifically. A growing body of literature from popular media, including BusinessWeek, the NY Times, and Scientific American supplements the few studies that explicitly investigate data sharing and open access literature in the biomedical sciences [Campbell EG et al 2002, Wren JD 2005, Piwowar HA 2007].

Thus, the stage is primed for additional research on the climate and culture of science, as well as tools and resources designed to facilitate Open Science. Papers can be solicited from a number of angles related to Open Science, such as from the bio-ontologies, BioNLP, or open source tools communities. We will also solicit research and policy papers from those involved in Open Access publishing and open data sharing. Importantly, however, we will invite those who are directly involved in the development or practice of Open Science, including, but not limited to: Jean-Claude Bradley (Drexel University), Cameron Neylon (University of Southampton), Rosie Redfield (University of British Columbia), Michael Barton (University of Manchester), Peter Suber (Open Access correspondent at the Scholarly Publishing And Resources Coalition), Bill Hooker (Shriner Hospital), and Heather Piwowar (University of Pittsburgh).

Adoption of Open Science, although widespread in public and government institutions, is still rare at the level of the individual researcher due to technological and cultural obstacles. Both types of obstacles can be addressed in an international, scientific forum exploring the tools, resources, and questions facing Open Science. By participating in a session on Open Science, the research community convened at PSB will be uniquely prepared to undertake much needed methodology development, scientific inquiry, and discussion necessary for advancing Open Science.

[Edit: thinking of adding a section at the end suggesting a format and structure for the session that would make it most in keeping with and productive for Open Science. i.e.

- All sessions have an intro tutorial the day before the conference. We should also have a tutorial, but I would prefer it not to be on ONS - save that for the actual session). Any suggestions here?

- Keynote on the history, importance, different aspects, and potential future of Open Science

- Research papers (primary talks) (2-4)

- Tools/demos/tutorials (2-4)

- Policy papers? (1-2)

- Panel discussion on some issue

- Open discussion on some question where action may be needed (maybe planning the next Open Science meeting)


Bill Hooker said...

I'm a bit out of my depth with a computing conference, but some quick ideas/points/attempts to help:

-- links for your standards examples:

-- the post to cite on ONS is

-- Open Science is a recurring theme at the NC Science Blogging conference -- there were a couple of sessions in 2007 too, if the wiki doesn't still have details Bora can surely find them

-- if you are willing to have other people mess with the document directly, Google Docs is a decent way to make it available; that's how Cam Neylon wrote his e-science proposal

-- I'm at Shriners Hospital, not OHSU; and I'm only a cheerleader for Open Science, I wouldn't say I'm really contributing anything but "yay team". Feel free to drop my name anywhere you want, but realize that it probably won't get you anything. :-)

shwu said...

Thanks, Bill. I'll put in a bigger plug for the SBC. And everyone I've read on the open science blogosphere points out your 3quarksDaily articles, so you must know something!

Cameron Neylon said...

Overall this looks really good. Bill has some good points though I think he undersells his experience.

I would also suggest as possible speakers: Jeremy Frey (Southampton Uni), Dave de Roure/Clare Goble (Southampton and Manchester Unis and MyExperiment), Peter Murray-Rust (Cambridge), GuntherEysenbach might also be a good speaker on Open Access and improved citation rates. Nature web team and PLoS might also be able to provide a paper on their systems and experiences thus far.

I am technically at STFC Rutherford Appleton Laboratory most of my time now. But it would be great to see it up on GoogleDocs to play with but it looks great so far.

Cameron Neylon said...

Sorry, another thought. Lets see if we can get a few people to commit to submitting papers with possible titles. I will work on UK people and see what I can get in the next few days or so.

Benjamin Good said...

I think this is a fantastic and very timely idea. Depending on how a few things progress in the next few months I'd be keen to submit a paper. Also, from the Canadian front, you might consider contacting Mark Wilkinson from the BioMoby project and Francis Ouellette (a heavy hitter from the early days of Genbank and an outspoken advocate of Open-Access) .

Benjamin Good said...

Mentioning that it would mean a trip to Hawaii in January never hurts.. - especially when recruiting from Canadian latitudes!

shwu said...

Thanks, Benjamin, very happy to hear of your interest! The traditional paper deadline is in July, but I think we will have a much more flexible submission schedule (if we get accepted), so you should have plenty of time. If you'd like to participate in the actual writing of the proposal, however, just let me know, either here or email (shwu19 at stanford dot edu). If you're just curious to see what it looks like though, the Google Doc is public:

Benjamin Good said...

I just read your proposal and I think it looks really good. I honestly don't have much to add to it right now, but would like to be kept informed of its progress.

One aspect that I found particularly interesting was the idea of doing something productive during the conference. (Aside from connecting with people and surfing). I actually had a paper in PSB a few years ago about a system for building a pseudo-ontology during the course of a conference that might be relevant. Whether its the descendant of that project or something better, it would be great to choose a specific, new open-collaborative tool being presented at the conference and actually use it to conduct the collaborative project you (or the collective?) select.