Would open science profit from a non-profit?

In my first foray organizing a formal meeting (the PSB workshop), I've learned that pretty much everything comes down to money. Having a successful meeting requires getting people to attend, and getting people to attend often involves money. Getting money to allow people to attend can even require money (for example, publishing costs for conference proceedings).

One idea Cameron's mentioned a few times during our fundraising discussions is the Open Science Collective, and though he hasn't fully described what this is to me, I get the impression that it would be some abstract entity comprising individuals, organizations, resources, and activities - some larger body that would provide support for open science-related endeavors. At the very least, I think it would provide a means to fund raise separate from any particular event such that we (in the collective sense) could act independently. By this I mean that the OSC could support individuals to go to meetings, sponsor meetings like the PSB workshop, or even organize its own meetings.

The idea hasn't really been taken further yet, with whimsical t-shirt ideas pretty much our only tangible revenue strategy so far. But to give the OSC a step towards reality, perhaps it's time to start talking about building a non-profit. From a quick glance through of one website's guide to starting a non-profit, it appears that we need to create a mission statement, obtain a board of directors, and eventually file for either incorporation (plus maybe other things, like tax-exempt or tax-deductible status). This is about where I start getting fuzzy on the details, so if anyone has experience with non-profits or foundations (I don't even know what the difference is) please feel free to enlighten me!

At the most basic level, it would be nice to have some external entity with a bank account into which we could funnel funds that we (again, the collective we) could apply towards open science activities. If that t-shirt shop ever sells anything, the proceeds should go into that account. What the best way to accomplish that is, I'm not quite sure. If it is to start a non-profit, then perhaps the first step is to see who else is interested and start drafting a mission statement together?

According to idealist.org, a mission statement should cover the purpose, the business, the values, and the beneficiaries of the organization; i.e. the what, how, why, and who/where. This can be accomplished in one line but can also be expanded into paragraphs. But let's start small - here's a stab at a one liner mission statement:

"The Open Science Collective is an international and interdisciplinary [non-profit] organization that promotes open exchange and collaboration in science, and provides resources and support for the advancement of open science."

So some concluding questions: Does it make sense to have something like the Open Science Collective? If so, what should it be and how do we get there? What would be the mission statement of the OSC? If not the OSC, what do we need?

Open Science at PSB - deadline approaching!

The initial deadline for proposals for the first Open Science workshop at PSB is coming up on June 1. We welcome submissions on almost anything related to Open Science - tools, platforms, and resources; applications, first-hand experiences, or case studies; cultural, social, and historical perspectives or studies; Open Access and open source; pretty much anything that will help us get a better picture of how Open Science has developed, where it is now, what's brewing on the horizon, and what's needed going forward. The call for participation has more detailed information on the workshop and submission instructions.

Note that the proposal need not be a fully mature or completely fleshed out abstract - a rough outline of the content of the proposed talk is sufficient. The early deadline is simply for us to get a better idea of what the workshop will look like, and there is ample time to continue refining abstracts thereafter.

There is no selection process for posters; anyone interested in presenting a poster may present. The deadline for submitting a poster abstract is Sept 12; however, early submissions are encouraged so that we may better organize the workshop!

Fellow bloggers and readers - please take a moment to post a short note about our workshop on your own blogs, or send notice of our call for participation to potentially interested friends and colleagues! Thanks in advance. :)

PSB Open Science workshop - call for participation

The call for participation for the Open Science workshop at PSB 2009 is now up! We welcome anyone with an interest in open science to submit proposals for talks. Note that although space is limited for talks and demos, anyone who registers for the conference can present a poster, so we also encourage poster submissions!

PSB proposal accepted for a workshop

The proposal we submitted for a session on Open Science at the Pacific Symposium on Biocomputing was accepted! They notified us yesterday that it would be included as a 3 hour workshop on the first day of the conference. Many thanks to all those who sent encouragement or letters of support - I'm sure it went a long way towards convincing the conference organizers that we are serious!

A call for participation will come out shortly, but just wanted to get the good news out!

PSB proposal up on Nature Precedings

Our proposal for an Open Science session at PSB is now available on Nature Precedings!

PSB Open Science session proposal submitted!

Thanks, everyone, for the encouraging and helpful comments, for spreading the word, or for writing in with a letter of support. You all helped us craft a very strong proposal, which was submitted yesterday! I'll post an update on that once I hear back, sometime around March 5th.

For those interested, the final version of the document is updated on GoogleDocs here, and a PDF can be downloaded here.

Call for letters of support for PSB proposal

Hi folks, so it's about a week until the proposal is due. So far, we have a draft up, which should be viewable by anyone. It almost there, so there should be no problems with getting it in come submission time. However, it could still use some help with coming up with what the session would actually look like, how much off the beaten path we want to go without turning off the conference organizers, and how much off the beaten path we need to go to make the session useful.

One thing that would really help outside of the proposal itself is to have actual letters of support. That way the organizers will know there is serious interest and commitment for a session on Open Science - it's a gamble for them, frankly, but much less of one if there is a good crowd on board.

So if you would like to support this proposal and are willing to commit to participating should it get accepted, please send me an email to that effect (with as many details of your anticipated participation as you can provide at this time), and I will include all the emails as "supplementary material" next Friday. Please also disseminate this call on your own blogs if you can. Many thanks in advance!

PSB proposal up on Google Docs

I've posted the proposal on Google Docs. If you've been commenting, I invited you. Does anyone know if it's possible to make the document open to everyone?

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!)

Instructions:
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

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SESSION TITLE:

“Open Science: tools, approaches, and implications”

INTRODUCTION & FOCUS:

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?)

JUSTIFICATION:

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)

Going forward on the PSB proposal

After finding out more information about conference logistics, it looks like we have enough momentum to start writing the proposal. Most of the discussion is taking place on Science in the Open, so let's just keep it there, at least until I get the draft of the proposal up. If you are interested in contributing to the proposal, please email me so I can set up editing permissions in the draft document!

An additional feeler for PSB

In an earlier post, I mentioned the possibility of submitting a proposal to PSB for a session on Open Science. Since then, I've gotten some informal feedback that the organizing committee is interested in the idea, but needs more information. The advice I received was to submit a regular session proposal detailing what kind of papers are expected and the people who would potentially participate. Essentially, the topic needs to be able to attract enough substantial, scientific papers for the committee to be convinced of its merit. Part of the process will involve soliciting paper submissions from specific people known to be working in the field.

On Cameron Neylon's blog, the point was made that PSB is an expensive conference to attend, and for this reason it could be a non-optimal choice for an Open Science meeting. However, if there are no strong objections to having multiple meetings on Open Science in the next year or two (if there are, then that is definitely worth discussing!), then we have nothing to lose (and probably some to gain) from submitting a proposal to (and if all goes well, hosting a session at) PSB. As Pedro Beltrao points out, it doesn't hurt to gain more exposure, even if it ends up being just a short tutorial. Also, I've been seeing a lot of Open Science activity in the US and Europe, but have yet to catch wind of it elsewhere; PSB, being located in the Pacific, draws a lot of attendees from Asia and Oceania, and it would be interesting to see what efforts and issues regarding Open Science are happening there.

So my big questions are these:

1. What should be the focus of this session on Open Science? (first, frame it as a traditional PSB session, then perhaps as a "creative" session)
2. What kind of substantial/technical/research papers can be written about Open Science?
3. Who are the major players in the field? Who would the session chair invite to submit a paper?
4. Who is willing to help write/organize the actual proposal and session?

But my most important question is this: Is anyone involved in the field interested in chairing this session?

Being a novice grad student who has very little experience with Open Science (this blog is it so far, and it only started a week ago!), I feel that such a session would be much more effective with a more senior Open Science advocate as chair. One of the duties of the session chair is to give a tutorial on the subject, another reason why someone with more experience would be better suited to this role.

Again, the deadline for session proposals is Feb 8th, so if it is going to happen, it will have to happen pretty fast. The community has already shown that bigger things (a grant proposal) can be accomplished in less time (a week), so I am not worried about getting it done if a consensus is reached.

If you have any answers or suggestions for the above 4 questions or about the session in general, and especially if you are interested in chairing, please respond to this post or email me!

* Edit: I originally mixed up Cameron's blog (Science in the Open) with JC Bradley's blog (UsefulChemistry), and have corrected it. Apologies to both!

Open Science at PSB 2009?

I attended a seminar today where we came up with a list of ideas for sessions for the 2009 meeting of the Pacific Symposium on Biocomputing (PSB). This group of people organized a session at PSB 2008 called "Multi-scale modeling", so many of the ideas were related to computational modeling. But since I am interested in Open Science, I asked whether there would be interest in having an Open Science session at PSB.

PSB is a pretty prestigious conference that prides itself on covering only the "hot topics" in biology and biocomputing. Combine that with their locale (Hawaii), and you can imagine it is fairly difficult to get accepted. But even though a session on Open Science would differ from their traditional sessions (less primary research papers, more tutorials / descriptions of experiences / discussion), I think it would be great to talk about Open Science there, since A) PSB is prestigious, B) attendees are probably pretty forward-thinking, C) by Jan 2009, we will be ready to have some really productive discussion, and D) did I mention Hawaii?

The deadline for submitting a session proposal is Feb 8th, which is in only a couple weeks. If there is support for this, I will try to carry it through. Here is the call for papers, which includes guidelines for what makes a good session, and responsibilities of a session chair. I'm not sure that I would be the best choice for a session chair since I have not participated in an open science endeavors yet and the session chair is required to give a 1 hr tutorial on the session topic, so if anyone is interested in being the session chair, please let me know! Ideas for what kind of papers could be solicited would also be appreciated.