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More on the PSB proposal

22 January 2008 23 views 16 Comments

Shirley Wu has followed up on her original proposal to submit a session proposal for PSB. She asks a series of important questions about going forward on this and I thought I would reply to these here to widen exposure.

I think it is worth going for a session and I am happy to lead the application but there may well be better people; Jean-Claude, Antony Williams, Peter Murray-Rust, Egon Willighagen to get to lead it depending on focus. I think the important question to ask is whether we can generate enough research papers to justify a session. I believe we can and should and I will commit to generating one if we go ahead, but we need at least another 3-4 to go ahead I think.

So, to answer Shirley’s questions:

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?

Given it is a computing symposium I would say that it should focus on tools and standards and how they effect what we can, or would like to do. This also gives us a chance to provide research type papers describing such tools and standards and investigating their implementation. So we could write papers describing different implementations of Open Notebooks and critical analysis of the differences, the organisation of Open Data, standards for describing data, and social and cultural aspects of what is happening etc etc.

People to invite to write papers include Jean-Claude Bradley, OpenWetWare group, Egon, Peter MR, Deepak Singh (willing to write a review/scoping type paper?), Antony Williams (ChemSpider), Simile Group (www.simile.mit.edu), other repository, data archival groups, Nature Publishing/PLoS/PMC/UK-PMC to describe systems, Heather Piwowar to analyse what happens, and social sciences groups that are becoming interested in what is going on.

Finally, as I say, I am willing to help, but as you can see time becomes a constraint for me and things have a habit if getting left to the last minute. If anyone else would like to step in to lead then I am more than happy to be a co-chair.  If no one else is available I am happy to lead. I at least have the advantage that I can probably source the resources so that I can get there!

I am going to tag this “Open Science PSB09″ if that seems a good tag to aggregate around.

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  • http://blog-di-j.blogspot.com/ Jeremiah Faith

    I think it might be a little early for a PSB session, given that so little of the Open Notebook efforts thus far have involved writing new code (it’s mainly been a search for what existing tools best fit our purpose for the moment). In the future, I think ONS will have a lot of purpose-built software options that might make for a session with real debate, instead of lots of proposals for what we’d like to have or implement (these types of hypothetical notebook proposals are useful, but perhaps at a different venue).

    If we were to try and organize something, I agree we’d definitely need to go with a bioinfo spin since it’s a bioinfo conference. I’d also suggest thinking further outside the Open Notebook box to try and invite bioinfo folks that helped earlier “open” efforts become more widespread successes. For example Michael Eisen for open access. Or even further back, Lincoln Stein whose helped organize and write and lot of the open source databases and code for biology.

    I think folks will definitely need to write some next-gen ONS software or at least provide some initial additions to the current-gen (e.g. incorporate microformats and experiment aggregators) for this to be an appropriate session for a PSB conference.

  • http://blog-di-j.blogspot.com/ Jeremiah Faith

    I think it might be a little early for a PSB session, given that so little of the Open Notebook efforts thus far have involved writing new code (it’s mainly been a search for what existing tools best fit our purpose for the moment). In the future, I think ONS will have a lot of purpose-built software options that might make for a session with real debate, instead of lots of proposals for what we’d like to have or implement (these types of hypothetical notebook proposals are useful, but perhaps at a different venue).

    If we were to try and organize something, I agree we’d definitely need to go with a bioinfo spin since it’s a bioinfo conference. I’d also suggest thinking further outside the Open Notebook box to try and invite bioinfo folks that helped earlier “open” efforts become more widespread successes. For example Michael Eisen for open access. Or even further back, Lincoln Stein whose helped organize and write and lot of the open source databases and code for biology.

    I think folks will definitely need to write some next-gen ONS software or at least provide some initial additions to the current-gen (e.g. incorporate microformats and experiment aggregators) for this to be an appropriate session for a PSB conference.

  • http://onebiglab.blogspot.com/ Shirley Wu

    Thanks, JC. I agree that your blog is a better place to gather feedback on this.

    There are at least 3 types of papers that could be written:
    1. social/cultural studies of open-ness/sharing in the biosciences (akin to Heather Piwowar’s poster at PSB a few weeks ago, includes Open Access)
    2. research in which Open Science in some form was an integral component
    3. resources, tools, or standards specifically developed or appropriated by our community (but these might be better suited as posters)

    #1 is a very flexible category, and one that I think many people would be interested in
    #2 is also very interesting, and I think it would be great to start cataloging “success stories” for Open Science, if something like that doesn’t already exist.
    #3 is very important, but hard to frame as a research talk

    We should definitely have a review/scoping talk as a keynote.

    The impression I got was that the organizing committee would consider a non-traditional session if they felt there was enough interest and enough value. So it may be worthwhile to gather people’s thoughts on what the big issues and questions are facing Open Science, what questions would make for good debate or panel discussion, what would make for good tutorials, etc.

  • http://onebiglab.blogspot.com Shirley Wu

    Thanks, JC. I agree that your blog is a better place to gather feedback on this.

    There are at least 3 types of papers that could be written:
    1. social/cultural studies of open-ness/sharing in the biosciences (akin to Heather Piwowar’s poster at PSB a few weeks ago, includes Open Access)
    2. research in which Open Science in some form was an integral component
    3. resources, tools, or standards specifically developed or appropriated by our community (but these might be better suited as posters)

    #1 is a very flexible category, and one that I think many people would be interested in
    #2 is also very interesting, and I think it would be great to start cataloging “success stories” for Open Science, if something like that doesn’t already exist.
    #3 is very important, but hard to frame as a research talk

    We should definitely have a review/scoping talk as a keynote.

    The impression I got was that the organizing committee would consider a non-traditional session if they felt there was enough interest and enough value. So it may be worthwhile to gather people’s thoughts on what the big issues and questions are facing Open Science, what questions would make for good debate or panel discussion, what would make for good tutorials, etc.

  • http://openwetware.org/wiki/User:Cameron_Neylon Cameron Neylon

    I think there could be enough papers. It would be slightly out of the ordinary, possibly too much, but perhaps we should leave that up to the organisers to decide?

    I had discussions with Jeremy Frey yesterday and we came up with the following possible suggestions as sources of papers. I think there is enough but that it really points up a key issue; that we shouldn’t be embarrased about treating what we are doing in this general area as research and development. Its not clear exactly how to publish it but I feel quite strongly we should – these ideas need to get into the ‘mainstream’ scientific consciousness and the best route to that is through the peer reviewed literature (IMO)

    Heather Piwowar- outcomes and benefits of Open Science
    My Experiment Group – tools and development
    ChemSpider – tools and development
    Southampton – tools for ONS and experiences in using them
    PLoS – Topaz system(?) or maybe A.N.Other publisher, NPG? (oh the irony of inviting the editor of Nature to submit a paper for peer review!)
    Peter M-R – tools for scraping the literature, the power of open data
    Social scientists – cultural aspects, but I don’t know who we would ask
    Repositories – again tools and coding

    and for a plenary/keynote/tutorial: Jean-Claude on making it all happen with what’s already available, or Peter Suber for an overall view, or Peter MR for all round general purpose polemic :)

  • http://openwetware.org/wiki/User:Cameron_Neylon Cameron Neylon

    I think there could be enough papers. It would be slightly out of the ordinary, possibly too much, but perhaps we should leave that up to the organisers to decide?

    I had discussions with Jeremy Frey yesterday and we came up with the following possible suggestions as sources of papers. I think there is enough but that it really points up a key issue; that we shouldn’t be embarrased about treating what we are doing in this general area as research and development. Its not clear exactly how to publish it but I feel quite strongly we should – these ideas need to get into the ‘mainstream’ scientific consciousness and the best route to that is through the peer reviewed literature (IMO)

    Heather Piwowar- outcomes and benefits of Open Science
    My Experiment Group – tools and development
    ChemSpider – tools and development
    Southampton – tools for ONS and experiences in using them
    PLoS – Topaz system(?) or maybe A.N.Other publisher, NPG? (oh the irony of inviting the editor of Nature to submit a paper for peer review!)
    Peter M-R – tools for scraping the literature, the power of open data
    Social scientists – cultural aspects, but I don’t know who we would ask
    Repositories – again tools and coding

    and for a plenary/keynote/tutorial: Jean-Claude on making it all happen with what’s already available, or Peter Suber for an overall view, or Peter MR for all round general purpose polemic :)

  • http://onebiglab.blogspot.com/ Shirley Wu

    Thanks Cameron, and sorry Jean-Claude for mixing things up in my earlier post and comment.

    Cameron’s list brings up another potential approach for papers – methods or tools that are not necessarily explicitly designed with open science in mind, but are easily related. Things like literature mining, tools that rely on (and add value to) open data, bibliometrics. There are also corollaries with scientific curation – Lawrence Hunter and Phil Bourne have published quite a bit on the state of our knowledgebases and curation efforts, and it is apparent that additional tools are needed to help with curation. These could be literature mining tools to help curators find knowledge or electronic annotation to automate the entire process, both of which benefit from Open-ness. Or tools for collaborative annotation (such as GeneRIFs) – a form of Open Curation?

  • http://onebiglab.blogspot.com Shirley Wu

    Thanks Cameron, and sorry Jean-Claude for mixing things up in my earlier post and comment.

    Cameron’s list brings up another potential approach for papers – methods or tools that are not necessarily explicitly designed with open science in mind, but are easily related. Things like literature mining, tools that rely on (and add value to) open data, bibliometrics. There are also corollaries with scientific curation – Lawrence Hunter and Phil Bourne have published quite a bit on the state of our knowledgebases and curation efforts, and it is apparent that additional tools are needed to help with curation. These could be literature mining tools to help curators find knowledge or electronic annotation to automate the entire process, both of which benefit from Open-ness. Or tools for collaborative annotation (such as GeneRIFs) – a form of Open Curation?

  • http://usefulchem.blogspot.com/ Jean-Claude Bradley

    Shirley – no problem for the mix-up :)

    I think there is an opportunity for some type of session on Open Science relating to biocomputing.

    The first question I have is how many people who were already planning to attend could contribute? If the number is not great then maybe a joint session might make sense this time around.

    I also have a concern about the requirement for submitting full papers. I usually avoid conference symposia where full papers are required to participate and I suspect many other do as well. It is hard enough to find time to write regular full papers and, at least in my field, symposium proceedings don’t count much in our academic evaluation. There is also the issue of giving up copyright to the conference publisher and that may be a concern for some of your target participants.
    What I don’t have a problem doing is recording my talk and publishing the transcript. That solves the problem of sharing the benefit of the symposium for those who can’t attend.

  • http://usefulchem.blogspot.com Jean-Claude Bradley

    Shirley – no problem for the mix-up :)

    I think there is an opportunity for some type of session on Open Science relating to biocomputing.

    The first question I have is how many people who were already planning to attend could contribute? If the number is not great then maybe a joint session might make sense this time around.

    I also have a concern about the requirement for submitting full papers. I usually avoid conference symposia where full papers are required to participate and I suspect many other do as well. It is hard enough to find time to write regular full papers and, at least in my field, symposium proceedings don’t count much in our academic evaluation. There is also the issue of giving up copyright to the conference publisher and that may be a concern for some of your target participants.
    What I don’t have a problem doing is recording my talk and publishing the transcript. That solves the problem of sharing the benefit of the symposium for those who can’t attend.

  • http://openwetware.org/wiki/User:Cameron_Neylon Cameron Neylon

    Jean-Claude’s points are good ones. In terms of copyright I think we would argue that it would be a condition of doing the session that the papers be CC-BY or appropriate licenses and that copyright wouldn’t be handed over.

    In terms of the hassle of papers I agree. I think PSB is ‘properly’ published in a real journal so not just proceedings which partly answers that. Shirley can you comment on that? I also think that the whole point of Open Science is its responsiveness so that only presenting work that is by definition 6 months out of date will be a bit odd. So we should argue for some papers to be presented that aren’t peer reviewed and are much more up to the minute.

    I think the concept is firming up as to what we would want to do and how we would want to do it. I am for putting the proposal in and seeing what the organisers make of it.

  • http://openwetware.org/wiki/User:Cameron_Neylon Cameron Neylon

    Jean-Claude’s points are good ones. In terms of copyright I think we would argue that it would be a condition of doing the session that the papers be CC-BY or appropriate licenses and that copyright wouldn’t be handed over.

    In terms of the hassle of papers I agree. I think PSB is ‘properly’ published in a real journal so not just proceedings which partly answers that. Shirley can you comment on that? I also think that the whole point of Open Science is its responsiveness so that only presenting work that is by definition 6 months out of date will be a bit odd. So we should argue for some papers to be presented that aren’t peer reviewed and are much more up to the minute.

    I think the concept is firming up as to what we would want to do and how we would want to do it. I am for putting the proposal in and seeing what the organisers make of it.

  • http://onebiglab.blogspot.com/ Shirley Wu

    Unfortunately, PSB papers are published in an “archival proceedings volume”, so not technically a real journal. I will be able to talk to one of the organizers today and maybe he can tell me more about the copyright issues. It appears that PDFs of at least 90% of proceedings are made available online within a month of the conference, though (http://psb.stanford.edu/psb-online/), which may already be sufficient? I don’t think there will be a problem with making transcripts available.

    Since the regular deadline for paper submissions is mid July, perhaps one way to structure the session would be to look for maybe 2 or 3 actual papers (if someone has already been working on something), allow a second round of “late-breaking papers” about 3 months from the conference date (this may be subject to their printing schedule, I will ask about this today too), and require the rest to be filled with posters and special talks/tutorials/discussion panels. These may also require a “late-breaking” submission date. We could ask for people to submit special talks or tutorials by providing as detailed an outline or abstract as they can with a formal introduction so the focus of the talk is clear, along with evidence that they have something of substance to present – links to projects or other web presence, a history of participation, etc. The big question is whether the conference (and we) can accommodate a later submission date, because this will mean turnaround will have to be extremely fast (maybe 2 weeks) to allow for travel plans at the very least, not to mention all the logistics that go into a planning a conference.

    Perhaps a better idea would be to accept paper and poster submissions with the understanding that they may change somewhat before the conference starts. 2 or 3 months prior to the conference (if the conference allows this), we can accept major revisions. That way the original submissions can be preliminary work if they have to be, and then more finalized work can be submitted later, while still allowing people to make travel plans and register in a timely fashion.

    I’ve never organized a conference, though, so all of this may just be way too much to ask.

    I don’t know if we can tell how many people are already planning to go, aside from the organizing committee, since attendance is highly dependent on which sessions are accepted. The topics can change a lot from year to year, though there will very likely be a session on text mining, a session on high-throughput data sets, and a session on translational bioinformatics – fields that all benefit from open-ness.

    I’ll see if I can get more information about potential logistics today. Stay tuned.

  • http://onebiglab.blogspot.com Shirley Wu

    Unfortunately, PSB papers are published in an “archival proceedings volume”, so not technically a real journal. I will be able to talk to one of the organizers today and maybe he can tell me more about the copyright issues. It appears that PDFs of at least 90% of proceedings are made available online within a month of the conference, though (http://psb.stanford.edu/psb-online/), which may already be sufficient? I don’t think there will be a problem with making transcripts available.

    Since the regular deadline for paper submissions is mid July, perhaps one way to structure the session would be to look for maybe 2 or 3 actual papers (if someone has already been working on something), allow a second round of “late-breaking papers” about 3 months from the conference date (this may be subject to their printing schedule, I will ask about this today too), and require the rest to be filled with posters and special talks/tutorials/discussion panels. These may also require a “late-breaking” submission date. We could ask for people to submit special talks or tutorials by providing as detailed an outline or abstract as they can with a formal introduction so the focus of the talk is clear, along with evidence that they have something of substance to present – links to projects or other web presence, a history of participation, etc. The big question is whether the conference (and we) can accommodate a later submission date, because this will mean turnaround will have to be extremely fast (maybe 2 weeks) to allow for travel plans at the very least, not to mention all the logistics that go into a planning a conference.

    Perhaps a better idea would be to accept paper and poster submissions with the understanding that they may change somewhat before the conference starts. 2 or 3 months prior to the conference (if the conference allows this), we can accept major revisions. That way the original submissions can be preliminary work if they have to be, and then more finalized work can be submitted later, while still allowing people to make travel plans and register in a timely fashion.

    I’ve never organized a conference, though, so all of this may just be way too much to ask.

    I don’t know if we can tell how many people are already planning to go, aside from the organizing committee, since attendance is highly dependent on which sessions are accepted. The topics can change a lot from year to year, though there will very likely be a session on text mining, a session on high-throughput data sets, and a session on translational bioinformatics – fields that all benefit from open-ness.

    I’ll see if I can get more information about potential logistics today. Stay tuned.

  • http://onebiglab.blogspot.com/ Shirley Wu

    So I talked to one of the conference organizers and got a little more information – not a lot, but enough to go on. Copyright shouldn’t be an issue; whenever authors have asked for copyright permissions they’ve received them, and this only matters for content published in the physical proceedings book. Which brings us to the other major issue, which was the timeline of submission. The paper submission deadline is very strict, but this is because they publish the proceedings in a physical book available at the conference. Material that doesn’t go in the physical proceedings book, however, seems like it will not necessarily be subject to the same timeline. I think it will be up to the session organizers (us?) to decide what makes sense in terms of dates and types of submissions, travel and registration, and how we are going to publish the proceedings if not in the printed book.

    At this point, I think I’m ready to draft a proposal (probably on Google Docs), which I will then post on my blog for feedback and revisions. I’m not sure how editing should work – interested contributors can email me so I can invite them to edit? Anyway, the draft should be up hopefully by Monday. Until then, comments and ideas always appreciated.

  • http://onebiglab.blogspot.com Shirley Wu

    So I talked to one of the conference organizers and got a little more information – not a lot, but enough to go on. Copyright shouldn’t be an issue; whenever authors have asked for copyright permissions they’ve received them, and this only matters for content published in the physical proceedings book. Which brings us to the other major issue, which was the timeline of submission. The paper submission deadline is very strict, but this is because they publish the proceedings in a physical book available at the conference. Material that doesn’t go in the physical proceedings book, however, seems like it will not necessarily be subject to the same timeline. I think it will be up to the session organizers (us?) to decide what makes sense in terms of dates and types of submissions, travel and registration, and how we are going to publish the proceedings if not in the printed book.

    At this point, I think I’m ready to draft a proposal (probably on Google Docs), which I will then post on my blog for feedback and revisions. I’m not sure how editing should work – interested contributors can email me so I can invite them to edit? Anyway, the draft should be up hopefully by Monday. Until then, comments and ideas always appreciated.