Comments on: First draft of PSB proposal http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/ I have severely improved my predicament Wed, 04 Nov 2009 21:49:47 +0000 http://wordpress.com/ hourly 1 By: Benjamin Good http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-19 Benjamin Good Thu, 31 Jan 2008 18:05:00 +0000 http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-19 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. <br/><br/>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. 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.

]]> By: shwu http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-18 shwu Wed, 30 Jan 2008 22:28:00 +0000 http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-18 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: http://docs.google.com/Doc?docid=dv4t5rx_33fpxx9pw5&hl=en 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: http://docs.google.com/Doc?docid=dv4t5rx_33fpxx9pw5&hl=en

]]> By: Benjamin Good http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-17 Benjamin Good Wed, 30 Jan 2008 18:11:00 +0000 http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-17 Mentioning that it would mean a trip to Hawaii in January never hurts.. - especially when recruiting from Canadian latitudes! Mentioning that it would mean a trip to Hawaii in January never hurts.. – especially when recruiting from Canadian latitudes!

]]> By: Benjamin Good http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-16 Benjamin Good Wed, 30 Jan 2008 17:36:00 +0000 http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-16 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) . 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) .

]]> By: Cameron Neylon http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-14 Cameron Neylon Tue, 29 Jan 2008 22:12:00 +0000 http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-14 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. 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.

]]> By: Cameron Neylon http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-13 Cameron Neylon Tue, 29 Jan 2008 22:11:00 +0000 http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-13 Overall this looks really good. Bill has some good points though I think he undersells his experience. <br/><br/>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. <br/><br/>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. 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.

]]> By: shwu http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-12 shwu Tue, 29 Jan 2008 17:20:00 +0000 http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-12 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! 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!

]]> By: Bill Hooker http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-11 Bill Hooker Tue, 29 Jan 2008 09:52:00 +0000 http://shirleywho.wordpress.com/2008/01/29/first-draft-of-psb-proposal/#comment-11 I'm a bit out of my depth with a computing conference, but some quick ideas/points/attempts to help:<br/><br/>-- links for your standards examples:<br/><br/>http://flowcyt.sourceforge.net/<br/>http://sbml.org/index.psp<br/>http://www.nlm.nih.gov/mesh/meshhome.html<br/>http://www.nlm.nih.gov/research/umls/<br/>http://www.biopax.org/<br/><br/>-- the post to cite on ONS is http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html<br/><br/>-- 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<br/><br/>-- 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<br/><br/>-- 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. :-) 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:

http://flowcyt.sourceforge.net/
http://sbml.org/index.psp
http://www.nlm.nih.gov/mesh/meshhome.html
http://www.nlm.nih.gov/research/umls/
http://www.biopax.org/

– the post to cite on ONS is http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html

– 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. :-)

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