Comments for Science in the open http://blog.openwetware.org/scienceintheopen An openwetware blog on the challenges of open and connected science Wed, 18 Nov 2009 23:47:21 +0000 http://wordpress.org/?v=2.3.1 http://creativecommons.org/licenses/by/3.0/ Comment on Google Wave in Research - Part II - The Lab Record by Lasse Buck http://feedproxy.google.com/~r/CommentsForScienceInTheOpen/~3/nYLra78dchE/ Lasse Buck Wed, 18 Nov 2009 09:07:54 +0000 http://blog.openwetware.org/scienceintheopen/2009/06/08/google-wave-in-research-part-ii-the-lab-record/#comment-288825 Hi Cameron - Great work! When we use a data modifying robot like the Reduction Robot, only the raw data and the resulting data is captured in the waves. The nature of the actual processing remains hidden. In your case, the goal is to create a versioned, provenanced, and shareable workflow. In many cases, versioned means that everything should also be trackable i.e. repeatable. In order to obtain that, proper effort must be made to: 1. Ensure the credentials of the robots used. 2. Record versioning of the robots used or make sure that they can not be altered. I expect my considerations are also relevant in your case? Hi Cameron - Great work!

When we use a data modifying robot like the Reduction Robot, only the raw data and the resulting data is captured in the waves. The nature of the actual processing remains hidden.

In your case, the goal is to create a versioned, provenanced, and shareable workflow. In many cases, versioned means that everything should also be trackable i.e. repeatable.
In order to obtain that, proper effort must be made to:
1. Ensure the credentials of the robots used.
2. Record versioning of the robots used or make sure that they can not be altered.

I expect my considerations are also relevant in your case?

]]> http://blog.openwetware.org/scienceintheopen/2009/06/08/google-wave-in-research-part-ii-the-lab-record/#comment-288825 Comment on Nature Communications Q&A by Twitter Trackbacks for Science in the open » Nature Communications Q&A [openwetware.org] on Topsy.com http://feedproxy.google.com/~r/CommentsForScienceInTheOpen/~3/bfQZxKiA32U/ Twitter Trackbacks for Science in the open » Nature Communications Q&A [openwetware.org] on Topsy.com Mon, 16 Nov 2009 12:01:14 +0000 http://blog.openwetware.org/scienceintheopen/2009/11/16/nature-communications-qa/#comment-288815 [...] Science in the open » Nature Communications Q&A blog.openwetware.org/scienceintheopen/2009/11/16/nature-communications-qa/ – view page – cached Science in the open - An openwetware blog on the challenges of open and connected science [...] […] Science in the open » Nature Communications Q&A blog.openwetware.org/scienceintheopen/2009/11/16/nature-communications-qa/ – view page – cached Science in the open - An openwetware blog on the challenges of open and connected science […]

]]> http://blog.openwetware.org/scienceintheopen/2009/11/16/nature-communications-qa/#comment-288815 Comment on Some (probably not original) thoughts about originality by Tzar Mohd Nizam http://feedproxy.google.com/~r/CommentsForScienceInTheOpen/~3/bpsgwXk_CBo/ Tzar Mohd Nizam Mon, 16 Nov 2009 01:28:15 +0000 http://blog.openwetware.org/scienceintheopen/2009/08/25/some-probably-not-original-thoughts-about-originality/#comment-288810 hi all! i'm new in this area. consider this situation: your paper has been accepted by a journal - problem is the journal is not indexed - therefore your work can't be shared with many people except for those who subscribe to that journal. can u republish your article in another indexed journal? tq hi all! i’m new in this area. consider this situation: your paper has been accepted by a journal - problem is the journal is not indexed - therefore your work can’t be shared with many people except for those who subscribe to that journal. can u republish your article in another indexed journal? tq

]]> http://blog.openwetware.org/scienceintheopen/2009/08/25/some-probably-not-original-thoughts-about-originality/#comment-288810 Comment on Google Wave in Research - Part II - The Lab Record by Cameron Neylon http://feedproxy.google.com/~r/CommentsForScienceInTheOpen/~3/S5q05SifOHM/ Cameron Neylon Fri, 13 Nov 2009 08:29:37 +0000 http://blog.openwetware.org/scienceintheopen/2009/06/08/google-wave-in-research-part-ii-the-lab-record/#comment-288802 Robert, I've played around a bit with an existing paper. This was mostly as an exercise to see what kind of tools we would need to aid the process. There are still some pretty big gaps, particularly in the data handling as well as the logistics of moving things around (i.e. blips that you might want to re-order in the drafting process which is currently not possible). So no, working towards it but I'm not aware of it be ing taken the whole way yet. I am hoping to put together a paper about the building tools to write a paper in wave, in wave, if that makes sense as a way of exploring the issues. Robert, I’ve played around a bit with an existing paper. This was mostly as an exercise to see what kind of tools we would need to aid the process. There are still some pretty big gaps, particularly in the data handling as well as the logistics of moving things around (i.e. blips that you might want to re-order in the drafting process which is currently not possible). So no, working towards it but I’m not aware of it be ing taken the whole way yet.

I am hoping to put together a paper about the building tools to write a paper in wave, in wave, if that makes sense as a way of exploring the issues.

]]> http://blog.openwetware.org/scienceintheopen/2009/06/08/google-wave-in-research-part-ii-the-lab-record/#comment-288802 Comment on Google Wave in Research - Part II - The Lab Record by Bobby James http://feedproxy.google.com/~r/CommentsForScienceInTheOpen/~3/0_i6jdq_ArI/ Bobby James Thu, 12 Nov 2009 22:15:53 +0000 http://blog.openwetware.org/scienceintheopen/2009/06/08/google-wave-in-research-part-ii-the-lab-record/#comment-288800 Has anyone yet tried to actually take a paper from first sentence through data analysis, figure production, and at least to submission? How has it worked? Where are the rough spots? I work as an epidemiologist/statistician and am wondering about Wave for all sorts of collaborative tasks, but I have yet to assemble a set of colleagues with accounts to actually skin our knees on the task. Has anyone yet tried to actually take a paper from first sentence through data analysis, figure production, and at least to submission? How has it worked? Where are the rough spots? I work as an epidemiologist/statistician and am wondering about Wave for all sorts of collaborative tasks, but I have yet to assemble a set of colleagues with accounts to actually skin our knees on the task.

]]> http://blog.openwetware.org/scienceintheopen/2009/06/08/google-wave-in-research-part-ii-the-lab-record/#comment-288800 Comment on The trouble with business models (Facebook buys Friendfeed) by Jodi Schneider http://feedproxy.google.com/~r/CommentsForScienceInTheOpen/~3/6eWGhp1zmmc/ Jodi Schneider Tue, 10 Nov 2009 15:21:44 +0000 http://blog.openwetware.org/scienceintheopen/2009/08/11/the-trouble-with-business-models-facebook-buys-friendfeed/#comment-288794 NEH has just funded MediaCommons to aggregate streams. See <a href="http://mediacommons.futureofthebook.org/blog/2009/11/10/mediacommons-digital-scholarly-network-unveiling-profile-system" rel="nofollow">http://mediacommons.futureofthebook.org/blog/2009/11/10/mediacommons-digital-scholarly-network-unveiling-profile-system</a> for details. NEH has just funded MediaCommons to aggregate streams. See http://mediacommons.futureofthebook.org/blog/2009/11/10/mediacommons-digital-scholarly-network-unveiling-profile-system for details.

]]> http://blog.openwetware.org/scienceintheopen/2009/08/11/the-trouble-with-business-models-facebook-buys-friendfeed/#comment-288794 Comment on Reflections on Science 2.0 from a distance - Part II by Cameron Neylon http://feedproxy.google.com/~r/CommentsForScienceInTheOpen/~3/v5W_Pw_jEdw/ Cameron Neylon Sun, 08 Nov 2009 07:59:46 +0000 http://blog.openwetware.org/scienceintheopen/2009/11/06/reflections-on-science-20-from-a-distance-part-ii/#comment-288789 I think I would give two answers to that question. One is whether there is a risk that describing things in terms of functional modules means we will find them. There is always a place for looking at things from multiple angles. The other is that I think what you are talking about is communicating knowledge and models, whereas I was focussed more on the capture. But over all I think most of this remains at an early stage. We should describe what we can with precisions, effectively capture what we are actually doing, but retain an open mind about the bigger picture. Although that's just really describing good science practice anyway I suppose. I think I would give two answers to that question. One is whether there is a risk that describing things in terms of functional modules means we will find them. There is always a place for looking at things from multiple angles.

The other is that I think what you are talking about is communicating knowledge and models, whereas I was focussed more on the capture. But over all I think most of this remains at an early stage. We should describe what we can with precisions, effectively capture what we are actually doing, but retain an open mind about the bigger picture. Although that’s just really describing good science practice anyway I suppose.

]]> http://blog.openwetware.org/scienceintheopen/2009/11/06/reflections-on-science-20-from-a-distance-part-ii/#comment-288789 Comment on Reflections on Science 2.0 from a distance - Part II by Rick Smith http://feedproxy.google.com/~r/CommentsForScienceInTheOpen/~3/7l4UrlJyqzY/ Rick Smith Sun, 08 Nov 2009 05:33:37 +0000 http://blog.openwetware.org/scienceintheopen/2009/11/06/reflections-on-science-20-from-a-distance-part-ii/#comment-288788 Given the nature of systems biology/complex systems with emergent behaviors, is it more instructive to build ontologies ad hoc, or to establish ontologies for known functional modules and then find them in unexplored systems? The latter idea was developed to a great extent in Miller's Living Systems, though they often feel less intuitive than they were probably meant to be Given the nature of systems biology/complex systems with emergent behaviors, is it more instructive to build ontologies ad hoc, or to establish ontologies for known functional modules and then find them in unexplored systems? The latter idea was developed to a great extent in Miller’s Living Systems, though they often feel less intuitive than they were probably meant to be

]]> http://blog.openwetware.org/scienceintheopen/2009/11/06/reflections-on-science-20-from-a-distance-part-ii/#comment-288788 Comment on Reflections on Science 2.0 from a distance - Part II by Twitter Trackbacks for Science in the open » Reflections on Science 2.0 from a distance - Part II [openwetware.org] on Topsy.com http://feedproxy.google.com/~r/CommentsForScienceInTheOpen/~3/6HTF5sSCfOc/ Twitter Trackbacks for Science in the open » Reflections on Science 2.0 from a distance - Part II [openwetware.org] on Topsy.com Sat, 07 Nov 2009 09:02:43 +0000 http://blog.openwetware.org/scienceintheopen/2009/11/06/reflections-on-science-20-from-a-distance-part-ii/#comment-288784 [...] Science in the open » Reflections on Science 2.0 from a distance - Part II blog.openwetware.org/scienceintheopen/2009/11/06/ – view page – cached Science in the open - An openwetware blog on the challenges of open and connected science [...] […] Science in the open » Reflections on Science 2.0 from a distance - Part II blog.openwetware.org/scienceintheopen/2009/11/06/ – view page – cached Science in the open - An openwetware blog on the challenges of open and connected science […]

]]> http://blog.openwetware.org/scienceintheopen/2009/11/06/reflections-on-science-20-from-a-distance-part-ii/#comment-288784 Comment on Reflections on Science 2.0 from a distance - Part I by Keith http://feedproxy.google.com/~r/CommentsForScienceInTheOpen/~3/_Xxc8uUgGng/ Keith Fri, 06 Nov 2009 18:59:53 +0000 http://blog.openwetware.org/scienceintheopen/2009/11/05/reflections-on-science-20-from-a-distance-part-i/#comment-288783 "The second key aspect of a blog post is that it natively comes with a unique URL" One problem that comes to mind would be the lack of permanence for web content. If a researcher decides to take down his or her blog, or even simply move the blog, then the URL's are no longer valid. Perhaps something between a blog and an online open-access journal with Wikipedia-like history tracking would fix the problem? “The second key aspect of a blog post is that it natively comes with a unique URL”

One problem that comes to mind would be the lack of permanence for web content. If a researcher decides to take down his or her blog, or even simply move the blog, then the URL’s are no longer valid. Perhaps something between a blog and an online open-access journal with Wikipedia-like history tracking would fix the problem?

]]> http://blog.openwetware.org/scienceintheopen/2009/11/05/reflections-on-science-20-from-a-distance-part-i/#comment-288783