Comments on: The case for open science http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/ Fri, 21 Nov 2008 19:13:10 +0000 http://wordpress.org/?v=2.6.2 By: Bioinformatics Zen » My open science notebook http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-2692 Bioinformatics Zen » My open science notebook Mon, 10 Sep 2007 18:06:14 +0000 http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-2692 [...] still very keen on the open notebook science movement: I think open collaboration will benefit everyone involved. So, when I should have been working on the Bio::Blogs special edition, I was instead tinkering [...] [...] still very keen on the open notebook science movement: I think open collaboration will benefit everyone involved. So, when I should have been working on the Bio::Blogs special edition, I was instead tinkering [...]

]]> By: Daniel Swan http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1317 Daniel Swan Tue, 26 Jun 2007 10:19:27 +0000 http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1317 Mike, you might be interested in similar musings from Frank Gibson at Newcastle: http://peanutbutter.wordpress.com/2007/06/26/do-scientists-really-believe-in-open-science/ Mike, you might be interested in similar musings from Frank Gibson at Newcastle:

http://peanutbutter.wordpress.com/2007/06/26/do-scientists-really-believe-in-open-science/

]]> By: Mike http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1307 Mike Mon, 25 Jun 2007 13:41:28 +0000 http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1307 @ Luca It is a shame that bioinformatics tools recieve little support once they are published. I think the scientific system does encourage this - once the tool has been published there is little reward for sustaining support. Also people leave labs, and funding runs out for projects which means that there is no able to support the tool. As an extreme example imagine a case where instead of contributing code to the linux codebase, everybody created their own distribution to include the feature they wanted. I think this something like the scenario you are describing. Perhaps if the journals encouraged tools to submitted with a GPL license, as well as papers that were based on improving already existing tools with new functionality. @Nanog Thanks for your comments. I'm working <a href="http://wiki.nodalpoint.org/open_science" rel="nofollow">another special edition</a> for bioblogs, the focus on open science. You're more than welcome to take and look and contribute. @ Luca
It is a shame that bioinformatics tools recieve little support once they are published. I think the scientific system does encourage this - once the tool has been published there is little reward for sustaining support. Also people leave labs, and funding runs out for projects which means that there is no able to support the tool.

As an extreme example imagine a case where instead of contributing code to the linux codebase, everybody created their own distribution to include the feature they wanted. I think this something like the scenario you are describing. Perhaps if the journals encouraged tools to submitted with a GPL license, as well as papers that were based on improving already existing tools with new functionality.

@Nanog
Thanks for your comments.
I’m working another special edition for bioblogs, the focus on open science. You’re more than welcome to take and look and contribute.

]]> By: nanog http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1299 nanog Sun, 24 Jun 2007 20:48:23 +0000 http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1299 Great topic! Thank you Mike! I think it's will be very useful for everybody who read this topic if we can give some best examples of Open Science projects, in my minds - http://www.plos.org http://www.biomedcentral.com http://precedings.nature.com Great topic!
Thank you Mike!
I think it’s will be very useful for everybody who read this topic if we can give some best examples of Open Science projects,
in my minds -

http://www.plos.org
http://www.biomedcentral.com
http://precedings.nature.com

]]> By: Medicine 2.0: The Second Edition « ScienceRoll http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1294 Medicine 2.0: The Second Edition « ScienceRoll Sun, 24 Jun 2007 15:09:21 +0000 http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1294 [...] Barton at Bioinformatics Zen tells us his opinion on Science 2.0. I loved this sentence: Despite all this I am very in favour of open science, and would like to [...] [...] Barton at Bioinformatics Zen tells us his opinion on Science 2.0. I loved this sentence: Despite all this I am very in favour of open science, and would like to [...]

]]> By: Luca Beltrame http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1273 Luca Beltrame Fri, 22 Jun 2007 21:19:28 +0000 http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1273 Mike, I can relate to that finding by experience. Over the three years I've been working in my group I've tested several microarray tools. Most of those (but luckily, not all of them) had been abandoned along the way, or had bugs that prevented proper use. Some even (which IMO is somewhat shameful) presented algorithms without proper implementations, which were of course impossible to test. Recently I was at a meeting over an improvement of a <a href="http://www.ducciocavalieri.org/bio.htm" rel="nofollow">pathway analysis tool</a> and the software engineer who wrote it said something like "We always reinvent the wheel because other groups don't share information". For these cases I <a href="http://www.dennogumi.org/2006/11/02/software-and-biological-research/" rel="nofollow">advocate the use of licenses such as the GPL</a> for biological software (or even BSD) so that at least someone else can pick an abandoned project and improve it. Mike, I can relate to that finding by experience. Over the three years I’ve been working in my group I’ve tested several microarray tools. Most of those (but luckily, not all of them) had been abandoned along the way, or had bugs that prevented proper use. Some even (which IMO is somewhat shameful) presented algorithms without proper implementations, which were of course impossible to test.

Recently I was at a meeting over an improvement of a pathway analysis tool and the software engineer who wrote it said something like “We always reinvent the wheel because other groups don’t share information”.
For these cases I advocate the use of licenses such as the GPL for biological software (or even BSD) so that at least someone else can pick an abandoned project and improve it.

]]> By: Mike http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1250 Mike Thu, 21 Jun 2007 21:41:00 +0000 http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1250 <p>Thanks Luca. I think your example of microarrays is a particularly good one. There are a lot of microarray analysis tools being published. I think that this leads to researchers suffering when they need to analyse their data, as there are a huge selection to choose from - it's difficult to know which one to pick. As you say, the publish or perish philosophy encourages bioinformaticians to create and publish a new microarray tool, rather than improve an already existing one. The latter option is the one more beneficial to the community. A related result, a <a href="http://www.ghastlyfop.com/blog/2007/03/software-availabilty-quick-survey-using.html" rel="nofollow">quick survey</a> carried out by Stew showed that 12% of applications published in bioinformatics one year ago were no longer available.</p> Thanks Luca. I think your example of microarrays is a particularly good one. There are a lot of microarray analysis tools being published. I think that this leads to researchers suffering when they need to analyse their data, as there are a huge selection to choose from - it’s difficult to know which one to pick. As you say, the publish or perish philosophy encourages bioinformaticians to create and publish a new microarray tool, rather than improve an already existing one. The latter option is the one more beneficial to the community. A related result, a quick survey carried out by Stew showed that 12% of applications published in bioinformatics one year ago were no longer available.

]]> By: Journal policies on preprint servers http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1249 Journal policies on preprint servers Thu, 21 Jun 2007 21:16:09 +0000 http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1249 [...] the theme of open science, I think one of the most important issues that needs clarification are the journals position to you [...] [...] the theme of open science, I think one of the most important issues that needs clarification are the journals position to you [...]

]]> By: Luca Beltrame http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1230 Luca Beltrame Thu, 21 Jun 2007 06:56:47 +0000 http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1230 I would really love to see a more open approach like the one you describe. As I see in the field of microarrays, the jealousy and the secrets surrounding the research sometimes are even against common sense. And sometimes secrecy is not worth it as the published results leave a lot to be desired. I believe that the concept of "publish or perish" needs an overhaul... right now it almost feels each lab is a secret society working on some (secret) plan for world domination. I would really love to see a more open approach like the one you describe. As I see in the field of microarrays, the jealousy and the secrets surrounding the research sometimes are even against common sense. And sometimes secrecy is not worth it as the published results leave a lot to be desired.
I believe that the concept of “publish or perish” needs an overhaul… right now it almost feels each lab is a secret society working on some (secret) plan for world domination.

]]> By: Mike http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1211 Mike Wed, 20 Jun 2007 16:16:31 +0000 http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1211 Thanks Pedro Could it be that open science is inevitable, it's just how long it takes to get there? The concept is definitely gaining more and more ground. It could move slowly through the research community, or a really good example it could convince a lot of people. Probably both. I'm sure blogging positively encourages open science too. Maybe it's part of the state of mind. Thanks Pedro
Could it be that open science is inevitable, it’s just how long it takes to get there? The concept is definitely gaining more and more ground. It could move slowly through the research community, or a really good example it could convince a lot of people. Probably both.
I’m sure blogging positively encourages open science too. Maybe it’s part of the state of mind.

]]> By: pedrobeltrao http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1170 pedrobeltrao Tue, 19 Jun 2007 09:23:38 +0000 http://www.bioinformaticszen.com/2007/06/the-case-for-open-science/#comment-1170 Best of luck :). Another possibility is also to share directions that you do not intend on pursuing. This is what I have been trying so far. Sharing ongoing research for me is hard because must of the stuff that I have been working recently have been collaborations and it is hard to talk several people into sharing results online (specially when it is a naive PhD student trying to convince them). Best of luck :). Another possibility is also to share directions that you do not intend on pursuing. This is what I have been trying so far. Sharing ongoing research for me is hard because must of the stuff that I have been working recently have been collaborations and it is hard to talk several people into sharing results online (specially when it is a naive PhD student trying to convince them).

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