http://www.nodalpoint.org/nodalpoint_tags/open_research Comments for "open research" en http://www.nodalpoint.org/2007/07/13/discussing_open_research#comment-3797 <p>Interesting question. A bug-tracker of sorts (for "bugs" in biological analysis) might be an effective tool to use. The difficulties with such an approach are:<br /> 1. Grouping the various "bugs" into logical groups. By that I mean any biological analysis is entered as a discrete project, with a listing of bugs and solutions. The "solutions" to a given problem (er, project) may then become a new bug in that evaluation of the "solutions" need to be listed, in the context where they are most appropriate. Each "solution" may of course include other "bugs" which would need to be linked together somehow (more than what bugzilla can do, for example - a "wikified" bug tracker? Which leads to the second difficulty).<br /> 2. There should be an intuitive way of browsing for, linking to, and posting said bugs and solutions that is restricts posts to accepted categories. Which might just mean boiling down bioinformatics research to the core procedural problems and enforcing those procedural steps as categories or grouping of the "bugs". Or it might mean looking in broad terms at biological analysis. Or a division between the two implementations - a low-level focus and a high-level focus of biological analysis and research wikibug-tracker.</p> <p>As a side note, you might be interested in a little project that I put online in June called "RiToJo" (<a href="http://subi.chem.ucla.edu/~mako/ritojo.html" title="http://subi.chem.ucla.edu/~mako/ritojo.html">http://subi.chem.ucla.edu/~mako/ritojo.html</a>) which is a tiddlyWiki-based code snippet repository for bioinformatics. Obstensively a "rosetta stone" of code procedures between different languages for bioinformatics tasks, it really is just meant as a starting point for an electronic bioinformatics lab notebook and that's what I use it for on a thumb-drive that I carry everywhere. Of course, there's a ton of stuff in my ELN that I don't share with RiToJo and most RiToJo users (there's three at UCLA, which accounts for many of the bioinformatics students at UCLA, not counting one professor for whom I harbor distinct disdain) also don't want to allow projects from their own RiToJo version to be read by the world (and possibly get scooped in the process) and like myself are too lazy to parse out non-sensitive parts of their local RiToJo ELN and merge changes. So after attempting to organize my view of bioinformatics code into RiToJo and make it chock-full of information I lost interest in it other than, like I said, as a somewhat useful starting point for someone to download and make their own ELN (tiddlyWiki's strength is that there is no install, and no web server necessary for running it locally - it's just one html file plus any associated image files).</p> <p>If you're serious about an open resource discussion, of course, then this discussion qualifies as the first "bug". How to present said information?</p> <p>---</p> <p>The major difference between a thing that might go wrong and a thing that cannot possibly go wrong is that when a thing that cannot possibly go wrong goes wrong, it usually turns out to be impossible to get at or repair.<br /> �Douglas Adams</p> <br class="clear" /> Thu, 19 Jul 2007 06:50:09 -0400 mako comment 3797 at http://www.nodalpoint.org http://www.nodalpoint.org/2007/07/13/discussing_open_research#comment-3743 <p>Yes, that sounds good. I would like to see some kind of resource for bioinformatics methods, review of methods, examples from real research, how-tos, cookbooks. We discussed this a little in response to the Bio::Blogs special edition a while ago.</p> <p>I also think the Nodal wiki is a natural repository for a lot of these things - it's set up, we know where to find it and it's relatively easy for people to create content there.</p> <br class="clear" /> Fri, 13 Jul 2007 20:26:02 -0400 Neil comment 3743 at http://www.nodalpoint.org http://www.nodalpoint.org/2007/07/13/discussing_open_research#comment-3742 <p>I have an interview with Dr Redfield coming to SciView where I asked about her views on Open Science. In fact there will be another new interview soon with Geneious' Alexei Drummond. Good timing maybe played a role here.</p> <p>Paulo</p> <br class="clear" /> Fri, 13 Jul 2007 10:23:11 -0400 nuin comment 3742 at http://www.nodalpoint.org http://www.nodalpoint.org/2007/07/13/discussing_open_research#comment-3741 <p>What do you think about putting in bioinformatic reviews ? I did once a mini review on analysis of protein evolution and I have been thinking of writing one on domain-domain interaction predictions methods. Maybe we could collect some of the best blog content into the wiki along the way for refinement etc. I think I would still post it on the blog and just mirror it on the wiki for possible participation for others and to have a place to build up.</p> <br class="clear" /> Fri, 13 Jul 2007 08:49:10 -0400 PedroBeltrao comment 3741 at http://www.nodalpoint.org