Hi, some time ago I was asking similar questions (and haven't really found the perfect answer. So please allow me to re-post my thoughts to widen the discussion a little bit. Some bits are a little specific to computational chemistry. It's about Data and Knowledge Management Tools for Computational Chemists.
I am looking for software, tools or general approaches to get hold of the wealth of information that accumulates (mostly) electronically. In particular emails, text/PDF/XML or similar documents, bookmarks to websites and bibliographic references. The main request would be to be able to "store" information as is without having to enter it individually into a curated database. Filtering, indexing or cataloging through a script would be ok, though. A powerful search should be possible. Some specific points: - concerning bibliographic references, there is a wide variety of formats like Pubmed, email-alerts, quotes on websites, ... sometimes with a comment by the person who sent the reference, sometimes with an URL link, ... I would like to be able to gather all information in a first pass without having to parse the format by hand (eg where are authors, title, etc). I have now started using CiteULike which is an amazing tool, but has the disadvantage that it sits on a server that is not under my control. So potentially it could disappear from one day to the other which would be bad. - concerning bookmarks, it would be nice to also have elimination of duplicates and of dead links - taking it one step further, indexing the sites listed in the bookmarks might also be an additional useful step After some extensive search of the web, I could not come up with a fully satisfactory solution. My current best bet would be to index text and other files and email with a search engine like eg namazu. For bookmarks I'd ideally like to store them in XBEL format, but there seem to be only a limited number of tools, and none or very few that eliminate duplicates and dead links. A useful bookmark tool might be bookmarker. FramerD (a database) seems also an interesting possibility, but probably requires quite some substantial coding. In an ideal world, I'd also love to make use of some artificial intelligence code (eg Self-organizing maps, textual data mining,..) or some machine-learning tools, but my feeling is that those are not (yet) usable by non-experts. My question is what do other people in the field use ? Are there any miracular packages that would do all that I want ? Are there other/better approaches ? Thanks very much in advance. Marc Baaden >>> David Andel said: >> Hi all >> >> [..] >> For quite some time I am thinking about a versatile system of managing >> my personal literature collection. >> [..] -- BioMolSim meeting 2&3 Sep 2005: http://www.iecb.u-bordeaux.fr/satellite2005/ Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
