[gmx-users] Data and Knowledge Management Tools for Computational Chemists
baaden at smplinux.de
Thu Jan 6 14:40:18 CET 2005
I hope this message is not too off-topic wrt Gromacs, but I think it
directly relates to the production, treatment and dissemination of
scientific results, eg those obtained with Gromacs.
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 (but eventually also results from calculations,
location of trajectories, ...).
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
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).
- 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.
Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
mailto:baaden at smplinux.de - http://www.marc-baaden.de
FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
More information about the gromacs.org_gmx-users