Chemical Informatics Letters

Volume 6, Issue 4; April 2003

Editor: Jonathan M Goodman

The Review Articles in Molecular Bioscience (RAMBIOS) database is available from its own web site and from the National Institute of Informatics, Japan, a computer science institute, and Kyushu University's Computing and Communications Centre. It covers more than eighty molecular bioscience journals currently from 1983 to 2002, from which articles are selected and supplied with keywords by experts.

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JISC resource guides

The Joint Information System Council (JISC) runs the Resource Discovery Network a collaboration of many educational and research organisations. Particularly relevant to chemistry are BIOME (health and life sciences), EEVL (Engineering, Mathematics and Computing) and PsiGate (physical sciences).

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SourceCode Repository

Where can you find small routines, solving a small problem which may be of use in a bigger program? Some of the following sites may be useful.

Open-source bioinformatics utilities and projects
Computational Chemistry List (last updated 1999; Whole programs)
CPAN Modules (Perl)
Giant Java Tree (Java)
NIST: Dictionary of Algorithms and Data Structures
Open Bioinformatics Foundation
The Open Science Project
Perl Monks Snippets
Planet Source Code (mainly packages, but some shorter routines, eg String Manipulation in Java)
Quantum Chemistry Program Exchange - not updated much recently. Charges a modest fee for each program.
SourceForge Snippets (many languages)
The Stony Brook Algorithm Repository

See also Survey of open-source molecular modelling programs some of which may be used to provide useful algorithms.

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SciELo

Scientific Electronic Library Online, run as a model for cooperative electronic publishing in developing countries, particularly Latin America and the Caribbean countries. A partnership between FAPESP (State of Sao Paulo Science Foundation), BIREME (Latin America and Caribbean Center on Health Sciences Information) and CNPq (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico). SciELo is a portal to the Brazilian, Chilean and the Cuban sites as well as a regional public health site.

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Cactus

The Erlangen/Bethesda Data and Online Services are a collaboration between the Computer Chemistry Centre at Erlangen-Nuremberg and the Laboratory of Medicinal Chemistry at the Centre for Cancer Research, National Cancer Institute, National Institutes of Health. Cactus is a distributed client/server system for the computation, management, analysis and visualisation of chemical information. The intention of these services is to provide to the public structures, data, tools, programs and other useful information. This includes a way to search the open NCI database of compounds - more than quarter of a million compounds.

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PASS

PASS (Prediction of Activity Spectra for Substances) predicts the biological activity spectrum for a compound from its structural formula, based on a training set of about forty six thousand biologically active compounds.

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Is XML any good?

A recent article by Tim Bray, who worked on the creation of XML, asked Is XML too hard? has catalysed debate about the merits of XML. A number of websites are run by people who do not like XML, including: Site A, Site B and Site C. The criticisms that it is verbose and offers users to much flexibility (for example, by allowing data to be stored both as elements and as attributes) are fairly easily refuted. A more serious criticism is that XML itself is fine, but XSL, XPATH, DTD, DOM, SAX, XML Schema, etc, etc. are complicated and unfriendly, and so the attractive simplicity of XML disappears as soon as it is actually used. After much discussion, the final conclusion is probably: XML is OK.

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Androgen database

The Androgen Receptor Gene Mutations Database is a database of mutations of the Androgen Receptor Gene, maintained by Bruce Gottlieb

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Pauling and DNA

The race to find the structure of DNA was won fifty years ago this month by Watson and Crick in Cambridge. Records from the archive of Linus Pauling give a documentary history of the events.

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Teaching Chemical Information

Many universities have courses on chemical information. The web sites listed range from introductions to using the library, to Masters degrees.

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ADMET

"ADMET in the 21st Century" is a conference run by the ACS in Florida, May 4-6, 2003. Speakers include: Scott Boyer (AstraZeneca), David D Christ (Bristol Myers Squibb), Sean Ekins (Concurrent Pharmaceuticals), Steve Hansel (Bristol Myers Squibb), Richard King (Merck), Paula Lapinskas (Vertex Pharmaceuticals), Scott Obach (Pfizer), Louis Plamondon, Donald Tweedie ( Boehringer Ingelheim), Daniel Verber, Ronald E White (Schering-Plough), Clive G Wilson (University of Strathclyde)

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Xapian

Xapian is an Open Source Probabilistic Information Retrieval library, released under the GPL.