Chemical Informatics Letters

Volume 8, Issue 1; January 2004

Editor: Jonathan M Goodman

Science Inventory
A searchable catalog of more than 4,000 science activities of the US environmental protection agency (EPA). The site allows keyword searches and highlights nine interdisciplinary topics: Aging Initiative; Contaminated Sediments; Ecological Assessment Tools; Genomics; Tribal Science; Children's Health; Cumulative Risk; Environmental Justice; Non-indigenous Species.

Systems Biology
What is 'Systems Biology'? A definition, from the American Chemical Society (C&EN, May 2003): Integrative approach in which scientists study pathways and networks will touch all areas of biology, including drug discovery. The Stuttgart University definition: Systematic approach, not focused on individual genes and individual proteins, instead interested in analyzing whole systems of genes or proteins by capturing information from many different elements of the overall system. The UMIST approach: Leroy Hood's definition is that it involves 'integrating technology, biology and computation'.

There are many websites, including: Systems Biology and Systems Biology! A Conference, Mass Spectrometry in Systems Biology, another Conference, software resources, SBML, CSBi, and PNNL, with interest from UCSF, Havard, Munich, Stuttgart, Jena, Japan, Italy, and Carnegie Mellon

A search using Google, gave the following numbers of hits:

  • "systems biology" 2003: 23500
  • "systems biology" 2002: 14800
  • "systems biology" 2001: 11200
  • "systems biology" 2000: 9990
  • "systems biology" 1999: 6650
A search of the scientific literature for "systems biology" gave almost 150 hits, most of which more than a hundred were from 2003, and nothing from before 1998. One of the first was a paper by Hood: 'Systems biology: New opportunities arising from genomics, proteomics and beyond' Experimental Hematology 1998, 26. Kitano wrote a brief overview in Nature 2002, 295, 1662.

EPA Right to know initiative
This project has been running since 1998, providing public access to information about high volume production chemicals.

Chemical Informatics Portal
This server, run by David Wild (Wild Ideas) at the University of Michigan's pharmaceutical engineering department, has a list of links and information about the Michigan 'Introduction to Chemoinformatics' class.

Heidelberg Central Spectroscopy Department - Molecular Modeling
Particular interested in sugar, but also web-based molecular modelling.

Information Retrieval in Chemistry
This page was updated in December 2003. It provides general chemistry links, rather than focussing on chemical informatics, despite describing itself as a "ChemInformatics host". The Ulysses search page holds classified listings of science-related search engines and sciences information directories.

Search Engines
Google is a very effective search engine, but it has many competitors. Can it retain dominance? Searching is a difficult problem. Search Engine Watch analyses the different programs which are available. Competitors to Google include Teoma which indexes fewer sites, and so may be more focussed, which tries to be comprehensive. Automatically grouping results ( Vivisimo; Grokker; Kartoo) may be a good approach. Subject-specific search engines may be appropriate for chemistry, although Google has done as good a job in many cases. Here are some science-specific search engines:


(7)CiteSeer - Scientific Literature Digital Library





Scholarly Publishing
The UK Parliament's Science and Technology Committee is to look into scientific publication, under the chairmanship of Ian Gibson, a former chemistry lecturer. The The Committee would welcome written evidence from interested organisations and individuals.

ChemInfoStream Barry Hardy's Chemical Informatics blog has news and views from the world of chemical information, modelling and informatics. There is also a Open source discussion - with access that is not open but requires registration and payment. (Correction - March 2004 - registration is required, but payment is not required to participate in the open source discussion))

Open source software
Mark Webbink, Senior Vice President and General Counsel of Red Hat, Inc., wrote this article for corporate attorneys, explaining free and open source software and comparing various open source licenses, detailing how the GPL really works, explaining US copyright law, and listing some corporate law office best practices for software, from the standpoint of what policies are prudent for the corporate environment. He comments on a series of myths about open source software, and comments on pitfalls to avoid.

ADMET-1 Conference
The ADMET-1 conference will be on February 11th-13th, 2004 in San Diego, California. Topics include: Computational Toxicology, Computational Metabolism/Excretion, Experimental ADMET, Computational Absorption/Distribution and a scientific workshop on Tox-ML.

Courses in Chemical Informatics

(Last surveyed December 2001 Chem. Inf. Lett. 2001, 3, #4.).

© 2004 J M Goodman, Cambridge
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