Volume 5, Issue 6; December 2002
Editor: Jonathan M Goodman
Molecular Modelling Programs
- Last reviewed in CIL 3, #6, December 2001. This year, more programs are included.
This list excludes the big commercial offerings and concentrates
on programs for which the source code is available in some form and which are available freely or cheaply.
Usually there is a license agreement restricting what may be done with the source code.
- A molecular mechanics and dynamics program written in C by Professor Robert Harrison at Georgia State's Computer Science Department.
- B, formerly Biomer; Free; Source Code; Java. Has moved from its old location to
Professor David Case' group at the Scripps Research Institute. The last update was in 2000.
- A plane wave/pseudopotential implementation of Density Functional Theory. The CPMD group is coordinated by Professor Michele Parrinello (Director of the Swiss Center of Scientific Computations and Professor at the ETH Zuerich) and Dr Wanda Andreoni (Manager of the Computational Material Science Group at IBM Zurich Research Laboratory). An e-mail discussion list is available to discuss the program.
- A quantum chemistry program using SCF, MP2, MCSCF or CC wave functions. The strengths of the program are mainly in the areas of magnetic and (frequency-dependent) electric properties, and for studies of molecular potential energy surfaces. It has been actively developed in 2002, by its authors in Denmark, Sweden and Norway. The main authors are T. Helgaker, H. J. A. Jensen, P. Jorgensen, J. Olsen, K. Ruud, H. Ågren.
- Ab initio calculations. Martyn Guest, of the Daresbury Laboratory, is the main author.
- Ab initio calculations. The program is maintained by Dr Mark Gordon's research group at the Ames Laboratory.
- A computational chemistry software package released under the
C++; Linux. Developed in Finland by Tommi Hassinen and collaborators, and updated in 2002.
- Ichmech incorporated in 2001. Free to academics; no changes in 2002.
- Open Source Project; Mainly written in Python,with a small amount of C;
Konrad Hinsen, from CNRS Orleans. Updated in 2002.
- A quantum chemistry package developed by Professor Peter Knowles at Birmingham University and Professor Hans-Joachim Werner
at Stuttgart University.
- A computational chemistry package that is designed both for workstations and high-performance parallel supercomputers, developed in the William R Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory, USA.
- A free, full source code (Fortran) molecular mechanics and dynamics program, written in the Ponder Lab. Updated in June 2002.
- Do you want access to your research articles to be restricted to those
who can afford a subscription to the relevant journals? There are alternatives,
including submission to a BioMed Central journal. There is a fee for having a paper published for many of these journals.
- PubScience was a free source of scientific information which was closed
because it was simulataneously so important that it was a major threat to
commercial publishers and so unimportant that no-one would be inconvenienced by
its disappearance. The
Software and Information Industry Association lobbied for the closure, following its postion statement:
(a) Pubscience enters into commerce;
(b) PubScience provides access to a database of bibliographic information that duplicates and competes with databases made available by private sector publishers.
The SIIA issued a press release commenting on the closure,
commending the decision, as "PubSCIENCE substantially duplicated private
Not everybody is happy.
Is it fairer to charge researchers for the articles they use
than to charge taxpayers for the cost of running a Web site that makes
them available for free? The latter may well be the most cost effective way
of distributing information to small institutions, who will feel the loss the most.
PSIdev: Proteomics Standards Initiative
- The Proteomics Standards Initiative aims to define community standards for data representation in proteomics to facilitate data comparision, exchange and verification. It was founded at a HUPO (Human Proteome Organisation) meeting. Its first step will be standards for protein mass spectrometry data and protein-protein interaction data.
- Scalable Vector Graphics (SVG) 1.1 and Mobile SVG now proposed recommendations by W3C - a step up from a candidate recommendation.
SVG is an XML-based graphics format, which allows any image to be encoded
as a text file, and does not depend on licensing data-compression programs.
- OASIS is a not-for-profit, global consortium that drives the development, convergence and adoption of e-business standards. It has a working group on an Open XML Format for Office Applications, which might provide an alternative to the ubiquitous MicroSoft .doc format. This standard will be used by OpenOffice, a free program.
- Organic Syntheses is a standard reference publication for organic chemists. It is now available on-line using a ChemDraw plug-in.
- One of the world's fastest computers, using 294 processors in a Beowulf cluster, was built using cheap components. The calculations of interest must not require too much bandwith between the nodes. It is in 85th place amongst the most powerful computers in the world (Top 500) but at less than $1000 per node, it scores well on price per Teraflop.
- DSpace is a a joint project of MIT Libraries and the Hewlett-Packard Company, providing long-term storage for the digital products of MIT faculty and researchers. MIT's OpenCourseWare already provides material from MIT's courses.
Free Electronic Journals
- Elektronische Zeitschriftenbibliothek (Electronic Journals Library) provides an index
of journals by subject for which the full text is freely available.
Free Medical Journals is a similar site, which is dedicated to the promotion of free access to medical journals over the internet. These lists of journals will change rapidly as publishers change their charging
mechanisms, and new journals become available.
- An Indian Chemistry Portal for ChemInformatics
- Chemical Information from the National Library of Medicine in the USA.
© 2002 J M Goodman, Cambridge