Cheminformatics Education, November 2008

The textbooks most commonly used in cheminformatics courses are those by Leach and Gillet²² and Gasteiger and Engel.²³ Books by Bajorath²⁴ and by Oprea²⁵ are also recommended. A few universities in China and India are also teaching cheminformatics but details of these are not well known in Europe and the United States.

The cheminformatics research group at Sheffield runs an intensive one week short course in cheminformatics (“A Practical Introduction to Chemoinformatics”) which provides hands-on training for scientists already in employment. It is sponsored by student bursaries from the Molecular Graphics and Modelling Society and CSA Trust. It has been run annually over four days since 2001, delivered to about 18 delegates from the United Kingdom, mainland Europe and the United States, mostly from industry. Numbers are restricted due to the intense nature and practical component of the course. The Institute of Cheminformatics Studies in India offers 12-month distance training programs²⁶ for industry. The Louis Pasteur University of Strasbourg will also be offering short courses for industry,²⁷ starting in May 2009.

Distance education at Indiana uses Web conferencing and teleconferencing. There are links with the University of Michigan, to run the class at both Universities (but centered in Indiana). Lectures are recorded. Out of 75 students, 39 have been distance education students. It has been reported18 that the benefits of distance education win out over the challenges. A wiki is used for the introductory cheminformatics class. The University of Erlangen-Nuremberg offers teaching modules for cheminformatics on the Web,²⁸ in collaboration with FIZ CHEMIE Berlin, developed within the scope of “Vernetztes Studium-Chemie”, a lead project of the German Federal Ministry of Education and Research. Currently, only some chapters are available.

DouglasConnect runs both public and private workshops and training programs in the areas of knowledge management and innovation. It has also an eCheminfo “community” and runs hands-on eChemInfo workshops.²⁹

One problem in developing cheminformatics teaching courses is the lack of freely available software. In bioinformatics much software has been developed in academia and is available at zero or low cost but only recently has free cheminformatics software begun to appear. For example, at Indiana, ChemBioGrid³⁰ is exploiting publicly available chemical information. Several databases are exposed through Web service wrappers, and the research team has also created Web service wrappers around several free and commercial cheminformatics tools. It also has a close working relationship with the Murray-Rust group in the Unilever Centre for Molecular Informatics at Cambridge University and has implemented several of their Web services locally, The researchers have also implemented a large amount of the functionality of the Chemistry Development Kit (CDK)³¹ as Web services, plus many services relating to the R statistical package.

In the Chemoinformatics Community Wiki³² a number of researchers and teachers in cheminformatics have joined forces to define the field in terms of a curriculum and to create open teaching materials in cheminformatics and chemical information based on open technologies and standards.

The practical sessions of FCT Lisbon’s cheminformatics course are based on software freely available to students (free cross-platform Java software available for different operating systems), as well as public data sets and Web services. All required resources are integrated into a Web portal for the course,³³ enabling students to study and practice on their own, at the practical sessions and after classes. Use of the material on the Web is authorized to other academic institutions provided the source is acknowledged.

Synergix Ltd. has developed commercial educational resources for drug design, molecular modeling, cheminformatics and medicinal chemistry. In 2002 the Company launched a computer-based course³⁴ entitled “Molecular Conceptor" which takes advantage of interactive multimedia systems.

The catalog of courses and resources compiled in this paper might suggest that cheminformatics education is flourishing. It is not. Many examples of isolated efforts are cited here but there is no European or international coordination. Cheminformatics practitioners have still not defined their discipline and its impact, let alone successfully made a case to governments and funding agencies. Perhaps the pharmaceutical industry, which has much to lose, should be further collaborating with academia to address the challenge.