Message to Users......

The field of computational biology has witnessed tremendous change in the years gone by. In its initial infancy stage, computation biology was used to solve only smaller biological problems. However, with the advancement in the field, scientists started using computational biological techniques heavily for solving even complex problems like protein modeling. In present era, computational biology is dominated by bioinformatics where managing, analyzing and mining biological data is a major challenge. And one of the major challenges for any computer or bioinformatics professional is to understand need of biologist and develop user-friendly software.

When I joined Institute of Microbial Technology (IMTECH), Chandigarh in 1986 as computer scientist, my primary duty was to provide computer services to IMTECH. At that time computer programs were developed for automation of institute. In 1990, first scientific program ELISA_eq was developed for computing antigen/antibody concentration from ELISA data in GW-BASIC. From 1990-93 computer programs for well defined biological problems like mapping restriction sites, calculation of DNA/protein size were also developed. During 1993-98, majority of computer programs were developed either for predicting proteins tertiary structure or for benchmarking the alignment methods. All these programs were standalone programs, developed for DOS/Windows using programming various languages like FORTRAN, PASCAL, C. These programs were distributed free for academic users via floppy or CD. Though these programs were user-friendly, but one needs to have a hardware/software compatibility and knowledge of installation, in order to run them. To overcome this problem, we started developing web services instead of standalone softwares. To use these webservers one only needs to have a computer with browser and access to internet.

In 1998, I established my group with few PhD students having an objective to solve biological problems. In last ten years our group has developed more than 100 web servers in the field of bioinformatics. These web servers can be grouped in following main categories

· Subunit vaccined design of epitope basec vaccine;

· Genome annotation (prediction of gene, repeat, polyadylation sites etc.).

· Functional annotation of proteomes.

· Computer-aided drug discovery.

These web servers are heavily used (≥ 20,000 hits per day) and cited (≥ 1500 citation) by scientific community worldwide.

One of the major challenges for bioinformaticians is to understand and solve biologist’s problems. At the same time the solution should be such that it is user-friendly so that a person having just a little knowledge of computer can also utilizes it. Though we have tried our best to help the biologist, our programs/services are still far from perfect. Our webservers perform well for single sequence queries or for a small number of sequences but they are unable to perform predictions for the whole genome or proteome (because we can't provide the required CPU time). Moreover, many a times due to the limitation of available bandwidth and other security reasons, users wish to run these servers on their local machines. In an urge to comply with these demands our group is releasing this software package, which is a collection and integration of computer programs developed at our group over the years.

The manual of this package has three major sections; first section is written for students working in the field bioinformatics particularly for software developers. This section describes I) commonly used major computational tools, frequently used for developing bioinformatics tools; ii) type of prediction methods and iii) procedure for evaluating of a newly developed method. Second section is written for users who wish to analyze the proteins. In this section, all small programs is described which are commonly used for building major software packages. Third section describes stanalone programs based on our servers/methods, important for users who want to run our methods on whole proteome. I wish all the best for our users.

(G.P.S. Raghava)