Web interface on computer libraries

A number of computer libraries have been developed in the past for providing reusable functions/subroutines. Examples include Biojava and Biopython. These libraries are very powerful and can be integrated in programs as they provide enormous flexibility. In order to install and use these libraries one need reasonable knowledge of computer programming and resources. However, most of the users (biologists, pharmacologists, research students) have limited knowledge of computer programming. In order to bridge the gap between the users and the existing libraries, we, at CRDD have made an attempt to develop web interfaces.

R based Libraries
R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. A number of libraries have been developed using R

  • Statistical Applications: R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible.
  • Bioconductor: Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data. Bioconductor is based primarily on the R programming language, but does contain contributions in other programming languages.

    Python based Libraries
    Python is a dynamic object-oriented programming language that can be used for many kinds of software development. It offers strong support for integration with other languages and tools, comes with extensive standard libraries, and can be learned in a few days.
  • Biopython: Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
  • MMTK: The Molecular Modelling Toolkit: The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications. MMTK is developed in and around Python, a high-level object-oriented general-purpose programming language.

    Java based Libraries
    The Java programming language is a high-level language that can be characterized by all of the following major features; i) Architecture neutral, ii) Portable, iii) High performance,iv) Robust and v) Secure.
  • BioJava : BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating biological sequences, file parsers.
  • CDK: Chemistry Development Kit: The Chemistry Development Kit is an open source Java library for Chemoinformatics and Bioinformatics.