Related Software Projects

producing free software component libraries useful for biomolecular computing

BioC++: The Biocpp project is new forum trying to coordinate/rationalize/standardize C++ based bioinformatics libaries   [2005]

BOOST: The Boost C++ libraries. A huge collection of standard libray extensions not specifically bioinformatics, but very much in line with the BTL philisopy.   [2002]

EMBOSS: The European Molecular Biology Open Software Suite - the descendant of EGCG [2002]

The Bioperl project is a collaborative effort to produce perl software for handling biosequence and alignment data. Links to other perl projects.  [ 1998 ]

SEALS-(A System for Easy Analysis of Lots of Sequences) a collection of perl modules designed to facilitate large-scale semi-automatic sequence analysis projects written by Roland Walker at the NCBI  [ 1998]

The OMF (Open Molecule Foundation) is a Sun sponsored collaboration between private companies and academic departments. Its aim is facilitate the production of a pool of bioinformatics and chemoinformatics software written in Java. Unlike the other projects on this page they do not necessarily plan to make their source code generally available. All the applets they produce will however be made freely available.  [ 1997 ]

Sean Eddy's Group have made some C programs available under the GNU General Public License. This software includes their well known HMMER package, which does sequence comparison using hidden Markov models. They also provide SQUID - a library of C functions and utility programs for sequence analysis.  [ 1998]

SCL (Sequence Class Library) consists of C++ classes that perform tasks commonly needed for analysing DNA or protein sequences. This work is published in Bioinformatics (then CABIOS) and is fully documented. [ 1996 ]

Andrew Martin at University College London has written some very useful C programs for analyzing and manipulating protein structures. [1997]

The bioWidget Consortium produces software components, written in Java, for the graphical display of genome data. The motivation behind this project is very similar to our own.  [ 1997 ]

NAMD is a parallel, object-oriented molecular dynamics program designed for high performance molecular dynamics simulations of large biomolecular systems. VMD is a molecular visualization and analysis program designed to be easy to use and modify. Both packages are written in C++. . [ 1998 ]

The UCSF Computer Graphics Laboratory provides several software packages of interest. These include the OTF (Object Technology Framework), which is a system designed to generate C++ classes that are tailored to the needs and specifications of biochemical application developers. [ 1996 ]. Also at this site are libpdb and libpdb++ which are C and C++ libraries for parsing Brookhaven Protein DataBank (PDB) formatted files.  [ 1994 ]

The PDBlib C++ class library is designed for modelling macromolecular structure at PDB levels of detail. Its home page is at the San Diego Supercomputing Center. [1998]. See the SDSC's extensive list of public domain software for other relevant stuff.

The Democritos package from Peter Murray-Rust has a variety of C++ classes useable by biologists, chemists and crystallographers. You can read about it at the CBMT (Collaborative BioMolecular Tools) site [ 1994 ]

GenTools is a collection of software for doing genetic analysis. [ 1993 ]

molbio++ is a C++ library for molecular biosequence analysis. It reads sequence data from a wide range of file formats and is described in a little detail in the BioCatalog software listings. [ 1993 ]

The Blitz++ Numerical Library: This project uses advanced C++ techniques to write scientific software that performs as well or better than equivalent programs written in Fortran.[ 1998]

TheTemplate Numerical Toolkit: Mathematical C++ software that carries out operations in linear algebra [ 1998]

The Visualization Toolkit (vtk) - a Visualization Textbook, C++ Library, and Tcl, Java, and Python Interpreters. This can be used for quick and (relatively) easy generation of novel cross-platform 3D data visualizaton programs. [ 1998 ]

LASSPTools is a collection of Unix utilities for numerical analysis and graphics written in C and Fortran [ 1995]

[ estimated last software update ] 

Go Back to the Software Engineering Home Page Any questions or comments to Mark Williams. This page was last updated on  19/06/05