RSS 205 projects tagged "Bioinformatics"

Download Website Updated 15 Mar 2002 BioJava

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Pop 157.65
Vit 2.38

BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.

Download Website Updated 27 Sep 2009 Bioperl

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Pop 98.71
Vit 8.04

Bioperl is set of Perl Modules for bioinformatics. It contains objects for Sequences, features on Sequences, and other important bioinformatics attributes.

No download Website Updated 02 Nov 2004 Cactus

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Pop 152.84
Vit 3.46

Cactus is a general, modular, parallel environment for solving systems of partial differential equations. The code has been developed over many years by a large international collaboration of numerical relativity and computational science research groups and can be used to provide a portable platform for solving any system of partial differential equations.

Download Website Updated 26 Oct 2011 E-Cell System

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Pop 132.77
Vit 12.63

E-Cell System is an object-oriented software suite for modelling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components, driven by multiple algorithms with different timescales, to coexist. The core library is written in C++ with a Python binding, and frontend software uses Python.

Download Website Updated 30 Jan 2001 EGO

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Pop 41.57
Vit 1.00

EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, Parsytec-CC under PARIX, and inhomogeneous clusters of UNIX workstations under PVM or MPI. EGO also runs sequentially on any decent UNIX workstation, even Windows95/NT PC's (with a GNU-C compiler) can be used.

No download Website Updated 15 Aug 2001 Ensembl

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Pop 18.28
Vit 1.83

Ensembl is an open source project to create and automatically maintain annotations on DNA sequence.

Download Website Updated 06 Jun 2001 Genpak

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Pop 38.50
Vit 2.96

Genpak is a small set of utilities designated to process DNA, RNA, and protein sequences in a very Un*x-like manner. This way, Genpak programs can be combined using pipes and redirections, as well as easily incorporated into CGI scripts. The utilities include a program for calculating GC content, Tm, translating DNA/RNA sequences into protein sequences, quick sequence retrieval, random sequence generation, and finding promoter sequences using a Hertz matrix.

Download Website Updated 24 Sep 2007 Ghemical

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Pop 148.92
Vit 6.69

Ghemical is a molecular modelling software package with some nice 3D visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). The geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms are included. Ghemical is written in C++, and hopefully offers a good framework for a generic freeware molecular modelling tool.

Download Website Updated 30 Jan 2001 Mavric

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Pop 12.53
Vit 1.00

Mavric is a python module/application that aims to be a user-friendly tool for manipulating phylogenetic trees on *NIX-like systems running X Windows. As such, it complements other phylogeny programs that currently lack a nice graphical interface.

Download Website Updated 28 Oct 2011 NAMD

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Pop 58.96
Vit 9.34

NAMD is a parallel, object-oriented molecular dynamics program designed for high-performance simulation of large biomolecular systems.

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