228 projects tagged "Bioinformatics"

Download Website Updated 21 May 2007 Python Macromolecular Library

Pop 45.35
Vit 3.48

The Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language. It is accessed via a layered, object-oriented application programming interface, and provides a range of useful software components for parsing mmCIF, PDB, and MTZ files, a library of atomic elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular viewer. The mmLib data model is designed to provide easy access to the various levels of detail needed to implement high-level application programs for macromolecular crystallography, NMR, modeling, and visualization. This includes specialized classes for proteins, DNA, amino acids, and nucleic acids.

Download Website Updated 04 Oct 2003 DrawTree

Pop 18.28
Vit 1.73

Drawtree is a program for visualisation of trees. It reads in trees in the Newick format and outputs them in a graphic format. Currently the only supported output format is Encapsulated PostScript, but other formats are planned.

Download No website Updated 08 Oct 2003 NeoBio

Pop 12.96
Vit 62.33

NeoBio is a Java class library of computational biology algorithms. The current version consists mainly of pairwise sequence alignment algorithms, such as the classical dynamic programming methods of Needleman and Wunsch (global alignment) and Smith and Waterman (local alignment). A more efficient approach, due to M. Crochemore, G. Landau, and M. Ziv-Ukelson (2002) is also available. All sequence alignment algorithms support simple scoring schemesm as well as substitution matrices such as standard BLOSUM and PAM matrices with constant (linear) gap penalty functions only. Future versions may contain related algorithms such as multiple sequence alignment, database search and protein structure prediction. NeoBio also also provides simple GUI and command line based tools to run the sequence alignment algorithms on DNA and protein sequences.

Download Website Updated 24 Oct 2003 The VolPack Volume Rendering Library

Pop 41.09
Vit 1.00

VolPack is a portable software library for volume rendering, based on a new family of extremely fast volume rendering algorithms. The library does not use any specialized hardware and is therefore portable to most platforms, yet it achieves very fast rendering times.

Download Website Updated 06 Apr 2011 Raster3D

Pop 52.65
Vit 3.67

Raster3D is a set of powerful tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm that is independent of any graphics hardware.

Download Website Updated 29 Dec 2004 Genome-Tools

Pop 22.18
Vit 1.49

Genome-Tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format. A CGI-based Web interface is also available.

No download Website Updated 18 Oct 2006 PerlPrimer

Pop 33.02
Vit 4.83

PerlPrimer is a GUI application that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR), and sequencing. It aims to automate and simplify the process of primer design. Current features include calculation of possible primer-dimers, retrieval of genomic or CDNA sequences from Ensembl (including both sequences automatically for QPCR), the ability to BLAST search primers using the NCBI server, ORF, and CpG island detection algorithms, the ability to add cloning sequences to primers, automatically adjusted to be in-frame, and QPCR primer design without manual intron-exon boundary entry.

No download Website Updated 28 Oct 2012 Renal Growth

Pop 27.06
Vit 8.13

Renal Growth is a tool for radiologists and paediatricians to plot renal length and volume measurements against nomograms for age and weight. It allows for multiple observations from birth to 13 years. Individual patient data files can be stored and reused. Length and volume charts can be exported as JPEG files for importing into a PACS system or other clinical record.

Download Website Updated 24 Dec 2003 Yawn: Yet Another W* Network

Pop 24.60
Vit 61.71

Yawn (Yet Another {Weird | Wacky | Witty | Wonderful | W*} Network) is a Java framework for training and testing neural networks independently from the neural model and the test environment being used. The models implemented so far are AppART, GasART, fuzzy ARTMAP, and Multi-Layer Perceptron (MLP).

Download Website Updated 31 Jan 2004 Brook for GPUs

Pop 51.81
Vit 1.00

Brook for GPUs is a compiler and runtime implementation of the Brook stream programming language for modern graphics hardware. The goals for this project are to demonstrate general purpose programing on GPUs, to provide a useful tool for developers who want to run applications on GPUs, and to research the stream language programming model, streaming applications, and system implementations.


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A command-line network analysis workbench.