226 projects tagged "Bioinformatics"
Updated 24 Feb 2011
Bioinformatics Benchmark System
| Pop | 30.74 |
|---|---|
| Vit | 1.00 |
The Bioinformatics Benchmark System is an attempt to build a reasonable testing framework, tests, and data, to enable end users and vendors to probe the performance of their systems. It is not trying to be the last word in informatics benchmarking, as there are simply too many codes, tests, data sets, and databases. The goal is to create a core of tests that all may download and use to probe specific elements of system performance. The end goal is to enable a pluggable set of tests, including the core tests, so that performance data may be gathered.
Updated 23 Feb 2011
Berkeley DB XML
| Pop | 150.96 |
|---|---|
| Vit | 3.26 |
Berkeley DB XML is a native XML database engine for use within your product. Made available as a C++ library with language bindings for Java, Perl, Python, PHP, and Tcl, it integrates directly into your application (it is not a standalone database server). It provides XQuery access into a database of document containers. XML documents are stored and indexed in their native format using Berkeley DB as the transactional database engine.
Updated 21 Dec 2010
Biogenesis
| Pop | 43.58 |
|---|---|
| Vit | 3.76 |
Biogenesis simulates in a visual fashion the processes involved in the evolution of unicellular organisms in nature. It tries to be a didactic approximation to the ideas of mutation or evolution, and can be enjoyed also as an entertainment. It's intended to serve as a support to show students some basic biological facts. The idea of Biogenesis is taken from Primordial Life, but it's an independent project.
Updated 18 Dec 2010
SwissParser
| Pop | 23.43 |
|---|---|
| Vit | 2.41 |
SwissParser allows you to define in a few lines a parser able to deal with the flat file format used in bioinformatics software such as UniProt, KEGG, etc.
Updated 07 Dec 2010
BALL
| Pop | 43.27 |
|---|---|
| Vit | 3.94 |
The Biochemical ALgorithms Library (BALL) is a framework for rapid application development in molecular modeling and structural bioinformatics. BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, NMR shift prediction, and visualization. Its extensibility results from an object-oriented and generic programming approach.
Updated 15 Nov 2010
OpenAlea
| Pop | 26.17 |
|---|---|
| Vit | 2.60 |
OpenAlea is a modeling and simulation framework in plant ecophysiology. It is based on the Python programming language and it provides different integration tools (for tasks such as installation and compilation), a visual programming interface, and different dedicated models and libraries.
Updated 10 Aug 2010
CanvasXpress
| Pop | 23.98 |
|---|---|
| Vit | 31.89 |
CanvasXpress is a JavaScript library based on the HTML5 canvas tag that provides a generic and simple way to display genomics data. It supports bar graphs, line graphs, bar-line combination graphs, box plots, dot plots, area graphs, stacked graphs, percentage-stacked graphs, correlation plots, Venn diagrams, heat maps, Newick trees, 2D-scatter plots, 2D-scatter bubble plots, 3D-scatter plots, pie charts, networks (or pathways), and a genome browser. It also supports a few data transformations like log and exponential transformation, z-score, percentile transformation, and ratio. It also supports grouping of samples, zooming, events, and more.
Updated 05 Aug 2010
CellProfiler
| Pop | 26.83 |
|---|---|
| Vit | 2.31 |
CellProfiler is a system for analyzing cell images. It is designed for biologists without training in computer vision or programming to make quantitative measurements of cells in thousands of images automatically. It is implemented using Matlab, but compiled standalone versions are available.
Updated 22 Jul 2010
COPASI
| Pop | 29.33 |
|---|---|
| Vit | 3.30 |
COPASI is a software application for modeling and simulation of biochemical networks. The software package has a GUI that lets users define biochemical network models by entering chemical reactions and kinetic equations. A powerful simulation engine can then perform simulations of the dynamics of the networks and carry out many different computational analyses. COPASI can simulate dynamics using either an ODE approach or a stochastic chemical kinetics approach (Gillespie-type algorithms).
Updated 24 May 2010
OBSearch
| Pop | 42.54 |
|---|---|
| Vit | 3.09 |
OBSearch is a distributed similarity search index. It can (for example) match programs and help to detect Open Source/Libre license violations, find music that sounds like Sisters of Mercy, or match huge vectors of randomly generated integers just for fun.
