- OS: Linux ×
Molecular Science
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Maliuvajka Interface to manipulate with 3d gragic,s reading initial data fron an XML file, created by user which represents 3d model and saves data in vectorized format.
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MitoMAS_membrane Mito-MAS-m is a simulator of the mitochondrial inner membrane and the enzymatic complexes embedded in it, implementing a coarse-grained (CG) model of the molecules using rigid structures and Dissipative Particules Dynamics (DPD) as motion equation.
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MolTools library The MolTools Java library provides tools for building applications that handle nucleotide sequence data. Features include sequence I/O, handling of lists/databases of sequences, calculation of Tm, and other utilities for sequence design.
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MolWgt Given the chemical formula, MolWgt calculates the molecular weight of a substance.
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Molevolve Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.
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NAncy_EX An open source code for the TDDFT excited states analysis. nto for the generation of natural transition orbitals and dadens code for attachment detachment density matrices. Codes are intended to postprocess gaussian 03 and 09 outputs.
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NMRC Genomics Software Bioinformatics tools and applications for the analysis of genomic sequence data.
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OOPS OOPS means Open Protein Simulator, it is a program designed to serve as a test bed for different algorithms for protein folding, dynamics and structure prediction. OOPS is based on a plugin architecture that makes it highly modular and extensible.
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PAICE: Rapid pathway visualization PAICE is a rapid bioinformatics pathway visualization tool for KEGG-compatible accessions derived from Illumina Solexa next-gen and Affymetrix datasets. It colors KEGG pathways while appreciating detection-calls and duplicate gene copies.
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PDBViz This is an open source Protien Data Bank (*.pdb) file format importer plug-in for Autodesk's Maya Unlimited/Complete Animation and Special Effects software. The plug-in is being created to facilitate dissemination of scientific research.
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Parentheses Classifier The Parenthesis Classifier takes the contents of a set of parentheses and classifies it into one of several categories. It includes a parenthesized-data extractor and the classifier.
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PepArML PepArML: An unsupervised, model-free, combining peptide identification arbiter for tandem mass spectra via machine learning.
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PocketDepth : binding site prediction PocketDepth helps determine binding grooves for protein molecules. Applicable in Bioinformatics and Drug discovery. Literature - http://www.ncbi.nlm.nih.gov/pubmed/17949996 Author's thesis - http://openwetware.org/wiki/Kalidas_Y
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PolyJen PolyJen: Polymerization in a digital laboratory
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Prequips A Java-based tool to visualize, integrate and analyze LC-MS/MS proteomics data.
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PyBact PyBact is an open source software written in Python for Bacterial Identification. The software generates simulated data matrix which accurately represents the probabilistic positive/negative results of the tested biochemical test.
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QRasmol QRasMol is a reimplementation of RasMol in C++ with updated CMake build systems.
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RAndom Network GEnerator RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.
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S-Cleaner This cleans unwanted textual information from DNA sequencing results
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SIPeS SIPeS - Site Identification from Paired-end Sequencing
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SPADE The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available.
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SPAS SPAS (Structure Property Analysis Software) is a Quantitative Structure-Property Relationship (QSPR) software.
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SPiM2Eclipse Eclipse plugin for Stochastic Pi Machine
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Sage Folding@Home Stats System Sage is a web-based stats system for your Folding@Home team. It is light, fast, and based on PHP and an assortment of SQL-based database management systems, so it is ideal for webservers.
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Simple Semantic Classifier The Simple Semantic Classifier classifies short chunks of natural language text into broad semantic classes that correspond to the OBO ontologies provided as input.
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