Open Source Linux Bio-Informatics Software

ConvertMAS - molecule converter; use to convert Chemical File Formats. It works on mol, mol2 and sdf files. It converts single file to respective formats. It will split sdf file with multiple molecules into seperate single files of any desired format. Also ConvertMAS creates sdf files from joining of mol, mol2 and sdf files. This is stand alone application; hence no need of internet connectivity to get results. It will generate output files in less time. Various online tools are available for conversion of Chemical file formats; but ConvertMAS mainly works on mol, mol2 and sdf effectively.

The Octet-CDK interoperability package.

Gnome-EMBOSS is an open-source application to help scientists handle DNA, RNA and protein sequences. It uses Gnome/GTK for the user interface and EMBOSS libraries for sequence handling routines. (See www.emboss.org for further info.)

AgED performs automatic feature extraction from your image data and allows for their visualization and management. AgED relies on Elliptic Fourier Transcriptors to extract features from large quantities of image data. These features can then be visualized and you can evaluate them in a statistical manner. This type of analysis is particularly worthwile in the assessment of biological experiments. Elliptic Fourier Descriptors have been applied in a large range of applications in biology. Examples include the distinguishing of leaf shapes, fish sex, organ size and so forth. AgED is intended for scientific use only. Use and distribution of this technology is subject to the Java Research License included herein. AgED comes with absolutely no warranty.

This is a project for Andre to share CellML related tools he works on that other people might find useful.

Anthill is a framework to support the design, implementation and evaluation of P2P applications based on ideas such as multi-agent and evolutionary programming borrowed from the complex adaptive systems area.

Arrayline is an extensible bioinfomatics data processing platform

The Automated Life Ecosystem Simulator is a microbe simulation environment developed in Java.

Biospha is a suite of perl scripts based on bioperl toolkit intended to help researches to manage large sequence file. With BIOSPHA you can classify each sequence according to the NCBI taxonomy. You also can get all taxonomic info from a GI or Taxid.

Bayesian Network tools in Java (BNJ) is an open-source suite of software tools for research and development using graphical models of probability. It is published by the Kansas State University Laboratory for Knowledge Discovery in Databases (KDD).

Large set of functions for biological records (ECG, EEG, phono), datastore, datamining and analysis (HRV, QT, RR, ST). The application is written in Java, so that it is assumed to work on all devices. It runs as a desktop or client-server application. It

A Perl Extension for modeling enzymatic (biochemical) reaction networks

Biological sample supervisor. Plant material and more (cellular, genetics).

BioCSharp is an open-source project designed to provide a bioinformatics .NET framework for processing biological data. It will include objects for manipulating sequences, file parsers, DAS, database access and analysis and statistical routines.

Visualize your bioinformatics analysis process.

The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!

Biological Annotation Tool is a general-purpose high speed environment for manipulating biological sequence annotations in multiple input and output formats. A plugin-style API permits much extensibility.

This is a collection of softwares that I have been using in my research on protein interaction network. By release them under the GPL 2.0 lience, I hope that they can be useful to others, as well.

BIRBU (BIological Relationship BUilder) is a Java tool for microarray gene expression data analysis. BIRBU identifies biologically significant relationship between genes using microarray data and prior knowledge on relationships between genes.

A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.

Source code for the Chemical Informatics and Cyberinfrastructure Collaboratory project.

Collection of tools for performing robust case-control disease and quantitative trait association studies using Copy Number Variants- Latest version should now be downloaded from Bioconductor

COB editor is a collaborative editor for biological ontology (e.g., Gene Ontology) building. Building on the idea of modular ontology from KR research, it supports multiple people to work on the same ontology.

The Canopy project is an initiative to merge and expand the functionality of Perl-speaks-NONMEM (PsN), Census, Xpose and PopED. The goal is to produce a coherent, inclusive and convenient platform for pharmacometric data analysis.

This is the prototype version of software for robust detecting and segmentation of cell nuclei in 3D fluorescence labeled microscopy images. First release coming soon...