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         Bio-Informatics
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948 projects in result set. Projects sorted by: Ranking (Top Ranked First)
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1. 3D Genome Tuner - 3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.

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2. 3D Viewer for Phylogenetic Trees - A 3D viewer for phylogenetic trees. Speciation events are displayed in the plane according to the species tree, while duplication events are displayed in the other dimension.

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3. 3v: Voss Volume Voxelator - Several RNA and protein structure volume calculation tools.

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4. 5DT DataGlove Driver - A driver for the 5DT datagloves written in pure C++ using only the STL. Meant to be cross-platform, but written on and developed for IRIX sytems.

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5. A database for musem specimens - A Content Management System for collection data of taxonomic specimens. Organize your museum specimens, collection vouchers in one user-friendly database.

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6. AAARF Genomic Repeat Investigation - AAARF, written in PERL and with numerous adjustable parameters, identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in a genome.

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7. ABAC - Algorithmic Based Automatic Contiguation of Shot-gun sequences (ABACAS) is an integrated platform for quickly contiguating reference based assemblies.

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8. ABACAS - Algorithm Based Automatic Contiguation of Assembled sequences (ABACAS) is an integrated platform for quickly contiguating reference based assemblies.

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9. Abeel Java Toolkit (AJT) - AJT is a set of utility classes for Java for handling some bioinformatics data, graphics file export, GUI widgets, and classes that should long have been added to the official Java API.

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10. aCell - a framework to build data-driven models of biological cells

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11. AcidMiner - Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.

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12. Adamant - Adamant is a java application for annotation of microarray array designs. The software enables MIAME-compliant annotation of sequences spotted onto arrays and can produce output files in MAGE-ML and other data formats used by public microarray data repos

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13. ADF MAGE-ML Tool - In order to facilitate standardization and exchange of microarray layout, this project provides an ADF (Array design File))/MAGE-ML converter.

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14. Adsat -- Sequence Analysis Tool - Automated Database-lookup and Sequence Analysis Tool for use specifically with BioPython. Used for obtaining Sequence and other Data from online databases and processing the data using open bioinformatics tools like BLAST and MEME.

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15. Agent-Based Multiscale Tissue Model - Agent-based multiscale model of cancer proliferation dynamics

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16. AgentCell - AgentCell is an agent-based model of cellular biochemical processes and biological behavior.

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17. AgentQ - AgentQ is a project aimed at the development of virtual agents that mimic human intelligence and attributes (such as language or commonsense), as well as environments for these agents to learn and function in.

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18. aisconvert - Toolkit for processing genetic data in RAW (23andme) format. Currently supports (command-line): Half-IBD (Identity by descent) aka HIRs - between 2 or any number of files (in distances and cM); RAW2PED conversion; regions of homozygousity

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19. AITools - This project is aimed at creating a set of highly universal AI tools to be used in AI modelling. So far the subject area includes: Neural Networks, Fuzzy Logic, Biological Methods, Genetic Computing. New tools will be devised as the project goes on.

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20. Akiva Discovery Manager - Discovery Manager for integrating components on CSF.

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21. ALinks - alinks is a set of POJO describing pedigree graphs.

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22. Ambit - chemical structures database - AMBIT consists of a MySQL database and functional modules providing storage of chemical compounds and allowing a variety of flexible structure, similarity and other queries. Written in Java, with the use of The Chemistry Development Kit.

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23. Amino Acid Finder - Ever got confused while remembering all the various physical properties of all the standard 20 amino acids? Then use Amino Acid Finder!! It has a built-in database and contains information about all the physical properties and lets you to search them

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24. AMORSS: redox enzymes simulation system - This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).

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25. Analytical Data Interchange - This project provides open software for working with analytical instrumentation data using the ASTM "ANDI" standard.

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26. Analytical Information Markup Language - This project supports ASTM E13.15 "Analytical Data Magement" in it's work defining AnIML, an XML standard for representing, managing and interchanging analytical chemistry data.

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27. Anna - Anna is lightweight Java framework to build pipeline systems of any kind. It will take care of recurrent needs such as dependency management, data serialisation and synchronization as well as parallelization of execution.

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28. AnnaF - AnnaF is an automatic gene annotation framework, that is used to do some automatic annotation for C. higginsianum. It was also tested on F. graminearum and should work well for fungi in general. AnnaF was build upon the pipeline framework Anna.

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29. Annotated Gel Markup Language Project - Annotated Gel Markup Language is a simple markup language that is being proposed to markup data obtained by 2D gel electrophorosis.The goal of AGML is to enable proteomics research move into the browsing mode of searching through existing databases.

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30. AnnotationQuery - A command-line program to manipulate annotated genetic sequences (initially in EMBL format). The user supplies a pattern to identify which features or qualifiers to process. These can then be deleted, renamed etc

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31. Anthill - 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.

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32. Antimony - Antimony is a human-readable, human-writable model definition language. libAntimony is a library that will read and write Antimony and SBML files and provides an API for other programs to import Antimony models into their own internal formats.

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33. APBS - APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://apbs.sf.net/>.

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34. Aqua - AQUA is a suite of programs for Analyzing the QUAlity of biomolecular structures that were determined via NMR spectroscopy. AQUA was developed by Ton Rullmann and Jurgen Doreleijers in the NMR Spectroscopy Department, Utrecht.

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35. Arcadia - Arcadia is a light-weight, cross-platform, C++ desktop application designed for visualizing biological networks such as metabolic pathways.

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36. Area-split proportional to pointinfluenc - Acre calculates growing-space or stand-density of trees and creats pictures of it. It can also be used to calculate weighted Voronoi-Diagrams (splits up an area to the neares point or to the point with the greatest influence at a certain place).

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37. array2net - Array2Net is a tool for visualizing gene co-expression network of expression profiling data.

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38. ArrayExpress Tab2MAGE - Tab2MAGE uses a flexible spreadsheet format for MIAME annotation of microarray experiments. Tab2MAGE spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.

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39. ArrayPipeline - ArrayPipeLine is a web-based Laboratory Information Management system, using MySQL, Perl CGI and R. It enables high-throughput analysis of microarray data, providing automation of data handling, and rapid creation and implementation of analysis pipelines

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40. arrayplex - ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture.

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41. ARTADE - ARTADE (ARabidopsis Tiling-Array-based Detection of Exons) is a standard tool for the automatic annotation of genome-wide tiling-array data in Arabidopsis. ARTADE is a program originally written by Dr. Tetsuro Toyoda, RIKEN, Japan.

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42. Artificial Anthill - The Artificial Anthill is an artificial life software (in Java) centered on theme of ants and their environment (other ants, other insect ar animals, plant, soil, weather,...). Project page: http://aanthill.org - Contact: aanthill@aanthil.org

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43. ASGARD - ASGARD is software for metabolic pathway reconstruction, but it can also generate other types of biological sequence annotation (EC and GO numbers, BLAST reports). This program is intended to be run in UNIX-like systems, and supports SGE or PBS.

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44. ASIML8 - A Simple Informatics Markup Language 8 (ASIML8) is an XML that stores a variety of bioinformatics and biological data. This project provides the DTD and a perl object library for creating and parsing ASIML8.

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45. ASKGene - ASKGene (Automated Sequence Knowledge GENErator) - a customizeable integration platform for sequence-processing bioinformatics tools.

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46. ASpipe - ASpipe is a pipeline to process GeneSeqer/GMAP alignments and identify alternative splicing (AS) events from the alignments. It requires unix bash, perl 5.0+ with DBI module and MySQL5.0+ to run properly.

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47. AssociationViewer - A Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.

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48. AutoDock Software in Parallel with GPUs - Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/

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

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50. Autosmooth - AutoSmooth is a compiled stand-alone graphical interface for signal and derivative extraction from time series with nonstationary noise structure. AutoSmooth is now part of the Signal Extraction Toolbox (SET).

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51. AVANA - Antigen Variability ANAlyzer - The Antigen Variability ANAlyzer (AVANA) tool uses information entropy to measure variability in protein sequence alignments. It also compares alignments using mutual information, identifying the mutations that characterize specific sequence sets.

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52. Avian Freeware Suite - Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)

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53. AW-clust - AWclust is easy to use non-parametric population structure analysis software written for R with a GUI interface. Just point and click and you will be on your way to discovering the important cluster information in your SNP data sets.

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54. baba - BABA stands for Basic-Algorithms-of-Bioinformatics Applet. This project aims to create a set of bioinformatic algorithms presented didactically. The algorithms available at the moment are: Needleman&Wunsch, Smith&Waterman, Four Russians and Nussinov.

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55. BACContigEditor - BACContigEditor is a simple sequence alignment editing tool, written in Java. It is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole genome project.

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56. BANNER Named Entity Recognition System - BANNER is a named entity recognition system intended primarily for biomedical text. It uses conditional random fields as the primary recognition engine and includes a wide survey of the best techniques described in recent literature.

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57. BARNACLE - BARNACLE is a Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.

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58. BasicLife - Basic life is an application that desires to simulate basic life based on some basic chemistry/physics rules. This environment provides particles that can bond, vibrate, react, etc. in order to create basic cells

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59. Bayesian Network tools in Java (BNJ) - 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).

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60. Bayesian Network Tools in Java (BNJ) - Java/XML toolkit for research using Bayesian networks and other graphical models of probability (exact and approximate inference, structure learning, etc.)

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61. BClib - A C++ library for Bayesian computation, including a collection of more generally-applicable utilities.

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62. bc_scatterplot - bc_scatterplot is a scatterplot plugin for the bioclipse project

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63. BEDTools - BEDTools is a suite of utilities for comparing genomic features in BED format. These utilities allow one to quickly address tasks such as: 1. Intersecting two BED files. 2. Merge overlapping features. 3. Paired-end overlaps.

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64. BGI-Codes - This is a project to create and maintain the Perl modules create by Beijing Genomics Institute members in daily work.

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65. BINViz - BINViz(Bidirectional Interactive Network Visualization) is a JavaScript library for network and graph visualization. The goal of this tool is to provide a better way to visualize complex graphical models and the underlying data in a web-based environment

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66. Bio-SPICE - Our goal is to create an open source framework and toolset for modeling dynamic cellular network functions, and to develop a user community committed to using, extending and exploiting these tools to further our knowledge of biologic processes.

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67. Bio-WormBase - Bio-WormBase provides a suite of software for the installation and monitoring of a WormBase mirror site.

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68. Bio::Metabolic - A Perl Extension for modeling enzymatic (biochemical) reaction networks

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69. Bio::NEXUS - Bio::NEXUS is an application programming interface (API) implemented in Perl that provides a thorough object-oriented interface to manipulating NEXUS files (Maddison et al, 1997) and the data they contain.

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70. Bio::Parse::SwissProt - perl module - A Perl module that provides methods for retrieving each and every field from a standard SwissProt file.

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71. BioAPI - A easy to use set of utilities for bioinformatics that work out of the box without having to import or include too many other libraries, these will form a workbench for the everyday work of a bioinformatician.

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

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73. BioBuilder - BioBuilder was a framework for building protein-centric databases using the Zope2. It's not maintained anymore. If you want to have a look to the latest snapshot of the code you can get it at http://biobuilder.sourceforge.net/ Contact us if you want to

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74. Biocentrica Voyager Antivirus - It moves by itself inside networks like virus infection & plagues, it is being written to solve computer virus problem drastically and responsibly. It is legal, free and open for public domain to improve W3 ICT Security.

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75. Bioclipse - An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).

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76. BioCommon - BioCommon is a Java library that provides API for common bioinformatic tasks such as parsing FASTA-, ACE- and BLAST-formatted files, statistically summarizing sequences and translating open reading frames.

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77. BioCSharp - 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.

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78. Biodiversity Information Group - Biodiversity Information Group develops software tools and data standards that enable herbaria and museums to create dynamic distributed queries of their online databases.

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79. BioDOM - BioDOM is a JAVA library for easy creation of XML files according to simple XML schemas for describing biological data. It can also be used to convert other commonly used biological (possibly non-)XML data into these new formats.

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80. BioEngine - Bioinformatic C++ library providing a central engine to other bio* libraries (BioPerl, BioPython, BioJava).

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81. BioEra - BioEra is DSP visual designer that can be used to create interfaces between human being and a machine with using bio signals like EEG, QEEG, HEG, EMG, ECG, GSR, EOG, visual/sound entrainment and others.

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82. BioEval - BioEval, a web-based evaluation platform for one or multiple biomedical text extraction systems and the collaborative creation of gold standards. Handles evaluation of extraction of one to many related entities, plus supporting evidence and normalization

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83. BioGeoTools: Biogeography Tools - BioGeoTools is a Java based package that is aimed at providing a program and libraries for biogeorgaphy analyses.

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84. bioGraph - bioGraph is a set of PHP scripts which can be used in enzyme assays. Currently, this includes pH, Temperature, Michaelis-Menten and Lineweaver-Burke plots.

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85. BioGRID - Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions. It strives to provide a comprehensive resource of Protein-Protein interactions for all major species.

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86. BioImageXD - BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.

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87. Bioinformatics Template Library - The original Bioinformatics Template Library (BTL) uses templates to implement generic programming in same way as the Standard Template Library (STL). Biolib aims at continue developing this library.

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88. Bioinfotracker - An Ajax based Functional Genomics Application Server to aid in functional analysis of entire genome in-silico.

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89. BioLayout3D - Tool for the visualisation and analysis of biological network or expression based data.

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0 / 0.00%

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90. Biologic Stylus - Biologic Institute's Stylus simulation software suite. (See the SVN repository for source code.)

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0 / 0.00%

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N/A / N/A

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0

91. Biological Annotation Tool - 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.

Click here to download.  
Rank/Activity Percentile
0 / 0.00%

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0

92. Biological Content Management - BioCM is Biological Content Manager: a Zope/Plone/Biopython product to manage, share and publish biological annotations on the web.

Rank/Activity Percentile
0 / 0.00%

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N/A / N/A

Downloads
0

93. Biological Network Analyzer - Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BN++ databases, but also as stand-alone tool.

Click here to download.  
Rank/Activity Percentile
0 / 0.00%

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N/A / N/A

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0

94. Biological Network Comparison Toolkit - A tool to construct the metabolic networks from KEGG, and compare the constructed metabolic networks. Phylogenetic trees can be constructed along the case.

Rank/Activity Percentile
0 / 0.00%

Registered/Updated
N/A / N/A

Downloads
0

95. Biological Pathway Exchange Language - BioPAX - A Data Exchange Format for Biological Pathway Information

Click here to download.  
Rank/Activity Percentile
0 / 0.00%

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N/A / N/A

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0

96. Biological Relationship Builder - 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.

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0 / 0.00%

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0

97. biom - Biom is an open source project related to bioinformatics. Biom is started for needs of university project related to statistics for Sars corona virus. It can work with any genome sequence, nucleo or amino.

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0 / 0.00%

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98. BioMa - BioMa is a specimen based Biodiversity database Manager. It is designed to store, organize, and manipulate biodiversity-related scientific data, either for the purposes of museums, scientific collections, or research projects.

Click here to download.  
Rank/Activity Percentile
0 / 0.00%

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N/A / N/A

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0

99. BioModels Database - BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models presented are annotated and linked to relevant data resources and are available in various format

Click here to download.  
Rank/Activity Percentile
0 / 0.00%

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N/A / N/A

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0

100. Biomolecule Toolkit - The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in structural biology to facilitate the development of molecular modeling, design and analysis tools.

Click here to download.  
Rank/Activity Percentile
0 / 0.00%

Registered/Updated
N/A / N/A

Downloads
0

948 projects in result set. Projects sorted by: Ranking (Top Ranked First)
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