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Bioinformatics.Org Full Project Listing
1 A program (CRNPRED) to predict secondary structures, contact numbers, and residue-wise contact orders of native protein structures from amino acid sequence. This program is based on the critical random networks method. A ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve. A python module for parsing ABI trace file (and hopefully ABI gel file too in the not-so-distant future). Gene finding accuracy evaluation tool and test datasets. It allows a nearly complete set of evaluation statistics to be easily generated on a customisable set of test sequences. AcE has nothing to do with ACEDB. You can download the program 'ace.pl' an A C++ library of efficient algorithms for bioinformatics Alkahest is an initiative to produce free open source software systems for high-throughput DNA sequence data management and analysis. Aminonet tool takes pdb file as input form local machine or from http://www.pdb.org and calculates different parameters of the network. Using AmonoNet one can visualize the network in an interactive way. Welcome to Ampred server,which predicts the Antimicrobial activity of given sequence. The activity may be antifungal, antiviral and antibacterial .This server works based on Multidimensional signatures of antimicrobial peptides (Yount and Yeaman.2004). AnnHyb is a free software for working with and managing nucleotide sequences in multiple formats. Features include sequence annotation, restriction analysis, pattern searching, retrieval from servers, etc. AnovArray is a set of SAS macros for the Analysis of Variance of Gene expression. It can be applied to the quantification of biological and technological variation and to the identification of differentially expressed genes in two or more conditions. ANTHEDNA is a package of integrated UNIX freeware tools for retrieving and analyzing sequence data. It is called ANTHEDNA because it was developed for analyzing the DNA sequence data obtained from the ribosomal database project. AntisenseML integrate sufficient information to provide fast, flexible access to the data. Moreover,XSLT transformation was made to render the antisenseML file into HTML view.Some useful tools to create update antisenseML will be released soon These documents may be useful as examples to help validate your application in compliance with FDA GxP regulations. ARGO (Antibiotic Resistance Genes Online) is intented to be a comprehensive web Resource for Scientists, Clinicians and other people who are interested in the looming problem of rise and spread of antibiotic resistant pathogens worldwide. Please visit http://bioinformatics.org/arrayalizer/ to see our website and for a detailed description of Array-A-Lizer - A serial DNA microarray quality analyzer. Executables and sourcecode of the project are also available at the website. We have derived novel clustering algorithm taking into consideration certain biological assumptions like conditional coregulation and properties of microarray data, uploaded at website www.asidb.com. Gene can be queried (only for Carbohydrate). Asterias is a set of web applications for the analysis of genomic (and, to a lesser extent, proteomic) data that cover from data normalization to development of prediction models for survival data. The Integrated Database Project is an effort to integrate multiple forms of biological, publication and ontological data under one query space for data mining. At its core sit relational databases whose tables model the data structure of the information. We are developing obesity control drug form taditional inadian medicinal plants, becouse medicines from plants have less side effects compare to allopathy medicines B This is a windows based base sequence editor. Search, complement, XNA to amino acid,amino acid to XNA,3 to1 & 1to 3 letter code, invert, find ORF,statistics of bps,2bp palindromes Bayallele is a Java-based application that uses bayesian inference and markov chain monte carlo methods to analyse genetic data. The analysis revolves around obtaining separate estimates of population size and migration rate for the sampled populations A nascent tutorial on bio-informatics, currently covering molecular biology basics and advanced topics like genomics. The project files will be updated every fortnight (2 weeks). Contributions welcomed. Bio-Linux is a bioinformatics-centred distrubution based on Debian GNU/Linux. Currently at version 4, it provides standard and cutting edge bioinformatics tools. It is freely distributed via the NERC Environmental Bioinformatics Centre (NEBC), Oxford, UK Bio-Wave is a Wavelet based semantic pattern & relation extractor and visualizer. It can be used for sequencing, pattern recognition, curve fitting and other similar processes, especially in gene sequencing and tissue viz. problems. Project Definition: Development of computational tools such as algorithms, software and databases for the collection, interpretation and dissemination of the vast quantities of complex mapping and sequencing data that are generated by human genome res BioBrew is a collection of open-source applications for life scientists and an in-house project at Bioinformatics.Org. BIOBROWSER is a portal to the existing bioinformatics universe. It encompasses in itself hyperlinked nodes to all major nucleotide, RNA, Protein sequences along with structural and genomics databases to name a few. Also links major related servers. The BioC# Project is an open-source project dedicated to providing C# tools for processing biological data. The BioC# library will provide a foundation upon which both free software and commercial packages can be developed. BALL (Biochemical Algorithms Library) is an application framework in C++ that has been specifically designed for this purpose. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparis Open source, Objective-C framework for parsing and writing sequence file formats 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. SERVING the bioinformatics requirements of experimentalists. DEFINING best practice. PROMOTING basic training. PROVIDING a service. BOOM, the Bioinformatics Object Oriented Modules, is a collection of reusable classes for efficient object-oriented bioinformatics modeling and application development; it has been used in several gene prediction programs including TIGRscan and TWAIN. This is a unique project that tries to make an informatic simulated system from a genetic /physiology well-known system. This project aims to create a list of functional requirements and technical specifications (flowcharts, classdiagrams, etc.) for the development of a complete workbench solution created in .NET/C# for researchers, students and others who are interested. In order to avoid re-inventing the wheel, a collection of FORTRAN code that may be useful for your scientific program. This BioPHP project aims to develop modules and, eventually, sample applications for bioinformatics in PHP both for web AND standalone applications (PHP's utility outside of the web is often overlooked.) BioQuery provides a single, powerful user interface for building search strategies to multiple biomedical databases, and provides a full update service that sends you new data matching your search criteria when new entries are added to the databases. promote the knowledge and application of bioinformatics in third world countries BIOSEG is a biological interval type for PostgreSQL. A PostgreSQL GiST index is used to improve the speed of overlap, contains and contained-in queries. A typical use is to store and query sequence base ranges in a biological database. BIRCH is comprehensive bioinformatics system, running on the Unix system. BIRCH consists of programs and databases for molecular biology that are useable either through a graphic interface or the Unix command line. The design of BIRCH lends itself to flex An easy to use script that creates a multiple alignment (relative to the query) from the database hits of a BLAST search. Multiple HSPs from a database sequence are combined or separated depending on their relationship to each other. Fast and easy to use script producing a graphical overview of blast results. BioLinux Goes Mobile A perl script that assembles families of orthologous genes by parsing a phylogenetic tree reconstructed from a mixture of orthologs and paralogs for a set of n taxa. Given a tree as input, the script reports families of orthologs, and it lists in- and out BSQuery 1.0 desktop utility that can be used to instantly retrieve sequence annotations from GenBank and other documents (e.g. AGAVE, etc),regardless of the document?s location (a local computer, LAN-based server, online, etc) The BTL provides generic mathematical components that allow C++ programmers to more rapidly construct applications that model biological entities. C CalPred is a "tool for EF-hand calcium binding protein prediction and calcium binding region identification" using machine learning techniques. It is a free web based software package and is accessible via world wide web from various platforms. Cardiovscular Gene Database provide you with VISTA system for the investigators in the Cardiovascular biology and pharmacology community. CD-HI/CD-HIT clusters protein sequence database at high sequence identity threshold. This program can remove the high sequence redundance efficiently. Program written by: Weizhong Li Celutil is an utilty to read&write, compare, convert, query Affymetrix CEL file in binary & ASCII format, gzipped or not. Celutil is a linux command line written in C++ and should compile and run on windows, MacOsX. Based on Affy File parsers & zlib. A web-based program that processes and displays information from the Codon Usage Database in an easy-to-read format. Analyze which codons your organism likes to use. WE strive to provide simple solutions for everyday life in a molbio lab A web-based program for comparing sequence conservation patterns to three-dimensional structures. D A Linux-based system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined) weight matrices. DeltaStat performs statistical calculations on data from 2D gel experiments quantified in Delta2D. DeltaStat combines the power of R with the efficiency of a database to handle the large amounts of data generated in proteomics experiments. A GNU/Linux-based system, called DEgenerate Oligonucleotide Design & Analysis System (DEODAS), for designing and electronically analyzing consensus-degenerate oligonucleotides is being developed by integrating published software tools from other authors. Providing tools for QFISH using free software (macros for NIH image) with examples of processed images; methods to calculate mean TRF length by southern blot with image processing and source code of macro for densitometry; and presentations Software and data for design of selector assays for targeted resequencing applications. The software is a Java and Perl pipeline that performs the tasks required to design selector probes for the coding regions of a set of target genes. Program to visualise patterns in DNA and RNA by using Chaos Game Representation A Live-CD Linux distribution based on Slackware. E This is portable and stable branch of the E-CELL project. Linux, Solaris, and MS-Windows versions are under developping. You will be able to run ecell2 not only in interactive mode but also in batch mode. EmblEx is a tool to retrieve subsequences as defined by complex descriptors in the Features qualifiers of the EMBL entries (ASCII files). Users can define complex keywords (or regular expressions) to be searched for. Many outputs are also possible. EnzymeLab is a program for the numerical and graphical analyses of enzyme kinetics data: the Micaelis-Menton parameters, inhibitor studies (both linear and non-linear), reaction rate/order and mechanism, and assay development/validation. ESPSim is an open source JAVA application designed to compute the similarity of protein electrostatic potential maps. ESP is a flexible platform to evaluate the discrimination abilities of user-defined expression signatures. Besides, it offers individual prediction information that could be useful for clinically prognosis and clinical management decisions. F FirstGlance in Jmol is a simple, free, browser-based tool for macromolecular visualization. It easily shows you the main features of any published macromolecular model (PDB file). It runs on all common browsers and platforms. FLIMS is reborn. I will be providing small UI components and code snippts that should add up to an application. The general purpose is to build a framework for bioinformatic programming. Maybe hooks into BioRuby and touching on experimental technologies s FragSize is a software tool designed to help molecular biologists in DNA band size determination. It use an graphic user interface, so, use FragSize is very easy. Just load the gel image and make the determinations. FreeMOL is an assembly of free and open source programs forming a framework for computational chemistry, informatics, structural biology and graphics. FreeMOL will be a credible alternative to high-priced commercial packages. fs_kit is a force spectroscopy toolbox, containing programs to fit, align and analyze spectra. It is currently a work in progress. The current state is best described as beta version. G G-language GAE is a software package aiming to provide a generic development and analysis environment for the analysis of complete genomes.Development at Bioinformatics.org is discontinued. Please proceed to the URL below. gBioSeq is in an early stage of development, but it is already running. The goal is to provide an easy to use software to edit DNA sequences under Linux, Windows, MacOsX, using GTK C# (Mono). Gemvid is a monitoring system that quantifies overall free movements of rodents without any markers, using a commercially available CCTV and a newly designed motion detection software developed on a GNU/Linux-operating computer. GO4J is a set of API to manipulate local GO vocabulary. It has four features: parsing four kinds of GO defintion; organize all GO ids with directed graph; evaluating semantic similarity between any two GO ids; visualizing relations between any ids. Data sets for training gene-finding software. GeneCite permits users to specify sophisticated sets of queries and generates a table of the number of citations found for each query. The table can be presented as a web page or in standard spreadsheet format. GeneGnome will allow users to build, in the GUI, nodular models of linked cellular enzyme networks in a GNOME environment with the goal of using the underlying calculational engine linked to the GUI to help make testable predictions in real cells. Gene Picker is a tool that is developed to display Genetic Information in an easy to use graphical format. The objective is to enable the scientist to access Genetic information archived in a back end database through a graphical representation. This woul Gints aims at the simulation of regulation networks. GeNetDB, contraction of Genetic Network Database, is a bioinformatic platform destined to the study of genetic regulatory networks. It contains in one place the data and the way to study them, providing the user an access to all tools needed for his work. The Genetic Data Analysis Library (GDL) is a collection of routines for performing standard and advanced genetical data analyses. The distribution contains also several command line programs based on the library. This Program has a core PHP function that generates venn diagrams, with user input as gene lists, through html forms using java script GeneZilla (formerly TIGRscan) is a state-of-the-art GHMM-based eukaryotic gene finder. It is faster and uses significantly less memory than GENSCAN, with comparable accuracy. GenLux is a project focused on the structural organisation of genes, e.g. promoters, splice-sites, etc. To elucidate certain aspects and verify data, modules (written in PERL, Java, etc) are released and put together in a "construction-set"-fashion. I think there is a need of a open forum especially made for genome assembly people so that we can share the knowledge with the world. This this the codebase for the Genopolis Gene Expression database (http://www.genopolis.it). It is presented here for futher puplic development or as a resource for similar projects. Genpak is a set of simple tools for manipulation of nucleic and protein sequences, written in ANSI C. The programs are supposed to be small, efective, use the Unix pipe/redirect and have a GUI via WWW/CGI. Browsing and Annotation of complete or incomplete genomes. Live GUI-manipiulation of the underlying database (with write access). Gene Function Identification Tool (GFIT) for post-sequencing analyses. UNIX+PERL enables us to query multi-entries and focus on what we want to see. Ghemical is a molecular modelling package. The graphical user interface is built on GTK2. Both quantum-mechanical and forcefield-based methods are supported, and it is also possible to add new methods. << Not released any file yet >> GOR-family algorithms for protein secondary structure prediction. Graphical User Interface for NCBI Stand alone BLAST. This is aimed to Windows users sice NCBI BLAST is only command line in Windows. But can be also used in UNIX. Requires Python, wxPython and BioPython. H under development A novel protein function prediction technique that helps identify the function of a protein when there are no known similar alignments. Calculations are performed without the need for computationally expensive alignment algorithms or databases. << Not released any file yet >> Spatial, 3D distribution of the hydrophobicity around the protein molecule, (M)olecular (H)ydrophobicity (P)otential (MHP) concept, intra- and inter-molecular interaction. The program calculates a hydrophobicity plot. Several sets of parameters can be used. (under construction) I The Immigrant genes database contains genes that have immigrated or been transferred from one species to another. Such knowledge is useful for studies that rely on phylogenetic and/or sequence similarity information. Ishmael is a standalone browser for the BioMOBY Biological Web Services system. Source is in CVS. IsoScan uses a 4-state Hidden Markov Model to predict isochores (regions of homogeneous G+C content) in genomic DNA. ISPyB Pocket Sample bridges the gap between the Crystalization information system (PIMS, ...) and the Information System for Protein crYstallography Beamlines : ISPyB. It keeps track of samples via datamatrix codes, ... J Java based Molecular Biologist's Workbench Jannotatix is a java-based Sequence and Annotation viewer. It's main purpose currently is to run different motif discovery programs on the sequences, supply the correct parameters and convert the results back to gff-format. A generic framework that could help research groups to design, accesss, search, share, and exchange bio-data. This project trys achieve this goal to help bio-data integration and management for small/middle sized research groups in avoid of purchasing exp Amaanova analysis in Java is intended to write the amaanova package in Java with interface to R. More bio-statitical module will be ported in this way. Comparative Analysis and Search Tool for prokaryotic genomes. The JCoast package provides a API and GUI that makes use of the standardised genome processing and storage system, GenDB. JDesigner is a tool that allows users to visually design biochemical networks. In addition JDesigner will output standard scripts such as SBML and Jarnac script. JDesigner is also SBW compliant. K [This project serves as a placeholder that meets all the projects (present and future) developed by Marek KochaÅ?czyk in one place.] L A science research project at the french school in brussels, created for the TPE projects in the french system. Deals with the perception of colors by the human eye. All information will be available to the public, but only in French. The LECB 2-D PAGE gel images database is for public use. It contains data sets from 4 types of experiments with 338 gif images with annotation and landmark data (various formats). It could be used for comparison with user data or software development. A database of leukemia genes Librarian is a tool for creation of annotated virtual library of PDF articles, designed for life science labs. Beta version of Ligand Database. << Not released any file yet >> An improvement of GOR-family algorithms for protein secondary structure prediction (LINK1, LINK2 and LINK+ methods). Based on GORx library. LuGenD is developed to help the Biological and Medical Sciences community to easily access all information on the genes that are involved in Lung Cancer. M The purpose of this project is two-fold. First of all, we would like to provide the average researcher with top-notch bioinformatics support. Second, we aim to provide a forum for bioinformaticians to distribute their work in a readily available form Phylogenetic analysis tools for distance matrix based clustering and comparison of trees. Mavric is both a library of phylogeny manipulation routines and a graphical interface for phylogenetic tree visualization and editing. Bioinformatics tools and lab admistrations tools developed by Tinghua H. at MBAB lab. * Knowledge and Technology Infrastructure for Marine Biological Resource Center(s)MBRC(s): Focusing on integration of presently separate knowledge bodies and technology platforms for monitoring , inventoring and managing biodiversity and bioprospecting. Microbial Diagnsotic Array Workstation (MDAW) is a webserver designed for manging, sharing and analysing diagnostic array data. This is a free resource which can be accessed at http://www.arraydb.org We describe an open source library written in the R programming language for Medline literature data mining. DNA melting simulator based on the algorithms of Poland, Scheraga, Fixman and Friere. Developed by Blake et al since 1980. More recent porting work done by Bizzaro. MetaBasis: A web based database (Basis) containing metadata (Meta) on software tools and databases in the field of Bioinformatics. Work done by: Vassilis Atlamazoglou PhD, Trias Thireou PhD, Yannis Hamodrakas MSc and George Spyrou PhD In Contrast to low-level Petri Nets (Place/Transition nets), Coloured Petri nets (CPN) belong to the high level nets. The idea of CPN is to overcome some limitations of low level Petri nets by adding of higher programming languages. MetaQTL is Java package for the meta-analysis of QTL mapping experiments. MetaQuant is a software for the automatic and accurate quantification of GC/MS based metabolome data. Develop a GUI interface using Perl/Tk to interact with Dr. Michael Zuker's web-based MFold. Will take in a sequence, GI, or accession number, obtain the sequence from GenBank, obtain folding parameters and results list, and then download results. Bioinformatics software has progressed a great deal from c++ code running on unix systems to user-friendly GUI based workbenches and visual tools. MobBioTools is a logical step forward towards bringing essential bioinformatics functionality to your mobile EMail list only: none of the Public Area resources are used. Multiplatform Molecular Visualization Program ProteinExplorer.Org (PE) makes slides of rotatable macromolecular structure views (MolSlides.Org). (PE) works on-line or off-line (from a downloaded copy) except for saving MolSlides. This project will facilitate saving MolSlides in more situations Development of a library and tools for object-oriented programming in Objective-C for macromolecular structure analysis. A Smalltalk-like interpreted scripting language gives access to all objects. Msatfinder is a simple Perl script that detects perfect microsatellite repeats (1-6 bp) in nucleic acid or protein sequences. Longer motif lengths can be detected if desired, and a variety of output files suitable for further processing are generated. MuGeN is a package for interactively exploring multiple annotated genomes simultaneously, possibly mixed with computational analysis results. Map information can be loaded from various sources, and resulting images can be exported in different formats. A multi-threaded standalone (no web interface needed) Java BLAST client. It can run BLAST similarity searches based on input sequence(s) or the Request IDs given out by NCBI's QBLAST in both batch and multi-threaded modes. Simple Windows GUI program to generate mutagenesis primer by inputting sequence, amino acid number, and letter of amino acid you want to mutate to. Also customize scoring scheme to make the primer fit your own need. The goal of this project is to develop a web-based user-friendly bioinformatics workstation where scientists can store and analyze their DNA/Protein sequences. A major goal is to have "plug-in" ability for developers and scientists to add tools/features t N NeoBio is a library of bioinformatics algorithms implemented in Java. The current version consists mainly of (pairwise) sequence alignment algorithms such as the classical dynamic programming methods of Needleman & Wunsch and Smith & Waterman. A series of workshops on advanced network tools for bioinformatics. 2001: CORBA and XML; 2002: Agents in Bioinformatics; 2003: Bioinformatics for Microarray data; 2004: Models and metaphors from Biology to Bioinformatics Tools O OligoCounter is a Java command line program which counts overrepresented 8-14bp oligonucleotides in DNA sequences. Simple text output is produced which can be visualised with a suite of associated Java applications, for example JCircleGraph or OligoViz. The Biomolecule Naming Service (BNS) is an LDAP directory of gene and protein information derived from NCBI's LocusLink database. The purpose of BNS is to quickly and easily convert between different name and identifier schemes. An open source laboratory information system designed aimed at small labs who want security and data exchange in an open system based on public protocols. OpenMMS (although defunct) has many nice features. Sure, you may use 'DBLoader', but can you make it work?... Perhaps I should rename this list... The goal of the OpenNotebook project is to create a modular framework for a client side cross-platform application to assist the end user of a web-based scientific resource in storing and maintaining returned data. The Operon Group is constituded of undergraduate students of Biology, Biochemistry, Informatics and Public Relations courses at the Federal University of Santa Maria (www.ufsm.br). More information in www.bioinformatics.org/operon/ Researching practical computational methods to solve the Chemical Master Equation (CME) using distrubuted/parallel algorithms executed on small PC clusters (10 processors). Cybernetic & Logitronic concepts to formulate variables (input/output) computations for the oxygen element throughout its electrochemical behavior, inside and outside the body. P A database of pancreatic cancer genes Is a parallel distributed framework for the design of oligonucleotides suitable for microarrays. PartiGene is an integrated sequence analysis suite consisting of a set of scripts; trace2dbEST, PartiGene.pl, prot4EST, annot8r and wwwPartiGene which process and organise EST data within a genomic context and facilitate large scale analysis. Patristic is a Java program that uses as input different tree files and computes their patristic distances. Patristic allows saving and editing in different ways those distances. Patristic provides different graphic views of the results. PCalc is a software designed to help molecular biologists in routine procedures of concentrations calculus in PCR, like calculus of primer concentration, calculus of annealing temperature (DNA/DNA and DNA/PNA), MW primer calculation and mass units convers pcb2png is a small utility that converts phosphoimager pcb/img files to png format PDBH aims to develop a searchable database of rasmol scripts, designed to visually integrate data in the PDB with data from other sources. Curently we maintain a set of scripts which DEFINE, color and annotate PDB entries with their SCOP domain definition User submits a protein sequence, and retrieves the positions which are well-conserved through several PSI-BLAST iterations. Conservation is parameterized by use of aa alphabet, use of priors, and voting scheme. Extension of perl OO system influenced by Frames / ontology research PES: Project For Endangered Species web based server side scripting backend with mysql or pgsql database. cataloging species and searching, adding functions. The Network for Integrative Multidisciplinary Bioinformatics Utilization Strategies (NIMBUS)-The Philippines' Bioinformatics Initiative Phoenix is a C++ parser for EMBL-Bank flat files. PHP Labware develops PHP software like the LabStoRe LIMS and OrderSys ordering/purchase systems for day-to-day usage by research groups/laboratories Built around independent modules that interact with each other, phpLabDB manages a variety of day-to-day useful laboratory information. It is also a high powered and highly customisable open-source laboratory database project. a web interface to manage biological samples (species, samples, DNA sequences, PCRs) phpPhylotree is a web application that is able to draw phylogenetic trees. it produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files. Poly is a program for the quantitative analysis of simple sequence repeats (SSRs) in DNA. polyxmass is a software suite for (bio)polymer mass spectrometry that is Free Software developed on GNU/Linux. It allows the definition of polymer chemistries and the simulation/analysis of mass spectrometric data obtained on (bio)polymers. Population genetic software: individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions. PREP is a Perl script designed to allow the usage of regexps within searches of Pubmed. PREP allows for the easy retrieval of Pubmed records that contain terms that can be more easy matched by a textual pattern than a traditional keyword query. Tools for aligning PCR primers or similar short DNA sequences against genomic sequence. Many options for constraining acceptable alignments and input/output formats. Automatically optimizes the sequence search stategy for search parameters. PrimerPy is a free GUI tool for optimal QPCR primer design, using "Primer3" as a backend engine. The design's been validated by laboratory experiences; applicable to conventional PCR too. A web-based program that automates design of mutagenic PCR primers for site-directed mutagenesis. PROMPT is a platform independent system for retrieval, analysis, mapping and comparison of protein sets. It allows easy mapping of different types of sequence identifiers, automatical data retrieval and integration, a multitude of analysis and comparison catalogs the available known prostate oncogenes. PyMsXML is a python script for converting vendor specific mass spectrometry data files from their proprietary binary format, to either of the emerging XML file formats for mass spectra: mzXML or mzData. Q R Automated molecular palaeontology of repetitive DNA elements. Input: RepeatMasker annotation. Outputs: 1) Defragmentation of elements. 2) Inference of nesting structure. 3) Estimates of the ages of LTR-elements. 4) Multiply aligned element sequences. S S2S is a tool able to easily manipulate, display and connect heterogeneous RNA data like sequences, secondary and tertiary structures. A bioinformatics data-updater. This small PHP code would retrieve the current release files from the premier databases, parse it, and then list only the salient features all in one single go. The Scriptome is a set of tools and protocols that helps biologists format, merge, and filter files. While designed for non-programmers, it can also help beginners learn Perl if they choose, and serve as a "cookbook" for experienced programmers. SEARCHPATTOOL is a program for analyzing DNA sequences in order to discover patterns or motifs for binding sites. It is based on exhaustive algorithm and is dedicated to prokaryotic species or genes with small promoter regions. seKs will be an easy to use sequence editor, running in the KDE3 environment. It will provide a nice GUI to edit, analyze and anotate DNA, RNA and protein sequences. Status: heavy development, nothing for the public yet Dependencies: QT3, boost SeqDoC (Sequence Difference of Chromatograms) aligns and performs a subtractive comparison of two ABI DNA sequence chromoatograms. The subtracted profile is processed to highlight differences characteristic of single base changes. Accepts a DNA sequence and a set of primer sequences and returns a textual figure showing the annealing positions of the primers, restriction cut sites, and protein translations. Nested JavaScript code makes the figure interactive. The Sequence Manipulation Suite 1 is a collection of web-based programs for analyzing and formatting DNA and protein sequences. The Sequence Manipulation Suite 2 is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, and for teaching purposes. The mailing list to ask all your SEQUENCE SEARCHING questions! Sequence Studio main package provides classes and interfaces for various kinds of sequence alignment SEQUEROME is a web-based Sequence profiling tool that provides a unique feature of completely profiling a BLAST report within a single browser interface by providing simplified access to web-distributed resources for protein and nucleic acid analysis. SeWeR is an very popular integrated, customizable, platform-independent web interface to bioinformatics services available over WWW. Sight, a java-based package that provides a user-friendly interface to create and connect agents for automatic genomic data mining for individual purposes. No programming skills are required, but very strong support for programmers is implemented. SiteFind is a molecular biology tool that enables a scientist performing site-directed mutagenesis to simultaneously introduce a restriction site as a maker for successful mutagenesis. The Samuel Lunenfeld Research Institute (SLRI) Bioinformatics Toolkit is a mainly C-based cross-platform toolkit for dealing with biological information, especially protein structure/function. Visit our project home page for more information. A Smith Waterman sequence alignment algorithm implemented to run on GreenTea P2P decentralized distributed network computing platform SNA is a Mathematica toolbox for stoichiometric network analysis. Among other things, it supports flux balance analysis and the enumeration of the elementary vectors of the flux and the conversion cone. Design primers for Snapshot to do allele specific analysis SNPsel generates allelic sequences by combining a single sequence with its SNPs, used as input for TFBS prediction programs (MULAN, MAPPER, MatInspector) to find TFBS affected by SNPs on both (allelic) sequences. A n illustrative example for the current situation in immunological research is the case of cytokine networks. Cytokines are small protein or glycoprotein messenger molecules that convey information from one cell to another. Various aspects of the immune The idea is to combine a 'wiki' system with SQL queries, allowing data driven pages to be constructed by the user. The most important aspects are results formatting and parameter passing between data driven pages. The major hurdle is security. The Short Sequence Assembly by K-mer search and 3' read Extension is a genomics application for aggressively assembling millions of short (25-36bp) nucleotide sequences. The StemNet project aims at designing and constructing a knowledge management system for the field of stem cell biology. Its goal will be to increase security and the quality of clinical treatment based on enhanced, web-based information supply. Strainer is a multi-platform visualization tool for metagenomics data. It allows the user to easily browse the variation present in assembled shotgun sequence data from non-clonal samples. The computer program STRAP supports the analysis of hundreds of proteins and integrates amino acid sequence, secondary structure, 3D-structure and genomic- and mRNA- sequence and residue annotation. The objective of the SCOL project is to produce a global hierarchical clustering of all the available small molecules and protein ligands using measures of structural and chemical 'similarity' between molecules. The project is to develop an efficient and useful clustering algorithm. The project currently includes computer code written in Matlab for performing singular value decomposition followed by fuzzy K-means clustering on adjacency matrices. T A Java taxonomy browser GUI designed to run as a plugin or standalone. Currently works with the NCBI taxonomy. This Database will give details of Drugs and the targets involved in the treatment of TB. Telemedicine Research Laboratory began its activities in the year 2000 at Bangalore, India. Some of the key objectives was to use technology for humanitarian purposes and synergise with international organisations like ITU and ISO. Text2Knowledge is aiming to provide text mining tools for medical texts. It utilizes natural language processing techniques to extract patterns for specific domains... Thaker RNAi Group was founded by a group of ambitious young scientists from Cambridge, Massachusetts. Combining the skill sets of Python, Ruby on Rails and Java, we intend to create a practical utility that connects scientists worldwide. Imagine that every web server was a generic CGI calculator, and you could compile code to 'run on the web'... Un "catalogue" de tous les TPE créés par les élèves de 1ère S au Lycée Francais de Belgique, pendant l'année scolaire 2001-2002. Trace Genetic Disease detects position and type of the mutation when disease causing protein sequences are given as input and displays original and mutated amino acid sequences with the probable diseases. TraceViewer provides several functionalities needed by any biologist who wants to efficiently analyse his/her trace data. The Tandem Repeat Occurrence Locator is a light weight SSR finder based on a slight modification of the Aho-Corasick algorithm. U The Dynamic Local Storage Tool is a simple PHP/Apache/MySQL application that downloads and maintains local databases containing relational UniGene keys for selected species. V [structural proteomics | JavaWebStart, OpenGL] Applies methods of defining conformational subspace for early-stage protein folding/structural similarity estimation by means of geometrical parameters of the polypeptide chain (see Bioinformatics papers) VLinux Bioinformatics workbench is a Linux distribution for Bioinformatics. It is easy to use, no installation required, CD-based distribution. It includes a variety of sequence and structure analysis packages.It is an Open source product released under G W The W-curve is a numerical mapping, pattern recognition algorithm that shows significant potential for achieving visual consensus for the class of long repetitive sequences found in long genomic strings. The name (without the a?s) stands for ?Web Services for Bioinformatics?. Wasabi is both an initiative to refactor popular informatics utilities as Web services and a piping infrastructure enabling those services to be linked to solve complex problems. WAX is general framework for tying together XML based applications on the web using RDF. Some code in CVS. Wikiposon is a collective framework to gather informations about TE, for study them or only to learn things. It is free to read but a registration is requested to edit the scientific content. WinBLAST is a Windows graphical front-end for NCBI BLAST. It is written completely in C#, utilizing Microsoft?s latest .NET framework. WinBLAST will run on any Windows machine that supports Microsoft .NET framework. WinBLAST has an intuitive user inter X Simple, declarative, bijective inter-conversion between MATLAB structured variables and XML strings. A specialized markup language, MbML, was defined to support string representation of any MATLAB variable: any XML --> MbML <--> MATLAB Y Yet Another Microbial/Metagenomic Annotation Pipeline/Program is a Perl application created for the NERC Microbial Metagenomics programme. It is designed to be a user-friendly way for Bio-Linux users to run a selection of first-pass annotation tools upon Your Lab Data is a free web-based LIMS (Laboratory Information Management System), aimed at a typical small molecular biology laboratory. It allows lab group members to have their own private forum, events (training or meetings), ELN and a LIMS area. Z The goal of this project is to discover new genes or splice variants from bioinformatic analysis on EST (Expressed Sequence Tag) hoping the interest of biologist for "wet" analysis on the produced data.
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