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Intrepid Bioinformatic's Integrative Genomics Viewer (IGV) modifications for viewing NGS files on IGV with data located on remote servers, accessed by web services.
Web application to make user-friendly requests on large XML database.
Tools to XML-ize large bodies of semi-formal texts (like floras).
Computer-assisted specimen identification.
Uses natural language processing, 2D/3D images analysis and generation.
The program versusSNP is a flexible tool for mining SNPs between two close related genomes. First, we align all the orthologous genes and select SNPs, then the SNPs are separated into categories based on their mutation types.
MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.
OpenVista(R) is the open-source version of VistA, an enterprise grade health care information system developed by the U.S. Veterans Affairs and deployed at 1,500 global facilities. OpenVista is a registered trademark of Medsphere Systems Corporation
This is a pipeline that is used to store an EST or Genome assembly information including reads and their alignment in a mysql database. Further more, it provides a set of scripts to mine SNPs and other statistics from the assembly.
Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.
HATS (Haplotype Amplification in Tumor Sequences) is a tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data. The amplified haplotype may reveal gene variants.
Executable program that measures sizes and other properties of colonies arrayed in a grid format (intended for 768, 384, or 96 colonies on agar plates) from jpeg images
The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.
An online database project with database and web interface to archive, manage, search and download individual-based life history data that have been collected from wild primate populations.
HeliconiusDB is a project to develop a database schema and web-based software tools for the study of Heliconius butterflies (and other organisms) in evolutionary biology.
It's a project to predict peptide fragmentation of mass spectrometry. Check the detail at Anal Chem. 2011 Feb 1;83(3):790-6. On the accuracy and limits of peptide fragmentation spectrum prediction. Li S, Arnold RJ, Tang H, Radivoja
A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.
Protein Data Bank transformed into an SQL database with a very powerful search engine and a rich web interface. The engine combines chemical, sequence and 3D structure searches. The interface provides statistics, sequence and 3D structure alignments.
Graphical editor using HTML5 canvas for input of chemical structures, molecule interactions, as well as protein sequence and 3D structural motifs. Facilitates searches in chemo-informatics, bioinformatics and structural biology .
BiVeS - Biochemical Model Versioning System BiVeS is a tool based on the XMLDiff algorithm. You can think of it as a kind of SVN for models with biological or chemical background encoded in XML.
Contextor is a light-weight simple-to-use Java based library to help developers and researchers working with the general concept of a resource; as examples, resources can be text resources, web resources, images and videos.
BorderFlow implements a general-purpose graph clustering algorithm. It maximizes the inner to outer flow ratio from the border of each cluster to the rest of the graph.