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ProteinShop is an interactive protein manipulation tool. Users apply their knowledge and intuition to quickly create a set of protein configurations that can be subjected to local or global optimization. More information at http://proteinshop.org
Knime (http://www.knime.org) nodes for sequence bioinformatics. Sequime is an eclipse plug-in for the KNIME data mining platform, providing additional nodes for reading, processing and visualizing sequence information.
AI-powered contract management that helps businesses track spending, negotiate smarter, and never miss deadlines.
Concord serves small and mid-sized businesses and Fortune 500 companies. This robust, web-based platform is used by human resource, sales, procurement, and legal teams, and virtually anyone who deals with contracts.
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.
GODASM is the brief of ".Gff Organized Data Analysis System for Microarray Studies". Private programs, GODA system, had been successful developed in 2008 at CGMH,Taiwan. Now the project will transfer GODAs to open-source based system.
The project is for developing libraries for visualizing biological sequence data on the web. The libraries are written in C and currently use a language (lex/yacc) based front end for presenting features on genomes, contigs, or any type of sequence.
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.
PeerGFS PEER Software - File Sharing and Collaboration
One Solution to Simplify File Management and Orchestration Across Edge, Data Center, and Cloud Storage
PeerGFS is a software-only solution developed to solve file management/file replication challenges in multi-site, multi-platform, and hybrid multi-cloud environments.
PheMaDB is a web-based data management system to store and analyze OmniLog Phenotype Microarray data. The manuscript can be accessed here: http://www.biomedcentral.com/1471-2105/12/109. Chang WE et al. BMC Bioinformatics. 2011 Apr 20;12(1):109.
H-mito is a mitochondrial DNA haplogroup prediction tool based on the phylogenetic tree http://www.phylotree.org/. Ancillary scripts: mitoP.py to extract mutation lists and clustal-2-fasta.zip to join, align through clustalw and convert data.
MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection
A database and a web front end for physiologic data on animal feeding, developed with PostgreSQL and Django at NESCent (http://www.nescent.org) for Mammalian Feeding Working Group (http://www.feedexp.org).
Current development of the codebase is on Github at http://github.com/NESCent/feedingdb.
Skittle is a 2D visualization of genome sequence files. The program assigns four colors to the four nucleotides and text wraps the sequence to create a 2D picture based on the DNA sequence. Great for researching tandem repeats and chromosome structure.
Compiled downloads available at http://dnaskittle.com/
Source maintained at https://github.com/josiahseaman/skittle
The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.
3D medical image platform for visualization and image processing. Segmentation with Levels sets. Surface reconstruction with marching Cubes, texture Mapping and Raycasting,DICOM support. Integration environment for VTK, ITK and vtkInria3D under wxWidgets
This is a MATLAB toolbox for the quality control and scoring of EMAP and SGA genetic interaction data. It includes a graphical user interface and some automatic plot-generating tools.
A population-based method for DNA copy number analysis: recurrent copy number aberration indentification in multiple samples (with no need of single-sample calling). Developed for a quick analysis of high resolution and large population data.
IMAS is a Visual Analytics system for the discovery of knowledge in genomic information. IMAS enables genomic scientists to rapidly analyze and visualize a set of microbial genomic sequences using tools such as Glimmer, Blast, Clustal-W, Primer3.