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DNA sequencing quality values, base calling and trace processing
Tracetuner is a tool for base and quality calling of trace files from DNA sequencing instruments. Originally developed by Paracel, a Celera Business, this code base was released as open source in 2006. TraceTuner was used by Celera to call 30+ million reads from both Drosophila and human genome sequencing projects. In 2000, Applied Biosystems bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the customers of these capillary electrophoresis sequencers. Later versions of...
Open Live Support aims at providing a free platform independent chat support system. The system currently works as a live chat support system. The team is currently working on integrating remote control capabilities to the system.
hxRender is a 2D graphics library built around OpenGL for rendering, and may be used with SDL for window setup. It was designed in mind to replace SDL's antiquated rendering methods.
Java Slideshow is a platform independent image viewer especially for huge collections. It provides an easy command line interface, supports tagging and view by category, zoom, move and has some file manager functions like delete file or find duplicates.
The Flow Cytometry Laboratory Information Management System (FlowLIMS) is a web-based software system that gives users the ability to create and manage experiment protocols for the DiVa and FACScan flow cytometers
RoofTop is a network/systems monitoring (NSM) tool that leverages SNMP standards to deliver critical health and performance monitoring through device based reports and graphs, event notifications, alerts, and configurable alarm thresholds.
Data and animal management software for large-scale phenotype screening Used by GNF for mouse ENU mutagenesis project. Data visualization & analysis, animal husbandry management, & automated QTL mapping. Usable as stand alone animal husbandry system.
Image Tagger is a simple graphical application to allow the tagging of images. It currently allows you to set title, commands, and keywords in the IPTC / EXIF tags. It's not very polished, but it is pretty stable. It uses ExifTool for editing tags.
@Note2 is now available in www.anote-project.org
@Note is a Biomedical Text Mining workbench that integrates current Biomedical Text Mining (BioTM) methods and provides biologists with intuitive tools capable of supporting their bibliographic searches and further literature curation.
MyJQuery is an operating system independent database utility written entirely in Java, for beginners MySQL 5.1+ Database & students.
Generating Perl,Perl/CGI,PHP,Java,JSP Code Snippet & export CSV,HTML,XML
execute any MySQL statement
SquidRestrict is a Web based tool that allows multiple time restrictions to be placed on internet usage for firewalls that use the Squid Web Cache (http://www.squid-cache.org/).
BioStream enables bioinformatics researchers to create, query and apply tools to their own databases. It supports sequence files and other data types by allowing the creation of metadata definition files.
Hyper Estraier is a full-text search system. It works as with Google, but based on peer-to-peer architecture. Using Hyper Estraier, we can construct a large-scaled search engine with cheap computers.
QDBM is a library of routines for managing a database. It is developed referring to GDBM for the purpose of the following three points: higher processing speed, smaller size of a database file, and simpler API..
hypKNOWsys aims at developing a Java-based workbench for knowledge discovery and knowledge management. Currently, hypKNOWsys has released two intermediate tools: DIAsDEM Workbench (text mining for semantic tagging) and WUMprep (Web mining pre-processing)
A Perl program to write characters (eg. a lot number) to an alphanumeric display via rs232. Includes JavaSwing GUI. Developed for production in pharma industry. Currently two lines included. German version.
SLIME (Scream LInux Middleware for Embedded systems) is a tiny and efficient cross-platform embedded middleware as a shared library with tools, which supports CBSD (component-based software development) to build application softwares quickly and easily.
The Genomic Diversity and Phenotype Data Model (GDPDM) captures molecular and phenotypic diversity data. MySQL databases are used to implement the schema. This project develops software tools (written in Java, Perl, etc.) associated with this model.
This is an experiment in creating the best database API I can come up with. It is an alternative to query languages. The latest version is being written in Scala using Berkeley DB Java and will run on the Java VM.