Open Source Java Scientific/Engineering Software - Page 70

Genevar (GENe Expression VARiation) is a platform of database and web services for the integrative analysis and visulization of SNP-gene assocaitaions in eQTL studies.

Geneview is a visualisation tool to display genetic sequence data stored in nucleic sequence databases like <A HREF="http://www.ncbi.nlm.nih.gov/Genbank/">GenBank</A>.

GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.

Identification of clines from allele frequency or genome-wide databases. Angular transformation. Sigmoid function. Parameterization of a cline: orientation, Pearson’s product-moment correlation coefficient, linear and sigmoid regression and coefficient of determination. Graphical representation of the cline. Confidence limits. Spatial autocorrelation. Moran's index. Isolation by distance. Exponential regression. Correlation Fst/Distance. Centroid method. Cline's expected vs. predicted heterozygosity. MDS. Sammon projection. Geographical distances. Fst distances. Export data to Arlequin, Phylip, Past and Poptree. User-friendly input data.

GenoGUARD is a DNA sequence screening software that implements the best match method recommended by the federal government to detect the presence of biosecurity threats in synthetic DNA orders.

Genome Data Visualization Toolkit (GDVTK) is a Java library for building bioinformatics visualization application. See Bioinformatics, 2004 Mar 22;20(5):727-34. Java-based application framework for visualization of gene regulatory region annotations.

This tool integrates and enhances publicly available genome data from different sources into a local database. Using a web browser, scientists may view and query the data, keep persistent notes, and schedule batch services (such as BLAST) from NIH.

GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded. This project has moved to GitHub: https://github.com/GenomeView/genomeview

Geo Sus is a software suit for use with the Bartington MS2 magnetic susceptibility meter. It was developed for the Victoria University Wellington Geophysics department to help out in their work. Created by team Geodudes in SWEN302 T2 2009

Geo4J is a Geographic Information System library for java. It is based on the java open source library named LWJGL. The principle is rendering data from source. It provides a tools set which permit user to initialize and handle geographics data.

The development community in building GIS solutions is sustaining an enormous level of effort. The GeoAPI project aims to reduce duplication and increase interoperability by providing neutral, interface-only APIs derived from OGC/ISO Standards.

GeoAr intends to be a rich client for WMS and WFS services. It's developed on LZX (OpenLaszlo), so it would serve dhtml(near future) and flash to the user's browser giving the chance of select between them, but having only one server's cource code.

The GeoCacher application for Geo caching enthousiasts and is used in conjunction with a SymbianOS or Android based phone and a location provider. It contains basic navigation as well as map-based navigation based on open street map data.

GDS is a project to check generic measured earth science data. It is also an interactive database management system to store all data in MySQL-DB. GDS rules as project based management system with unlimited stations. Each station manages 20 sensors.

GeoDress is a program for reverse geocoding of JPEG pictures with a simple GUI and even a command-line interface.

Dynamic Geometry Software both for Drawing and Proving Geometry Statements

GeoGebra is free and multi-platform dynamic mathematics software for learning and teaching geometry, algebra, statistics, and calculus. Download the free software at http://www.geogebra.org. Find the source code at http://www.geogebra.org/trac

Welcome to the GeoGig project, exploring the use of distributed management of spatial data. GeoGig draws inspiration from Git, but adapts its core concepts to handle versioning of geospatial data. Users are able to import raw geospatial data (currently from Shapefiles, PostGIS or SpatiaLite) in to a repository where every change to the data is tracked. These changes can be viewed in a history, reverted to older versions, branched in to sandboxed areas, merged back in, and pushed to remote repositories.

Integration of multithread calculation and 2D/3D visualization

Photo Geo-Tagging application for easily adding GPS coordinates to EXIF based images.

GeoLab3D is a java application that let the user play with geometrical concepts in 3D.

geolocate is a front-end java program that works with google maps to provide dynamic maps to users. Combined with the flexibility of XML and the power of javascript, users can see various relationships on their map to draw conclusions.

geoLucene is an extension of Lucene that allows to effectively index and search documents that contain locational information (longitude/latitude). It uses R-tree as a spacial index. See http://www.gossamer-threads.com/lists/lucene/java-dev/53378.

GeoMondrian is a "spatially-enabled" version of Mondrian. GeoMondrian brings to the Mondrian OLAP server what PostGIS brings to the PostgreSQL DBMS, i.e. a consistent and powerful support for geospatial data. It also provides geo-extensions to MDX.

GeoPMS is a project based full paper management system to archive, search and manage scientific papers. GeoPMS has full text search, search by author, search by title and citation import functionality direct from the PDF header, PDF text or RIS. Reference list design can be selected for each project.