Open Source Java Scientific/Engineering Software - Page 91

CAXO (Component for Accessing XML based Objects) is mapping any xml based object to a multiline and editable tree structure. CAXO is a JComponent, and direct implementable in any swing container. In default configuration, CAXO is an xml browser or editor

The Celera Genome Browser, developed at Celera Genomics as part of Celera's sequencing and annotation of the human genome, and released as open source in 2006.

Celerity, an open-source, Java based data-flow architecture that provides high performance with fine data granuality. Celerity offers a module based programming environment, which can parrellelize across processors, machines and architectures.

Help us to improve Cell Culture. We want to hear your feedback! Request new Cell Culture feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/fw Cell Culture is a highly specialized protocol-driven system designed to support development of the cell lines. Cell Culture manages activities related to the growth and maintenance of cell lines, provides stable cell lines development and incorporates laboratory methods facilitating faster and more accurate inventory lifecycle management: from the procurement of cell lines and request processing to tracking of tubes and other items in the laboratories. Cell Culture provides easy to follow, step-by-step protocols, with tips and notes and is of interest to researchers, technicians and process engineers using cell culture within the biotechnology, biomedicine and pharmaceutical industries.

A bioinformatics tool, developed as a Cytoscape plugin, for elucidating small molecule signalling mechanisms that drive cell fate into a specific direction.

CellGIS is a wireless planning tool that uses Java and ASCII Raster maps format. It allows to implement more propagation models and funcionalities by means of plug-ins.

An IDE for CellML 1.1 user models developed in UNSW as an open source project. Author: Mitchell Lanesbury 2012

Cellontro models and simulates cells, other biological entities, and biochemical networks. Specify your models using XML and Java, or SBML. Cellontro is now completely contained within the Xholon sourceforge project.

This software simulates cellular behavior based on specific rules (e.g. Game of Life or Wireworld). The UI will be replaceable and there will be a feature for importing rules from a file based on a format developed for this purpose.

Cerebrum intends to be a state of the art web 2.0 Electronic health record management solution.

Chemical Entities of Biological Interest (ChEBI) is a freely available database of chemical compounds and other small molecular entities. WE HAVE MIGRATED TO GITHUB. To create new issues/comments, please use the following link: https://github.com/ebi-chebi/ChEBI/issues

UIMA solution for analysing web-server logs, that does things like analyze the user behavioral patterns in the channels followed by users from the log files, report current and the past behaviour of the visitors in selfservice systems.

Distributed phrase-based machine translation training tool based on Hadoop.

A simple utility to check a dicom cdrom for patient, studies, series and images It extracts data directely from dicomdir.

The CheckCML project is a collection of modules for the production and checking of chemical experimental data represented as CML. The core CheckCML library provides classes for the checking process; tools such as OscarData allow for the production of CML

Mathematics, Chemistry and Bio-informatics semantic knowledge editor and simulation environment. It should serve as interactive science learning program or science classroom notebook and workshop.

A Java program to parse chemical names using IUPAC nomenclature. The output can be either a visualisation of the molecule, or in a form for other programs to use (e.g. CML).

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 .

The Chemical Manager application can be of great help to Organic Chemistry Departments. University research groups will benefit from using this application, since it was optimized for their needs. Currently, Technion Chemistry department is benefiting from it.

CherBot is an information bot for Crossfire, Daimonin and good old plain IRC that keeps track of which players collect which items, who's been online, determines a level ranking, provides a mail system for mailing offline players, manages clans and

Cherokee is a fully extensible and scriptable automation engine for any and all java applets. To make it work for your favorite java applet the most you have to do is write is two classes.

Calculate the number of solutions to place n queens on an n*n chess board, without any queen attacking each other. Options allow using rooks instead of queens, disabling knight attacks and setting the minimum distance between queens.

ChiBE (Chisio BioPAX Editor) is an open source pathway editor for biological pathways in BioPAX format. ChiBE converts BioPAX graphs into process diagrams where complexes and compartments are represented with compound nodes. !!! For latest version, please see !!! http://code.google.com/p/chibe

Chipster is a biologist-friendly analysis software for high-throughput data. It contains over 200 analysis tools for next generation sequencing (NGS), microarray and proteomics data. Users can combine tools in automatic analysis workflows, which can be shared. Chipster's interactive visualizations allow users to select datapoints and create new gene lists. For NGS data Chipster contains a built-in genome browser, which highlights SNPs and automatically indexes BAM files and calculates coverage. Chipster’s ability to provide a biologist-friendly access to a powerful analysis platform is technically based on a desktop application user interface, a flexible distributed architecture, and the ability to integrate many types of analysis tools (command line, R/Bioconductor, Java, Web Services etc). The platform is generic and easily extendable to other areas, even beyond bioinformatics. For more information, please see http://chipster.csc.fi and http://genomebiology.com/1471-2164/12/

A visualization software for BioPAX files. Uses compound graphs for showing complexes and compartments. Can also export to SIF and display SIF files.