Open Source Java Bio-Informatics Software - Page 11

Care4G is a web-based software, as forking of the most famous care2x, it will be a complete HIS for the II Millennium...

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.

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

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.

Cervelletto is a neural network simulator. It uses a new neural model based on biological, neurological and psychological studies. [it's not yet completed... just give me some weeks! sorry!]

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

An integrated bioinformatics toolkit for analysis of ChIPseq data from the Illumina DNA sequencing platform. Includes filtering, quality control, simulation, peakfinding, visualization, and comparison of samples.

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).

Chemical Evaluation Framework (CEF) is a molecular structure based software to assist in hazard assessment. Download requires Java 6 update 1. Source code is contained in jar files. Download contains GSH reactivity plugin.

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 .

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.

Cloe (Closure Editor) is a graphical, Java based tool used for editing contigs, resolving contig features, and closing both sequencing and physical gaps.

Application for visualisation of Chromosomal LOcations of Gene Expression.

A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.

A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.

CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.

Comprehensive Meta Prediction and Annotation Services for Proteins: The new all-in-one prediction tool that can be easily extended to include any SOAP/WSDL-enabled prediction servers. A concise user interface lets you use the results instantly.

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.

The Comparative Toxicogenomics Database (under development) will be a publicly-available, web-based database of genes and proteins of human toxicological significance. It is being developed using an Oracle 9i database, Tomcat, and Python.

The increasing wealth of transcriptomic data and current computational tools enable to infer how protein interactomes and complexomes may be assembled in specific samples. With CompleXChange this information can be exploited to conduct differential analyses of the dynamic protein complexome in a quantitative manner. The corresponding publication can be found on https://doi.org/10.1186/s12859-019-2852-z.

CSBI is a component based framework that allows for inter-component data sharing and access. GINY is an Open Source Graph Library.