Open Source Java Bio-Informatics Software - Page 12

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.

The development and curation of a range of XML-based tools for using Chemical Markup Language (CML), including XSD XML Schemas for validation, datatyping and constraining CML documents and XSLT Stylesheets for transforming, filtering and rendering.

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.

CompuCell3D is a software framework for multimodel simulations of biocomplexity problems. It has been developed as an ongoing project for the Interdisciplinary Center for the Study of Biocomplexity at the university of Notre Dame.

CILib is a framework for developing Computational Intelligence software in swarm intelligence, evolutionary computing, neural networks, artificial immune systems, fuzzy logic and robotics.

Conrad is both a high performance Conditional Random Field engine which can be applied to a variety of machine learning problems and a specific set of models for gene prediction using semi-Markov CRFs.

Contextor is a light-weight simple-to-use Java based library to help developers and researchers working with the general concept of a resource; as examples, resources can be text resources, web resources, images and videos.

ConvertMAS - molecule converter; use to convert Chemical File Formats. It works on mol, mol2 and sdf files. It converts single file to respective formats. It will split sdf file with multiple molecules into seperate single files of any desired format. Also ConvertMAS creates sdf files from joining of mol, mol2 and sdf files. This is stand alone application; hence no need of internet connectivity to get results. It will generate output files in less time. Various online tools are available for conversion of Chemical file formats; but ConvertMAS mainly works on mol, mol2 and sdf effectively.

Corra [BMC Bioinformatics 2008] is a computational framework & tools for discovery proteomics using label free LC-MS and ATAQS [BMC Bioinformatics 2011] is a computational framework & tools for validation proteomics using SRM LC-MS method.

For comparative plus/minus spreadsheet data, Coulson Plot Generator application creates a multiple pie diagram, for a rapid visual comparison of subunit occupancy across a range of entities. Numbers of pies, segments, labels and colours are customisable. Creates an editable PDF from a comma separated text file. Now with zoom capability and more memory, for larger datasets. Save images in several formats including SVG.

The Cybertory™ Virtual Molecular Biology Laboratory is an on-line virtual environment for conducting simulated experiments in molecular genetics.