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ATOM is an OMERO client which allows automated import of image data into OMERO. ATOM is provided as is without any guarantees or warranty. The author is not responsible for any damage or losses of any kind caused by the use or misuse of the programs.
BioX (pronounce as bio cross) is a system for the management of local and remote (currently supporting RMI, CORBA and SOAP Web Services) components such as files and services (e.g. BLAST). Additionally, the components can be composed to workflows.
iso2l (ˈaisəutuːl, spoken isotool) is a software to calculate the isotopic distribution of a chemical formula or a amino acid chain.
The development has been MOVED TO https://github.com/binfalse/iso2l
BAMStats is a GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API.
Soaplab is a generator of Web Services providing a programmatic access to command-line (and other) applications on remote computers (an example of its usage is available at http://www.ebi.ac.uk/soaplab/)
The creation of quantitative SBML models is a time-intensive manual process. Saint, an automated SBML annotation integration tool, aids the modeller and reduces development time by providing information about a model in an easy-to-use interface.
OpenVista(R) is the open-source version of VistA, an enterprise grade health care information system developed by the U.S. Veterans Affairs and deployed at 1,500 global facilities. OpenVista is a registered trademark of Medsphere Systems Corporation
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Executable program that measures sizes and other properties of colonies arrayed in a grid format (intended for 768, 384, or 96 colonies on agar plates) from jpeg images
The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.
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.
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
Visualize chromatographic properties for peptides from replicate, multi-site HPLC-MRM Mass Spectrometry experiments. RT Viewer was developed to easily visualize and troubleshoot chromatographic properties of a study across multiple laboratories.
EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
BorderFlow implements a general-purpose graph clustering algorithm. It maximizes the inner to outer flow ratio from the border of each cluster to the rest of the graph.
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.
Memomics Forge is a meta-project for software that utilizes the Memomics Semantic Service.
Memomics Semantic Service provides semantic data which can be embedded in applications via webservices.
PowerTalk automatically speaks Microsoft PowerPoint presentations. For presenters who find speaking difficult, audiences containing people with visual impairments and fun educational uses. Uses synthesised computer speech provided with Windows
h2:www is an easily extendable online interface for bioinformatical command-line tools, providing convenient project-oriented working facilities for multiple users.
DimReduction project provide an open-source multiplatform (Java) graphical environment for bioinformatics problems that supports many feature selection algorithms, pattern recognition techniques, criterion functions and graphic visualization tools.
TaxonFinder is an application that annotates taxon found in literature. The application harnesses a hybrid algorithm that is necessarily a combination of morphological analysis, dictionary lookup and Levenstein Distance algorithm.