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Basic Electronical Medical Management (BEMM) is an application to control medical data of a set of patients. It is built on top of open source technologies, to provide an integration skeleton of mvn, Datanucleus, Spring, Vaadin, Acceleo technologies.
This library is a lightweight implementation of genetic algorithm, contains the most popular types of chromosomes and the basic algorithms for selection, elitism, crossing and mutation.
CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74
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Molecular Graphics and Dynamics. Molecular model builder. Part of the Ascalaph Designer http://sourceforge.net/projects/asc-designer/ project. Windows & Linux.
--UPDATE-- New Version is now integrated in the official PyMOL plugin repository! --UPDATE--
The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.
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.
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.
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This is a C library with a set of functions that allow the user to evolve biological networks. The user provides a fitness function in C, and the library will do the rest. A few simulation algorithms and examples are included.
RefineHMM refines an original hidden Markov model (HMM) to find an optimal fit
against the evolutionary group that the HMM models, and it does this using
through iterative database searches and incremental subsequent adaptation of
the seed set.
Anna is lightweight Java framework to build pipeline systems of any kind.
It will take care of recurrent needs such as dependency management, data serialisation and synchronization as well as parallelization of execution.
Trial Criteria Online Data Entry (trialCODE): a Java-based user interface that codifies eligibility requirements used to automate the screening of potential subjects to clinical trials. Used for caMATCH screening engine on BreastCancerTrials.org site.
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.
IBIS - Interactive Biodiversity Informatics Software - is software to identify species or other taxa. Intended users range from school children or citizen scientists to ecologists or taxonomists. The identification keys can be embedded in CMS or Wiki
Ruby Research Wiki (RRiki) can be used to keep notes and organize references for research. It uses a browser interface, an intuitive plain text formatting language (markdown), and facilities to cross-reference and hierarchically organize notes
h2:www is an easily extendable online interface for bioinformatical command-line tools, providing convenient project-oriented working facilities for multiple users.
GAME stays for Generic Architecture based on Multiple Experts.
Its main purpose is to make easy prototyping, test and release of prediction systems.
Released by IASC group, university of Cagliari
BioPerl implemented in JavaScript. The library aims to promote and aid the development of bioinformatics applications in JavaScript much the same way as BioPerl helps bioinformatics development in Perl.