Open Source Frameworks

An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).

Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework.

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.

The BMF is a Software Framework developed in Java language for the creation of web applications on the server platform also Open source, in clinical, administrative and management for a healthcare company.

BioEval, a web-based evaluation platform for one or multiple biomedical text extraction systems and the collaborative creation of gold standards. Handles evaluation of extraction of one to many related entities, plus supporting evidence and normalization

The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.

BioSunMS, a flexible software platform for submission, management, retrieval of sample and MS data(MALDI or SELDI), and clinical proteomics-related statistical analysis. BioSunMS integrated all functions into a user-friendly desktop RCP application.

The BioUtils - Proteomics package is a lightweight Java framework for handling commonly used data produced and needed in the field of Mass spectrometry in general and especially in the field of Proteomics. It's stable, intuitive to use and good integrated with Java 6 SDK and later.

The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in structural biology to facilitate the development of molecular modeling, design and analysis tools.

Coati is a web development framework and API for genome databases that supports multiple database vendors and database schemas.

Wienert S, Heim D, Kotani M, Lindequist B, Stenzinger A, Ishii M, Hufnagl P, Beil M, Dietel M, Denkert C, Klauschen F. CognitionMaster: an object-based image analysis framework. Diagn Pathol 2013, 8:34

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.

DASS-GUI is a graphical user interface for pattern search in non-sequential data.

The Genomic Diversity and Phenotype Connection (GDPC) written in JAVA uses web services to make XML formatted data publicly available. The GDPC Browser (front-end GUI) can access these services, and other applications can use the API.

GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein interactions, gene expression, disease-causing probabilities, genomic context). GEPETTO is written in Java/Python and supported by an advanced modular architecture, which means that it can easily be modified and extended by the user, in order to include alternative scoring methods and new data sources. We intend to extend the system from gene-level to variant-level prioritization, by exploiting the variant data in the MSV3D database. Contact: bmhoan@gmail.com or walter.vincent.fr@gmail.com

Before year 2045, we want to create a "software development lab" that will allow to write "from scratch" the DNA of a creature, the "content" of it's first cell, and the components of the solution in which it will grow, to simulate it's life.

ISYS (Integrated SYStem) is a Java-based plugin framework for loosely-coupled integration of independently developed components. It provides both service-oriented and event-based communication whose semantics may be contributed by component developers.

Java bio-informatics library to analyze and convert genomic sequence and assembly data. This library was created and used by the J. Craig Venter Institute (JCVI)

OpenMedic is a set of open source software and hardware building blocks written in C# for building computer-based medical instrumentation and controls using the .NET framework.

El proyecto central es la conformación de un Sistema de Información Hospitalaria, se pretende ir por subproyectos los cuales formaran las piezas fundamentales que se integraran mediante perfiles IHE que vayan estableciéndose para la norma HL7v3

Web application providing analysis of biomedical relationships. Built using the Grails web application framework (http://grails.org/) with MySQL (http://www.mysql.com/) as a back-end datastore and utilizing R (http://www.r-project.org/) for statistical analysis. Developed by the Dana Farber Cancer Institute (http://compbio.dfci.harvard.edu/) and Entagen (http://www.entagen.com).

The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE.

TRMSim-WSN (Trust and Reputation Models Simulator for Wireless Sensor Networks) is a Java-based simulator aimed to test Trust and Reputation models for WSNs. It provides several Trust and Reputation models and new ones can be easily added.

Generic ASP.NET XML interface to heterogeneous databases for the TAPIR protocol

XMPP Web Services for Java (XWS4J) is an implementation of machine to machine communication over XMPP. The communicated content is encoded in XML, according to customized definitions of input and output in W3C XML Schemata.