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The program fuses 2 sets of molecules. It tries different relative positions of molecules before binding them, so that there is no or minimal intersection in the resulting molecule. The atom to be fused in a molecule is labeled with an R symbol.

eagle-i is an ontology-driven, RDF-based distributed platform for creating, storing and searching semantically rich data. eagle-i is built around semantic web technologies and adheres to linked open data principles.

SAAT Semi-Automated Annotation Tools The Medical University Graz, in cooperation with the Fraunhofer Institute for Biomedical Engineering IBMT is developing the SAAT - Semi-Automated Annotation Tools in the CRIP context.

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

EOS stands for Entity Oriented Search. The project is a toolkit to support EOS projects on a Lucene and Hadoop platform.

Danaides stores meta-data from biological banks in a graph databases as well as OBO formatted ontologies. It also provides a web query interface to parse ontologies or extract nodes based on ontology requirements. Example: Get all known elements that are in family of Fish (species ontology) AND a RNA (sequence ontology).

XMAS supports a new kind of “sit forward” time series microarray analysis through visual interaction and interoperable operators. Domain knowledge is integrated directly into the system to aid users in their analysis.

GraphSpider is a pattern matcher which searches parsed text in phrase-structure tree or dependency graph format for syntactic structures matching a set of patterns in MPL, a regexp-like pattern language. Applications: information extraction, text mining.

A biological data warehouse that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. Website: http://bioinformatics.ubc.ca/atlas

Shred is a fast and scalable faceted data browser. The application allows users to navigate the data in an intuitive way and by any path they wish to take. Immediate intuitive information regarding the data is apparent.

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).

Decision support tool that assesses breast cancer risk and identifies risk-reducing interventions. Includes web service implementations of established models -- BRCAPRO, Gail, Claus, BCSC Density -- for calculating breast cancer risk.

Multimedia consumption at social events - if available - can be considered as a complex problem. People use their smart phones and tablets to take pictures and videos, leading to a high number of production places. If we enable those visitors to share their content at the event, new challenges emerge. Visitors move, go online and offline, and build a dynamic network. One can say a complex adaptive network emerges, with all its problems. We tackle these problems by introducing a bio-inspired...

The JAQPOT3 web services are OpenTox API-1.2 compliant web services. JAQPOT3 is a web application that supports model training and data preprocessing algorithms such as MLR, SVM, ANN and more.

** IMPORTANT NOTICE ** 10 Feb 2006 Code is being moved to the SMI subversion repository (http://smi-protege.stanford.edu/svn/owl/trunk/) Project will continue to be open source. ProtegeOWL info at: http://protege.stanford.edu/overview/protege-owl.html

The OBO-Annotator is a semantic NLP tool that is designed to give its end-users a great deal of flexibility to combine any number of OBO ontologies from the OBO foundry regardless of their format and use them to annotate text-bases.

The Integrative Biology VRE is a web-based graphical user interface and repository that provides an environment where biological simulation experiments can be constructed without the need for any knowledge of unix, cluster computing, or shell scripting.

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.