Foundations of the Whole Brain Catalog
From Whole Brain Catalog
The Whole Brain Catalog looks to bring together many efforts in neuroscience, computational neuroscience, and other open source development projects.
Contents |
[edit] Neuroscience Efforts
Neuroscience Information Framework
- A dynamic inventory of web-based neuroscience resources, data, and tools accessible via the Internet.
- Provides the NIFSTD ontology which populates NeuroLex.org
[edit] Computational Neuroscience
- Produced animations of neuron activity
- Produces animations of neuron activity, convert from several formats into NeuroML
- Used as a standard way of representing neuron structures
- Produced animations of molecular activity
- Incorporated mouse brain meshes
http://www.cs.ucl.ac.uk/research/medic/camino/guide.htm
- Extracted fiber tracts from DTI data
[edit] Semantic Web
- Processed OWL ontologies
- Used as a triple store for semantic web knowledge
Semantic Mediawiki
- Used to provide an open community for contributing to neuroscience vocabularies and definitions
[edit] Open Source Development
- All 3D visualization
- Used as a standard way of describing 3D shapes
- Backbone language. Also taking advantage of webstart technologies
- Build maintenance
- Repository for libraries
- Client / server networking
- XML / object / relational mapping
- Object / relational mapping
- Backend database
- Lightweight database
- Test cases
- Testing framework
- Image serving
- XML processing
- Integrated development environment
- Continuous integration server
OpenLayers
[edit] Data
- Source of some neuronal morphologies
- Cell images and 3D models
http://www.rcsb.org/pdb/home/home.do
- Protein models
- Gene expression lookup
[edit] Other
- Mesh processing
- 3D object processing
[edit] Code dependencies
- A full report of the code dependencies of the Whole Brain Catalog can be found in the following locations
