FIND RESOURCES
Research Tools
Biositemaps
The Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC) (www.ncbcs.org) has developed technologies to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site ‘'biositemap.rdf' which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources.
BIRN Data Repository
This sustainable archive supports the sharing and exchange of biomedical research data, accepts data generated by the biomedical research community and makes these data freely available. Biomedical imaging data from humans and animal models are available for download with descriptive metadata, and in some cases, associated clinical, microarray, or other biomedical data.
Brain Machine Interface Platform
The Brain Machine Interface Platform (BMI PF) accumulates BMI (Brain Machine Interfaces)-related experimental data, mathematical models, and tools generated in neuroscience, computational theory, and robotics.
Cerebellar Development Transcriptome Database
The Cerebellar Development Transcriptome Database (CDT-DB) provides spatio-temporal gene expression profile information on the postnatal development of mouse cerebellum. It seeks to reproduce the genetic blueprint of cerebellar development.
Cerebellar Platform
The Cerebellar Platform is a digital research archives for the cerebellar research. Available resources include mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation.
Entrez Gene
Entrez Gene is a searchable database of genes based on sequenced genomes; its content includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases.
Entrez Genome
The Genome database provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps. The database is organized in six major organism groups: Archaea, Bacteria, Eukaryotae, Viruses, Viroids, and Plasmids and includes complete chromosomes, organelles and plasmids as well as draft genome assemblies.
GeneNetwork
The GeneNetwork consists of a set of linked resources for systems genetics. It has been designed for multiscale integration of networks of genes, transcripts, and traits such as toxicity, cancer susceptibility, and behavior. This open resource combines more than 25 years of legacy data generated by hundreds of scientists with full genome sequence and deep transcriptome data sets.
Google App Engine
Google App Engine provides a fully-integrated application environment that permits web applications to run on Google's infrastructure. The environment includes: dynamic web serving, with full support for common web technologies, persistent storage with queries, sorting and transactions, automatic scaling and load balancing, APIs for authenticating users and sending email using Google Accounts, and a fully featured local development environment.
Google Code
Invertebrate Brain Platform
The Invertebrate Brain Platform (IVB PF) integrates experimental data, mathematical models, and research tools relevant to the study of invertebrate brains, neurons, and behavior.
Japan Node
This portal provides information about neuroinformatics platforms in Japan that share experimental data, mathematical models, as well as techniques and tools developed for neuroscience research.
Mouse Brain Library
The primary goal of the MBL is to systematically map and characterize genes that modulate architecture of the mammalian CNS. You can search the MBL for cases by strain, age, sex, body or brain weight. The MBL is a collaborative project between Robert W. Williams (Center for Genomics and Bioinformatics, University of Tennessee) and Glenn D. Rosen (Department of Neurology, Beth Israel Deaconess Medical Center, Boston).
Mouse Genome Informatics
This site provides search tools for Genes, Genomic Features and Maps, Phenotypes, Alleles and Disease Models, Gene Expression, Gene Ontology Functional Annotations, Strains, SNPs and Polymorphisms, and Mammalian Orthology of the mouse.
Neurodebian
The Debian Neuroscience repository provides mostly neuroscience-related packages to be used on Debian systems (or Debian-derivatives like Ubuntu).
NeuroImaging Platform
The NeuroImaging Platform collects information about neuroimaging research and provides them to researchers all over the world. You can access bibliographic information of text book and peer reviewed journal papers. For practical purposes, programs to present the stimuli, analysis software, and raw data in neuroimaging experiments with various methods such as functional MRI (fMRI), MEG, and NIRS are also included.
Neuron-Glia Platform
- Publicize and archive models and related data and tools regarding Neuron-Glia functions. (Visitors can only browse and download limited items. Need to register as a user to submit and download items.)
- Provide workspace for sharing models, data, tools and memos privately among group members of registered users. (Need to register as a user to do this. Upon e-mailed request to the administrator, a group of users will be established.)
Neuroscience Information Framework
The Neuroscience Information Framework (NIF) is the largest collection of neuroscience and biomedical data, materials, tools and resources available on the web. The dynamic inventory is accessible via a semantically-enhanced search portal and available to anyone connected to the internet. NIF provides best practices and tools for resource providers to share their data, make their resources more discoverable, and increase interoperability with other data resources. Additionally, for developers, NIF provides tools and services for accessing NIF's content and vocabularies (ontologies). Find what you need, faster, with NIF.
NeuroTools
NeuroTools is a set of tools written in Python to manage, store and analyze simulations. NeuroTools provides modules to facilitate simulation setup, parameterization and instrumentation, and data management, analysis and visualization. The data-related tools are equally suited to analysis of experimental data, although that is not the primary motivation for their development.
NITRC
The Neuroimaging Informatics Tools and Resources Clearinghouse facilitates the finding and comparison of neuroimaging resources for fMRI and related structural analyses. Individuals can contribute their own tools and resources. NITRC also hosts a number of datasets, most notably the 1000 Functional Connectomes resting state fMRI project.
Scientific Tools for Python
Visiome Platform
The Visiome Platform is a digital research resource archive for vision science. The available resources include mathematical models, experimental stimuli, experimental data, and analytical tools.
