Research Tools

The Allen Brain Atlas encompasses several large-scale projects and makes the data and tools freely available online to scientists worldwide. These projects include the Mouse Spinal Cord, Human Cortex Study, Sleep Study, and Mouse Brain.

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.

The Basic Local Alignment Search Tool (BLAST) is an algorithm for comparing regions of local similarity across biologic sequences. The program compares nucleotide or protein sequences to online databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it. If you don't know the name but can locate the structure in the Template Atlas of the Primate Brain, BrainInfo will tell you its name and other facts about it. The NeuroMaps application also lets you map and display any kind of mouse or macaque data on standard atlas templates and print or download figures for presentation or publication.

The CCDB is a publicly-accessible resource that allows researchers to query and download unique datasets derived from high resolution light microscopy and electron tomography. The CCDB accepts data contributions from the community and is developing a set of tools for management of imaging data.

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.

EEG.pl is an open repository of software, publications, and datasets related to the analysis of brain potentials.

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.

The GENSAT project is a collection of pictorial gene expression maps of the brain and spinal cord of the mouse. Using EGFP BAC-transgenics, this project provides the scientific community with tools to catalog, map, and electrophysiologically record from individual cells. The transgenic mice created by this project are available to the scientific community.

The Invertebrate Brain Platform (IVB PF) integrates experimental data, mathematical models, and research tools relevant to the study of invertebrate brains, neurons, and behavior.

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.

Neural ElectroMagnetic Ontologies (NEMO) is an NIH-funded project researching the design and implementation of ontologies to address a critical need for tools to support representation, storage, and sharing of brain electromagnetic data. NEMO ontologies include concepts related to ERP data (including spatial and temporal features of specific ERP patterns), data provenance, and the experimental paradigms that were used to collect data. The NEMO database is a repository that stores raw and processed data, ontology-based tools for ERP analysis, and annotated results.

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.

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.

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.

PhysioNet offers free access via the web to large collections of recorded physiologic signals and related open-source software. In addition to providing free electronic access to PhysioBank data and PhysioToolkit software, the PhysioNet web site offers service and training via on-line tutorials at entry and advanced levels.

The SenseLab Project contains 8 related databases that support experimental research on, and computational modeling of, information processing in nerve cells and microcircuits. The databases include dendritic membrane properties, a large inventory of computational models of neurons and microcircuits, and a comprehensive inventory of olfactory receptors. The neuronal databases are provided with tools which allow searches for motifs of properties across different neuron types.

This website is a portal for activities of the Spike Train Analysis Network. The network was originally funded by the EPSRC to promote collaboration and the development of novel analysis techniques for neural data analysis. The network hosts seminar series in Newcastle on spike train analysis topics which is broadcast live over the internet and archived for later viewing.

SumsDB is a repository of brain-mapping data (surfaces and volumes; structural and functional data) from many laboratories. This site also provides WebCaret, an online visualization tool for viewing SumsDB datasets.

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.