Research Tools

This section provides pointers to Software Tools, Computing Services, and Data Repositories.

Allen Brain Atlas

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.

Hosted by: Allen Institute for Brain Science


The Laboratory for Bioimages & Bioengineering provides a "virtual reality" platform for the interaction of bioimages, medical data, and 3D models.

Hosted by: Department of Computer Science, University of Genoa


The Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC) ( 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.


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.

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.


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.


CARMEN is a consortium effort to create a virtual laboratory for neurophysiology that enables sharing and collaborative exploitation of data, analysis code, and expertise. Neural activity recordings (signals and image series) are the primary data types.

Hosted by: Newcastle University

Cell Centered Database

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.

Hosted by: University of California, San Diego

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.

Collaborative Research in Computational Neuroscience

This website provides a marketplace and discussion forum for sharing tools and data in neuroscience. It hosts experimental datasets for testing computational models of the brain and new analysis methods. The data include physiological recordings from sensory and memory systems, as well as eye movement data.

Hosted by: Redwood Center for Theoretical Neuroscience, UC Berkeley is an open repository of software, publications, and datasets related to the analysis of brain potentials.

Hosted by: Department of Biomedical Physics, University of Warsaw

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.


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.

Hosted by: University of Tennesse

GENSAT Project

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.

Hosted by: Rockefeller University

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.

Hosted by:

Google Code

Project Hosting on Google Code is a free service to the open source community.
Hosted by:

ICBM Subject Database

The ICBM Subject Database is a web-based database infrastructure that simplifies image dataset collection, organization and dissemination. The data can be queried using a combination of subject demographics and scan-related attributes. Authorized users may view representations of the data and form collections of datasets that can be downloaded or fed directly into the Pipeline environment for distributed processing and analysis.

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.


Launchpad is a hosting service for open source projects.

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).

Hosted by: University of Tennessee

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.

Hosted by: The Jackson Laboratory

National Database for Autism Research (NDAR)

NDAR hosts genetic, imaging, and phenotypic research data relevant to autism, making these data available to qualified researchers. NDAR also has the capability to let investigators use NDAR as a space in which to share data with select collaborators in ongoing studies. Through its Data Dictionary, NDAR will foster the development of a shared, common understanding of the complex data-landscape that characterizes autism research.

Neural Electro-Magnetic Ontologies (NEMO)

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 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.

NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. It contains contributions from over two dozen labs and is continuously updated as new morphological reconstructions are collected, published, and shared.

Hosted by: Krasnow Institute for Advanced Study, George Mason University

Neuron-Glia Platform

The Neuron-Glia Platform serves two purposes:
  1. 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.)
  2. 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 Database Gateway

The SfN Neuroscience Database Gateway (NDG) is a centralized gateway for accessing neuroscience-related databases. It provides links to five main types of databases: (1) databases of experimental data, (2) knowledge bases, (3) software tools for neuroscience, (4) bioinformatics resources, and (5) providers of research materials.

Hosted by: Society for Neuroscience

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.

Hosted by: University of Cailfornia, San Diego


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.


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.

Pediatric MRI Data Repository

This website serves as the portal through which neuroimaging data (anatomical MRI, diffusion tensor imaging (DTI), and MR spectroscopy) from the NIH MRI Study of Normal Brain Development can be obtained by qualified researchers. Clinical and behavioral measures such as neurological examinations, behavioral ratings, neuropsychological testing, structured psychiatric interviews, and hormonal measures from urine and saliva samples are also available.

Hosted by: McConnell Brain Imaging Center, McGill University


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.

Hosted by: Massachusetts Institute of Technology

Scientific Tools for Python

SciPy is open-source software for mathematics, science, and engineering.


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.

SourceForge provides free hosting to open source software development projects.

Spike Train Analysis Network

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.

SPM Anatomy Toolbox

This software allows researchers to combine probabilistic cytoarchitectonic maps with functional imaging data.

Hosted by: Institut für Neurowissenschaften und Biophysik (INB), Forschungszentrum Jülich

Surface Management System Database (SumsDB)

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.

Hosted by: Washington University School of Medicine, St. Louis

Talairach Software

The Talairach software provides spatial normalization of human neuroimaging data, and includes three components: (1) Talairach Client: a Java application for finding individual and batch labels as well as command-line tools for accessing the daemon, (2) Talairach Applet: a web application for the daemon which includes graphical overlays and nearest gray matter searches, (3) Talairach Daemon: a high-speed database server for querying and retrieving data about human brain structure over the internet.

Hosted by: University of Texas Health Science Center San Antonio

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.

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