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Research Tools
This section provides pointers to Software Tools, Computing Services, and Data Repositories.
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, Control Systems and Telecommunications, University of Genoa
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.
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.
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
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
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.
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.
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
EEG.pl 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 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.
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
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 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.com
Project Hosting on Google Code is a free service to the open source community.
Hosted by:
google.com
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.
Hosted by:
Laboratory of Neuro Imaging, UCLA
The INCF provides access to a Blue Gene supercomputer, which is housed at the Parallel Computer Center of the Royal Institute of Technology in Stockholm. During a first evaluation phase a limited number of large-scale computing projects will be selected, based on the suitability of the project for supercomputers. Approved projects will then be re-evaluated on a regular basis.
A resource that makes it easy for neuroscientists to find, use, and share software tools.
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 portal provides information about neuroinformatics platforms in Japan that share experimental data, mathematical models, as well as techniques and tools developed for neuroscience research.
Hosted by:
RIKEN BSI Neuroinformatics Japan Center
Launchpad is a hosting service for open source projects.
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
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
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. Finally, its architecture facilitates linkage of NDAR with
other significant data resources, regardless of their location or
ownership and in ways that respect the policies and implementations of
those other data resources. As these, and other, features are used over
time, NDAR is expected to become a portal to the autism research
community for the autism research community.
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.
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
The Neuron-Glia Platform serves two purposes:
- 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.)
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
NIF is an inventory of information and other resources within a framework that enables neuroscientists to identify resources relevant to their research needs. Resources include databases, software tools, experimental reagents and tools, knowledge bases and portals, and other entities, spanning multiple levels of biological organization and function. It represents collaboration across the 16 NIH Institutes, Centers and Offices that support neuroscience research.
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 also contribute their own tools and resources.
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
SciPy is open-source software for mathematics, science, and engineering.
The SenseLab Project contains 6 related neuronal and olfactory databases that support experimental and theoretical research on the membranes that mediate information processing in nerve cells, using the olfactory pathway as a model system. The neuronal databases are provided with tools which allow searches for combinations of properties across different neuron types.
Hosted by:
Yale University
SourceForge.net provides free hosting to open source software development projects.
This software allows researchers to combine probabilistic cytoarchitectonic maps with functional imaging data.
Hosted by:
Institut für Neurowissenschaften und Biophysik (INB), Forschungszentrum Jülich
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
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
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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