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http://www.open-ephys.org/pulsepal

Open source pulse train generator that allows users to create and trigger software defined trains of voltage pulses with high temporal precision. Generates precisely timed pulse sequences for use in research involving electrophysiology or psychophysics.

Proper citation: Pulse Pal (RRID:SCR_017203) Copy   

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https://github.com/felixfiederling/SpinalJ/blob/main/SpineRack.stl

Software tool extension to ImageJ for spinal cord. Used for efficient preparation and imaging of whole spinal cord and the absence of 3D reference atlas.

Proper citation: SpinalJ (RRID:SCR_025437) Copy   

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http://www.mitomap.org/

Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf.

Proper citation: MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) Copy   

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http://www.gensat.org/daily_showcase.jsp

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 19, 2012. Due to budgetary constraints, the National Center for Biotechnology Information (NCBI) has discontinued support for the NCBI GENSAT database, and it has been removed from the Entrez System. The Gene Expression Nervous System Atlas (GENSAT) project involves the large-scale creation of transgenic mouse lines expressing green fluorescent protein (GFP) reporter or Cre recombinase under control of the BAC promoter in specific neural and glial cell populations. BAC expression data for all the lines generated (over 1300 lines) are available in online, searchable databases (www.gensat.org and the Database of GENSAT BAC-Cre driver lines). If you have any specific questions, please feel free to contact us at info_at_ncbi.nlm.nih.gov The GENSAT project aims to map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques. Search criteria include gene names, gene symbols, gene aliases and synonyms, mouse ages, and imaging protocols. Mouse ages are restricted to E10.5 (embryonic day 10.5), E15.5 (embryonic day 15.5), P7 (postnatal day 7), and Adult (adult). The project focuses on two techniques * Evaluation of unmodified mice lines for expression of a given gene using radiolabelled riboprobes and in-situ hybridization. * Creation of transgenic mice lines containing a BAC construct that expresses a marker gene in the same environment as the native gene

Proper citation: GENSAT at NCBI - Gene Expression Nervous System Atlas (RRID:SCR_003923) Copy   

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http://ibvd.virtualbrain.org/

A database of brain neuroanatomic volumetric observations spanning various species, diagnoses, and structures for both individual and group results. A major thrust effort is to enable electronic access to the results that exist in the published literature. Currently, there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the dissemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies, as well as metaanalysis. Extensions that permit pre-published, non-published and other representation are planned, again to facilitate comparative analyses. Design strategy: The principle organizing data structure is the "publication". Publications report on "groups" of subjects. These groups have "demographic" information as well as "volume" information for the group as a whole. Groups are comprised of "individuals", which also have demographic and volume information for each of the individuals. The finest-grained data structure is the "individual volume record" which contains a volume observation, the units for the observation, and a pointer to the demographic record for individual upon which the observation is derived. A collection of individual volumes can be grouped into a "group volume" observation; the group can be demographically characterized by the distribution of individual demographic observations for the members of the group.

Proper citation: Internet Brain Volume Database (RRID:SCR_002060) Copy   

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http://proteomics.ucsd.edu/Software/NeuroPedia/index.html

A neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species.

Proper citation: NeuroPedia (RRID:SCR_001551) Copy   

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http://stemcelldb.nih.gov/public.do

Database characterizing and comparing pluripotent human stem cells. The growth and culture conditions of all 21 human embryonic stem cell lines approved under the August 2001 Presidential Executive Order have been analyzed. Available to the scientific community are the results of our rigorous characterization of these cell lines at a more advanced level.

Proper citation: StemCellDB (RRID:SCR_006305) Copy   

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http://www.wwpdb.org/

Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations.

Proper citation: Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) Copy   

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http://www.nitrc.org/projects/ibsr

Data set of manually-guided expert segmentation results along with magnetic resonance brain image data. Its purpose is to encourage the development and evaluation of segmentation methods by providing raw test and image data, human expert segmentation results, and methods for comparing segmentation results. Please see the MediaWiki for more information. This repository is meant to contain standard test image data sets which will permit a standardized mechanism for evaluation of the sensitivity of a given analysis method to signal to noise ratio, contrast to noise ratio, shape complexity, degree of partial volume effect, etc. This capability is felt to be essential to further development in the field since many published algorithms tend to only operate successfully under a narrow range of conditions which may not extend to those experienced under the typical clinical imaging setting. This repository is also meant to describe and discuss methods for the comparison of results.

Proper citation: Internet Brain Segmentation Repository (RRID:SCR_001994) Copy   

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http://krasnow1.gmu.edu/cn3/L-Neuron/database/

A database of virtually generated anatomically plausible neurons for several morphological classes, including cerebellar Purkinje cells, hippocampal pyramidal and granule cells, and spinal cord motoneurons. It presently contains 542 cells. In the trade neurons collection the database contains an amaral cell archive, neuron morpho reconstructions, and mouse alpha motoneurons. Their collection of generated neurons include motoneurons, Purkinje cells, and hippocampal pyramidal cells.

Proper citation: Virtual NeuroMorphology Electronic Database (RRID:SCR_007118) Copy   

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http://senselab.med.yale.edu/odordb

OdorDb is a database of odorant molecules, which can be searched in a few different ways. One can see odorant molecules in the OdorDB, and the olfactory receptors in ORDB that they experimentally shown to bind. You can search for odorant molecules based on their attributes or identities: Molecular Formula, Chemical Abstracts Service (CAS) Number and Chemical Class. Functional studies of olfactory receptors involve their interactions with odor molecules. OdorDB contains a list of odors that have been identified as binding to olfactory receptors.

Proper citation: Odor Molecules DataBase (RRID:SCR_007286) Copy   

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http://www.commondataelements.ninds.nih.gov

The purpose of the NINDS Common Data Elements (CDEs) Project is to standardize the collection of investigational data in order to facilitate comparison of results across studies and more effectively aggregate information into significant metadata results. The goal of the National Institute of Neurological Disorders and Stroke (NINDS) CDE Project specifically is to develop data standards for clinical research within the neurological community. Central to this Project is the creation of common definitions and data sets so that information (data) is consistently captured and recorded across studies. To harmonize data collected from clinical studies, the NINDS Office of Clinical Research is spearheading the effort to develop CDEs in neuroscience. This Web site outlines these data standards and provides accompanying tools to help investigators and research teams collect and record standardized clinical data. The Institute still encourages creativity and uniqueness by allowing investigators to independently identify and add their own critical variables. The CDEs have been identified through review of the documentation of numerous studies funded by NINDS, review of the literature and regulatory requirements, and review of other Institute''s common data efforts. Other data standards such as those of the Clinical Data Interchange Standards Consortium (CDISC), the Clinical Data Acquisition Standards Harmonization (CDASH) Initiative, ClinicalTrials.gov, the NINDS Genetics Repository, and the NIH Roadmap efforts have also been followed to ensure that the NINDS CDEs are comprehensive and as compatible as possible with those standards. CDEs now available: * General (CDEs that cross diseases) Updated Feb. 2011! * Congenital Muscular Dystrophy * Epilepsy (Updated Sept 2011) * Friedreich''s Ataxia * Parkinson''s Disease * Spinal Cord Injury * Stroke * Traumatic Brain Injury CDEs in development: * Amyotrophic Lateral Sclerosis (Public review Sept 15 through Nov 15) * Frontotemporal Dementia * Headache * Huntington''s Disease * Multiple Sclerosis * Neuromuscular Diseases ** Adult and pediatric working groups are being finalized and these groups will focus on: Duchenne Muscular Dystrophy, Facioscapulohumeral Muscular Dystrophy, Myasthenia Gravis, Myotonic Dystrophy, and Spinal Muscular Atrophy The following tools are available through this portal: * CDE Catalog - includes the universe of all CDEs. Users are able to search the full universe to isolate a subset of the CDEs (e.g., all stroke-specific CDEs, all pediatric epilepsy CDEs, etc.) and download details about those CDEs. * CRF Library - (a.k.a., Library of Case Report Form Modules and Guidelines) contains all the CRF Modules that have been created through the NINDS CDE Project as well as various guideline documents. Users are able to search the library to find CRF Modules and Guidelines of interest. * Form Builder - enables users to start the process of assembling a CRF or form by allowing them to choose the CDEs they would like to include on the form. This tool is intended to assist data managers and database developers to create data dictionaries for their study forms.

Proper citation: NINDS Common Data Elements (RRID:SCR_006577) Copy   

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http://ligand-expo.rutgers.edu/

An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components.

Proper citation: Ligand Expo (RRID:SCR_006636) Copy   

•   Source: SciCrunch Registry

https://fitbir.nih.gov/

Platform for Traumatic Brain Injury relevant data. System was developed to share data across entire TBI research field and to facilitate collaboration between laboratories and interconnectivity between informatics platforms. FITBIR implements interagency Common Data Elements for TBI research and provides tools and resources to extend data dictionary. Established submission strategy to ensure high quality and to provide maximum benefit to investigators. Qualified researchers can request access to data stored in FITBIR and/or data stored at federated repositories.

Proper citation: Federal Interagency Traumatic Brain Injury Research Informatics System (RRID:SCR_006856) Copy   

•   Source: SciCrunch Registry

http://www.regardsstudy.org/

The REasons for Geographic and Racial Differences in Stroke (REGARDS) project, sponsored by the National Institutes of Health (NIH), is a national study focusing on learning more about the factors that increase a person''s risk of having a stroke. REGARDS is an observational study of risk factors for stroke in adults 45 years or older. 30,239 participants were recruited between January 2003 and October 2007. They completed a telephone interview followed by an in-home physical exam. Measurements included traditional risk factors such as blood pressure and cholesterol levels, and an echocardiogram of the heart. At six month intervals, participants are contacted by phone to ask about stroke symptoms, hospitalizations and general health status. The study is ongoing and will follow participants for many years. The purpose of the REGARDS project is to understand why people in some parts of the country develop more strokes than people in other parts of the country, and why blacks develop more strokes than whites. We hope to learn how to reduce the number of people having strokes.

Proper citation: REGARDS - REasons for Geographic and Racial Differences in Stroke (RRID:SCR_007228) Copy   

•   Source: SciCrunch Registry

http://jaxmice.jax.org/list/ra1642.html

Produce new neurological mouse models that could serve as experimental models for the exploration of basic neurobiological mechanisms and diseases. The impetus for the program resulted from the recognition that: * The value of genomic data would remain limited unless more information about the functionality of its individual components became available. * The task of linking genes to specific behavior would best be accomplished by employing a combination of different approaches. In an effort to complement already existing programs, the Neuroscience Mutagenesis Facility decided to use: a random, genome-wide approach to mutagenesis, i.e.N-ethyl-N-nitrosourea (ENU) as the mutagen; a three-generation back-cross breeding scheme to focus on the detection of recessive mutations; behavioral screens selective for the detection of phenotypes deemed useful for the program goals. The resulting mutant mouse lines have been available to the scientific community for the last five years and over 700 NMF mice have been sent to interested investigators for research; these mutant mouse lines will remain available as frozen embryos (which can be re-derived on request) and can be ordered through the JAX customer service at 1-800-422-6423 (or 207-288-5845). The results of the work of the Neuroscience Mutagenesis Facility and that of two other neurogenesis centers, i.e. The Neurogenomics Project at Northwestern University, and the Neuromutagenesis Project of the Tennessee Mouse Genome Consortium, can also be seen at Neuromice.org, a common web site of these three research centers; in addition, information about all mutants produced by these groups has been recorded in MGI.

Proper citation: JAX Neuroscience Mutagenesis Facility (RRID:SCR_007437) Copy   

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http://www.cidr.jhmi.edu/

Next generation sequencing and genotyping services provided to investigators working to discover genes that contribute to disease. On-site statistical geneticists provide insight into analysis issues as they relate to study design, data production and quality control. In addition, CIDR has a consulting agreement with the University of Washington Genetics Coordinating Center (GCC) to provide statistical and analytical support, most predominantly in the areas of GWAS data cleaning and methods development. Completed studies encompass over 175 phenotypes across 530 projects and 620,000 samples. The impact is evidenced by over 380 peer-reviewed papers published in 100 journals. Three pathways exist to access the CIDR genotyping facility: * NIH CIDR Program: The CIDR contract is funded by 14 NIH Institutes and provides genotyping and statistical genetic services to investigators approved for access through competitive peer review. An application is required for projects supported by the NIH CIDR Program. * The HTS Facility: The High Throughput Sequencing Facility, part of the Johns Hopkins Genetic Resources Core Facility, provides next generation sequencing services to internal JHU investigators and external scientists on a fee-for-service basis. * The JHU SNP Center: The SNP Center, part of the Johns Hopkins Genetic Resources Core Facility, provides genotyping to internal JHU investigators and external scientists on a fee-for-service basis. Data computation service is included to cover the statistical genetics services provided for investigators seeking to identify genes that contribute to human disease. Human Genotyping Services include SNP Genome Wide Association Studies, SNP Linkage Scans, Custom SNP Studies, Cancer Panel, MHC Panels, and Methylation Profiling. Mouse Genotyping Services include SNP Scans and Custom SNP Studies.

Proper citation: Center for Inherited Disease Research (RRID:SCR_007339) Copy   

•   Source: SciCrunch Registry

http://www.ninds.nih.gov/research/parkinsonsweb/amr/amr_mice_ucla_repository.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 26, 2011. Information for depositors Investigators who are willing to share mice with the PD research community through this resource should send an email to PDMice_at_ninds.nih.gov describing the mouse. The submission will be reviewed by the PD Models Repository Oversight Committee and, if accepted, a copy of the MTA will be sent by return email. NINDS is most interested in distributing mice that have been characterized in a peer-reviewed publication, but other models will certainly be considered. The email should describe the following: The protocol for identification from tail DNA. The health report of the mice to be shipped (the report has to be less than 2 months old). Information about the strain and any special needs for care and breeding. Information about any publications involving the mice Certification that mice are not encumbered by continuing intellectual property or other rights to any research, data or discovery utilizing the animals. Information for consumers Investigators desiring to study the mice available through the repository should send a request via email to PDMice_at_ninds.nih.gov. Requests will be reviewed by the PD Models Repository Oversight Committee and priority will be determined on a first come, first served basis; two breeding pairs will typically be shipped to any single requester. As detailed in the MTA, mice are not available for commercial research, including but not limited to drug screening. Neither the creator nor UCLA have a role in the governance of the Repository, and specifically, cannot impose conditions upon availability or distribution. It is anticipated that until the Repository is in a mode of steady state production, requests will be collected and mice distributed as supply allows. The email requesting mice should include: A brief description of the protocol Either a copy of the IACUC approval letter or numberNINDS/UCLA Repository for Parkinson's Disease Mouse Models: One of the most immediate and important benefits of discoveries regarding the genetic or environmental causes of Parkinson's disease (PD) is the subsequent development of animal models wherein therapeutic and/or preventative interventions may be studied. The widespread availability of such models is critically important to making progress against a disorder that affects more than 500,000 Americans at any given time. The National Institute of Neurological Disorders and Stroke (NINDS) fully recognizes the burden placed on investigators by the financial and logistical realities of distributing high demand research resources. Some investigators have deposited their mice with national distribution facilities but many mouse models are not available through such resources. Developing means to facilitate greater sharing of mouse models of PD is one of the goals developed by the PD research community at the July 2002 summit meeting convened by the NIH Director. Accordingly, as part of the effort to accelerate PD research, NINDS and the University of California at Los Angeles (UCLA) created a resource that will distribute transgenic mouse models of human PD that are not yet available through national commercial resources. Investigators who are willing to share mice with the PD research community can simply arrange with NINDS to have the mice deposited at UCLA and investigators desiring to study the mice may arrange with NINDS to obtain two breeding pairs. The process will use Material Transfer Agreements created specifically for this arrangement.

Proper citation: NINDS/UCLA Repository for Parkinson's Disease Mouse Models (RRID:SCR_007319) Copy   

•   Source: SciCrunch Registry

https://bams1.org/

Knowledge management system designed to handle neurobiological information at different levels of organization of vertebrate nervous system. Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. Handles data and metadata collated from original literature, or inserted by scientists that is associated to four levels of organization of vertebrate nervous system. Data about expressed molecules, neuron types and classes, brain regions, and networks of brain regions.

Proper citation: Brain Architecture Management System (RRID:SCR_007251) Copy   

•   Source: SciCrunch Registry

http://enhancer.lbl.gov/

Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth.

Proper citation: VISTA Enhancer Browser (RRID:SCR_007973) Copy   

•   Source: SciCrunch Registry