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http://clarityresourcecenter.org/

Protocols and other training materials related to the CLARITY protocol, a technique for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable.

Proper citation: Clarity resources (RRID:SCR_001387) Copy   

•   Source: SciCrunch Registry

https://www.genome.wisc.edu/tools/asap.htm

Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ASAP (RRID:SCR_001849) Copy   

•   Source: SciCrunch Registry

http://www.columbia.edu/cu/biology/faculty/yuste/

Laboratory that aims to understand the function of the cortical microcircuit by reverse-engineering of the cortical microcircuit using the mouse neocortex in vitro and in vivo as their experimental preparations. The techniques applied are electrophysiology, anatomy, and a variety of optical methods, including infrared-DIC, voltage- and ion-sensitive dye imaging with confocal, two-photon and second harmonic microscopy. They also use laser uncaging, biolistics, electroporation, electron microscopy and numerical simulations, and make extensive use of genetically modified mouse strains. They focus is on two major questions: (1) What is the function of dendritic spines? (2) What are the multicellular patterns of activity under spontaneous or evoked activation of the circuit? Resources include: * Cell Reconstructions: Cell Database, PDF Images, .DAT Files * Circuit Diagrams: Full Circuit Diagram, Inhibitory Circuit Diagram, Excitatory Circuit Diagram, Simplified Circuit Diagram, Layer to Layer Simplified Circuit, Circuit diagram references

Proper citation: Rafael Yustes Laboratory (RRID:SCR_001845) Copy   

•   Source: SciCrunch Registry

http://bmi.neuroinf.jp/

Databases of accumulating BMI (Brain Machine Interfaces)-related experimental data, mathematical models, and tools generated in neuroscience, computational theory, and robotics. Databases include: # Database of BMI (Brain Machine Interfaces)-related papers: More than 3500 BMI-related papers are registered. Each paper has original tags, for example, recording method and subject, for easy searching. # Database of original contents: BMI-related materials (Movie, Picture, Data, Program) provided by scientists. # Database of BMI-related research sites: 185 BMI-related research sites in the world (university, institute and company) are registered. The research site can be searched either by the location using clickable map or by the field of interest. # Database of BMI-related materials: Links to BMI-related materials (Movie, Picture, Document, Data, Program) are listed. You can easily find materials of your interest since each material is classified into research field. # BMI-related column: The columns are written by researchers specialized in BMI. Original contents include: * Neuronal activity during performance of a memory-guided movement * Reconstructed visual images from human fMRI activity * fMRI data and program for visual image reconstruction * Brain sections of monkeys, stained for several gene markers * Cortical Box Method: The Cortical box method is an analytical method that standardizes the serial coronal sections of rodent cortex for quantitative analysis. * Multineuron activity in monkey prefrontal cortex * Monkey Atlas: **Brain sections of monkeys, stained for AChE, ER81 mRNA and Sema3E mRNA - These pictures are low-resolution photos of serial brain sections of monkeys, stained for AChE as well as for ER81 and Sema3E mRNAs. The compressed file contains JPEG photos and html files for web browser navigation. Other materials are available at our website BraInSitu dedicated for in situ hybridization resources for brains. BraInSitu http://www.nibb.ac.jp/brish/indexE.html ** MRI Brain Atlas of Japanese Snow Monkey (Macaca Fuscata) at different ages - MRI Brain Atlas of Japanese Snow Monkey (Macaca Fuscata) at different ages ** The Stereotaxic MRI Brain Atlas of Japanese Snow Monkey - The Stereotaxic MRI Brain Atlas of Japanese Snow Monkey * Monkey M1 BMI ** m-file for checking the results of wrist angle estimation- This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/uln ** m-file for training of wrist angle estimation -This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation.ar deviation. ** M1 Neuronal Activity during monkey performing a motor task - video/x-ms-wmv ** Muscle tension - To estimate muscle tension from raw emg signal ** raw EMG signal - Raw EMG signal for 5 seconds ** training data of wrist angle and emg signal - This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation. ** Weight file of neural network - This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation. * Multineuron activity in monkey prefrontal cortex: Multineuron activity in monkey prefrontal cortex recorded by 3 tetrodes. Vertical 4 lines indicate one tetrode. Adjacent tetrodes are around 500 micron apart to each other.

Proper citation: Brain Machine Interface Platform (RRID:SCR_001813) Copy   

•   Source: SciCrunch Registry

https://gene.sfari.org/database/human-gene/

Curated public database for autism research built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The genetic information includes data from linkage and association studies, cytogenetic abnormalities, and specific mutations associated with ASD. New gene submissions are welcome. Modules: * Human Gene: thoroughly annotated list of genes that have been studied in the context of autism, with information on the genes themselves, relevant references from the literature, and the nature of the evidence. Uniquely, SFARI Gene incorporates information on both common and rare variants. * Animal Model: information about lines of genetically modified mice that represent potential models of autism. This information includes the nature of the targeting construct, the background strain and, most importantly, a thorough summary of the phenotypic features of the mice that are most relevant to autism. * Protein Interaction (PIN): compilation of all known direct protein interactions for those gene products implicated in autism. It presents both graphical and tabular views of interactomes, highlighting connections between autism candidate genes. Each protein interaction is manually verified by consultation with the primary reference. * Copy Number Variant (CNV): a parallel resource providing genetic information about all known copy number variants linked to autism. * Gene Scoring: includes a "score" for each autism candidate gene, based on an assessment of the strength of human genetic evidence.

Proper citation: AutDB (RRID:SCR_001872) Copy   

•   Source: SciCrunch Registry

http://www.addgene.org

Non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Facilitates archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources.

Proper citation: Addgene (RRID:SCR_002037) Copy   

•   Source: SciCrunch Registry

http://www.candidagenome.org/

Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome.

Proper citation: Candida Genome Database (RRID:SCR_002036) Copy   

•   Source: SciCrunch Registry

http://videocast.nih.gov/

VideoCasting of special NIH events, seminars, conferences, meetings and lectures available to viewers on the NIH network and the Internet from the VideoCast web site. VideoCasting is the method of electronically streaming digitally encoded video and audio data from a server to a client. VideoCast is often referred to as streaming video. Streaming files are not downloaded, but rather are broadcast in a manner similar to television broadcasts. The videos are processed by a compression program into a streaming format and delivered in a staggered fashion to minimize impact upon the network and maximize the experience of the content for the viewer. When users request a streaming file they will receive an initial burst of data after a short delay (file latency). While content is being viewed, the streaming server machine and software continues to stream data in such a manner that the viewer experiences no break in the content. CIT can broadcast your seminar, conference or meeting live to a world-wide audience over the Internet as a real-time streaming video. The event can be recorded and made available for viewers to watch at their convenience as an on-demand video or a downloadable podcast. CIT can also broadcast NIH-only or HHS-only content.

Proper citation: NIH VideoCasting (RRID:SCR_001885) Copy   

•   Source: SciCrunch Registry

https://datashare.nida.nih.gov

Website which allows data from completed clinical trials to be distributed to investigators and public. Researchers can download de-identified data from completed NIDA clinical trial studies to conduct analyses that improve quality of drug abuse treatment. Incorporates data from Division of Therapeutics and Medical Consequences and Center for Clinical Trials Network.

Proper citation: NIDA Data Share (RRID:SCR_002002) Copy   

•   Source: SciCrunch Registry

http://biogps.org/dataset/tag/kawasaki%20disease/

Collection of data sets on Kawasaki disease, a rare childhood illness that affects the blood vessels. The data includes biochemical measurements of myocardial strain, oxidative stress, and cardiomyocyte injury as well as protein level analysis.

Proper citation: Kawasaki Disease Dataset (RRID:SCR_001451) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/resources/Tools/record/nlx_144509-1/6b508d2a-fd5f-56f2-93cf-462fcd52548e/search?q=*&l=&facet%5B%5D=Parent%20Organization:University%20of%20Michigan;%20Michigan;%20USA&sort=added

THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 12, 2017.

Dataset in Bilingual exposure optimizes left-hemisphere dominance for selective attention processes in the developing brain by Arredondo, Su, Satterfield, & Kovelman (XX) Does early bilingual exposure alter the representations of cognitive processes in the developing brain? Theories of bilingual development have suggested that bilingual language switching might improve children''s executive function and foster the maturation of prefrontal brain regions that support higher cognition. To test this hypothesis, we used functional Near Infrared Spectroscopy to measure brain activity in Spanish-English bilingual and English-monolingual children during a visuo-spatial executive function task of attentional control (N=27, ages 7-13). Prior findings suggest that while young children start with bilateral activation for the task, it becomes right-lateralized with age (Konrad et al., 2005). Indeed monolinguals showed bilateral frontal activation, however young bilinguals showed greater activation in left language areas relative to right hemisphere and relative to monolinguals. The findings suggest that bilingual experience optimizes attention mechanisms in the language hemisphere, and highlight the importance of early experiences for neurodevelopmental plasticity of higher cognition. These data are made available from Ioulia Kovelman''s Language and Literacy Lab at University of Michigan and may be exported through the NIF Data Federation. To cite these data please use this text Data were published by Arredondo et al. (XX) and made available via the NIF at XX

Proper citation: Arredondo ANT fNIRS dataset1 (RRID:SCR_002653) Copy   

•   Source: SciCrunch Registry

http://www.humanconnectome.org/documentation/S500/

Behavioral and 3T MR imaging data from over 500 healthy adult participants with 14 subjects also scanned in resting-state MEG (rMEG) and task MEG (tMEG). Highlights: * Behavioral and demographic data on 550 subjects. * MR imaging data preprocessed using updated pipelines (structural pipeline v3.1, functional pipeline v3.1, diffusion pipeline v3.1, task analysis pipeline v3.3). * Updates to pipelines include a new intersubject registration method called MSMSulc. All MR data from Q1-Q3 releases have been reprocessed. HCP strongly advises against mixing data from this release with previously-released data. * Individual task fMRI grayordinate-based analysis results (available at 2mm, 4mm, 8mm, and 12mm smoothing levels) and volume-based analysis results (4mm smoothing) are available for all complete 500 Subjects tfMRI data, using an updated task analysis pipeline v3.3. * New extensively processed 100- and 400+-subject group-average functional MR data. * Updates to MEG data and access in ConnectomeDB. Structural MRI-based MEG anatomical models and MR data for the 14 MEG1 Release subjects. * Improvements to behavioral data organization and data dictionary, including the addition of previously unreleased restricted behavioral and demographic data. * All imaging data soon to be available on the cloud through Amazon S3. (More information to come!)

Proper citation: WU-Minn HCP 500 Subjects MR and MEG Release (RRID:SCR_003922) Copy   

•   Source: SciCrunch Registry

http://www.lifetable.de/

A collection of population life tables covering a multitude of countries and many years. Most of the HLD life tables are life tables for national populations, which have been officially published by national statistical offices. Some of the HLD life tables refer to certain regional or ethnic sub-populations within countries. Parts of the HLD life tables are non-official life tables produced by researchers. Life tables describe the extent to which a generation of people (i.e. life table cohort) dies off with age. Life tables are the most ancient and important tool in demography. They are widely used for descriptive and analytical purposes in demography, public health, epidemiology, population geography, biology and many other branches of science. HLD includes the following types of data: * complete life tables in text format; * abridged life tables in text format; * references to statistical publications and other data sources; * scanned copies of the original life tables as they were published. Three scientific institutions are jointly developing the HLD: the Max Planck Institute for Demographic Research (MPIDR) in Rostock, Germany, the Department of Demography at the University of California at Berkeley, USA and the Institut national d''��tudes d��mographiques (INED) in Paris, France. The MPIDR is responsible for maintaining the database.

Proper citation: Human Life-Table Database (RRID:SCR_006248) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-8/search?q=*

A data set of connectivity statements from BAMS, CoCoMac, BrainMaps, Connectome Wiki, the Hippocampal-Parahippocampal Table of Temporal-Lobe.com, and Avian Brain Circuitry Database. The data set lists which brain sites connectivity is to and from, the organism connectivity is mapped in, and journal references.

Proper citation: Integrated Nervous System Connectivity (RRID:SCR_006391) Copy   

•   Source: SciCrunch Registry

The record is no longer available at this source.

A list of snippets for databases in NIF data federation.

Proper citation: Integrated Snippets (RRID:SCR_009031) Copy   

•   Source: SciCrunch Registry

https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-2

A virtual database of annotations made by 50 database providers (April 2014) - and growing (see below), that map data to publication information. All NIF Data Federation sources can be part of this virtual database as long as they indicate the publications that correspond to data records. The format that NIF accepts is the PubMed Identifier, category or type of data that is being linked to, and a data record identifier. A subset of this data is passed to NCBI, as LinkOuts (links at the bottom of PubMed abstracts), however due to NCBI policies the full data records are not currently associated with PubMed records. Database providers can use this mechanism to link to other NCBI databases including gene and protein, however these are not included in the current data set at this time. (To view databases available for linking see, http://www.ncbi.nlm.nih.gov/books/NBK3807/#files.Databases_Available_for_Linking ) The categories that NIF uses have been standardized to the following types: * Resource: Registry * Resource: Software * Reagent: Plasmid * Reagent: Antibodies * Data: Clinical Trials * Data: Gene Expression * Data: Drugs * Data: Taxonomy * Data: Images * Data: Animal Model * Data: Microarray * Data: Brain connectivity * Data: Volumetric observation * Data: Value observation * Data: Activation Foci * Data: Neuronal properties * Data: Neuronal reconstruction * Data: Chemosensory receptor * Data: Electrophysiology * Data: Computational model * Data: Brain anatomy * Data: Gene annotation * Data: Disease annotation * Data: Cell Model * Data: Chemical * Data: Pathways For more information refer to Create a LinkOut file, http://neuinfo.org/nif_components/disco/interoperation.shtm Participating resources ( http://disco.neuinfo.org/webportal/discoLinkoutServiceSummary.do?id=4 ): * Addgene http://www.addgene.org/pgvec1 * Animal Imaging Database http://aidb.crbs.ucsd.edu * Antibody Registry http://www.neuinfo.org/products/antibodyregistry/ * Avian Brain Circuitry Database http://www.behav.org/abcd/abcd.php * BAMS Connectivity http://brancusi.usc.edu/ * Beta Cell Biology Consortium http://www.betacell.org/ * bioDBcore http://biodbcore.org/ * BioGRID http://thebiogrid.org/ * BioNumbers http://bionumbers.hms.harvard.edu/ * Brain Architecture Management System http://brancusi.usc.edu/bkms/ * Brede Database http://hendrix.imm.dtu.dk/services/jerne/brede/ * Cell Centered Database http://ccdb.ucsd.edu * CellML Model Repository http://www.cellml.org/models * CHEBI http://www.ebi.ac.uk/chebi/ * Clinical Trials Network (CTN) Data Share http://www.ctndatashare.org/ * Comparative Toxicogenomics Database http://ctdbase.org/ * Coriell Cell Repositories http://ccr.coriell.org/ * CRCNS - Collaborative Research in Computational Neuroscience - Data sharing http://crcns.org * Drug Related Gene Database https://confluence.crbs.ucsd.edu/display/NIF/DRG * DrugBank http://www.drugbank.ca/ * FLYBASE http://flybase.org/ * Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/ * Gene Ontology Tools http://www.geneontology.org/GO.tools.shtml * Gene Weaver http://www.GeneWeaver.org * GeneDB http://www.genedb.org/Homepage * Glomerular Activity Response Archive http://gara.bio.uci.edu * GO http://www.geneontology.org/ * Internet Brain Volume Database http://www.cma.mgh.harvard.edu/ibvd/ * ModelDB http://senselab.med.yale.edu/modeldb/ * Mouse Genome Informatics Transgenes ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt * NCBI Taxonomy Browser http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html * NeuroMorpho.Org http://neuromorpho.org/neuroMorpho * NeuronDB http://senselab.med.yale.edu/neurondb * SciCrunch Registry http://neuinfo.org/nif/nifgwt.html?tab=registry * NIF Registry Automated Crawl Data http://lucene1.neuinfo.org/nif_resource/current/ * NITRC http://www.nitrc.org/ * Nuclear Receptor Signaling Atlas http://www.nursa.org * Olfactory Receptor DataBase http://senselab.med.yale.edu/ordb/ * OMIM http://omim.org * OpenfMRI http://openfmri.org * PeptideAtlas http://www.peptideatlas.org * RGD http://rgd.mcw.edu * SFARI Gene: AutDB https://gene.sfari.org/autdb/Welcome.do * SumsDB http://sumsdb.wustl.edu/sums/ * Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat http://www.temporal-lobe.com/ * The Cell: An Image Library http://www.cellimagelibrary.org/ * Visiome Platform http://platform.visiome.neuroinf.jp/ * WormBase http://www.wormbase.org * YPED http://medicine.yale.edu/keck/nida/yped.aspx * ZFIN http://zfin.org

Proper citation: Integrated Manually Extracted Annotation (RRID:SCR_008876) Copy   

•   Source: SciCrunch Registry

http://www.nia.nih.gov/research/blog

Blog intended for grantees of the National Institute on Aging (NIA) at the NIH, as well as applicants for funding, those with an application in mind, application reviewers, and students pursuing careers in research on aging and Alzheimer's disease.

Proper citation: Inside NIA: A Blog for Researchers (RRID:SCR_012812) Copy   

•   Source: SciCrunch Registry

http://scicrunch.org/resources

Portal providing identifiers for Antibodies, Model Organisms, and Tools (software, databases, services) created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in their system where more than one identifier exists for a single resource.

Proper citation: Resource Identification Portal (RRID:SCR_004098) Copy   

•   Source: SciCrunch Registry

http://erin.sfn.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A database that lists, reviews, and rates resources for teaching neuroscience at the graduate and undergraduate level.

Proper citation: Educational Resources in Neuroscience (RRID:SCR_000169) Copy   

•   Source: SciCrunch Registry

http://mindhacks.com/

Mind Hacks: Neuroscience and psychology tricks to find out what's going on inside your brain. Mind Hacks is also a book by Tom Stafford and Matt Webb.

Proper citation: Mind Hacks (RRID:SCR_000170) Copy   

•   Source: SciCrunch Registry