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http://national_databank.mclean.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. A publicly accessible data repository to provide neuroscience investigators with secure access to cohort collections. The Databank collects and disseminates gene expression data from microarray experiments on brain tissue samples, along with diagnostic results from postmortem studies of neurological and psychiatric disorders. All of the data that is derived from studies of the HBTRC collection is being incorporated into the National Brain Databank. This data is available to the general public, although strict precautions are undertaken to maintain the confidentiality of the brain donors and their family members. The system is designed to incorporate MIAME and MAGE-ML based microarray data sharing standards. Data from various types of studies conducted on brain tissue in the HBTRC collection will be available from studies using different technologies, such as gene expression profiling, quantitative RT-PCR, situ hybridization, and immunocytochemistry and will have the potential for providing powerful insights into the subregional and cellular distribution of genes and/or proteins in different brain regions and eventually in specific subregions and cellular subtypes.

Proper citation: National Brain Databank (RRID:SCR_003606) Copy   

•   Source: SciCrunch Registry

http://www.ninds.nih.gov/news_and_events/proceedings/20101217-NEXT.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 26,2022. A unique clinical trial network open to studies of more than 400 neurological diseases, allowing investigators to more efficiently pursue new therapies based on scientific opportunity. The network has a centralized IRB serving 25 sites, which will allow trials to move faster, without the need to coordinate IRBs at each individual site. It is not necessary to be part of the NeuroNEXT infrastructure to propose and conduct a study within the network. The Network for Excellence in Neuroscience Clinical Trials, or NeuroNEXT, was created to conduct studies of treatments for neurological diseases through partnerships with academia, private foundations, and industry. The network is designed to expand the National Institute of Neurological Disorders and Stroke''s (NINDS) capability to test promising new therapies, increase the efficiency of clinical trials before embarking on larger studies, and respond quickly as new opportunities arise to test promising treatments for people with neurological disorders. The NeuroNEXT program aims to: * Provide a robust, standardized, and accessible infrastructure to facilitate rapid development and implementation of protocols in neurological disorders affecting adult and/or pediatric populations. The network includes multiple Clinical Sites, one Clinical Coordinating Center (CCC) and one Data Coordinating Center (DCC). * Support scientifically sound, possibly biomarker-informed, Phase II clinical trials that provide data for clear go/no-go decisions. * Energize and mobilize federal, industry, foundations and patient advocacy partners by leveraging existing relationships between NINDS and NeuroNEXT to organize high impact Phase II clinical trials for neurological disorders. * Expand the pool of experienced clinical investigators and research staff who are prepared to be leaders of multicenter clinical research trials. * Working with NeuroNEXT is a cooperative venture between NINDS, the NeuroNEXT network and the applicant.

Proper citation: NeuroNEXT (RRID:SCR_006760) Copy   

•   Source: SciCrunch Registry

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

Collection of images from cell type-specific protein expression in retina using BAC transgenic mice. Images from cell type-specific protein expression in retina using BAC transgenic mice from GENSAT project.

Proper citation: Retina Project (RRID:SCR_002884) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.tbi-impact.org/?p=impact%2Fcalc&btn_calc=GO+TO+CALCULATOR

A calculator that calculates the prediction models for 6 month outcome after Traumatic Brain Injury. Based on extensive prognostic analysis the IMPACT investigators have developed prognostic models for predicting 6 month outcome in adult patients with moderate to severe head injury (Glasgow Coma Scale <=12) on admission. By entering the characteristics into the calculator, the models will provide an estimate of the expected outcome at 6 months. We present three models of increasing complexity (Core, Core + CT, Core + CT + Lab). These models were developed and validated in collaboration with the CRASH trial collaborators on large numbers of individual patient data (the IMPACT database). The models discriminate well, and are particularly suited for purposes of classification and characterization of large cohorts of patients. Extreme caution is required when applying the estimated prognosis to individual patients. The sequential prediction models may be used as an aid to estimate 6 month outcome in patients with severe or moderate traumatic brain injury (TBI). However, the prediction rule can only complement, never replace, clinical judgment and can therefore be used only as a decision-support system.

Proper citation: IMPACT Prognostic Calculator (RRID:SCR_004730) Copy   

•   Source: SciCrunch Registry

https://github.com/danbider/lightning-pose

Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools.

Proper citation: Lightning Pose (RRID:SCR_024480) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.gaitor.org

Software suite to analyse gait trials collected with Experimental Dynamic Gait Arena for Rodents. Used for rodent gait analysis.

Proper citation: GAITOR Suite (RRID:SCR_023031) Copy   

•   Source: SciCrunch Registry

https://cells.ucsc.edu/

Web based tool to visualize gene expression and metadata annotation distribution throughout single cell dataset or multiple datasets. Interactive viewer for single cell expression. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster specific marker genes.

Proper citation: UCSC Cell Browser (RRID:SCR_023293) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://datascience.uth.edu/medcis

NIH funded center to provide system for sharing multimodal epilepsy data for Sudden Unexpected Death in Epilepsy. Modality Epilepsy Data Capture and Integration System (MEDCIS) is cross cohort query interface for SUDEP (Sudden Unexpected Death in EPilepsy) research.

Proper citation: University of Texas Health Science at Houston Center for SUDEP Research (RRID:SCR_024700) Copy   

•   Source: SciCrunch Registry

http://neuromab.ucdavis.edu/

A national mouse monoclonal antibody generating resource for biochemical and immunohistochemical applications in mammalian brain. NeuroMabs are generated from mice immunized with synthetic and recombinant immunogens corresponding to components of the neuronal proteome as predicted from genomic and other large-scale cloning efforts. Comprehensive biochemical and immunohistochemical analyses of human, primate and non-primate mammalian brain are incorporated into the initial NeuroMab screening procedure. This yields a subset of mouse mAbs that are optimized for use in brain (i.e. NeuroMabs): for immunocytochemical-based imaging studies of protein localization in adult, developing and pathological brain samples, for biochemical analyses of subunit composition and post-translational modifications of native brain proteins, and for proteomic analyses of native brain protein networks. The NeuroMab facility was initially funded with a five-year U24 cooperative grant from NINDS and NIMH. The initial goal of the facility for this funding period is to generate a library of novel NeuroMabs against neuronal proteins, initially focusing on membrane proteins (receptors/channels/transporters), synaptic proteins, other neuronal signaling molecules, and proteins with established links to disease states. The scope of the facility was expanded with supplements from the NIH Blueprint for Neuroscience Research to include neurodevelopmental targets, the NIH Roadmap for Medical Research to include epigenetics targets, and NIH Office of Rare Diseases Research to include rare disease targets. These NeuroMabs will then be produced on a large scale and made available to the neuroscience research community on an inexpensive basis as tissue culture supernatants or purified immunoglobulin by Antibodies Inc. The UC Davis/NIH NeuroMab Facility makes NeuroMabs available directly to end users and is unable to accommodate sales to distributors for third party distribution. Note, NeuroMab antibodies are now offered through antibodiesinc.

Proper citation: NeuroMab (RRID:SCR_003086) Copy   

•   Source: SciCrunch Registry

https://syngoportal.org/

Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms.

Proper citation: SynGO (RRID:SCR_017330) 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

http://www.jneurosci.org/supplemental/18/12/4570/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 29, 2013. Supplemental data for the paper Changes in mitochondrial function resulting from synaptic activity in the rat hippocampal slice, by Vytautas P. Bindokas, Chong C. Lee, William F. Colmers, and Richard J. Miller that appears in the Journal of Neuroscience June 15, 1998. You can view digital movies of changes in fluorescence intensity by clicking on the title of interest.

Proper citation: Hippocampal Slice Wave Animations (RRID:SCR_008372) Copy   

•   Source: SciCrunch Registry

https://bams1.org/ontology/viewer.php

Ontology designed for neuroscience. Includes complete set of concepts that describe parts of rat nervous system, growing set of concepts that describe neuron populations identified in different brain regions, and relationships between concepts.

Proper citation: BAMS Neuroanatomical Ontology (RRID:SCR_004616) Copy   

•   Source: SciCrunch Registry

http://www.tbidx.net

Network evaluating consensus-based common data elements (CDE) for traumatic brain injury (TBI) and psychological health (TBI-CDE, www.commondataelements.ninds.nih.gov/TBI.aspx) while extensively phenotyping a cohort of TBI patients across the injury spectrum from concussion to coma. Institutions that participate in the TBI Network will be able to track the outcomes of patients through a 3, 6 and 12-month followup program and compare outcomes with other participating institutions. For the three acute care centers, patients were enrolled that presented to the emergency department within 24 hours of head injury and required computed tomography (CT). For the rehabilitation center, referrals from acute hospitals were enrolled. Patients were consented to participate in components: clinical profile; blood draws for measurement of proteomic and genomic markers; 3T MRI within 2 weeks; three-month Glasgow Outcome Scale-Extended (GOS-E); and six-month TBI-CDE Core outcome assessments. A web-enabled database, imaging repository, and biospecimen bank was developed using the TBI-CDE recommendations. A total of 605 patients were enrolled. Of these subjects, 88% had a GCS 13-15, 5% had a GCS 9-12, and 7% had a GCS of 8 or less. Three-month GOS-E''s were obtained for 78% of the patients. Comprehensive 6-month outcome measures, including PTSD assessment, are ongoing until September 2011. Blood specimens were collected from 450 patients. Initial CTs for 605 patients and 235 patients with 3T MRI studies were transferred to an imaging repository. The TRACK TBI Network will provide qualified institutions access to a web-based version of key forms in tracking TBI outcomes for Quality Improvement and institutional benchmarking.

Proper citation: TRACK TBI Network (RRID:SCR_004723) Copy   

•   Source: SciCrunch Registry