Curator Dashboard

A freely editable semantic wiki for community-based curation of the terms used in Neuroscience. Entries are curated and eventually incorporated into the formal NIFSTD ontology. NeuroLex also includes a Resource branch for community members to freely add neuroscience relevant resources that do not become part of NIFSTD ontology but rather make up the NIF Registry. As part of the NIF, we provide a simple search interface to many different sources of neuroscience information and data. To make this search more effective, we are constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g., neuron is a cell. These categories provide the means to perform more effective searches and also to organize and understand the information that is returned. But an important adjunct to this activity is to clearly define all of the terms that we use to describe our data, e.g., anatomical terms, techniques, organism names. Because wikis provide an easy interface for communities to contribute their knowledge, we started the NeuroLex.

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• SciCrunch
• 15 years ago - by Anonymous

Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data.

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• RRID-Legacy
• 7 years ago - submitted by Edyta Vieth

Software ensembl based annotation R package. Exposes annotation databases generated from Ensembl. This package loads SQL connection to database containing annotations from Ensembl.

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• RRID
• 1 year ago - by Anonymous

It assists in the compilation and identification of repeat sequences in plant genomes. All of the repetitive sequences in the database are coded for the convenience of future analyses. In plants, ploidy levels and repetitive sequences contribute significantly to genome size. A number of different repetitive sequences have been reported in the plant genome and these can be classified into super-classes, classes, and subclasses based on structure and sequence composition. The transposable element (TEs) super-class includes retrotransposons, transposons, and miniature inverted-repeat transposable elements (MITEs). Other repetitive sequences are associated the centromere and telomere. Another super-class of repetitive sequences are rDNAs which encode the structural RNA components of ribosomes.

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• SciCrunch
• 17 years ago - by Anonymous

Software tool as full text search engine for COVID-19 Open Research Dataset. Used to explore dataset and identify potential research efforts.

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• rapid-viraldb
• 7 years ago - submitted by Jeffrey Grethe

Core offers mass spectrometry services. Provided instruments include

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• RRID
• 1 year ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 24, 2017.

Platform to enable dissemination of scientific findings, foster open peer commentary and promote collaboration among the research community. Widespread participation in OneLab will increase the quality, transparency and reproducibility of data thus accelerating the pace of scientific discoveries. The result will be a streamlined process from the bench to the clinic with tremendous benefits for the well-being of the general public. OneLab is a private professional network that mirrors the hierarchy of real world research laboratories. Users are designated as either principal investigators (PI) or lab members. PIs can invite lab members to join and data posted by lab members cannot be shared without PI approval. In this way the PI retains FULL CONTROL over the dissemination of scientific content thus safeguarding the primacy of authorship. This professional network will serve as a backdrop for sharing scientific findings, promote collaborations, and provide a basis for open peer commentary. Semantic Search of Structured Content OneLab implements a powerful search functionality that is based on structured content. Users describe their Single Figure Posts (SFPs) using defined fields such as model organism, genes, proteins and assay. This additional layer of structure provides the basis for a smarter and more accurate search engine that understands searcher intent and therefore generates more relevant results. Structured content allows OneLab to go one step further by offering recommendations based on similarities that might not be intuitive, thus increasing potential collaborations among scientists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 15 years ago - by Anonymous

Software tool that can match tandem mass spectra with peptide sequences, in process known as protein identification. Database search engine for matching tandem mass spectra with protein sequences. Command line tool for matching tandem mass spectra with peptide sequences.

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• RRID-Legacy
• 7 years ago - by Anonymous

Core specializes in precise measurements of rare isotopologues such as “clumped” isotopes of carbonate and CO2 and triple oxygen isotope distributions in waters, carbonates, phosphates and recently organics. Houses Nu Perspective IRMS mass spectrometers, EuroVector EA3000 and HT-PyrOH, NuCarb device for traditional carbon and oxygen isotopes, Thermo Fisher ISQ 7000 GC-MS, fully automated clumped isotope preparation line, semi-automated triple oxygen isotope preparation line, manual water fluorination line, multi-purpose vacuum extraction line, and ovens, balances, glassware, fume hoods, and other equipment used in experiments and sample preparation.

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• RRID
• 1 year ago - submitted by Edyta Vieth

Software tool for biomarker assessment and outcome based cut point optimization.

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• SciCrunch
• 13 years ago - by Anonymous

Probabilistic programming language for specifying statistical models. Defines log probability function over parameters conditioned on specified data and constants. Platform for statistical modeling and high performance statistical computation. Provides full Bayesian inference for posterior expectations including parameter estimation and posterior predictive inference by defining appropriate derived quantities of interest.

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• SciCrunch
• 6 years ago - submitted by Nathan Anderson

Core offers services and instrumentation including Renishaw inVia microscopes, High sensitivity ultra low noise RenCam CCD detector,Multiple lasers on hand (532nm, 633nm, 785nm),< 1 cm-1 spectral resolution capability. Supports sampling accessories such as fiber optic probes and temperature control stages (liq. He – 300ºC). Offers Automated XYZ stage with 100nm positioning control and Compositional mapping.

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• RRID
• 1 year ago - submitted by Edyta Vieth

Software for identifying differentially methylated regions between unique samples using array based methylation profiles. It allows researchers to compare n greater than or equal to 2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishesit from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance.

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• SciCrunch
• 12 years ago - by Anonymous

Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation.

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• RRID-Legacy
• 6 years ago - submitted by Nathan Anderson

Core provides imaging and expert technical assistance and instrumentation in support of investigators.

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• RRID
• 1 year ago - submitted by xuezhi cui

Collect, share, and distribute information about protein three-dimensional structures. It serves as a portal for the scientific community to learn about protein structures solved by SG centers, and also to contribute their expertise in annotating protein function. The premise of the TOPSAN project is that, no matter how much any individual knows about a particular protein, there are other members of the scientific community who know more about certain aspects of the same protein, and that the collective analyses from experts will be far more informative than any local group, let alone individual, could contribute. They believe that, if the members of the biological community are given the opportunity, authorship incentives, and an easy way to contribute their knowledge to the structure annotation, they would do so. Therefore, borrowing elements from successful, distributed, collaborative projects, such as Wikipedia (the free encyclopedia anyone can edit) and from other open source software development projects, TOPSAN will be a broad, collaborative effort to annotate protein structures, initially, those determined at the JCSG. They believe that the annotation of proteins solved by structural genomics consortia offers a unique opportunity to challenge the extant paradigm of how biological data is collected and distributed, and to connect structural genomics and structural biology to the entire biological research community. TOPSAN is designed to be scalable, modular and extensible. Furthermore, it is intended to be immediately useful in a simplistic way and will accommodate incremental improvements to functionality as usage becomes more sophisticated. Their annotation pages will offer the end user a combination of automatically generated as well as expert-curated annotations of protein structures. They will use available technology to increase the speed and granularity of the exchange of scientific ideas, and use incentive mechanisms that will encourage collaborative participation.

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• SciCrunch
• 15 years ago - by Anonymous

Collection of human pancreas data and images. Platform to share data from human pancreas samples. Houses reference datasets from human pancreas samples, achieved through generosity of organ donors and their families.

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• dkNET
• 6 years ago - submitted by Ko-Wei Lin

Core provides resources and services to prepare samples for analysis in epigenetic regulation in both genome-wide and locus-specific manners.

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• RRID
• 1 year ago - submitted by Edyta Vieth

GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations. # GOChase-History resolves the whole modification history of GO IDs. # GOChase-Correct highlights merged GO IDs and redirects to the correct primary term into which the secondary ID was merged. For obsolete GO terms, the nearest non-discarded parent term is recommended by GOChase. This function may be used by GO browsers such as AmiGO and QuickGO to fix broken hyperlinks. # A whole database (such as LocusLink) as a flat file can be loaded into GOChase, reporting the annotation errors and GOChase corrections. # When one inputs a GO ID, GOChase will resolve all gene products annotated with the GO ID across all the major databases. Platform: Online tool

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• SciCrunch
• 15 years ago - by Anonymous

Established to produce immortalized cell lines from human blood (EBV transformations). Offers genomics applications for single cells, including RNA-seq, gene expression profiling by qPCR and DNA amplification for whole-genome or targeted (exome or PCR-based analysis) through 10x Genomics Chromium platform (similar to Drop Seq). Offers custom genotyping to analyze short tandem repeats, variable number tandem repeats and single nucleotide polymorphisms.

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• SciCrunch
• 6 years ago - submitted by Edyta Vieth