Curator Dashboard

Research infrastructure for the EU Human Brain Project. Provides digital tools and services which can be used to address challenges in brain research and brain inspired technology development. Digital research infrastructure, created by EU-funded Human Brain Project, that gathers extensive range of data and tools for brain-related research. EBRAINS will capitalize on the work performed by the Human Brain Project teams in digital neuroscience, brain medicine, and brain-inspired technology.You can share your neuroscience data, models and software.

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• NIF
• 6 years ago - submitted by Maryann Martone

Core offers consulting and support services for detection of different fluorescent parameters simultaneously, RBC contaminated samples, and high throughput analysis using 96 or 384-well plates. Cell sorter allows for collecting cells/particulates of interest, after screening for positively selected markers, downstream applications, and is capable of sorting four separate cell populations simultaneously.

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• SciCrunch
• 13 years ago - by Anonymous

Open community of researchers, educators, and professionals with goal of improving way we develop, share, use, and re-use agent based and computational models for study of social and ecological systems. Develops and maintains CoMSES Model Library, digital repository that supports discovery and good practices for software citation, digital preservation, reproducibility, and reuse.

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• RRID-Legacy
• 7 years ago - submitted by Anita Bandrowski

Core facility that provides the following services: DNA extraction from whole blood, saliva, isolated cell pellet, RNA extraction from whole blood with PaxGene tubes, Lymphoblast transformation, Isolation and cryo-preservation of white blood cells. The BioSample Services Facility (BSF) provides sample handling and preparation resources to investigators in the Partners research community. Our goal is to efficiently and effectively process specimens enabling the generation of high quality data via down stream processes. All projects containing subject samples and submitted to the BSF for handling must be IRB approved in advance. All specimens must be entered into our Laboratory Information Management System (GIGPAD) prior to delivery to the BSF. Our staff will work with you to design an implementation plan that would best fit your research needs.

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• SciCrunch
• 13 years ago - by Anonymous

Facility housed within Center for Genes, Environment and Health, provides Next-Gen Sequencing services from expert planning through data analysis including RNA-Seq, Whole Exome Sequencing, Single-Cell sequencing and customized panels.Data is stored onsite and is ready for future data mining by our team or others when needed. Our team is trained to utilize both Illumina and Thermo Ion Sequencing Platforms, including many other technologies, to provide the best mix of capabilities for your genomics needs.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 30, 2023. Core facility that provides the following services: Microscopy consultation services, Technical microscopy service, Microscopy training services, Conventional immunofluorescence microscopy service, Confocal microscopy service, Live-cell imaging service, Conventional electron microscopy service, EM immunogold labeling service, Tissue sectioning service, Tissue fixation, Computer based image analysis and quantification.

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• SciCrunch
• 13 years ago - by Anonymous

Open source software Python library for sensitivity analysis. Useful in systems modeling to calculate effects of model inputs or exogenous factors on outputs of interest.

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• RRID
• 4 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. A database with information about a variety of vectors, including phage, plasmid, phagemid, phasmid, cosmid, virus and YAC vectors. It also contains information on drosophilia, C. elegans, yeast and drosophilia vectors, including vector functions, hosts and copy number.

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• SciCrunch
• 17 years ago - by Anonymous

Core has developed library of natural product extracts derived from unique collection of diverse marine and terrestrial actinomycetes, fungi and cyanobacteria. Provides technology and expertise to develop candidates identified through high-throughput screening into unique, bioactive, patentable, small molecules.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

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• SciCrunch
• 15 years ago - by Anonymous

Software package for QC and visualization of ATAC-seq results. Used to examine aligned reads and report basic metrics, including reads mapped in proper pairs, optical or PCR duplicates, reads mapping to autosomal or mitochondrial references, ratio of short to mononucleosomal fragment counts, mapping quality, various kinds of problematic alignments.

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• RRID
• 4 years ago - submitted by Ipek Selcen

Software application providing a comprehensive modelling framework and a multiple-imputation approach to haplotypic analysis of population-based data. It uses biallelic SNP genotype data to impute haplotype frequencies at the individual level. SimHap also tests for haplotype associations with outcomes of interest while incorporating the uncertainty around inferred haplotypes into the modelling procedure. SimHap allows epidemiological (ie, non-genetic) and both single SNP and haplotype association analyses of quantitative Normal, binary, longitudinal and right-censored outcomes under a range of genetic models. SimHap can accommodate large data sets, and can model genetic and environmental effects, including complex haplotype:environment interactions. SimHap features cross-platform functionality via Java, and a sophisticated graphical user interface (GUI). SimHap will also perform association analysis on more simple epidemiological models, with or without the inclusion of genetic covariates. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Astrobiology Habitable Environments Database (AHED) is a new data system being developed as a long-term, open-access repository for astrobiology data. AHED is intended to store user-contributed results from NASA or externally-funded research in astrobiology, and to encourage sharing and synergy within the astrobiology community.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software package for simulating RNA-seq library preparation with parameter estimation.

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• SciCrunch
• 13 years ago - by Anonymous

Comparative database with clinical and resource utilization data for inpatient, ambulatory surgery, emergency department and observation unit encounters for more than 49 children's hospitals.

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• RRID
• 4 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. Database to access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. They developed an automated method for discovering human tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs), which involves classifying human EST libraries according to tissue categories and Bayesian statistical analysis. They use the UniGene clusters of human Expressed Sequence Tags (ESTs) to identify splices. The UniGene EST's are clustered so that a single cluster roughly corresponds to a gene (or at least a part of a gene). A single EST represents a portion of a processed (already spliced) mRNA. A given cluster contains many ESTs, each representing an outcome of a series of splicing events. The ESTs in UniGene contain the different mRNA isoforms transcribed from an alternatively spliced gene. They are not predicting alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. They have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with 2.1 million human mRNA and EST sequences, they mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus. After constructing a tissue list of 46 human tissues with 2 million human ESTs, they generated a database of novel human alternative splices that is four times larger than our previous report, and used Bayesian statistics to compare the relative abundance of every pair of alternative splices in these tissues. Using several statistical criteria for tissue specificity, they have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. They have validated our results by comparison with independent studies. This genome-wide analysis of tissue specificity of alternative splicing will provide a useful resource to study the tissue-specific functions of transcripts and the association of tissue-specific variants with human diseases.

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• SciCrunch
• 16 years ago - by Anonymous

Light microscopy facility. Offers microscopes and training to image cell and tissues, live or fixed, BSL1/BSL2.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 15 years ago - by Anonymous

Core assists with production, characterization and differentiation of human pluripotent stem cells. Offers services related to research on human ES and iPS cells. Provides reprogramming of iPS cell lines from patients and healthy donors, for example for in vitro disease modeling. Offers already established human ES cell lines and large bank of human iPS cell lines established through ongoing REK-approved projects. Provides ES and iPS cell characterization services, and training in the culture and maintenance of human ES and iPS cells.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

A manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker's yeast and Brewer's yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases. YMDB contains metabolites arising from normal S. cerevisiae metabolism under defined laboratory conditions as well as metabolites generated by S. cerevisiae when used in baking and in the production of wines, beers and spirits. YMDB currently contains 2027 small molecules with 857 associated enzymes and 138 associated transporters. Each small molecule has 48 data fields describing the metabolite, its chemical properties and links to spectral and chemical databases. Each enzyme/transporter is linked to its associated metabolites and has 30 data fields describing both the gene and corresponding protein. Users may search through the YMDB using a variety of database-specific tools. The simple text query supports general text queries of the textual component of the database. By selecting either metabolites or proteins in the search for field it is possible to restrict the search and the returned results to only those data associated with metabolites or with proteins. Clicking on the Browse button generates a tabular synopsis of YMDB's content. This browser view allows users to casually scroll through the database or re-sort its contents. Clicking on a given MetaboCard button brings up the full data content for the corresponding metabolite. A complete explanation of all the YMDB fields and sources is available. Under the Search link users will find a number of search options listed in a pull-down menu. The Chem Query option allows users to draw (using MarvinSketch applet or a ChemSketch applet) or to type (SMILES string) a chemical compound and to search the YMDB for chemicals similar or identical to the query compound. The Advanced Search option supports a more sophisticated text search of the text portion of YMDB. The Sequence Search button allows users to conduct BLASTP (protein) sequence searches of all sequences contained in YMDB. Both single and multiple sequence (i.e. whole proteome) BLAST queries are supported. YMDB also supports a Data Extractor option that allows specific data fields or combinations of data fields to be searched and/or extracted. Spectral searches of YMDB's reference compound NMR and MS spectral data are also supported through its MS, MS/MS, GC/MS and NMR Spectra Search links. Users may download YMDB's complete textual data, chemical structures and sequence data by clicking on the Download button.

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• SciCrunch
• 15 years ago - by Anonymous