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on page 1 showing 20 out of 623 results

Cite this (1000 Fungal Genome Project, RRID:SCR_016463)

URL: https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf

Resource Type: Resource, topical portal, data access protocol, database, web service, organism-related portal, portal, software resource, project portal, data or information resource

Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment.

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Cite this (3D de novo assembly, RRID:SCR_017227)

URL: https://github.com/theaidenlab/3d-dna.git

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly.

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Cite this (Accelerating Medicines Partnership Type 2 Diabetes, RRID:SCR_003743)

URL: http://www.type2diabetesgenetics.org/

Resource Type: Resource, disease-related portal, topical portal, database, service resource, portal, storage service resource, data repository, data or information resource

Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease.

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Cite this (Addiction Research GPCR Assay Bank, RRID:SCR_002895)

URL: http://www.duke.edu/web/gpcr-assay/index.html

Resource Type: Resource, production service resource, biomaterial supply resource, material service resource, service resource, cell repository, material resource, biomaterial manufacture

Describes data from and access to permanent cell lines containing beta-arrestin fluorescent protein biosensors. This assay Bank provides plasmids, cells lines, and resulting data to the NIDA/NIH funded research community in order to better understand and combat addiction.

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Cite this (Advanced 3D Visualization and Volume Modeling, RRID:SCR_007353)

URL: http://www.fei.com/software/amira-3d-for-life-sciences/

Resource Type: Resource, data analysis software, data processing software, software application, data visualization software, 3d visualization software, software resource

Software tool for visualizing, manipulating, and understanding data from tomography, microscopy, MRI and other imaging processes.Used to import and export options, to processes 3D image filtering and DTI based fiber tracking to visualization, volume and surface rendering, author tools for virtual reality navigation, video generation, and more.

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    affydata

Cite this (affydata, RRID:SCR_016976)

URL: http://bioconductor.org/packages/release/data/experiment/html/affydata.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software, data or information resource

Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.

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    affy

Cite this (affy, RRID:SCR_012835)

URL: http://www.bioconductor.org/packages/release/bioc/html/affy.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.

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Cite this (Africa Centre Biobank, RRID:SCR_000638)

URL: http://www.africacentre.ac.za/Biobank/tabid/460/Default.aspx

Resource Type: Resource

THIS RESOURCE IS NO LONGER IN SERVICE, documented November 30, 2015. Extensive collection of biological specimens of various kinds that are mostly collected from the population around the Africa Centre in northern KwaZulu-Natal, but there are also specimens collected from populations in and around Durban and elsewhere in KwaZulu-Natal. The results of tests carried out on these specimens are generally stored in the main databases of the various studies involved, and are linkable back to the demographic and other data collected from the individuals concerned. The Biobank is curated by staff of the Africa Centre's Virology Laboratory in Durban, where all the specimens are currently stored, mostly in -80C freezers. A particular strength of its holdings are the dried blood spot (DBS), specimens five drops of blood on a filter-paper card, obtained via a finger-prick - of which there are now nearly 115,000. The following is a list of its holdings (May 2011): * 67,700 DBS specimens collected since late 2002 primarily for HIV prevalence estimation of the population covered by the Africa Centre Demographic Surveillance population. All have at least been tested for HIV, and just over 21% give a Positive result. Specimens are collected annually, so for some individuals we might have a sequence of 8-10 specimens covering 2002-2011. * 36,601 DBS specimens collected by the Vertical Transmission Study (VTS) between Sep 2001 and Dec 2006. This study focussed on mother-child pairs and investigated the vertical transmission of HIV from mother to child. DBS specimens were collected from both the mothers (at initial screening, and then from their children at Birth, 6, 10, 14, 18, 22 weeks, and 7, 8, 9, 12, 15, 18, 21 and 24 months. * 6,585 DBS specimens collected as part of the KZN IMPACT study of PMTCT effectiveness in six districts of kwaZulu-Natal. The specimens were collected during 2004-2006 from infants aged 4-8 weeks when mothers brought them to clinics for immunisation. These DBS specimens are stored at room temperature, not in freezers. * 3,524 DBS specimens collected as part of the Kesho Bora study from Sep 2007 . They were collected from mothers at enrollment, and from the infants at delivery, 2 weeks, and at 4, 5, 7, 8 and 15 months. * 50,068 Plasma specimens * 28,775 breastmilk specimens * 11,277 breastmilk products (Pellets and lactoserum). These have all been extracted from the BM specimens in prev. item? * 11,188 RNA and DNA products extracted from DBS and plasma specimens from all our major studies. * 5,735 Serum specimens * 3,505 cell pellets * 1,778 whole blood specimens * 1,284 Peripheral Blood Mononuclear Cells from the Kesho Bora study mothers (665) and their children (619) * 179 skin tissue specimens from the KST study (Kaposi's Sarcoma) * 176 foreskins

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Cite this (Agilent Masshunter Qualitative Analysis, RRID:SCR_016657)

URL: https://www.agilent.com/en/products/software-informatics/masshunter-suite/masshunter-qualitative-analysis-gcms

Resource Type: Resource, data analysis software, data processing software, software application, data analytics software, software toolkit, software resource, data acquisition software

Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise.

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Cite this (Agile Protein Interactomes DataServer, RRID:SCR_008871)

URL: http://apid.dep.usal.es

Resource Type: Resource, data analysis service, data access protocol, database, analysis service resource, production service resource, web service, service resource, software resource, data or information resource

APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.

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Cite this (Allen Brain Atlas, RRID:SCR_017001)

URL: http://portal.brain-map.org/

Resource Type: Resource, atlas, project portal, portal, data or information resource

Projects within the Allen Institute for Brain Science for creating Mouse and Human Brain atlases. Combine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases.

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Cite this (Allen Developing Mouse Brain Atlas, RRID:SCR_002990)

URL: http://developingmouse.brain-map.org/

Resource Type: Resource, atlas, database, expression atlas, reference atlas, data or information resource

Map of gene expression in developing mouse brain revealing gene expression patterns from embryonic through postnatal stages. Provides information about spatial and temporal regulation of gene expression with database. Feature include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases may be viewed alongside in situ hybridization (ISH) data as well as by itself.

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Cite this (Allen Human Brain Atlas, RRID:SCR_007416)

URL: http://human.brain-map.org/

Resource Type: Resource, data processing software, database, software application, data visualization software, software resource, atlas, data or information resource

Multi modal atlas of human brain that integrates anatomic and genomic information, coupled with a suite of visualization and mining tools to create an open public resource for brain researchers and other scientists. Data include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is a desktop software application for viewing the human brain anatomy and gene expression data in 3D. It is available for download.

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Cite this (Allen Institute for Brain Science, RRID:SCR_006491)

URL: http://www.brain-map.org

Resource Type: Organization, atlas, topical portal, portal, data or information resource

Seattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain.

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Cite this (Allen Institute for Brain Science Sleep Study, RRID:SCR_002983)

URL: http://sleep.alleninstitute.org

Resource Type: Resource, data set, atlas, data or information resource

Collection of gene expression data in mouse brain for five different conditions of sleep and wakefulness to understand sleep deprivation and dynamic changes underlying sleep and wake cycles. Platform to generate cellular resolution expression data.

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Cite this (Allen Institute, RRID:SCR_005435)

URL: https://alleninstitute.org/

Resource Type: Resource, atlas, organization portal, database, portal, data or information resource

Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes.

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Cite this (Allen Mouse Brain Atlas, RRID:SCR_002978)

URL: http://mouse.brain-map.org/

Resource Type: Resource, atlas, database, data or information resource

Project for 3D genome map of gene expression in the adult mouse brain. Reveals the expression patterns of genes throughout entire adult mouse brain down to cellular level. Interactive, genome wide image database of gene expression with ISH and Nissl images. Combination of RNA in situ hybridization data, detailed Reference Atlases and informatics analysis tools are integrated to provide searchable digital atlas of gene expression.

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Cite this (Allen Mouse Brain Connectivity Atlas, RRID:SCR_008848)

URL: http://connectivity.brain-map.org/

Resource Type: Resource, atlas, spatially referenced dataset, data or information resource

Map of neural connections in mouse brain, built on an array of transgenic mice genetically engineered to target specific cell types. In addition to the connectivity data, information about the transgenic mouse lines and genetic tracers is available. Consists of high resolution 2-D projectivity image data that can be viewed side-by-side with the associated reference atlas and other reference datasets. Enables 3-D visualization and spatial/ontological search of connectivity models through a combination of manual and informatics analyses.

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Cite this (Allen Mouse Spinal Cord Atlas, RRID:SCR_007418)

URL: http://mousespinal.brain-map.org/

Resource Type: Resource, atlas, data or information resource, database

Platform for exploring spinal cord at cellular and molecular levels. Map of gene expression for adult and juvenile mouse spinal cord. Provides map of normal mouse when used to compare gene expression in diseased or injury models. Interactive database of gene expression mapped across all anatomic segments of mouse spinal cord at postnatal days 4 and 56. Indexed set of images based on RNA in situ hybridization data, searchable and sortable by gene, age, expression, cervical, thoracic, lumbar, sacral, and coccygeal segments.

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Cite this (Altered States Database, RRID:SCR_016350)

URL: http://www.nitrc.org/projects/asdb/

Resource Type: Resource, data or information resource, database

Database as an open science framework with a scientific data extracted from scientific literature about various altered states of consciousness assessed with questionnaires.
Used to compare what experiences are elicited by different drugs and non-pharmacological methods that induce altered states to help to understand human consciousness functions.
Is listed by Neuroimaging Informatics Tools.

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