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http://www.utsa.edu/claibornelab/

The long-term goals of my research are to understand the relationship between neuronal structure and function, and to elucidate the factors that affect neuronal morphology and function over the lifespan of the mammal. Currently we are examining 1) the effects of synaptic activity on neuronal development; 2) the effects of estrogen on neuronal morphology and on learning and memory; and, 3) the effects of aging on neuronal structure and function. We have focused our efforts on single neurons in the hippocampal formation, a region that is critical for certain forms of learning and memory in rodents and humans. From the portal, you may click on a cell in your region of interest to see the complete database of cells from that region. You may also explore the Neuron Database: * Comparative Electrotonic Analysis of Three Classes of Rat Hippocampal Neurons. (Raw data available) * Quantitative, three-dimensional analysis of granule cell dendrites in the rat dentate gyrus. * Dendritic Growth and Regression in Rat Dentate Granule Cells During Late Postnatal Development.(Raw data available) * A light and electron microscopic analysis of the mossy fibers of the rat dentate gyrus.

Proper citation: University of Texas at San Antonio Laboratory of Professor Brenda Claiborne (RRID:SCR_008064) Copy   

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http://www.snprc.org/

Center that supports studies of nonhuman primate models of human diseases, including common chronic diseases and infectious diseases and the effects that genetics and the environment have on physiological processes and disease susceptibility. SNPRC encourages the use of its resources by investigators from the national and international biomedical research communities.

Proper citation: Southwest National Primate Research Center (RRID:SCR_008292) Copy   

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http://cprc.rcm.upr.edu/

Center for the study of non-human primates. Its mission is the study and use of non-human primates as models for studies of social and biological interactions and for the discovery of methods of prevention, diagnosis and treatment of diseases that afflict humans. Through the stewardship of three unique facilities—Cayo Santiago Field Station, Sabana Seca Field Station, and the Laboratory of Primate Morphology supports a diverse range of research programs that enhance understanding of primate biology and behavior, with direct applications in biomedical and translational research.

Proper citation: Caribbean Primate Research Center (RRID:SCR_008345) Copy   

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http://www.brainvoyager.de/BV2000OnlineHelp/BrainVoyagerWebHelp/Talairach_brain_atlas.htm

The Talairach brain atlas visualized via BrainVoyager (Commercial software) can be used to visualize Brodmann areas as they were defined for the Talairach brain (Talairach & Tournaux, 1988) and to compare regions of subjects with respect to the Brodmann areas. The demarcated areas are based on the Talairach demon, which is a digitized version of the Talairach atlas and which has been transferred into BrainVoyager VOI files by Matthias Ruf, Mannheim. Using the Brodman.voi file you may ask questions like the following: What is the signal time course of subject N in experiment A within Brodmann area X ?. Note, however, that the defined areal boundaries should be used only as a rough guideline for determining the location of activated regions: There is substantial variation of histologically defined areas between subjects. Since cytoarchitectonically defined Brodmann areas are not available in vivo, we advise to use the provided information with care. The TalairachBrain.vmr file is located in the same folder as your BrainVoyager executable file. It can be loaded as any VMR project by using the Open... item in the File menu (or the Open icon). The TalairachBrain.vmr file is also loaded automatically when using the glass brain visualization tool.

Proper citation: BrainVoyager: Talairach Brain Atlas (RRID:SCR_008800) Copy   

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http://www.pathonet.org

PathoNet is a virtual meeting place for pathologists from all over the world. They can use it as a virtual pathology laboratory in which they can exchange their views on their cases. Join us and share your experience. Special or rare cases maybe very useful in the diagnostic practice. Everybody who would like to use digital microscopy in human, veterinary or forensic pathology; in laboratory medicine, in human anatomy; in experimental research, and when teaching can benefit from this resource. Additionally, practicing physicians, students, tutors, experts and researchers can all contribute and benefit from PathoNet. Sponsors: This resource is supported by 3DHISTECH Ltd.

Proper citation: PATHONET (RRID:SCR_008674) Copy   

•   Source: SciCrunch Registry

http://www.muschealth.com/multimedia/Podcasts/index.aspx?type=main

The MUSChealth.com Podcast Library, featuring podcasts on a variety of topics related to your health and our services here at MUSC. These medical podcasts are hosted by MUSC faculty, physicians and special guests and are produced and directed by Linda Austin, M.D. Current topics include: * Academics and Education * Aging, Geriatrics and Caregiving * Alcohol and Drug Dependency * Allergies and Asthma * Ashley River Tower * Bones, Joints, Muscles and Spine * Cancer * Children''s Health * Cosmetic Surgery * Dental * Dermatology/Skin Problems * Diabetes, Endocrinology and Metabolism * Digestive Health * ENT: Ear, Nose and Throat * Executive Health * Eye Health * General Health and Wellness * Heart and Vascular Health * Hospice * Kohl''s Take a Minute for Kids * Lungs and Breathing * Men''s Health * Mental Health * MUSC News and Events * Neurological Health * Organ Transplant * Osteoporosis * Pregnancy - Week by Week * Pregnancy and Childbirth * Radiology * Research and Clinical Trials * SC Health, Leadership and Policy * Sports Medicine * Stroke * Urology * Weight Loss Surgery Follow-up * Weight Management * Women''s Health

Proper citation: MUSC Health Podcast Library (RRID:SCR_008827) Copy   

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https://omictools.com/l2l-tool

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 26, 2019.

Database of published microarray gene expression data, and a software tool for comparing that published data to a user''''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don''''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: L2L Microarray Analysis Tool (RRID:SCR_013440) Copy   

•   Source: SciCrunch Registry

http://www.brainsimagebank.ac.uk

A searchable collection of anonymised images and associated clinical data. It includes normal individuals at all ages (from prenatal to old age). The image bank contains integrated data sets already collected as part of research studies which include control subjects. New data is added as they become available.

Proper citation: BRAINS Imagebank (RRID:SCR_014576) Copy   

•   Source: SciCrunch Registry

https://www.rebuildingakidney.org

A consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function. Their goal is to coordinate and integrate research to support the development and implementation of strategies such as de novo repair of nephrons, the re-generation of nephrons, and the in vitro engineering of a biological kidney to enhance renal repair and promote the generation of new nephrons in the postnatal organ. Investigators may apply for funding of a kidney-related project through the RBK Partnership Project. Funded projects would join the consortium.

Proper citation: ReBuilding a Kidney (RRID:SCR_014442) Copy   

•   Source: SciCrunch Registry

http://www.loni.ucla.edu/~thompson/thompson.html

The UCLA laboratory of neuroimaging is working in several areas to enhance knowledge of anatomy, including brain mapping in large human populations, HIV, Schizophrenia, methamphetamine, tumor growth and 4d brain mapping, genetics and detection of abnormalities.

Proper citation: University of California at Los Angeles, School of Medicine: Neuro Imaging Lab of Thompson (RRID:SCR_001924) Copy   

•   Source: SciCrunch Registry

http://ww2.sanbi.ac.za/Dbases.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The STACKdb is knowledgebase generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACK project aims to generate a comprehensive representation of the sequence of each of the expressed genes in the human genome by extensive processing of gene fragments to make accurate alignments, highlight diversity and provide a carefully joined set of consensus sequences for each gene. The STACK project is comprised of the STACKdb human gene index, a database of virtual human transcripts, as well as stackPACK, the tools used to create the database. STACKdb is organized into 15 tissue-based categories and one disease category. STACK is a tool for detection and visualization of expressed transcript variation in the context of developmental and pathological states. The data system organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index

Proper citation: Sequence Tag Alignment and Consensus Knowledgebase Database (RRID:SCR_002156) Copy   

•   Source: SciCrunch Registry

http://www.ibiblio.org/dnam/mainpage.html

This site provides access to mutation databases and software including the human hprt database, Human p53 database, Transgenic lacZ database, and Transgenic lacI database. Other avaialble programs include Mutational spectra comparison and relational database data entry. The most recent hprt database contains information on over 2,300 mutations found in vivo and in vitro in the human hprt gene and runs under Windows. The version for evaluation on this homepage has fewer mutations and is a DOS program. The database contains information on the mutagen, dose, spontaneous and induced mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, cell type, citation, and other items. In addition, information regarding the cause and effect of mutations affecting splicing is given. Routines have been developed for the analysis of single base substitutions. The p53 database contains information on nearly 5,867 mutations found in the human p53 gene. The database itself has been updated in April of 1997. The database contains information on the cancer type, loss of heterozygosity, base position, amino acid position, amino acid change, local DNA sequence,citation, and other items. Routines have been developed for the analysis of single base substitutions. The Transgenic lacZ database contains information on 405 mutations found in vivo in the transgenic lacZ gene. It has last been updated in January of 1998. It provides information on the mutagen, dose, organ, mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, citation, and other items. The Transgenic lacI database contains information on over 1700 mutations found in vivo in the transgenic lacI gene and on nearly 8000 mutations in the lacI gene in native E. coli. The database was updated in January 1998. The database contains information on the mutagen, dose, organ, mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, citation, and other items. Routines have been developed for the analysis of single base substitutions for each of the databases. The software runs only on IBM-compatible PCs.

Proper citation: Neal's DNA Mutation Site (RRID:SCR_002947) Copy   

•   Source: SciCrunch Registry

http://www.patika.org/

The human pathway database which contains different biological entities and reactions and software tools for analysis. PATIKA Database integrates data from several sources, including Entrez Gene, UniProt, PubChem, GO, IntAct, HPRD, and Reactome. Users can query and access this data using the PATIKAweb query interface. Users can also save their results in XML or export to common picture formats. The BioPAX and SBML exporters can be used as part of this Web service.

Proper citation: Pathway Analysis Tool for Integration and Knowledge Acquisition (RRID:SCR_002100) Copy   

•   Source: SciCrunch Registry

http://circadb.hogeneschlab.org/

Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans.

Proper citation: CircaDB (RRID:SCR_018078) Copy   

•   Source: SciCrunch Registry

https://www.humancellatlas.org

Software tool as a catalog of comprehensive reference of human cells based on their stable properties, transient features, locations and abundances. Map to show the relationships among its elements. Open data international collaborative project involving diverse scientific communities to provide a framework for understanding cellular dysregulation in human disease.

Proper citation: Human Cell Atlas (RRID:SCR_016530) Copy   

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http://www.broadcvdi.org/

Platform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data.

Proper citation: Cardiovascular Disease Knowledge Portal (RRID:SCR_016536) Copy   

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https://commonfund.nih.gov/hubmap

Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows.

Proper citation: The Human BioMolecular Atlas Program (RRID:SCR_016922) Copy   

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https://kpmp.org

Project to ethically obtain and evaluate human kidney biopsies from participants with Acute Kidney Injury (AKI) or Chronic Kidney Disease (CKD), create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways, and targets for novel therapies. Used to develop the next generation of software tools to visualize and understand the various components of kidney diseases and to optimize data collection. Multi site collaboration comprised of patients, clinicians, and investigators from across the United States.

Proper citation: Kidney Precision Medicine Project (RRID:SCR_016920) Copy   

•   Source: SciCrunch Registry

https://github.com/zuoxinian/CCS

Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies.

Proper citation: Connectome Computation System (RRID:SCR_017342) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/homology.shtml

MGI contains homology information for mouse, human, rat, chimp, dog and other species. Complete set of human, chimpanzee, rhesus macaque, dog, cattle, rat, chicken, western clawed frog and zebrafish Homology Classes for mouse genes. Report includes Chromosome and EntrezGene and OMIM IDs. Report of Human and Mouse Homology Classes sorted by HomoloGene ID includes associated nucleotide and protein sequences, Chromosome and OMIM IDs. Report of Human and Mouse Homology with phenotype annotations. Several additional MGI reports are available, including those for Gene Ontology, Phenotypes and Nomenclature.

Proper citation: Vertebrate Homology (RRID:SCR_017517) Copy   

•   Source: SciCrunch Registry