Curator Dashboard

Matlab toolbox for the analysis of functional neuroimages (PET, fMRI). The toolbox contains a number of models: FIR-filter, Lange-Zeger, K-means clustering among others, visualizations and reading of neuroimaging files.

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• SciCrunch
• 17 years ago - by Anonymous

A brain bank which collects postmortem human brains to meet the needs of neuroscientists investigating specific psychiatric and neurological disorders. NYBB disburses tissue samples to investigating clinicians or scientists whose research has been approved by their Institutional Review Board. The tasks of the NYBB include: collection and processing of human postmortem brain samples for research; neuropathological evaluation and diagnosis; storage and computerized inventory of brain samples; and distribution of brain samples to investigating clinicians and scientists. Brains from individuals without neurological or psychiatric disorders are used as normal controls.

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• SciCrunch
• 16 years ago - by Anonymous

BOA is an R/S-PLUS program for carrying out convergence diagnostics and statistical and graphical analysis of Monte Carlo sampling output. It can be used as an output processor for the BUGS software or for any other program which produces sampling output. BOA includes all of the analysis options found in CODA, plus a few others. It is designed to be faster, more efficient, and offer more flexible data management than CODA. BOA can be used at the command-line or with the supplied menu-driven interface. Either way, the program enables the user to focus on the analysis at hand rather than on the manipulation of data. Sponsors: This resource is supported by the University of Iowa. Keywords: Bayesian, Analysis, Program, Diagnostics, Statistical, Graphical, Software,

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. DMAPS database contains pre-computed multiple structure alignments for protein chains in the Protein Data Bank (PDB). Automated structure alignments have been generated for classified protein families using CE-MC algorithm. Alignments have been built only for those families with at least three members. Currently, multiple structure alignments are available for 3050 SCOP-, 3087 CATH-, 664 ENZYME- and 1707 CE-based families. Users will be able to retrieve multiple alignments for a given PDB chain classified by one of these criteria.

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• SciCrunch
• 17 years ago - by Anonymous

A database for phylogenetic classification for proteins encoded in complete genomes. Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. Please be aware that COGs hasn't been updated in many years and will not be.

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• SciCrunch
• 16 years ago - by Anonymous

Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical representations from Geno Ontology (GO) annotated interaction data maintained by The Grid. The following list describes some of the important characteristics of the Osprey Network Visualization System: * Portability ( cross platform availability ) o Osprey is available on almost all Platforms that support the latest Java Plugin * Tools for Biological Analysis o Osprey provides many features such as network filters, connectivity filters, advanced layouts, and dataset superimposing which are extremely useful to biologists who are interested in analyzing their data * Powerful Support Database o Integrated with Osprey is a powerful database of interactions and annotation, see section 8. The GRID ( The General Repository of Interaction Datasets ). * Ease of use o Osprey provides an extremely user friendly interface for working with interaction data * Online Database Add-on Ability o Osprey can be incorporated as a standard visualization tool with online databases such as The GRID * Support for figures o Osprey networks can be saved in SVG, PNG and JPG format so they can be used with image programs Sponsors: Development of Osprey was funded by a grant from the Canadian Institutes of Health Research.

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• SciCrunch
• 17 years ago - by Anonymous

The Yeast Microarray Global Viewer (yMGV) is an on-line database providing a synthetic view of the transcriptional expression profiles of yeast genes among most of the published expression datasets. yMGV displays a one-screen graphical representation of gene expression variations for each published genome-wide experiments, allowing a quick retrieval of experimental conditions having an effect upon expression of this gene. It can show expression data for orthologs of supported yeasts, and also provides tools to isolate groups of genes sharing similar transcription profiles in a defined subset of experiments. Additionally, yMGV provides a set of statistical tools allowing a critical assessment of the published data.

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• SciCrunch
• 17 years ago - by Anonymous

Annotea is a W3C LEAD (Live Early Adoption and Demonstration) project under Semantic Web Advanced Development (SWAD). Annotea enhances collaboration via shared metadata based Web annotations, bookmarks, and their combinations. By annotations we mean comments, notes, explanations, or other types of external remarks that can be attached to any Web document or a selected part of the document without actually needing to touch the document. When the user gets the document he or she can also load the annotations attached to it from a selected annotation server or several servers and see what his peer group thinks. Similarly shared bookmarks can be attached to Web documents to help organize them under different topics, to easily find them later, to help find related material and to collaboratively filter bookmarked material. Annotea is part of the Semantic Web efforts. It provides a RDF metadata based extendible framework for rich communication about Web pages while offering a simple annotation and bookmark user interface. The annotation metadata can be stored locally or in one or more annotation servers and presented to the user by a client capable of understanding this metadata and capable of interacting with an annotation server with the HTTP service protocol.

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• SciCrunch
• 17 years ago - by Anonymous

Public university in Reading, Berkshire, England. It was founded in 1892 as University College, Reading, a University of Oxford extension college.

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• SciCrunch
• 12 years ago - submitted by Stephen Larson

Database containing the DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented; the most up to date collation of sequence, gene, and other annotations from all databases (eg. Celera published, NCBI, Ensembl, RIKEN, UCSC) as well as unpublished data. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. The objective of this project is to generate a comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications. There are over 360 disease-associated genes or loci on chromosome 7. A major challenge ahead will be to represent chromosome alterations, variants, and polymorphisms and their related phenotypes (or lack thereof), in an accessible way. In addition to being a primary data source, this site serves as a weighing station for testing community ideas and information to produce highly curated data to be submitted to other databases such as NCBI, Ensembl, and UCSC. Therefore, any useful data submitted will be curated and shown in this database. All Chromosome 7 genomic clones (cosmids, BACs, YACs) listed in GBrowser and in other data tables are freely distributed.

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• SciCrunch
• 14 years ago - by Anonymous

Standard brain atlas of the honeybee presented as an interactive three-dimensional surface model with integrated neuron and neuronal tracts. The standard atlas was created as an average-shape atlas of 22 neuropils, calculated from 20 individual immunostained whole-mount bee brains. After correction for global size and positioning differences by repeatedly applying an intensity-based nonrigid registration algorithm, a sequence of average label images was created. The Honeybee, Apis mellifera has been studied extensively with respect to its sensory and neural capacities in navigation, communication, visual and olfactory learning and memory processing. The goal is to integrate the entirety of information into a Virtual Atlas of the Honeybee Brain. This common spatial reference map will potentiate the representation of structural and functional data obtained in different experiments and from different individuals.

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• SciCrunch
• 17 years ago - by Anonymous

A community website for Huntington''s Disease (HD) research that currently contains Y2H and Mass spectrometry protein-protein interaction data centered around the HD protein (huntingtin) and information on therapeutic studies in mouse. Also available are raw Human and Mouse Affymetrix Microarray data. The protein interaction data is from several sources, including interactions curated from the literature by ISB staff, experimentally determined interactions produced by Bob Hughes and colleagues at Prolexys (currently password protected), and interactions reported in a recent publication by Goehler et al from Eric Wanker''s lab. Content areas that may be covered by the site include the following: * Therapeutic studies in mouse, primarily drug screens. * HD mouse models with a focus on timelines of disease progression. * Antibodies used in HD research. * Microarray gene expression studies. * Genes and proteins relevant to HD research. This includes HD itself, the growing list of proteins thought to interact directly or indirectly with huntingtin (Htt), and other genes and proteins implicated in the disease process. * Molecular pathways thought to be involved in the disease process. * Timelines of disease for Mouse models

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• SciCrunch
• 13 years ago - by Anonymous

Randomized, multicenter, double blind, placebo controlled clinical trial of phytotherapy for benign prostate symptoms among men. The CAMUS trial will test Saw palmetto in about 369 men. Men who decide to be part of the CAMUS trial will be given one out of two possible treatments at random. One out of every two men would get an inactive placebo treatment. One out of every two men would get Saw palmetto pills. This kind of scientific study is the best way to find out if the plant extracts really work to prevent men with benign prostatic hyperplasia (BPH) from getting worse. During the study, men will not know which of the two treatments they are assigned to. They will be followed very closely by a study team every 12 weeks to see how they are doing. Men in the CAMUS trial will be studied over 72 weeks. Ten clinical centers will participate in the trial. They are located at: Columbia University, NY, NY; New York University, NY, NY; University of Texas Southwestern Medical Center, Dallas, Texas; University of Colorado, Denver, CO; Washington University, St. Louis, MO; Yale University, New Haven, CT; Queens University, Hamilton, Ontario, Canada; Northwestern University, Chicago, IL; University of Maryland, Baltimore, MD; University of California at San Francisco, San Francisco, CA.

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• dkNET
• 14 years ago - by Anonymous

Network of collaborative research centers that tested the effects of treatment with cyclosporine to treatment with mycophenalate mofetil combined with oral pulse dexamethasone in children and young adults with focal segemental glomerulosclerosis. Efficacy was assessed in terms of induction of remission of proteinuria after 52 weeks of treatment and sustained remission after 26 weeks off treatment. The clinical sites were State University of New York, Stony Brook; Montefiore Medical Center; Seattle Children''''s Medical Center; Medical City Dallas Hospital; and the University of North Carolina. The Cleveland Clinic is the data-coordinating center, and NephCure will fund ancillary studies.

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• dkNET
• 14 years ago - by Anonymous

A tool that can be used to predict caspase cleavage sites from human protein sequences.

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• SciCrunch
• 13 years ago - by Anonymous

The Dinucleotide Property Database is designed to collect and analyse thermodynamic, structural and other dinucleotide properties. The table presenting all the dinucleotide properties can be pruned and rearranged by different criteria. The database contains different export and analysis functions.

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• SciCrunch
• 17 years ago - by Anonymous

High-resolution electronic atlases for mouse strains c57bl/6j, a/j, and dba/2j in either coronal or horizontal section. About this Atlas: The anterior-posterior coordinates are taken from an excellent print atlas of a C57BL/6J brain by K. Franklin and G. Paxinos (The Mouse Brain in Stereotaxic Coordinates, Academic Press, San Diego, 1997, ISBN Number 0-12-26607-6; Library of Congress: QL937.F72). The abbreviations we have used to label the sections conform to those in the Franklin-Paxinos atlas. A C57BL/6J mouse brain may contain as many as 75 million neurons, 23 million glial cells, 7 million endothelial cells associated with blood vessels, and 3 to 4 million miscellaneous pial, ependymal, and choroid plexus cells (see data analysis in Williams, 2000). We have not yet counted total cell number in DBA/2J mice, but the counts are probably appreciably lower.The brain and sections were all processed as described in our methods section. The enlarged images have a pixel count of 1865 x 1400 and the resolution is 4.5 microns/pixel for the processed sections.Plans: In the next several years we hope to add several additional atlases of the same sort for other strains of mice. A horizontal C57BL/6J atlas and a DBA/2J coronal atlas were completed by Tony Capra, summer 2000, and additional atlases may be made over the next several years. As describe in the MBL Procedures Section is not hard to make your own strain-specific atlas from the high resolution images in the MBL.

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• SciCrunch
• 17 years ago - by Anonymous

Randomized clinical trial to determine the efficacy and safety of three treatments for benign prostatic hyperplasia (BPH): transurethral needle ablation (TUNA), transurethral microwave therapy (TUMT), and medical therapy with alfuzosin and finasteride. The study has been terminated. (Inability to recruit required sample size.)

• Resource
• dkNET
• 14 years ago - by Anonymous

Database of known enzyme structures that have been deposited in the Protein Data Bank (PDB). The enzyme structures are classified by their E.C. number of the ENZYME Data Bank. Browse the classification hierarchy or enter an EC number or search-string. There are currently 45,638 PDB-enzyme entries in the PDB (as at 23 February, 2013) involving 38,109 separate PDB files - some files having more than one E.C. number associated with them.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Neuropsychiatric Imaging Research Laboratory (NIRL) analyze magnetic resonance images to research numerous psychiatric disorders including depression, bipolar disorder, and post traumatic stress disorder. NIRL also develop new methods for MR image processing to improve quality and reliability of research in the field of neuroimaging. The laboratory computer resources include Sun MicroSystems SPARC workstations, Windows PCs, over 3 terabytes of online hard disk space, and a web server system. The lab has a site filtered anonymous ftp server system for data transfer. There are individual offices for visiting fellows and analysts for image processing as well as shared work-study rooms and conference facilities.

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• SciCrunch
• 17 years ago - by Anonymous