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• Resource
• NIF
• 4 years ago - by Anonymous

The Histology and Cellular Localization Core provides training and research support in microscopy, anatomy and histology of chemosensory systems. Core personnel work with Monell researchers to develop and optimize in-house procedures and to establish cutting-edge techniques in histology and cell anatomy. The Core provides centralized services such as tissue sectioning and in situ probe preparation. The Core facility is equipped with cryostats, fluorescence microscopes, confocal microscopes, and a two-photon microscope.

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• SciCrunch
• 13 years ago - by Anonymous

Offers genomic technologies to academic laboratories and biotechnology companies.Application portfolio includes Whole genome (re)sequencing, including the identification of variants (SNVs, mutations, indels, CNVs);Targeted sequencing, for instance exomes; Transcriptome analyses (RNA-Seq, small RNA-Seq, microarrays), including in single cells (single-cell 3 RNA-seq); Determination of chromatin structure and dynamics (ChIP-Seq, FAIRE-Seq, Hi-C); Epigenetic analyses (ChIP-Seq, RRBS, Bisulphite-Seq);Genotyping (RAD-Seq, GBS, microarrays).

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

A database of new exon boundaries induced by pathogenic mutations in human disease genes.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Core provides services, access to instruments, and training to facilitate production of animal tissue samples for morphological and molecular analyses. Supports multiplex immunofluorescence staining, RNA in situ hybridization (ISH), and imaging analysis. Services include tissue preparation, processing, and sectioning, as well as histochemistry and immunohistochemistry of fresh, frozen, and fixed animal tissues, can optimize and validate commercial or proprietary antibodies for chromogenic or fluorescence-based immunohistochemistry including seven-color multiplexing.Provides access to database listing antibodies that have been tested in lab to date and are currently in stock.Offers basic imaging resources and digital whole-slide scanning of stained tissue sections, which allows researchers to view their slides online at their convenience.Researchers can also rent our self-service instruments. These include embedding station, microtome, cryostat, and vibratome. Provides access to brightfield and fluorescence upright and dissecting microscopes,laser capture microdissection scope, and high-throughput multispectral imaging system.To reserve time on instrument, faculty, staff, and investigators must be registered in iLab.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

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.

• Resource
• dkNET
• 14 years ago - by Anonymous

Software R package for nonnegative matrix factorization. Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms.

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• RRID
• 4 years ago - by Anonymous

A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity.

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• SciCrunch
• 15 years ago - by Anonymous

Repository allows all researchers at Birkbeck to upload data, and get DOI.Data in the Birkbeck Data Repository is stored on Arkivum server.This is a very secure storage space, which will allow our data to remain unchanged and accessible for many years after it is deposited.

• Resource
• SciCrunch
• 4 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) and the program that calculates DSSP entries from PDB entries. DSSP is distributed on a basis of trust and instructions are available on the site. * Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead: dsspcmbi source.pdb destination.dssp > messages.txt * Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code. * FTP access to the DSSP files resides at the CMBI: ftp.cmbi.kun.nl/pub/molbio/data/dssp or ftp://ftp.ebi.ac.uk/pub/databases/dssp/. If you have problems downloading the DSSP files, it is likely that your FTP program is not able to handle tens of thousands of files in one directory. In this case, install a proper FTP program, for example NCFTP. However, it is recommended that you download DSSP files with the rsync command.

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• SciCrunch
• 17 years ago - by Anonymous

Software R package to calculate various intraclass correlation coefficients. Used to quantify inter-rater and intra-rater reliability.

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• RRID
• 4 years ago - by Anonymous

Database of apo and holo structure pairs of proteins before and after binding. Various protein functions have been shown directly associated with conformational transitions triggered by binding other molecules. Tertiary structures determined in the unbound and bound state are usually named apo and holo structures, respectively. AH-DB is the largest database of apo-holo structure pairs and provides a sophisticated interface to search and view the collected data. It contains 746314 apo-holo pairs of 3638 proteins from 702 organisms.

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• SciCrunch
• 16 years ago - by Anonymous

Core provides and supports gold standard of high quality mouse, rat and zebrafish modeling services for VAI investigators, collaborators and greater research community.Facility includes high containment barrier. All procedures are conducted according to the National Institutes of Health Guide for the Care and Use of Laboratory Animals. The Institute is accredited at the highest standard of care through the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) International.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool

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• SciCrunch
• 15 years ago - by Anonymous

Software application as machine learning model for image colorization.

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• RRID
• 3 years ago - by Anonymous

This is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins. The nearly completed sets of MIPs have been identified from the completed genome sequence of organisms available at NCBI. The structural models of MIP proteins were created by defined protocol. The database aims to provide key information of MIPs in particular based on sequence as well as structures. This will further help to decipher the function of uncharacterized MIPs. For each MIP entry, this database contains information about the source, gene structure, sequence features, substitutions in the conserved NPA motifs, structural model, the residues forming the selectivity filter and channel radius profile. For selected set of MIPs, it is possible to derive structure-based sequence alignment and evolutionary relationship. Sequences and structures of selected MIPs can be downloaded from MIPModDB database.

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• SciCrunch
• 15 years ago - by Anonymous

Software R package to implement model selection and multimodel inference based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc) from various model object classes. Package implements classic model averaging for given parameter of interest or predicted values, as well as shrinkage version of model averaging parameter estimates or effect sizes. Package includes diagnostics and goodness-of-fit statistics for certain model types including those of 'unmarkedFit' classes estimating demographic parameters after accounting for imperfect detection probabilities.

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• RRID
• 3 years ago - by Anonymous

This is a topical portal dedicated to the communication of news, science, and information of interest to the brain mapping community, and to sharing and promoting the science of brain mapping. The purpose and goal of brain mapping is to advance the understanding of the relationship between structure and function in the human brain. Scientists in this field seek to gain knowledge of the physical processes that underly human sensation, attention, awareness and cognition. These results are immediately applicable to surgical intervention, to the design of medical interventions and to the treatment of psychological and psychiatric disorders.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2019. Analyzing protein structure projection on exon-intron structure of corresponding gene through years led to several fundamental conclusions about structural and functional organization of the protein. According to these results we decided to map the protein functional sites. So we created the database SitEx that keep the information about this mapping and included the BLAST search and 3D similar structure search using PDB3DScan for the polypeptide encoded by one exon, participating in organizing the functional site. This will help: # to study the positions of the functional sites in exon structure; # to make the complex analysis of the protein function; # to exposure the exons that took part in exon shuffling and came from bacterial genomes; # to study the peculiarities of coding the polypeptide structures. Currently, SitEx contains information about 9994 functional sites presented in 2021 proteins described in proteomes of 17 organisms.

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• SciCrunch
• 15 years ago - by Anonymous

A set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina''''s Solexa, Roche''''s 454 and Applied Biosystems'''' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format.

• Resource
• SciCrunch
• 13 years ago - by Anonymous