Curator Dashboard

Provides computational and storage tools needed to efficiently and effectively process data. High performance computing cluster housing compute cores, graphical processing unit cores, and directly attached high speed storage.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

The Biocontainment Core Facility supports researchers whose experiments require a Biosafety Level 2 enhanced (BL2+) containment level. The Biocontainment Core adheres to Biosafety Level 3 (BL3) practices. Protective apparel, equipment, and other materials are provided by the core. Two core facilities are available: one is located at the Jimmy Fund building at Dana Farber; the second at The Center for Life Science. Authorized core users may have access to both facilities. Use of the facility is limited to researchers who receive training in BL3 procedures and comply with authorized user requirements. Training is provided by the Biosafety Officer, Core Manager, and authorized users.

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• SciCrunch
• 13 years ago - by Anonymous

A professional, social network and publication database geared to researchers where the latest field specific publications can be read, publications with other specialists can be discussed, and collaboration with colleagues is facilitated. They provide researchers with access to around 40 million abstracts and tens of thousands of Full texts, uploaded by the authors themselves. Researchers can search through 7 of the largest databases simultaneously, such as PubMed, IEEE & CiteSeer.

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• SciCrunch
• 16 years ago - by Anonymous

Core facility that provides the following services: Autoantibody determination, HLA typing and Genotyping for the best recognized susceptibility loci (INS, PTPN22, CTLA4).

The Human Sample Procurement Core will support translational research endeavors within the JDRF Center by providing the Center''s laboratories access to well-characterized blood samples from patients with diabetes at different stages of the disease. This availability will greatly facilitate the translational exploration of concepts and targets emerging from the basic research projects. Individuals with T1D (recent onset, long-standing Type-1 diabetes) and matched controls (healthy or T2D) will be recruited from the patient population at the Joslin Diabetes Center and neighboring institutions. The Core will perform and record a basic characterization of patients and their samples. This analysis will include a thorough evaluation of clinical characteristics from a diabetes and autoimmune standpoint, and an immunogenetic workup (outsourced to Joslin or other cores): autoantibody determination, HLA typing and genotyping for the best recognized susceptibility loci (INS, PTPN22, CTLA4). A relational database will be adapted to record all patient information, copies of which will be provided in a de-identified manner to the investigators.

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• SciCrunch
• 13 years ago - by Anonymous

Provides full service precision machine shop specializing in design and construction of custom equipment for scientific research and teaching.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core facility that provides the following services: 96-well plasmid preparation service.

The Center for Computational and Integrative Biology (CCIB) Automation Core provides the greater Partners research community with high-throughput automation services as well as special automation project design and implementation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

THIS IS A TEST

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• 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.

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• 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.

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• 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.

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• 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
• 4 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