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http://www.chori.org/Services/Elemental_Analysis_Facility/elemental_analysis.html

Core provides sample preparation, metal extraction, dissolved solids measurement, analytic consultation, and technical writing assistance) in support of wide range of clinical and biomedical research projects.Instruments include Agilent 5100 SVDV Inductively-Coupled Plasma-Optical Emission Spectrometer, SPS3 Robotic Autosampler,MARS5 Microwave Sample Digestion Oven,ICPExpert Advanced Workstation.Analytic Capabilities:Simultaneous, multi-element quantitation over wide dynamic range;Broad elemental detection capability with high precision and sensitivity;Compatible with range of clinical, nutritional, basic research, and pharmaceutical samples;Tolerant of high total dissolved solids and complex matrix components;NIST-traceable calibrants, standards, and other QA/QC controls included in analyses.

Proper citation: Children's Hospital Oakland Research Institute Elemental Analysis Core Facility (RRID:SCR_017927) Copy   

•   Source: SciCrunch Registry

https://www.purdue.edu/discoverypark/bioinformatics/

Core to facilitate, amplify, and accelerate biological research and discovery through application of bioinformatics. Provides bioinformatic analysis services for Next Generation Sequencing (NGS) data.

Proper citation: Purdue University Bioinformatics Core Facility (RRID:SCR_017896) Copy   

•   Source: SciCrunch Registry

https://ki.mit.edu/sbc/bioinformatics

Core provides support, assistance and training in wide range of bioinformatics topics. Maintains high-performance computing resource offering many bioinformatics applications, substantial processing power and secure storage. Provides support for desktop computing and poster printing. Services include Data Analysis, Software Support (access to proprietary bioinformatics resources Ingenuity Pathway Analysis and GeneGO MetaCore, Training sessions covering various bioinformatics topics, Linux compute cluster, data storage.

Proper citation: Massachusetts Institute of Technology Koch Institute Bioinformatics and Computing Core Facility (RRID:SCR_017894) Copy   

•   Source: SciCrunch Registry

https://www.brown.edu/research/projects/superfund/cores/core-d

Core provides equipment and technical expertise for evaluation of molecular and morphological changes in cells, tissues, and organs following exposure to complex environmental contaminants. Provides equipment, including automated tissue processor, paraffin embedding center, two automated microtomes, cryostat, vibratome for soft-tissue sectioning, multiheaded light microscope with projection capabilities, system for laser capture microdissection, and slide scanner with analysis software for identification and quantification of morphological structures.Offers expertise in histopathological and immunocytochemial methods, including fixation, dehydration, embedding, sectioning, histological staining, immunolabeling, high-resolution imaging, and quantitative image analysis. Services in sample preparation, offers assistance in imaging and image analysis and provides consultation for ongoing or future research projects, training program for students and investigators who use centrally available equipment.

Proper citation: Brown University Molecular Pathology Core Facility (RRID:SCR_017898) Copy   

•   Source: SciCrunch Registry

http://ssom.luc.edu/genomics/

Core provides next-generation sequencing capabilities using Illumina MiSeq. Helps with experimental design, quality control analysis, library preparation, and data analysis. MiSeq desktop sequencer allows to access applications such as targeted gene sequencing, metagenomics, small genome sequencing, targeted gene expression, amplicon sequencing, and HLA typing.MiSeq is capable of delivering up to 15 Gb of output with 25 million sequencing reads and 2x300 basepair read lengths.

Proper citation: Loyola University Genomics Core Facility (RRID:SCR_017857) Copy   

•   Source: SciCrunch Registry

http://nic.ucsf.edu/

Core provides light microscopy instrumentation, microscopy training and education and can provide assistance with experiment design, data acquisition, and image analysis. Provides training for users.Services include:Fluorescence imaging (up to 5 colors) Brightfield, phase contrast, and DIC imaging;High speed imaging (over 100 frames per second);Automated imaging, including multiwell plates;Super-resolution imaging (SIM / STORM / PALM);Single molecule imaging;3D confocal imaging;Gigapixel image stitching;Live cell time lapse imaging;Photoactivation and photobleaching;Light sheet imaging of cleared tissues.

Proper citation: University of California at San Francisco, Nikon Imaging Center Core Facility (RRID:SCR_017862) Copy   

•   Source: SciCrunch Registry

http://health.usf.edu/medicine/corefacilities/flowcytometry

Core is equipped with two benchtop analyzers from BD Immunocytometry Systems (3 laser/8 color BD Canto II and 4 laser/17 color BD LSR II). These instruments support large variety of applications, including multicolor cell phenotyping, apoptosis, cell cycle and bead arrays. After orientation and training, equipment is available for use directly by investigators. Alternatively experiments can be run and analyzed by Core Facility staff.For sorting purposes facility is equipped with high speed BD FacsAria IIu sorter (4 laser/11 colors), as well as magnetic sorter (AutoMacs Pro) from Miltenyi Biotech. FacsAria IIu is enclosed in Baker Bioprotect III to support sort of biohazardous agents level 1 and 2.

Proper citation: South Florida University College of Medicine Fred Wright Jr Flow Cytometry Core Facility (RRID:SCR_017901) Copy   

•   Source: SciCrunch Registry

https://www.biotech.iastate.edu/metabolomics/

Core facility that conducts fee for service mass spectrometry-based non-targeted and targeted metabolomic studies. The facility serves and partners with both on- and off-campus clients.

Proper citation: Iowa State University W.M. Keck Metabolomics Research Laboratory Core Facility (RRID:SCR_017911) Copy   

•   Source: SciCrunch Registry

http://mhpl.facilities.northwestern.edu/

Core provides assistance with standard and customized research specific histology services for variety of tissues (i.e., mouse, rat, sheep, pig, zebrafish, etc.) for routine histology, and immunohistochemistry. Provides Pathologist consultation to help develop strategies to elucidate phenotypes and gain mechanistic insight regarding biologic actions of targeted molecule(s) or toxicity of exogenously administered substances.Provides training opportunities for learning histology techniques and phenotyping analysis.Services include Immunohistochemistry (IHC) . Using tyramide signal amplification (TSA) and ABC methods (automated), with DAB chromogenic substrate; Immunofluorescence (IF)- Single and multiple staining;TUNEL assay; Freezing and embedding of tissues for histology;Frozen sections;Paraffin block processing and Paraffin sections;Hematoxylin and Eosin staining of sections;Specialized histochemical staining of sections (e.g. Trichrome, PAS, Luxol fast blue, Cresyl violet, and many other stains);Dissection and tissue collection;Histopathology (slide interpretation);Histopathology toxicity evaluation;Training in necropsy techniques including perfusion of mice and special tissue dissection;Assistance with development of animal pathology protocols.

Proper citation: Northwestern University Mouse Histology and Phenotyping Laboratory Core Facility (RRID:SCR_017870) Copy   

•   Source: SciCrunch Registry

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

Enables comparative phenotype analysis, searches for human disease models, and hypothesis generation by providing access to spontaneous, induced, and genetically engineered mutations and their strain-specific phenotypes.

Proper citation: Phenotypes and Mutant Alleles (RRID:SCR_017523) Copy   

•   Source: SciCrunch Registry

https://www.sourcebioscience.com/products/life-sciences-research/clones/rnai-resources/c-elegans-rnai-collection-ahringer/

C. elegans RNAi feeding library distributed by Source BioScience Ltd. Designed for genome wide study of gene function in C. elegans through loss of function studies.

Proper citation: C. elegans RNAi Collection (Ahringer) (RRID:SCR_017064) Copy   

•   Source: SciCrunch Registry

https://ualr.edu/bioinformatics/midsouth-bioinformatics-center/

Core provides bioinformatics consulting, training, technical assistance, and access to computational infrastructure for faculty, students, and researchers in region with their bioscience computational needs. Offers private sessions, workshops and training on specialty topics. Computing resources including software, computing cluster, technical advice.

Proper citation: University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility (RRID:SCR_017168) Copy   

•   Source: SciCrunch Registry

https://git.io/vAeKZ

It is non-graphical user interface in MATLAB which relies on keyboard callback functions. Used for analyzing big data sets.

Proper citation: ROIs selection with a non-graphical user interface (RRID:SCR_016352) Copy   

•   Source: SciCrunch Registry

http://www.kcl.ac.uk/ioppn/depts/neuroimaging/research/imaginganalysis/Software/PIPR.aspx

Software toolbox designed to provide machine learning methods for pre-processed imaging data allowing for two (or more) class classification in the context of drug development. The Toolbox includes implementations of Gaussian Process Classification, Support Vector Machines, Ordinal Regression and Sparse Multinomial Logistic Regression for fMRI, Structural and ASL imaging data.

Proper citation: Pharmacological Imaging and Pattern Recognition toolbox (RRID:SCR_003874) Copy   

•   Source: SciCrunch Registry

http://www.blast2go.com/b2ghome

An ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher''''s Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: Blast2GO (RRID:SCR_005828) Copy   

•   Source: SciCrunch Registry

http://www.bcgsc.ca/platform/bioinfo/software/alea

A computational software toolbox for allele-specific (AS) epigenomics analysis. It incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. It provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project) to reconstruct diploid in-silico genomes for human or hybrid mice under study. Then, for each accompanying ChIP-seq or RNA-seq dataset, it generates two Wiggle track format (WIG) files from short reads aligned differentially to each haplotype.

Proper citation: ALEA (RRID:SCR_006417) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

Proper citation: Bioconductor (RRID:SCR_006442) Copy   

•   Source: SciCrunch Registry

http://www.cgat.org/~andreas/documentation/cgat/cgat.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 3, 2023. A collection of tools for the computational genomicist written in the python language to assist in the analysis of genome scale data from a range of standard file formats. The toolkit enables filtering, comparison, conversion, summarization and annotation of genomic intervals, gene sets and sequences. The tools can both be run from the Unix command line and installed into visual workflow builders, such as Galaxy. Please note that the tools are part of a larger code base also including genomics and NGS pipelines. Everyone who uses parts of the CGAT code collection is encouraged to contribute. Contributions can take many forms: bugreports, bugfixes, new scripts and pipelines, documentation, tests, etc. All contributions are welcome.

Proper citation: Computational Genomics Analysis Tools (RRID:SCR_006390) Copy   

•   Source: SciCrunch Registry

http://www.gaworkshop.org/

The Genetic Analysis Workshops (GAWs) are a collaborative effort among genetic epidemiologists to evaluate and compare statistical genetic methods. For each GAW, topics are chosen that are relevant to current analytical problems in genetic epidemiology, and sets of real or computer-simulated data are distributed to investigators worldwide. Results of analyses are discussed and compared at meetings held in even-numbered years. The GAWs began in 1982 were initially motivated by the development and publication of several new algorithms for statistical genetic analysis, as well as by reports in the literature in which different investigators, using different methods of analysis, had reached contradictory conclusions. The impetus was initially to determine the numerical accuracy of the algorithms, to examine the robustness of the methodologies to violations of assumptions, and finally, to compare the range of conclusions that could be drawn from a single set of data. The Workshops have evolved to include consideration of problems related to analyses of specific complex traits, but the focus has always been on analytical methods. The Workshops provide an opportunity for participants to interact in addressing methodological issues, to test novel methods on the same well-characterized data sets, to compare results and interpretations, and to discuss current problems in genetic analysis. The Workshop discussions are a forum for investigators who are evolving new methods of analysis as well as for those who wish to gain further experience with existing methods. The success of the Workshops is due at least in part to the focus on specific problems and data sets, the informality of sessions, and the requirement that everyone who attends must have made a contribution. Topics are chosen and a small group of organizers is selected by the GAW Advisory Committee. Data sets are assembled, and six or seven months before each GAW, a memo is sent to individuals on the GAW mailing list announcing the availability of the GAW data. Included with the memo is a short description of the data sets and a form for requesting data. The form contains a statement to be signed by any investigator requesting the data, acknowledging that the data are confidential and agreeing not to use them for any purpose other than the Genetic Analysis Workshop without written permission from the data provider(s). Data are distributed by the ftp or CD-ROM or, most recently, on the web, together with a more complete written description of the data sets. Investigators who wish to participate in GAW submit written contributions approximately 6-8 weeks before the Workshop. The GAW Advisory Committee reviews contributions for relevance to the GAW topics. Contributions are assembled and distributed to all participants approximately two weeks before the Workshop. Participation in the GAWs is limited to investigators who (1) submit results of their analyses for presentation at the Workshop, or (2) are data providers, invited speakers or discussants, or Workshop organizers. GAWs are held just before the meetings of the American Society of Human Genetics or the International Genetic Epidemiology Society, at a meeting site nearby. We choose a location that will encourage interaction among participants and permit an intense period of concentrated work. The proceedings of each GAW are published. Proceedings from GAW16 were published in part by Genetic Epidemiology 33(Suppl 1), S1-S110 (2009) and in part by Biomed Central (BMC Proceedings, Volume 3, Supplement 7, 2009). Sponsors: GAW is funded by the Southwest Foundation for Biomedical Research.

Proper citation: Genetic Analysis Workshop (RRID:SCR_008350) Copy   

•   Source: SciCrunch Registry

http://www.nmrfam.wisc.edu/

Provides access and developes NMR technology to advance range of applications and improves the efficiency, rigor and reproducibility of NMR data acquisition and analysis. Houses NMR spectrometers equipped with state-of-the-art probe technology and protocols to support acquisition of high-quality data. Spectrometers range from 500 MHz to 1100 MHz. Service is tailored to the needs of individual users and projects. Provides training and advice on experimental design, best practices for data acquisition, and data analysis. Experienced staff support users with training opportunities including workshops, video tutorials and protocols.

Proper citation: National Magnetic Resonance Facility at Madison (RRID:SCR_001449) Copy   

•   Source: SciCrunch Registry