Curator Dashboard

One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. The T-profiler tool hosted on this website uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can submit their microarray data for analysis by clicking on one of the two organism-specific tabs above. Platform: Online tool

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• SciCrunch
• 17 years ago - by Anonymous

Software as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation.

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• RRID-Legacy
• 9 years ago - by Anonymous

Biorepository resource with mission of proper collection, handling, processing and storage of irreplaceable biological specimens to support spectrum of related basic science, translational and clinical research. Provides expertise in nucleic acid extractions, quantification, aliquoting and quality assurance; liquid specimen centrifugation, processing and aliquoting; histological tissue processing, immunohistochemistry and tissue microarray microtomy; pathologist consultation services. Tissue Core operations are divided into four distinct pillars of service that work collaboratively to ensure specimen quality is maintained from procurement to preservation.

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• SciCrunch
• 14 years ago - by Anonymous

MiMi Web gives you an easy to use interface to a rich NCIBI data repository for conducting your systems biology analyses. This repository includes the MiMI database, PubMed resources updated nightly, and text mined from biomedical research literature. The MiMI database comprehensively includes protein interaction information that has been integrated and merged from diverse protein interaction databases and other biological sources. With MiMI, you get one point of entry for querying, exploring, and analyzing all these data. MiMI provides access to the knowledge and data merged and integrated from numerous protein interactions databases and augments this information from many other biological sources. MiMI merges data from these sources with deep integration into its single database with one point of entry for querying, exploring, and analyzing all these data. MiMI allows you to query all data, whether corroborative or contradictory, and specify which sources to utilize. MiMI displays results of your queries in easy-to-browse interfaces and provides you with workspaces to explore and analyze the results. Among these workspaces is an interactive network of protein-protein interactions displayed in Cytoscape and accessed through MiMI via a MiMI Cytoscape plug-in. MiMI gives you access to more information than you can get from any one protein interaction source such as: * Vetted data on genes, attributes, interactions, literature citations, compounds, and annotated text extracts through natural language processing (NLP) * Linkouts to integrated NCIBI tools to: analyze overrepresented MeSH terms for genes of interest, read additional NLP-mined text passages, and explore interactive graphics of networks of interactions * Linkouts to PubMed and NCIBI's MiSearch interface to PubMed for better relevance rankings * Querying by keywords, genes, lists or interactions * Provenance tracking * Quick views of missing information across databases. Data Sources include: BIND, BioGRID, CCSB at Harvard, cPath, DIP, GO (Gene Ontology), HPRD, IntAct, InterPro, IPI, KEGG, Max Delbreuck Center, MiBLAST, NCBI Gene, Organelle DB, OrthoMCL DB, PFam, ProtoNet, PubMed, PubMed NLP Mining, Reactome, MINT, and Finley Lab. The data integration service is supplied under the conditions of the original data sources and the specific terms of use for MiMI. Access to this website is provided free of charge. The MiMI data is queryable through a web services api. The MiMI data is available in PSI-MITAB Format. These files represent a subset of the data available in MiMI. Only UniProt and RefSeq identifiers are included for each interactor, pathways and metabolomics data is not included, and provenance is not included for each interaction. If you need access to the full MiMI dataset please send an email to mimi-help (at) umich.edu.

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• SciCrunch
• 17 years ago - by Anonymous

Center for Animal Resources and Development is an international repository and distribution center for production, cryopreservation, and supply of genetically engineered mice.Provides a summary of institutions, organizations, and individuals contributing mouse resource information to the IMSR database.

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• SciCrunch
• 9 years ago - submitted by Mason Pairish

Flow cytometry analyzer system for individual labs that performs up to 100 different tests in single reaction volume and can use either magnetic beads or plain polystyrene beads.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

A manually curated resource of signal transduction pathways in humans. All pathways are freely available for download in BioPAX level 3.0, PSI-MI version 2.5 and SBML version 2.1 formats. The slim pathway models representing only core reactions in each pathway are available at NetSlim. All the NetPath pathway models are also submitted to WikiPathways., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

Software to help users of targeted high throughput genomic sequencing data to accurately detect copy number variants (CNVs). Framework for running and evaluating other copy number detection tools.Used for evaluating and improving performance of CNV detection in exome and targeted sequencing data.

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• SciCrunch
• 8 years ago - by Anonymous

RARAF is dedicated to providing user-friendly radiation sources and bio-labs for research in biology, radiation biology, and radiation physics.

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• SciCrunch
• 14 years ago - by Anonymous

Assessment test that measures both a participant''s attention and inhibitory control. The test requires the participant to focus on a given stimulus while inhibiting attention to stimuli (fish for ages 3-7 or arrows for ages 8-85) flanking it. Sometimes the middle stimulus is pointing in the same direction as the flankers (congruent) and sometimes in the opposite direction (incongruent). Scoring is based on a combination of accuracy and reaction time, and the test takes approximately 3 minutes to administer. This test is recommended for ages 3-85.

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• SciCrunch
• 13 years ago - by Anonymous

Microbial stock center. Collaborative platform for the pan-European research infrastructure for microbial resources. Provides access to microorganisms, their derivatives, associated data and services for research, development and application.

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• RRID-Legacy
• 8 years ago - submitted by Anita Bandrowski

Core offers mass spectral proteomic analysis. Assists with qualitative and quantitative characterization of proteins in biological matrices such as plasma/serum, tissue, cell lines and other biological material to gain understanding of physiological pathways, molecular interactions and regulatory signaling.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Assessment test that measures the perceived intensity of quinine (a bitter tastant) and salt administered in liquid solutions. The tastants are applied to the tip of the tongue as well as the whole mouth and rated on a generalized labeled magnitude scale (ranging from no sensation at all to strongest sensation of any kind). The test is recommended for administration to participants ages 12-85 and takes approximately six minutes to administer.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool used in visual object recognition software research to analyze images for scenes, objects, faces, and other content. A convolutional neural network for large scale image recognition. Weights for the VGG-16 model architecture trained on an image database Imagenet.

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• RRID-Legacy
• 8 years ago - by Anonymous

Interdisciplinary research, teaching and service facility equipped with scanning and transmission electron microscopes, an atomic force microscope, and the ancillary instruments. Provides microscopic imaging, X-ray analysis, and specimen preparation services for biological, pharmaceutical, and materials scientific research. The MMRL consist of four individual microscope rooms, the Histology laboratory, and sample preparation and chemical storage areas.Graduate- and upper-undergraduate-level training is offered in the operation of electron microscopes, sample preparation, and thick/thin sectioning. Currently, MMRL houses transmission electron, scanning electron microscopes, and atomic force microscope. The microscopes available for use include: - Hitachi H-7500 transmission electron microscope - Hitachi S-3400N variable pressure scanning electron microscope with x-ray analysis and digital imaging - Hitachi S-2460N scanning electron microscope with x-ray analysis In addition, the following items are also available for MMRL users: - Three Leica 2030 rotary paraffin microtome - Two LKB ultramicrotomes - A LKB 7800 glass knife maker - Leica Reichert Ultratrim - Denton critical point dryer - Denton sputter coaters (Desk II and Desk IV) - Denton Vacuum evaporators (DV-502A) - Liquid nitrogen dewars (various sizes) - A Leica stereo dissecting microscope - A Tissue-TeK VIP Tissue Processor - A Tissue-TeK II Embedding Center

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• SciCrunch
• 14 years ago - by Anonymous

A non-profit consortium of Boston academic medical centers and universities (and growing) to accelerate the healthcare innovation cycle by fostering interdisciplinary, inter-institutional collaboration among experts in translational research, medicine, science, engineering, healthcare implementation and entrepreneurship in concert with industry, foundations and government to rapidly improve patient care. It concentrates on early stage, high-risk ideas, projects and supports them through to a commercial exit from academia. It provides innovators with resources to explore, develop and implement novel technological solutions for today's most urgent healthcare problems. CIMIT is dedicated to helping develop medical technology that will help both military and civilian patients.

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• Consortia-pedia, a FasterCures Project
• 13 years ago - by Anonymous

A data-driven educational resource pertaining to opioid addiction and how it is likely to happen with prescription drugs. It also includes information pertaining to state-by-state legislation. Insufficient information. Waiting for PMID or manuscript info

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• D3R
• 8 years ago - by Anonymous

Core offers statistical analysis of genomics data. Provides suite of standardized analysis pipelines for common data types like RNA-seq, ATAC-seq, and genome assembly. For more complex datasets, such as single-cell genomics, provides tailored analysis solutions. Core team assists with all project stages, from experimental design to publication support and data management. GDSC hosts several multi-day bioinformatics workshops designed to introduce fundamental concepts for analysis of genomics data.

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• RRID
• 2 years ago - by Anonymous

Research informatics and analytics platform for the IMI OncoTrack consortium.

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• Consortia-pedia, a FasterCures Project
• 13 years ago - by Anonymous

Python library for materials analysis codes. Defines core object representations for structures and molecules.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth