Curator Dashboard

Part of Department of Health program for collecting, analyzing, and publishing information on all cancer cases in Puerto Rico. Information collected is obtained through active search for cancer cases, in places where cancer patients are studied, diagnosed or treated.

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• RRID
• 3 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. An open source software tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by finding fusions directly and verifying them, differentiating it from all other existing tools by finding the candidate regions and searching for the fusions afterwards.

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• SciCrunch
• 13 years ago - by Anonymous

A large scale functional connectivity data mining software package which enables large-scale seed-based analysis and brain-behavior analysis. It can examine a large number of seed regions with minimal user input. ACA has a brain-behavior analysis component to delineate associations among imaging biomarkers and one or more behavioral variables.

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• SciCrunch
• 11 years ago - submitted by David Kennedy

Core provides services involved with the latest multiplexed immunoassays.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression.

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• SciCrunch
• 13 years ago - by Anonymous

Open source, platform-independent application for the visualization and analysis of complex, high-dimensional imaging data such as Diffusion Tensor Imaging (DTI) and High Angular Resolution Diffusion Imaging (HARDI). It has a plugin-based architecture which allows third parties to develop new plugins to extend the tool. Overview of the many features: * vIST/e is programmed in C++. It uses the Visualization Toolkit for visualization and pipelined data processing, as well as the cross-platform toolkit Qt Framework for an easy-to-use Graphical User Interface. * vIST/e introduces a powerful new plugin system, which allows for modular development with increased extensibility and stability. * Powerful GPU-based visualization techniques allow for smooth, real-time visualization of large data sets. Using custom ray tracing algorithms created with OpenGL, vIST/e can render DTI ellipsoids and HARDI spherical harmonics glyphs up to 4th order. The high frame rates offered by modern GPU technology allows for interactive exploration of this complex data. * Diffusion Tensor Imaging data can be visualized and interactively explored in a number of ways, including multiple cross-sections, volume rendering, and tensor glyphs. Derived scalar volumes, including various different anisotropy measures, can be computed and visualized. Data from other modalities, such as structural MRI, can be shown alongside the DTI data. * Various fiber tracking methods allow for fast and accurate reconstruction of fiber pathways. Interactively defined Regions of Interest (ROIs) can be used for seeding and filtering of fibers. Fibers are visualized either as lines, optionally using a powerful, GPU-based lighting engine, or as 3D structures such as tubes. * Scalar volumes, glyphs, and fibers can be colored using a wide array of coloring option. Customizable color loop-up tables allow for highly flexible visualization of scalar data. * Visualization and processing of various different HARDI formats is supported. HARDI data is interactively visualized using highly detailed glyphs rendered on the GPU. HARDI glyphs can be visualized in combination with DTI glyphs, for a better overview of complex diffusion data. * vIST/e includes support for NVIDIA's Compute Unified Device Architecture (CUDA), which enables highly parallel, GPU-based data processing, allowing for significant speed-up of computationally expensive algorithms.

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• SciCrunch
• 14 years ago - by Anonymous

Software R package and jamovi module for simplifying agreement and reliability analyses. Functions within this package include simple tests of agreement, agreement analysis for nested and replicate data, and provide robust analyses of reliability.Used for calculating absolute agreement and estimating required sample sizes for studies of absolute agreement.

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• RRID
• 3 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software package for the prediction of calpain cleavage sites.

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• SciCrunch
• 13 years ago - by Anonymous

A portable, highly integrated, internet-enabled, hardware / software platform and patient management system, which includes an online Patient Manager module which complies with the HIPAA Final Security Rule, an event-related potential (ERP) Viewer module to view and analyze raw and average ERP waves, and a Protocol Editor module to simplify the choice and administration of selected ERP protocols. It is also easy to train and administer with non-specialized personnel, and is designed to be used in an out-patient setting. COGNISION TM with auditory or visual event-related potential (ERP) technology, provides a direct physiologic measure of patients' cognitive processing (i.e., a cognitive biomarker).

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• SciCrunch
• 14 years ago - by Anonymous

Provides specimens with annotated data for clinical and basic science research purposes.Biorepository functions as centralized tissue bank to provide researchers access to cancer- and non-cancer-related specimens including fresh or frozen tissue, paraffin blocks,sections and fluids, procured and stored using international standards of best practices and protocols compliant with Office for Human Research Protection. Specimens can be obtained prospectively as part of clinical trials or accessed through UC Davis Health Clinical Laboratories, where over 5.5 million blood specimens are processed annually.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff.

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• SciCrunch
• 13 years ago - by Anonymous

Commercial technology solutions for NIRS neuroscience imaging applications.

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• SciCrunch
• 14 years ago - by Anonymous

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• NIF
• 3 years ago - by Anonymous

Software package that contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).

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• SciCrunch
• 13 years ago - by Anonymous

A Problem Solving Environment (PSE) for modeling, simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE, as well as BioMesh3D. BioMesh3D is a free, easy to use program for generating quality meshes for the use in biological simulations. The most recent stable release is version 4.6.

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• SciCrunch
• 14 years ago - by Anonymous

MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters.

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• dkNET
• 3 years ago - submitted by Maryann Martone

Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14, 2026. A fully automated software application for the processing of fMRI data using SPM. It is fully automated from the point of data acquisition at the MRI scanner. It incorporates tools for automated data transfer, archiving, real-time SPM5 batch script generation with distributed grid processing, automated error-recovery procedures, full data-provenance, email notifications, optional conversion back to DICOM (Digital Imaging and Communications in Medicine), and picture archiving and communications systems (PACS) insertion. The architecture allows for an infinite number of easily definable analyses that are fully automated from the point of acquisition. Requirements: * MATLAB 7.3 or greater with the Image Processing Toolbox * SPM5

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• SciCrunch
• 14 years ago - by Anonymous

Provides biomarker testing for human clinilcal research studies across multiple disciplines.Provides expertise with chemistry, special chemistry, radioimmunoassay, nephelometric and ELISA and multiplexing assay methods utilizing automated and manual procedures. Laboratory has Clinical Laboratory Improvement Act certification and follows guidelines established by CLIA for quality control and proficiency testing to ensure results. Core coordinates proper pre-analytical sample collection and processing procedures with project leaders; performs biochemical assays on samples submitted to the laboratory by investigators in manner that assures strict quality control both within and between assay runs; reports results to project staff in timely fashion; makes available expertise and technical assistance for establishing and validating new methodologies to support University of Miami investigators.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

An R package developed for the large-scale analysis of gene expression signatures. It gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.

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• SciCrunch
• 12 years ago - by Anonymous