Curator Dashboard

Prucka CardioLab system delivers the EP data and visualization we need for electrophysiological study and catheter ablation.

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• RRID-Legacy
• 9 years ago - by Anonymous

System to record continuous measurements of left ventricular pressure with a conductance pressure-volume catheter.

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• RRID-Legacy
• 9 years ago - by Anonymous

The InterLex project - a core component of SciCrunch and supported by projects such as the Neuroscience Information Framework project (NIF), the NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury - is a dynamic lexicon of biomedical terms. Unlike an encyclopedia, a lexicon provides the meaning of a term, and not all there is to know about it. InterLex is being constructed to help improve the way that biomedical scientists communicate about their data, so that information systems like NIF and dkNET can find data more easily and provide more powerful means of integrating that data across distributed resources. One of the big roadblocks to data integration in the biomedical sciences is the inconsistent use of terminology in databases and other resources such as the literature. When we use the same terms to mean different things, we cannot easily ask questions that span across multiple resources. For example, if three databases have information about what genes are expressed in cortex, but they all use different definitions of cerebral cortex, then it is hard to compare them. InterLex allows for the association of data values (i.e. the value of a field or text within a field) to terminologies enabling the crowdsourcing of data-terminology mappings. InterLex was built on the foundation of NeuroLex (see Larson and Martone 2013 Neurolex: An online framework for neuroscience knowledge. Frontiers in Neuroinformatics, 7:18) and contains all of the existing NeuroLex terms. The initial entries in NeuroLex were built from the NIFSTD ontologies. NIFSTD currently has about 60,000 concepts (includes both classes and synonyms) that span gross anatomy, cells, subcellular structures, diseases, functions and techniques. InterLex models terms using primitives of the Web Ontology Language (OWL) and can export directly to a variety of standard ontology formats. A primary goal of interlex is to provide a stable layer on top of the many other existing terminologies, lexicons, and ontologies (i.e. provide a way to federate ontologies for data applications) and to provide a set of inter-lexical and inter-data-lexical mappings. In the future, InterLex will support user specific namespaces so that users can customize the exact definitions or ontologies they source from, as well as the relationships on those terms. Importantly, however, InterLex enforces a simple rule which is that terms which represent the same concept under the same superclass will maintain the same identifier fragment (i.e. 'ilx_1234567'). However, each user will be able to 'fork' a term into their own namespace (e.g. http://uri.interlex.org/user/ilx_1234567). This enables the various perspectives on a term or concept to have equal space so that the full diversity of views on a term can be seen and expressed. Sign-up for updates to get notified about updates to InterLex and when new features are available.

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• RRID-Legacy
• 9 years ago - submitted by Tom Gillespie

LINCS L1000 characteristic direction signatures search engine. Software tool to find consensus signatures that match user’s input gene lists or input signatures. Underlying dataset is LINCS L1000 small molecule expression profiles generated at Broad Institute by Connectivity Map team. Differentially expressed genes of these profiles were calculated using multivariate method called Characteristic Direction.

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• dkNET
• 9 years ago - submitted by Ko-Wei Lin

Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources.

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• dkNET
• 9 years ago - submitted by Ko-Wei Lin

Web application that provides interactive visualization of drug and small-molecule induced gene expression signatures. L1000FWD enables coloring of signatures by different attributes such as cell type, time point, concentration, as well as drug attributes such as MOA and clinical phase.

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• dkNET
• 9 years ago - submitted by Ko-Wei Lin

Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools.

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• dkNET
• 9 years ago - submitted by Ko-Wei Lin

Web application for a code and text writing environment. It uses javascript and can be used to produce executable papers.

• SciCrunch
• 9 years ago - submitted by Anita Bandrowski

Biomaterial supplier that links organ and tissue donors with the scientific community. After securing the appropriate consent, IIAM provides non-transplantable organs and tissues to researchers for use in medical discovery and education.

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• dkNET
• 9 years ago - submitted by Ko-Wei Lin

IDEPI is a domain-specific and extensible software library for supervised learning of models that relate genotype to phenotype for HIV-1 and other organisms. IDEPI makes use of open source libraries for machine learning (scikit- learn, scikit-learn.org/), sequence alignment (HMMER, hmmer.janelia.org/), sequence manipulation (BioPython, biopython.org), and parallelization (joblib, pythonhosted.org/joblib), and provides a programming interface to allow the users to engineer sequence features and select machine learning algorithms appropriate for their application.

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• RRID-Legacy
• 9 years ago - by Anonymous

Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data. PMID: 26044712, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• RRID-Legacy
• 9 years ago - by Anonymous

CytoBackBone is an R package for merging of phenotype information from different cytometric profiles. Single-cell technologies are the most suitable techniques for the characterization of cells by the differential expression of the molecules that define their roles and functions in tissues. Among these techniques, mass cytometry represents a leap forward by increasing the number of available measurements to approximately 40 cell markers. Thanks to this technology, detailed immune responses were described in several diseases. However, the study of immune responses, such as that due to viral infections or auto-immune diseases, could be further improved by increasing the number of simultaneously measurable markers. To increase this number, we designed an algorithm, named CytoBackBone, which combines phenotypic information of different cytometric profiles obtained from different cytometry panels.

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• SciCrunch
• 9 years ago - submitted by Nicolas Tchitchek

Image reconstruction software for MRI. Its library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms.

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• RRID-Legacy
• 9 years ago - by Anonymous

Virtual Slide Microscope Software by Olympus. This software will be read the data captured by VS120/cellSens. Images saved with VSI or Multi-Tiff file format can be read.

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• RRID-Legacy
• 9 years ago - by Anonymous

This pipeline and the included scripts are used to filter useful reads for SSPACE.

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• SciCrunch
• 9 years ago - submitted by Fu-Hao Lu

NGSimple (Next-Generation illumina SIMulation PipeLinE), mainly written in perl is designed to simulate NGS parameters (illumina sequencing type, read length, insert size and coverage) based on a given reference, and give a report to choose the best parameter combination that could contribute to a good assembly.

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• SciCrunch
• 9 years ago - submitted by Fu-Hao Lu

Standalone software tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Music composition and manipulation software.

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• RRID-Legacy
• 9 years ago - by Anonymous