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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Authority Synonyms Record Last Update Mentions Count
Integrated DNA Technologies OligoAnalyzer
 
Resource Report
Resource Website
500+ mentions
Integrated DNA Technologies OligoAnalyzer (RRID:SCR_001363) OligoAnalyzer data analysis software, data processing software, sequence analysis software, software application, software resource, web application Web-based application for analyzing oligonucleotides. Analysis proceeds after the sequence has been entered and the calculations modified based on target type, oligo concentration, sodium ion concentration, magnesium ion concentration, and dNTP concentration. oligos, oligonucleotides, sequence, web, analyzer Free, Freely Available nif-0000-07754 SCR_001363 SciCrunch Registry IDT OligoAnalyzer, OligoAnalyzer, IDT Oligo Analyzer, OligoAnalyzer 3.1 2026-09-26 02:12:59 620
Bioinformatics Jobs Board
 
Resource Report
Resource Website
Bioinformatics Jobs Board (RRID:SCR_001484) bioinformatics.ca Job Postings job resource Job postings available to Bioinformatics.ca members. To become a member please sign up for an account. DISCLAMER: OICR and the Canadian Bioinformatics Workshops are not affiliated with and have not investigated the companies listing jobs on this site. OICR is not making any representations with respect to the positions and is not acting as an agent for the companies listed. bioinformatics is related to: Canadian Bioinformatics Workshops
has parent organization: Ontario Institute for Cancer Research
Free, Freely available nlx_152739 SCR_001484 SciCrunch Registry 2026-09-26 02:13:00 0
UNAFold
 
Resource Report
Resource Website
100+ mentions
UNAFold (RRID:SCR_001360) data analysis software, data processing software, software application, software resource Software package for nucleic acid folding and hybridization prediction. It has capabilities to predict folding for single-stranded RNA or DNA through a combination of free energy minimization, partition function calculations and stochastic sampling. The program runs on Unix and Linux platforms as well as Mac OS X and Windows. software, nucleic acid, folding, hybridization, prediction, rna, dna, stochastic sampling, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: University at Albany; New York; USA
Free, Available for download, Freely available biotools:unafold, nif-0000-07753 http://mfold.rna.albany.edu/ SCR_001360 SciCrunch Registry The UNAFold Web Server, UNAFold Web Server 2026-09-26 02:12:59 373
LPE
 
Resource Report
Resource Website
LPE (RRID:SCR_001364) LPE software resource Software library used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional "BH" or "BY" procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. differential expression, microarray is listed by: OMICtools
has parent organization: Bioconductor
PMID:18450812 Free, Available for download, Freely available OMICS_01978 SCR_001364 SciCrunch Registry Local Pooled Error 2026-09-26 02:12:59 0
Multiple-Path Particle Dosimetry Model
 
Resource Report
Resource Website
10+ mentions
Multiple-Path Particle Dosimetry Model (RRID:SCR_001486) MPPD software resource Computational model that can be used for estimating human and rat airway particle dosimetry. The model is applicable to risk assessment, research, and education. The MPPD model calculates the deposition and clearance of monodisperse and polydisperse aerosols in the respiratory tracts of rats and human adults and children (deposition only) for particles ranging in size from ultrafine (0.01 micrometers) to coarse (20 micrometers). The models are based on single-path and multiple-path methods for tracking air flow and calculating aerosol deposition in the lung. The single-path method calculates deposition in a typical path per airway generation, while the multiple-path method calculates particle deposition in all airways of the lung and provides lobar-specific and airway-specific information. Within each airway, deposition is calculated using theoretically derived efficiencies for deposition by diffusion, sedimentation, and impaction within the airway or airway bifurcation. Filtration of aerosols by the nose and mouth is determined using empirical efficiency functions. The MPPD model includes calculations of particle clearance in the lung following deposition. model, computational model, particle dosimetry, risk assessment, adult human, child, aerosol, deposition, clearance, lung is related to: The Hamner Institute for Health Sciences: BMDExpress and The multiple-path particle dosimetry PMID:8566482 Free, Freely available nlx_152744 http://www.ara.com/products/mppd.htm SCR_001486 SciCrunch Registry Multiple Path Particle Dosimetry Model 2026-09-26 02:13:00 15
Globin Gene Server
 
Resource Report
Resource Website
10+ mentions
Globin Gene Server (RRID:SCR_001480) Globin Gene Server analysis service resource, data analysis service, data or information resource, database, narrative resource, production service resource, resource, service resource, software resource, source code, training material Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles. dna sequence, hemoglobin, mutation, globin gene cluster, sequence comparison, functional genomics, gene, alignment, genetic analysis, variant, gene expression, protein, thalassemia, globin gene, genome, pairwise alignment, multiple alignment, annotation, sequence analysis, dna is listed by: NIDDK Information Network (dkNET)
has parent organization: Pennsylvania State University
NLM R01LM05773;
NLM R01LM05110;
NIDDK DK27635
PMID:11857738
PMID:11480780
PMID:9799599
PMID:9576329
PMID:8088828
Free, Freely available nlx_152723 SCR_001480 SciCrunch Registry 2026-09-26 02:13:00 30
Pediatric Acute Liver Failure Study
 
Resource Report
Resource Website
Pediatric Acute Liver Failure Study (RRID:SCR_001478) PALF data or information resource, disease-related portal, portal, research forum portal, resource, topical portal Study group and network for a 2008 longitudinal study for the etiology, diagnosis, treatment, and outcome of acute liver failure in infants, children, and adolescents. Data from patients include urine, bile, serum, liver tissue, cell lines derived from fibroblast culture, and DNA. management strategy, infant, child, adolescent, clinical, liver, patient care, rare disease, blood, tissue, longitudinal, urine, bile, serum, liver tissue, cell line, fibroblast culture, dna, etiology, diagnosis, treatment, outcome is listed by: NIDDK Information Network (dkNET)
is related to: Acute Liver Failure Study Group
has parent organization: University of Pittsburgh; Pennsylvania; USA
Acute liver failure NIDDK U01DK072146 Free, Freely available nlx_152715 http://www.palfstudy.org/ SCR_001478 SciCrunch Registry Pediatric Acute Liver Failure (PALF) Study, Pediatric Acute Liver Failure (PALF) Study Group 2026-09-26 02:13:00 0
Happy
 
Resource Report
Resource Website
10+ mentions
Happy (RRID:SCR_001395) HAPPY data analysis software, data processing software, software application, software resource, source code THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download). qtl, quantitative trait locus, r, c, gene, genetic, genomic, ansi c, unix, irix, sunos, linux, animal model, trait, map, genotype, phenotype, haplotype, linear regression, data set, qtl mapping is listed by: Genetic Analysis Software
is listed by: Debian
has parent organization: Wellcome Trust Centre for Human Genetics
Wellcome Trust PMID:11050180
DOI:10.1073/pnas.230304397
THIS RESOURCE IS NO LONGER IN SERVICE nlx_152594 http://www.well.ox.ac.uk/~rmott/happy.html https://sources.debian.org/src/r-other-mott-happy.hbrem/ SCR_001395 SciCrunch Registry reconstructing HAPlotYpes 2026-09-26 02:12:59 46
Retinal Topography Maps Database
 
Resource Report
Resource Website
1+ mentions
Retinal Topography Maps Database (RRID:SCR_001399) Retinal Topography Maps Database data or information resource, data repository, database, service resource, storage service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A database of over 700 retinal topography maps of a wide variety of species published in a diversity of journals. It has been assembled to assist vision and neuroscience researchers to locate and compare the distribution of retinal neurons within and across species. The maps can be searched by taxonomic or common name classification, cell type sampled, type of retinal specialization and staining/visualization method. Maps can be compared by selecting multiple maps and clicking the Compare Selected button. An interactive spreadsheet can be also downloaded. retinal map, retina, vision, retinal neuron, topography, eye has parent organization: University of Western Australia; Perth; Australia PMID:26230981 THIS RESOURCE IS NO LONGER IN SERVICE nlx_152606 SCR_001399 SciCrunch Registry Retinal topography maps, retinalmaps.org 2026-09-26 02:12:59 1
Online Neuroscience Lectures - Maintained by the Kilgard Lab
 
Resource Report
Resource Website
Online Neuroscience Lectures - Maintained by the Kilgard Lab (RRID:SCR_001397) data or information resource, portal, slide, topical portal, video resource List of lectures, slides and videos concerning neuroscience and neurophysiology. neuroscience, neurophysiology, lecture, slide, video Free, Freely Available nif-0000-08126 SCR_001397 SciCrunch Registry Online Neuroscience Lectures 2026-09-26 02:12:59 0
MRI Studio
 
Resource Report
Resource Website
100+ mentions
MRI Studio (RRID:SCR_001398) data processing software, data visualization software, image analysis software, image processing software, software application, software resource An image processing program running under Windows suitable for such tasks as tensor calculation, color mapping, fiber tracking, and 3D visualization. Most of operations can be done with only a few clicks. This tool evolved from DTI Studio. Tools in the program can be grouped in the following way: * Image Viewer * Diffusion Tensor Calculations * Fiber Tracking and Editing * 3D Visualization * Image File Management * Region of Interesting (ROI) Drawing and Statistics * Image Registration tensor calculation, color mapping, fiber tracking, 3d visualization, dti, image registration, mri, diffusion mr fiber tracking, microsoft, c++, analyze is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Diffusion Tensor Imaging ToolKit
has parent organization: Johns Hopkins University; Maryland; USA
works with: UManitoba - JHU Functionally Defined Human White Matter Atlas
NCRR ;
Biomedical Informatics Research Network ;
NIBIB
Free, Freely Available nif-0000-00291 http://www.nitrc.org/projects/mri_studio SCR_001398 SciCrunch Registry dtiStudio, DTI Studio 2026-09-26 02:12:59 180
PNEUMA
 
Resource Report
Resource Website
1+ mentions
PNEUMA (RRID:SCR_001391) PNEUMA simulation software, software application, software resource, software toolkit A set of modules that are used to simulate the autoregulation of the cardiovascular and respiratory systems under conditions of changing sleep-wake state and a variety of physiological and pharmacological interventions. It models the dynamic interactions that take place among the various component mechanisms, including those involved in the chemical control of breathing, heart rate, and blood pressure, as well as the effects of changes in the sleep-wake state and arousal from sleep. PNEUMA includes the autonomic control of the cardiovascular system, chemoreflex and state-related control of breath-to-breath ventilation, state-related and chemoreflex control of upper airway potency, as well as respiratory and circulatory mechanics. The model is capable of simulating the cardiorespiratory responses to sleep onset, arousal, continuous positive airway pressure, the administration of inhaled carbon dioxide and oxygen, Valsalva and Mueller maneuvers, and Cheyne-Stokes respiration during sleep. In PNEUMA 3.0, we have extended the existing integrative model of respiratory, cardiovascular, and sleepwake state control, to incorporate a sub-model of glucoseinsulinfatty acid regulation. The extended model is capable of simulating the metabolic control of glucoseinsulin dynamics and its interactions with the autonomic nervous system. The interactions between autonomic and metabolic control include the circadian regulation of epinephrine secretion, epinephrine regulation on dynamic fluctuations in glucose and free fatty acids in plasma, metabolic coupling among tissues and organs mediated by insulin and epinephrine, as well as the effect of insulin on peripheral vascular sympathetic activity. This extended model represents a starting point from which further in silico investigations into the interaction between the autonomic nervous system and the metabolic control system can proceed. Features in PNEUMA 3.0 * Incorporates metabolic component based on prior models of glucose-insulin regulation and free fatty acid (FFA) regulation. * Changes in sympathetic activity from the autonomic portion of PNEUMA produce changes in epinephrine output, which in turn affects the metabolic sub-model. * Inputs from the dietary intake of glucose and external interventions, such as insulin injections, have also been incorporated. * Also incorporated is autonomic feedback from the metabolic component to the rest of PNEUMA: changes in insulin level lead to changes in sympathetic tone. System Requirements: PNEUMA requires Matlab R2007b or higher with the accompanying version of Simulink to be installed on your computer. matlab, simulate, autoregulation, cardiovascular system, respiratory system, sleep-wake state, physiological intervention, pharmacological intervention, drug, breathing, heart rate, blood pressure, respiration, glucose, insulin, fatty acid, regulation, autonomic nervous system, chemoreflex, ventilation, circulation, cardiorespiratory, metabolic control system, circadian, regulation, epinephrine has parent organization: Biomedical Simulations Resource NIBIB P41-EB001978;
NCRR P41-RR01861
PMID:17271149 Free, Freely Available nlx_152572 SCR_001391 SciCrunch Registry 2026-09-26 02:12:59 3
NIH Common Data Element Repository
 
Resource Report
Resource Website
1+ mentions
NIH Common Data Element Repository (RRID:SCR_001390) NIH CDE Resource Portal, CDE Resource Portal common data element, data or information resource, narrative resource, standard specification A repository of Common Data Elements (CDE). The CDE is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. Forms in the Repository might be original, or might recreate the format of real-world data collection instruments or case report forms. NIH has endorsed collections of CDEs that meet established criteria. NIH-endorsed CDEs are designated with a gold ribbon. Users can Browse NIH-Endorsed CDEs, Browse All CDEs, or Browse Forms. clinical research, clinical, patient registry, human subject research, human subject, data element, case report form, interoperability, data sharing has parent organization: National Library of Medicine Free, Freely Available nlx_152564 https://cde.nlm.nih.gov/home, http://www.nlm.nih.gov/cde/ SCR_001390 SciCrunch Registry NIH Common Data Element (CDE) Resource Portal, Common Data Element (CDE) Resource Portal 2026-09-26 02:12:59 8
Center for Gamma Ray Imaging
 
Resource Report
Resource Website
Center for Gamma Ray Imaging (RRID:SCR_001384) Center for Gamma-Ray Imaging instrument manufacture, material service resource, production service resource, service resource Biomedical technology resource center that develops new gamma-ray imaging instruments and techniques that yield substantially improved spatial and temporal resolutions. The Center makes its imagers and expertise available to a wide community of biomedical and clinical researchers through collaborative and service-oriented interactions. The collaborative research applies these new imaging tools to basic research in functional genomics, proteomics, cancer, cardiovascular disease and cognitive neuroscience, and to clinical research in tumor detection and other selected topics. There are five core research projects: * Detector technology research and development * Reconstruction algorithms and system modeling * Data acquisition, signal processing, and system development * Image-quality assessment and system optimization * Techniques for molecular imaging spect, ct, imaging, clinical, gamma-ray, imaging instrument, basic research, functional genomics, cardiovascular disease, cognitive neuroscience, breast cancer, tumor detection, proteomics, cancer has parent organization: University of Arizona; Arizona; USA NIBIB EB002035-14 nlx_152567 SCR_001384 SciCrunch Registry 2026-09-26 02:12:59 0
Semantic Measures Library
 
Resource Report
Resource Website
Semantic Measures Library (RRID:SCR_001383) SML software library, software resource, software toolkit Open source Java library dedicated to semantic measures computation and analysis. Tools based on the SML are also provided through the SML-Toolkit, a command line software giving access to some of the functionalities of the library. The SML and the toolkit can be used to compute semantic similarity and semantic relatedness between semantic elements (e.g. concepts, terms) or entities semantically characterized (e.g. entities defined in a semantic graph, documents annotated by concepts defined in an ontology). semantic measure, semantic similarity, semantic relatedness, functional similarity, gene ontology, annotation, parse, gene, disease ontology, mesh, rdf, owl, umls, snomed-ct, java, semantic, command line is listed by: FORCE11
is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Ecole des Mines d'Ales; Ales; France
Ecole des Mines d'Ales; Ales; France ;
LGI2P Research Center
PMID:24108186 Free, Available for download, Freely available nlx_152555 http://www.semantic-measures-library.org SCR_001383 SciCrunch Registry SML-Toolkit, Semantic Measures Library and ToolKit, Semantic Measures Library & ToolKit 2026-09-26 02:12:59 0
CODR: C PATH On Line Data Repository
 
Resource Report
Resource Website
1+ mentions
CODR: C PATH On Line Data Repository (RRID:SCR_001388) CODR analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource A repository of de-identified control arm data of patients from clinical studies of Alzheimer's disease and Mild Cognitive Impairment. It provides the ability to analyze the data online with the R statistical analysis program, create and download standard reports, run complex queries, or download data to a desktop for further analysis. Additional data will be added to the database over time. Critical Path Institute consortia members and qualified researchers may upload and work on scientific data relevant to biomarkers of drug toxicity, neurodegenerative diseases, and patient-reported outcomes. clinical data, alzheimer's disease, camd, biomarker, drug toxicity, neurodegenerative disease, patient-reported outcome, patient outcome, metadata standard, data repository has parent organization: CAMD Neurodegenerative disease, Drug toxicity, Alzheimer's disease, Mild Cognitive Impairment Free, Freely Available nlx_152562 SCR_001388 SciCrunch Registry C-Path Online Data Repository (CODR), CPATH online data repository, C-PATH Online Data Repository, C PATH On Line Data Repository 2026-09-26 02:12:59 2
CAMD
 
Resource Report
Resource Website
1+ mentions
CAMD (RRID:SCR_001389) CAMD consortium, data or information resource, organization portal, portal THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 8, 2022. Consortium developing new technologies and methods to accelerate the development and review of medical products for neurodegenerative diseases. It is focused on accelerating drug development for patients with chronic neurodegenerative disease, namely, Alzheimer's disease (AD) and Parkinson's disease (PD), by advancing drug development tools for evaluating drug efficacy, conducting clinical trials, and streamlining the process of regulatory review. The consortium focuses on sharing precompetitive patient-level data from the control arms of legacy clinical trials, developing new tools to be submitted to the regulatory agencies, and developing consensus data standards. CAMD has the following areas of focus: (1) qualification of biomarkers, (2) development of common data standards, (3) creation of integrated databases for clinical trials data, and (4) development of quantitative model-based tools for drug development. Regulatory milestones include a qualification opinion with EMA for the use of low baseline hippocampal volume for patient enrichment in pre-dementia trials, and most recently, positive regulatory decisions from the FDA and EMA for the use of a clinical trial simulation tool to aid in trials for mild to moderate stages of AD., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. data set, clinical trial, mild cognitive impairment, clinical, biomarker, metadata standard, disease progression model, consortium, drug, data sharing, disease modeling, drug development, disease model, imaging, cerebral spinal fluid is listed by: Consortia-pedia
has parent organization: Critical Path Institute; Arizona; USA
is parent organization of: CODR: C PATH On Line Data Repository
Publicly funded THIS RESOURCE IS NO LONGER IN SERVICE nlx_152563 SCR_001389 SciCrunch Registry Coalition Against Major Diseases 2026-09-26 02:12:59 6
Salk Institute for Biological Studies - Slesinger Lab
 
Resource Report
Resource Website
Salk Institute for Biological Studies - Slesinger Lab (RRID:SCR_001850) data or information resource, portal, topical portal THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This lab is investigating the molecular details of how potassium ion channels open and close (i.e. gating), the cellular regulation of potassium channels in nerve cells, and more recently, their role in drug addiction and mental disorders. There are currently two related areas of focus in the lab. One main area of research is investigating the G protein regulation of GIRK channels, utilizing structural, biochemical and electrophysiological strategies. The other area extends from the G protein regulation experiments to studies that examine the role of GIRK channels in the neural response to drugs of abuse, utilizing biochemical, electrophysiological and behavioral strategies. drug, electrophysiological, gating, abuse, addiction, behavioral, biochemical, cell, cellular, channel, disorder, girk channel, g protein, ion, mental, molecular, nerve, neural, potassium, regulation, structural THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10413 SCR_001850 SciCrunch Registry Salk Institute (Slesinger) 2026-09-26 02:13:05 0
Farsight Toolkit
 
Resource Report
Resource Website
1+ mentions
Farsight Toolkit (RRID:SCR_001728) FARSIGHT data processing software, image analysis software, image processing software, software application, software resource, software toolkit THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A collection of software modules for image data handling, pre-processing, segmentation, inspection, editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks. All of the modules are written in accordance with software practices of the Insight Toolkit Community. Importantly, all modules are accessible through the Python scripting language which allows users to create scripts to accomplish sophisticated associative image analysis tasks over multi-dimensional microscopy image data. This language works on most computing platforms, providing a high degree of platform independence. Another important design principle is the use of standardized XML file formats for data interchange between modules. editing, 2d, 3d, algorithm, analysis, bio-format, computational, data, graphical, inspection, metadata, microscopy, morphological, morphology, pixel, processing, segmentation, taxonomy, image has parent organization: University of Houston; Texas; USA NIBIB R01-EB005157;
NSF EEC-9986821;
NIBIB R01EB005157
PMID:24808857 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10227 SCR_001728 SciCrunch Registry FARSIGHTWiki 2026-09-26 02:13:03 2
CCAT
 
Resource Report
Resource Website
50+ mentions
CCAT (RRID:SCR_001843) CCAT software resource THIS RESOURCE IS OUT OF SERVICE, documented on April 5, 2017, A software package for the analysis of ChIP-seq data with negative control., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Genome Institute of Singapore; Singapore; Singapore
PMID:20371496 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00428, biotools:ccat https://bio.tools/ccat SCR_001843 SciCrunch Registry Control based ChIP-Seq Analysis Tools 2026-09-26 02:13:05 76

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