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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SimulAdren Resource Report Resource Website |
SimulAdren (RRID:SCR_027314) | software application, software resource | Software tool as simulation program of hypothalamus-pituitary-adrenal axis (HPA axis, aka corticotropic feedback control) for education and research, based on nonlinear MiMe-NoCoDI model and implemented with CyberUnits Bricks library. | simulation program, hypothalamus-pituitary-adrenal axis, nonlinear MiMe-NoCoDI model, CyberUnits Bricks library, |
uses: CyberUnits uses: Free Pascal Compiler uses: Lazarus IDE |
DOI:10.13140/2.1.2400.2568 | Free, Available for download, Freely available | https://zenodo.org/records/16324704 | SCR_027314 | 2026-08-04 09:46:10 | 0 | ||||||||
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Human Brain Connectivity Database Resource Report Resource Website |
Human Brain Connectivity Database (RRID:SCR_001594) | Human Brain Connectivity Database | data or information resource, data set, bibliography | Preliminary database of neuroanatomical connectivity reports specifically for the human brain, which have been manually curated. It includes details (based on manual literature curation) of tract tracing or related connectivity studies conducted in human brain tissue. This database and user interface will be expanded and improved in the near future. | neuroanatomy, brain, tract tracing, connectivity | has parent organization: Brain Architecture Project | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153841 | SCR_001594 | 2026-08-05 10:43:24 | 0 | ||||||||
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TOMUS Resource Report Resource Website |
TOMUS (RRID:SCR_001549) | TOMUS | clinical trial, resource, bibliography, data or information resource | Study that compared the outcomes of two minimally invasive surgical procedures to treat stress urinary incontinence in women. These procedures are called mid-urethral slings. The procedures insert a mesh sling or hammock to support the bladder neck so that urine does not leak. Both procedures have been approved by the FDA and have been shown to be safe and successful in treating stress urinary incontinence. However, it is not known if one is better than the other. This study answers that question. The secondary aims of the trial are to compare other outcomes for the two surgical procedures, including quality of life, sexual function, satisfaction with treatment outcomes, complications, and the need for other treatments(s) after surgery. Follow-up will be a minimum of two years. Stress urinary incontinence is the accidental leakage of urine during activities such as coughing, laughing, sneezing, or lifting heavy objects. | surgical procedure, female, mid-urethral sling, treatment, outcome, quality of life, sexual function, complication, retropubic mid-urethral sling, transobturator mid-urethral sling, adult human |
is listed by: ClinicalTrials.gov is listed by: NIDDK Information Network (dkNET) has parent organization: Urinary Incontinence Treatment Network |
Stress urinary incontinence, Urinary incontinence | NIDDK U01DK060401; NIDDK U01DK060379; NIDDK U01DK060397; NIDDK U01DK058234; NIDDK U01DK060393; NIDDK U01DK058229; NIDDK U01DK058225 |
PMID:20479459 PMID:22378483 PMID:21422865 PMID:21925636 PMID:23635737 |
Free, Freely available | nlx_152859 | SCR_001549 | Trial Of Mid-Urethral Slings, TOMUS-Trial Of Mid-Urethral Slings | 2026-08-05 10:43:23 | 0 | ||||
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HALT-C Trial Resource Report Resource Website |
HALT-C Trial (RRID:SCR_001534) | HALT-C Trial, HALT-C | clinical trial, resource, bibliography, data or information resource | Multi-center, randomized controlled study designed to determine if continuing interferon long term over several years will suppress the Hepatitis C virus, prevent progression to cirrhosis, prevent liver cancer and reduce the need for liver transplantation. Patient enrollment began in 2000 and was completed in 2003 at 10 clinical centers, which were supported by a data coordinating center, virological testing center, and central sample repository. Patients with chronic hepatitis C and advanced fibrosis or cirrhosis on liver biopsy who failed to respond to a previous course of interferon alfa were enrolled in this study. Patients were initially treated with a 24-week course of peginterferon alfa-2a and ribavirin. Patients who remained hepatitis C virus RNA positive were then randomized to receive maintenance, low-dose peginterferon or to be followed on no treatment. Liver biopsies were done before enrollment and after 2 and 4 years of treatment or follow-up. The endpoints were development of cirrhosis, hepatic decompensation, hepatocellular carcinoma, death, or liver transplantation. 1050 patients were randomized and followed through the 4 year randomized phase of the trial and as long as 4 years off treatment. Serum samples collected at multiple time points, DNA and liver tissue are available for scientific investigation. | interferon, progression, cirrhosis, prevention, liver cancer, liver transplantation, liver, pegylated interferon, clinical, outcome, adult human, dna, liver tissue, serum, blood, b lymphoblastoid cell-line, epstein-barr virus infection in peripheral blood mononuclear cell, peripheral blood mononuclear cell, biomaterial supply resource, formalin fixed, histology, frozen, stained liver slide, unstained liver slide, advanced fibrosis, liver biopsy, peginterferon alfa-2a, ribavirin |
is listed by: One Mind Biospecimen Bank Listing is listed by: ClinicalTrials.gov is listed by: NIDDK Central Repository is listed by: NIDDK Research Resources is listed by: NIDDK Information Network (dkNET) |
Hepatitis C virus, Chronic hepatitis C | NIDDK | Free, Freely available | nlx_152835 | http://archives.niddk.nih.gov/haltctrial/displaypage.aspx?pagename=haltctrial/index.htm | http://www.haltctrial.org/ | SCR_001534 | Hepatitis C Antiviral Long-term Treatment against Cirrhosis, Hepatitis C Antiviral Long-term Treatment against Cirrhosis (HALT-C) Trial, Hepatitis C Antiviral Long-term Treatment against Cirrhosis Trial | 2026-08-05 10:43:23 | 0 | |||
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Dendritica: Software Tools for Studying Dendritic Signaling Resource Report Resource Website 1+ mentions |
Dendritica: Software Tools for Studying Dendritic Signaling (RRID:SCR_001865) | software application, simulation software, software resource | Dendritica is a program package for relating dendritic geometry and signal propagation. The programs are based on those used for the simulations described in the following paper: Vetter, P., Roth, A. & Husser, M. (2001). Action potential propagation in dendrites depends on dendritic morphology. Journal of Neurophysiology, 85: 926-937. Dendritica can functionally be divided into three main parts: - Interactive morphological analysis and electrophysiological simulation of single cells - Automated batch simulations across a set of morphologies using the same simulation parameters - Automated analysis of batch simulation runs Dendritica requires NEURON 4.1.1 with some modifications described in Appendix 1. It was tested for NEURON 4.1.1 on Linux and SGI IRIX. Some modifications to the Dendritica code may be necessary in order to run it on older or newer versions of NEURON. Sponsors: This work was supported by the Wellcome Trust, the European Community, the Max-Planck-Gesellschaft, the Wellcome Trust 4-year PhD Programme in Neuroscience. | electrophysiological simulation, dendritic geometry, interactive, morphological, morphology, neuron, sigle cell, signal propagation | Free | http://www.dendrite.org/software.html | SCR_001865 | Dendritica | 2026-08-05 10:43:28 | 1 | |||||||||
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MCML and CONV Resource Report Resource Website |
MCML and CONV (RRID:SCR_002419) | MCML, MCML & CONV, CONV | software application, simulation software, software resource | MCML is a Monte Carlo simulation program for Multi-layered Turbid Media with an infinitely narrow photon beam as the light source. The simulation is specified by an input text file called, for example, sample.mci, which can be modified by any simple text editor. The output is another text file called, for example, sample.mco. (The names are arbitrary.) CONV is a convolution program which uses the MCML output file to convolve for photon beams of any size in a Gaussian or flat field shape. CONV can provide a variety of output formats (reflectance, transmission, iso-fluence contours, etc.), which are compatible with standard graphics applications. | optical imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Oregon Health and Science University; Oregon; USA |
PMID:9421660 PMID:19256707 |
Free, Available for download, Freely available | nlx_155791 | http://www.nitrc.org/projects/mcml | SCR_002419 | Monte Carlo for Multi-Layered media | 2026-08-05 10:43:38 | 0 | |||||
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Virtual brain Resource Report Resource Website 10+ mentions |
Virtual brain (RRID:SCR_002249) | tvb | software application, simulation software, software resource | Simulation software for modeling the entire human brain by combining structural and functional data from empirical neuroimaging data. It can generate local field potentials, EEG, MEG and fMRI BOLD data based on neural mass models. The user can also modify the model parameters to match clinical conditions from focal lesions or degenerative disorders. | dti, simulation, modeling, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Toronto; Ontario; Canada |
James S. McDonnell Foundation | PMID:23442172 PMID:23774395 |
Free, Freely available | nlx_155567 | http://www.nitrc.org/projects/tvb | SCR_002249 | thevirtualbrain.org, The Virtual Brain, thevirtualbrain | 2026-08-05 10:43:36 | 39 | ||||
|
Mason Resource Report Resource Website 100+ mentions |
Mason (RRID:SCR_002476) | software application, simulation software, software resource | Collection of software tools for simulating biological sequences, including simulations of genome fragment sampling, random genomic sequences, methylation levels, and NGS reads. | read simulating software, sequencing simulation, haplotype simulation | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_00252 | SCR_002476 | Mason2 | 2026-08-05 10:43:39 | 164 | ||||||||
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Nirfast Resource Report Resource Website 10+ mentions |
Nirfast (RRID:SCR_002503) | NIRFAST | software toolkit, software resource | Software package for modeling Near-Infrared light transport in tissue and image reconstruction. This includes: Standard single wavelength absorption and reduced scatter, Multi-wavelength spectrally constrained models and Fluorescence models. | optical imaging, tissue |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Dartmouth College; New Hampshire; USA |
PMID:20182646 PMID:23942632 |
Free, Available for download, Freely available | nlx_155902 | http://www.nitrc.org/projects/nirfast | SCR_002503 | 2026-08-05 10:43:39 | 35 | ||||||
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Orphelia Resource Report Resource Website 1+ mentions |
Orphelia (RRID:SCR_000119) | software application, simulation software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A metagenomic open reading frame (ORF) finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin. The resource is based on a two-stage machine learning approach that uses linear discriminants to extract features from the ORFs. An artificial neural network then combines the features and computes a gene probability for each ORF fragment. | metagenomic open reading frame, tool, resource, protein, genes, DNA, phyologenetic origin, machine learning, linear discriminates, artificial neural network, computation, scientific computing, fragment | is listed by: OMICtools | PMID:19429689 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01492 | SCR_000119 | 2026-08-05 10:43:06 | 2 | ||||||||
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Glide Resource Report Resource Website 10+ mentions |
Glide (RRID:SCR_000187) | Glide | software application, simulation software, software resource | Software package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Used in drug development for predicting protein ligand binding modes and ranking ligands via high throughput virtual screening. | ligand, receptor, docking, computation, virtual, screening, drug, discovery |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger works with: Ligprep |
PMID:18428795 | Restricted | OMICS_01601 | SCR_000187 | 2026-08-05 10:43:07 | 15 | |||||||
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forqs Resource Report Resource Website |
forqs (RRID:SCR_000643) | forqs | software application, simulation software, software resource | Software for forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. It also also models quantitative traits and selection on those traits. | c++, linux, osx, windows, command line, simulation, recombination, quantitative trait, selection, haplotype pattern |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA has parent organization: Bitbucket |
NHGRI HG002536; NHGRI R01 HG007089; NSF EF-0928690 |
PMID:24336146 | Free, Available for download, Freely available | OMICS_02196 | SCR_000643 | Forward-in-time simulation of Recombination, and Selection, Quantitative traits | 2026-08-05 10:43:12 | 0 | |||||
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Compound Discoverer Resource Report Resource Website |
Compound Discoverer (RRID:SCR_028693) | software application, software resource | Software platform by Thermo Fisher Scientific designed for identifying, comparing, and interpreting small molecules in complex biological, environmental, and forensic samples. It uses customizable workflow, known as nodes, to automate mass spectrometry data processing, spectral library searching, and statistical analysis.Compound Discoverer is integrated with SIRIUS (via a custom workflow node) to bridge the gap between high-resolution MS/MS data and confident molecular identification. While Thermo Scientific’s Compound Discoverer excels at library searching and statistical analysis, SIRIUS provides powerful in silico tools to accurately predict molecular formulas, chemical classes, and de novo structures. High-resolution mass spectrometry (HRMS) data analysis software for untargeted metabolomics, lipidomics, and contaminant screening. Utilizes modular workflows to extract features, match spectra against libraries like mzCloud, and confidently identify complex organic compounds. | High-resolution mass spectrometry (HRMS) data analysis, small molecule data processing and metabolomics, identifying, comparing, interpreting, small molecules, | PMID:41919739 | Restricted | SCR_028693 | Thermo Scientific Compound Discoverer | 2026-08-04 09:46:29 | 0 | |||||||||
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Stoelting ANY-maze Video Tracking Software Resource Report Resource Website |
Stoelting ANY-maze Video Tracking Software (RRID:SCR_028718) | software application, software resource | Automated platform used in behavioral neuroscience to track and analyze the movements and behaviors of lab animals, such as mice and rats. Standardizes experiments like the Elevated Plus Maze, Open Field, Barnes Maze, and Fear Conditioning. Tracks whole-body movement, distance traveled, freezing/immobility, and zone entries. Connects to external devices like food dispensers, shockers, and lasers to trigger automated responses based on the animal's actions. | behavioral neuroscience, track, analyze, movements and behaviors, lab animals, mice, rats | is used by: Medical University of South Carolina MUSC Mouse Behavior Phenotyping Core Facility | Restricted | SCR_028718 | ANY-maze Video Tracking | 2026-08-04 09:46:34 | 0 | |||||||||
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hivebench Resource Report Resource Website |
hivebench (RRID:SCR_000915) | commercial organization, software resource | A commercial software laboratory notebook. | protocol sharing tool | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158032 | SCR_000915 | 2026-08-04 09:40:16 | 0 | ||||||||||
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National Resource for Automated Molecular Microscopy Resource Report Resource Website 1+ mentions |
National Resource for Automated Molecular Microscopy (RRID:SCR_001448) | NRAMM | biomedical technology research center, training resource | Biomedical technology research center that develops, tests and applies technology aimed toward completely automating the processes involved in solving macromolecular structures using cryo-electron microscopy. The goal is to establish a resource that will serve both as a center for high-throughput molecular microscopy as well as for transferring this technique to the research community. Current Core Technology Research and Development is focused on 4 areas: improving grid substrates and specimen preparation; further automation and optimization of image acquisition; development of an integrated single particle analysis and processing pipeline; and the development of automated high throughput EM screening. NRAMM welcomes applications of both collaborative and service projects. | macromolecular structure, cryo-electron microscopy, macromolecule, structure, microscopy, automation, high throughput, specimen handling, image acquisition, data processing, data information integration, structural biology technology center | NIGMS 9 P41 GM103310; NCRR 2P41RR017573 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152671 | SCR_001448 | 2026-08-04 09:40:23 | 2 | ||||||||
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National Biomedical Center for Advanced ESR Technology Resource Report Resource Website 1+ mentions |
National Biomedical Center for Advanced ESR Technology (RRID:SCR_001444) | ACERT | biomedical technology research center, training resource | Biomedical technology research center that develops methods, both experimental and theoretical, of modern electron spin resonance (ESR) for biomedical applications. Center technologies are applicable to the determination of the structure and complex dynamics of proteins. Principal areas of expertise: * Pulsed Fourier Transform and Two Dimensional ESR * High Frequency-High Field (HFHF) ESR * High Resolution ESR Microscopy * Theory and Computational Methods for Modern ESR Activities include: * making resources available to the biomedical community, * publishing results, * running workshops on the new methodologies, * addressing the need to bring these new technologies to other laboratories. | electron spin resonance, spectrometer, electron spin resonance spectrometer, structure, dynamics, protein, structural biology technology center | has parent organization: Cornell University; New York; USA | NIGMS P41GM103521; NCRR P41RR016292 |
Free, Freely Available | nlx_152669 | SCR_001444 | ACERT National ESR Center, National Biomedical Center for Advanced Electron Spin Resonance Technology | 2026-08-04 09:40:23 | 1 | ||||||
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Center for Integrative Biomedical Computing Resource Report Resource Website 1+ mentions |
Center for Integrative Biomedical Computing (RRID:SCR_001961) | CIBC | biomedical technology research center, training resource | Biomedical technology research center that produces open-source software tools for biomedical image-based modeling, biomedical simulation and estimation, and the visualization of biomedical data. The Center works closely with software users and collaborators in a range of scientific domains to produce user-optimized tools and provides advice, technical support, workshops, and education to enhance user success. Biological projects and collaborations drive their development efforts, all with a single unifying vision: to develop the role of image-based modeling and analysis in biomedical science and clinical practice. The CIBC has a strong, ongoing emphasis on software simulation of bioelectric fields, with clinically oriented collaborations in cardiac defibrillation and the diagnosis/treatment of epilepsy. In addition, the CIBC has expanded in recent years to include applications of statistical shape analysis and three-dimensional visualization to mouse genetics and neuroimaging and applications of image and geometry processing to cell biology. | cardiac defibrillation, epilepsy, software, biomedical, image, modeling, simulation, estimation, visualization, computing, informatics, computing and informatics technology center | has parent organization: University of Utah; Utah; USA | NIGMS P41GM103545 | nif-0000-10535 | SCR_001961 | NIH/NIGMS Center for Integrative Biomedical Computing | 2026-08-04 09:40:31 | 1 | |||||||
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GenVision Resource Report Resource Website 1+ mentions |
GenVision (RRID:SCR_001166) | GenVision | commercial organization, software resource | A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig. | genome, image, visualization, graphic, map, gene expression, contig, genetics |
is listed by: OMICtools works with: Lasergene's SeqMan Pro |
Commercial | OMICS_02135 | SCR_001166 | GenVision - Software for Publication-Quality Illustrations, DNASTAR GenVision | 2026-08-04 09:40:19 | 1 | |||||||
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NIH Center for Macromolecular Modeling and Bioinformatics Resource Report Resource Website 10+ mentions |
NIH Center for Macromolecular Modeling and Bioinformatics (RRID:SCR_001435) | Center for Macromolecular Modeling and Bioinformatics, TCBG | biomedical technology research center, training resource | Biomedical technology research center focusing on the structure and function of supramolecular systems in the living cell as well as on the development of new algorithms and efficient computing tools for physical biology. They bring the most advanced molecular modeling, bioinformatics, and computational technologies to bear on questions of biomedical relevance. They extend, refine and deliver these technologies in response to experimental progress and emerging needs of the wide biomedical research community. They magnify the impact of their work through direct collaboration with experimental researchers, the distribution of cutting-edge and user-friendly software, and via extensive training, service, and dissemination efforts. The multidisciplinary team is engaged in the modeling of large macromolecular systems in realistic environments, and has produced ground-breaking insights into biomolecular processes coupled with mechanical force, bioelectronic processes in metabolism and vision, and with the function and mechanism of membrane proteins. They are committed and work towards further advancement of * Molecular modeling tools which can integrate structural information with bioinformatics databases and molecular dynamics simulations, and which can be used by a wide audience; * High performance molecular visualization and simulation software, capable of modeling biomolecules in realistic environments of 100,000,000 atoms or more; * Conceptual and methodological foundations of molecular modeling in the fields of quantum biology, mechanobiology, and interactive modeling; * Biomedical science through collaborations between theoretical and experimental researchers; * Support of the entire research process and training through a web-enabled collaborative environment; and * Service, training, and dissemination by leveraging web-based molecular graphics and integrated modeling technologies. | supramolecular system, living cell, cell, algorithm, computing, physical biology, software, molecular dynamics, simulation, molecule, visualization, biomolecule, molecular modeling, bioinformatics, computational technology, computing and informatics technology center, model, macromolecule | has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA | NIGMS P41GM104601 | Free, Freely Available | nlx_152659 | SCR_001435 | Resource for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling & Bioinformatics | 2026-08-04 09:40:23 | 33 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
