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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BOC Sciences Protein Ubiquitination Service Resource Resource Report Resource Website |
BOC Sciences Protein Ubiquitination Service Resource (RRID:SCR_022127) | service resource | Service in field of drug discovery and research. BOC Sciences service in one stop Proteolysis Targeting Chimeric based molecular drug discovery which has become strategy in area of drug discovery. | BOC Sciences, biomedical service, PROTAC, Proteolysis Targeting Chimeric, molecular drug discovery, drug discovery | is related to: BOC Sciences | Restricted | SCR_022127 | BOC Sciences PROTAC Protein Ubiquitination Service, BOC Sciences Protein Ubiquitination Services, Protein Ubiquitination Services | 2026-09-12 01:00:05 | 0 | |||||||||
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BOC Sciences Small molecule target protein ligand Service Resource Resource Report Resource Website |
BOC Sciences Small molecule target protein ligand Service Resource (RRID:SCR_022126) | service resource | Provides small molecule target protein ligand service to customers to meet new drug discovery goals. | BOC Sciences, biomedical service, small molecule target protein ligand, protein, ligand, PROTAC | Restricted | SCR_022126 | Small molecule target protein ligand, BOC Sciences PROTAC Small molecule target protein ligand, BOC Sciences Small molecule target protein ligand | 2026-09-12 01:00:05 | 0 | ||||||||||
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BOC Sciences Peptide ligand for target protein Service Resource Resource Report Resource Website |
BOC Sciences Peptide ligand for target protein Service Resource (RRID:SCR_022125) | service resource | Service provider in drug discovery and development. Provides one stop PROTA development, which has become strategy in field of small molecular drug discovery. Provides peptide ligand design for target protein to customers to meet new drug discovery goals. | Peptide ligand for target protein, peptide ligands, target protein, PROTAC, BOC Sciences, biomedical service | is related to: BOC Sciences | Restricted | SCR_022125 | 2026-09-12 01:00:05 | 0 | ||||||||||
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ToppCluster Resource Report Resource Website 100+ mentions |
ToppCluster (RRID:SCR_001503) | ToppCluster | analysis service resource, data analysis service, production service resource, resource, service resource | A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene. | term enrichment, gene, analysis, gene enrichment analysis, connectivity, heatmap, ortholog, microarray, function, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GenitoUrinary Development Molecular Anatomy Project is related to: ToppGene Suite |
NIDDK 1U01DK70219; NIDDK P30DK078392; NCRR U54 RR025216; NIDCR U01DE020049 |
PMID:20484371 | Free | OMICS_02225, nlx_152801, biotools:toppcluster | https://bio.tools/toppcluster | SCR_001503 | ToppCluster: A multiple gene list feature analyzer for the dissection of biological systems | 2026-09-12 01:00:07 | 152 | ||||
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vIST/e Resource Report Resource Website 1+ mentions |
vIST/e (RRID:SCR_001627) | vIST/e | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | 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. | diffusion tensor imaging, high angular resolution diffusion imaging, visualization, cross-section, volume rendering, tensor glyph, mri, fiber tracking |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion MRI of Traumatic Brain Injury has parent organization: Eindhoven University of Technology; North Brabant; Netherlands |
Free, Available for download, Freely available | nlx_153923 | http://www.nitrc.org/projects/viste | SCR_001627 | DTITool | 2026-09-12 01:00:07 | 4 | ||||||
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Mind Research Network - COINS Resource Report Resource Website 10+ mentions |
Mind Research Network - COINS (RRID:SCR_000805) | COINS | data or information resource, data repository, data set, service resource, storage service resource | A web-based neuroimaging and neuropsychology software suite that offers versatile, automatable data upload/import/entry options, rapid and secure sharing of data among PIs, querying and export all data, real-time reporting, and HIPAA and IRB compliant study-management tools suitable to large institutions as well as smaller scale neuroscience and neuropsychology researchers. COINS manages over over 400 studies, more than 265,000 clinical neuropsychological assessments, and 26,000 MRI, EEG, and MEG scan sessions collected from 18,000 participants at over ten institutions on topics related to the brain and behavior. As neuroimaging research continues to grow, dynamic neuroinformatics systems are necessary to store, retrieve, mine and share the massive amounts of data. The Collaborative Informatics and Neuroimaging Suite (COINS) has been created to facilitate communication and cultivate a data community. This tool suite offers versatile data upload/import/entry options, rapid and secure sharing of data among PIs, querying of data types and assessments, real-time reporting, and study-management tools suitable to large institutions as well as smaller scale researchers. It manages studies and their data at the Mind Research Network, the Nathan Kline Institute, University of Colorado Boulder, the Olin Neuropsychiatry Research Center (at) Hartford Hospital, and others. COINS is dynamic and evolves as the neuroimaging field grows. COINS consists of the following collaboration-centric tools: * Subject and Study Management: MICIS (Medical Imaging Computer Information System) is a centralized PostgreSQL-based web application that implements best practices for participant enrollment and management. Research site administrators can easily create and manage studies, as well as generate reports useful for reporting to funding agencies. * Scan Data Collection: An automated DICOM receiver collects, archives, and imports imaging data into the file system and COINS, requiring no user intervention. The database also offers scan annotation and behavioral data management, radiology review event reports, and scan time billing. * Assessment Data Collection: Clinical data gathered from interviews, questionnaires, and neuropsychological tests are entered into COINS through the web application called Assessment Manager (ASMT). ASMT's intuitive design allows users to start data collection with little or no training. ASMT offers several options for data collection/entry: dual data entry, for paper assessments, the Participant Portal, an online tool that allows subjects to fill out questionnaires, and Tablet entry, an offline data entry tool. * Data Sharing: De-identified neuroimaging datasets with associated clinical-data, cognitive-data, and associated meta-data are available through the COINS Data Exchange tool. The Data Exchange is an interface that allows investigators to request and share data. It also tracks data requests and keeps an inventory of data that has already been shared between users. Once requests for data have been approved, investigators can download the data directly from COINS. | mri, fmri, neuropsychological assessment, neuroimaging, diffusion tensor imaging assay, magnetic resonance imaging assay, functional mri assay, diffusion magnetic resonance imaging, magnetoencephalography, electroencephalography, brain, behavior, data sharing, data management, clinical, computed tomography, magnetic resonance, single photon emission computed tomography, positron emission tomography, clinical assessment clinical neuroinformatics, image collection, mri 2d image, database application |
is used by: Consortium for Reliability and Reproducibility is used by: DataLad is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NKI-RS Enhanced Sample has parent organization: Mind Research Network is parent organization of: MCIC |
Aging | NIBIB 1 R01 EB 000840; NIBIB 1 R01 EB 006841; NIBIB 1 R01 EB 005846 |
PMID:22275896 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144067 | http://www.nitrc.org/projects/coins | SCR_000805 | Mind Research Network - Collaborative Informatics and Neuroimaging Suite, Collaborative Informatics Neuroimaging Suite, Collaborative Informatics and Neuroimaging Suite | 2026-09-12 01:00:06 | 20 | |||
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Tandem Repeats Finder Resource Report Resource Website 500+ mentions |
Tandem Repeats Finder (RRID:SCR_022193) | TRF | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to locate and display tandem repeats in DNA sequences. Program to analyze DNA sequences. | nucleotides pattern, pattern copies, DNA tandem repeat, DNA sequences, locate tandem repeats | NSF CCR9623532 | PMID:9862982 | Free, Available for download, Freely available | https://tandem.bu.edu/trf/trf.html | SCR_022193 | 2026-09-12 01:00:06 | 544 | |||||||
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BWA-MEM2 Resource Report Resource Website 5000+ mentions |
BWA-MEM2 (RRID:SCR_022192) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for sequence mapping.The next version of BWA-MEM. Used for aligning sequencing reads against large reference genome. | Intel Corporation, sequence mapping, aligning sequencing reads, large reference genome, Burrows-Wheeler Aligner, | is related to: BWA | DOI:10.1109/IPDPS.2019.00041 | Free, Available for download, Freely available | SCR_022192 | BWA-MEM | 2026-09-12 01:00:06 | 5566 | ||||||||
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Thermo Fisher: EVOS XL Core Imaging System Resource Report Resource Website 1+ mentions |
Thermo Fisher: EVOS XL Core Imaging System (RRID:SCR_022190) | instrument resource | Designed to eliminate complexities of microscopy, EVOS XL Core system captures high-quality brightfield cell images right at your benchtop within minute. Instrument for monitoring cell cultures, either within hood or in cell culture room. | EVOS XL Core Microscope, instrument, equipment, USEDit | is listed by: USEDit | Restricted | SCR_022190 | 2026-09-12 01:00:06 | 3 | ||||||||||
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StatAlign Resource Report Resource Website 1+ mentions |
StatAlign (RRID:SCR_001892) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for Bayesian analysis of protein, DNA and RNA sequences. It utilizes multiple alignments, phylogenetic trees and evolutionary parameters to quantify uncertainty in these analyses. It is written in Java. | software package, bayesian, protein, dna, rna, sequencing, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
PMID:23335014 | Free, Available for download, Freely available | biotools:StatAlign, OMICS_03743 | https://bio.tools/StatAlign | SCR_001892 | StatAlign 2.0 | 2026-09-12 01:00:07 | 1 | ||||||
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Near Infrared Camera Resource Report Resource Website |
Near Infrared Camera (RRID:SCR_022113) | NIRCam | instrument resource | Instrument aboard the James Webb Space Telescope. It has two major tasks, as imager from 0.6 to 5 micron wavelength, and as wavefront sensor to keep 18-section mirrors functioning as one. Imager covers infrared wavelength range 0.6 to 5 microns. NIRCam detects light from the earliest stars and galaxies in process of formation, population of stars in nearby galaxies, as well as young stars in Milky Way and Kuiper Belt objects. NIRCam is equipped with coronagraphs, instruments that allow astronomers to take pictures of very faint objects around central bright object, like stellar systems. | instrument, equipment, USEDit, imager, Webb, NASA | is listed by: USEDit | SCR_022113 | Near Infrared Camera | 2026-09-12 01:00:05 | 0 | |||||||||
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Creative Peptides Resource Report Resource Website |
Creative Peptides (RRID:SCR_022112) | commercial organization | Creative peptides is specialized in process development and manufacturing of bioactive peptides.Offers custom peptide synthesis, process development, manufacturing as well as catalog products for customers in industry and research area. Creative Peptides is staffed by scientific teams with experts in the fields of peptide technology, antibodies and synthetic chemistry. | bioactive peptides, custom peptide synthesis, process development, manufacturing, peptide technology, antibodies, synthetic chemistry |
is parent organization of: Creative Peptides Antibody Protein Bacteria Interactions Service Resource is parent organization of: Creative Peptides Backbone Cyclized Peptides Service Resource is parent organization of: Creative Peptides Cell Penetrating Peptide Design and Synthesis Service Resource is parent organization of: Creative Peptides Cosmetic Peptides Service Resource is parent organization of: Creative Peptides Design Platform Service Resource is parent organization of: Creative Peptides Peptide Drug Discovery Service Resource is parent organization of: Creative Peptides Target Validation in Peptide Drug Discovery Service Resource is parent organization of: Creative Peptides Target Analysis In Silico Service Resource is parent organization of: Creative Peptides Target Analysis in Bioscience Service Resource is parent organization of: Creative Peptides Hit Identification in Peptide Drug Discovery Service Resource is parent organization of: Creative Peptides PNA Synthesis Service Resource is parent organization of: Creative Peptides PNA Oligomer Synthesis Service Resource is parent organization of: Creative Peptides Chemical Synthesis of PNA Oligomers with Fmoc Service Resource is parent organization of: Creative Peptides Synthesis by Mmt Chemistry Service Resource is parent organization of: Creative Peptides PNA/DNA Chimera Synthesis Service Resource is parent organization of: Creative Peptides Total Peptide Library Construction Service Resource is parent organization of: Creative Peptides Peptide Drug Bioconjugations Service Resource is parent organization of: Creative Peptides: Peptide Lead Optimization Service Resource is parent organization of: Creative Peptides: Formulation Development Service Resource is parent organization of: Creative Peptides PNA Modification Service Resource is parent organization of: Creative Peptides PNA Modification of Connection between Nucleobase and Backbone Service Resource is parent organization of: Creative Peptides PNA Backbone Modification Service Resource is parent organization of: Creative Peptides PNA N/C Terminal Modification Service Resource is parent organization of: Creative Peptides PNA Modification by C Replacement Service Resource is parent organization of: Creative Peptides: Peptide Synthesis Service Resource is parent organization of: Creative Peptides Active Peptide Ingredients from Natural Products Service Resource is parent organization of: Creative Peptides Peptide Drug Biosynthesis Service Resource is parent organization of: Creative Peptides Peptide Drug Chemical Synthesis Service Resource is parent organization of: Creative Peptides Custom Peptide Synthesis Service Resource |
SCR_022112 | 2026-09-12 01:00:05 | 0 | |||||||||||
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Ruffus Resource Report Resource Website 1+ mentions |
Ruffus (RRID:SCR_022196) | software library, software resource, software toolkit | Software lightweight Python library for computational pipelines. Reproducible pipeline framework. | computational pipelines creation, computational pipelines | Medical Research Council | DOI:10.1093/bioinformatics/btq524 | Free, Available for download, Freely available | SCR_022196 | 2026-09-12 01:00:06 | 3 | |||||||||
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MashMap Resource Report Resource Website 10+ mentions |
MashMap (RRID:SCR_022194) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as fast approximate aligner for long DNA sequences. Used for computing local alignment boundaries between long DNA sequences. | mapping genome assembly, long DNA sequences, long reads, reference genome, long DNA sequences aligner | National Human Genome Research Institute ; NIH ; NSF CCF1816027 |
PMID:30423094 DOI:10.1007/978-3-319-56970-3_5 |
Free, Available for download, Freely available | SCR_022194 | 2026-09-12 01:00:06 | 31 | |||||||||
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TORTOISE Resource Report Resource Website 100+ mentions |
TORTOISE (RRID:SCR_001645) | TORTOISE | data processing software, image analysis software, image processing software, software application, software resource | An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data. | diffusion mri, dti, image motion correction, distortion correction, tensor computation, visualization, analysis, tensor fitting, modeling, magnetic resonance, tensor metric |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion MRI of Traumatic Brain Injury has parent organization: National Institute of Child Health and Human Development |
NICHD | Free, Available for download, Freely available | nlx_153921 | http://www.nitrc.org/projects/tortoise | SCR_001645 | Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble | 2026-09-12 01:00:07 | 108 | |||||
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GRS Resource Report Resource Website 1+ mentions |
GRS (RRID:SCR_001008) | data analysis software, data management software, data processing software, software application, software resource | A compression tool for efficient storage of Genome Re-Sequencing data. GRS processes genome sequence data without use of reference SNPs and other variants. It can also automatically rebuild the individual genome sequence data using the reference genome sequence. | data analysis software, data management software, compression tool, data compression, storage, genome, resequencing | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00960 | SCR_001008 | 2026-09-12 01:00:07 | 2 | |||||||||
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FACTA+. Resource Report Resource Website 1+ mentions |
FACTA+. (RRID:SCR_001767) | FACTA+ | data access protocol, service resource, software resource, web service | Text mining tool to discover associations between biomedical concepts from MEDLINE articles. Use the service from your browser or via a Web Service. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner - the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds. There is also a FACTA+ visualization service that can be found here: http://www.nactem.ac.uk/facta-visualizer/ | text mining, gene, protein, disease, symptom, drug, enzyme, compound, biomedical, association, machine learning, chemical, text-mining software, bio.tools |
is listed by: OMICtools is listed by: FORCE11 is listed by: bio.tools is listed by: Debian is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | PMID:18772154 | Free, Freely available | biotools:facta_plus, nif-0000-10272, OMICS_01181 | http://refine1-nactem.mc.man.ac.uk/facta/, https://bio.tools/facta_plus | SCR_001767 | Finding Associated Concepts with Text Analysis | 2026-09-12 01:00:07 | 2 | ||||
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NTAP Resource Report Resource Website 10+ mentions |
NTAP (RRID:SCR_001488) | NTAP | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for tiling array data analysis to survey the genome-wide binding sites of transcription factor HY5 in Arabidopsis and the genome-wide histone modifications/DNA methylation level in rice. It was developed in the process of generating NimbleGen analysis. Written in R and Perl. | software, tiling array, data analysis, rice, arabidopsis, hy5, transcription factor, genome |
is listed by: OMICtools has parent organization: Peking University; Beijing; China |
PMID:19468055 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00808 | SCR_001488 | NimbleGen Tiling array Analysis Package, NimbleGen Tilingarray Analysis Package | 2026-09-12 01:00:07 | 10 | ||||||
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BOC Sciences Ligand Design for Target Protein Service Resource Resource Report Resource Website |
BOC Sciences Ligand Design for Target Protein Service Resource (RRID:SCR_022124) | service resource | Service provider in drug discovery and development. Provides one stop development, which has become strategy in field of small molecular drug discovery. Provides ligand design for target protein to customers to meet new drug discovery goals. | Ligand Design for Target Protein, PROTAC, BOC Sciences, biomedical service | is related to: BOC Sciences | Restricted | SCR_022124 | BOC Sciences Ligand Design for Target Protein, BOC Sciences PROTAC Ligand Design for Target Protein | 2026-09-12 01:00:05 | 0 | |||||||||
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BOC Sciences Target Protein Services Service Resource Resource Report Resource Website |
BOC Sciences Target Protein Services Service Resource (RRID:SCR_022123) | service resource | Service provider in drug discovery and research. Provides one stop proteolysis targeting molecular drug discovery based on chimeric. Provides target protein services to customers to meet new drug discovery goals. | Target Protein, Protein Degradation, PROTAC, BOC Sciences, biomedical service, proteolysis targeting, molecular drug discovery | is related to: BOC Sciences | Restricted | SCR_022123 | BOC Sciences Target Protein Services, Target Protein Services, BOC Sciences PROTAC Target Protein Services | 2026-09-12 01:00:05 | 0 |
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