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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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SYCAMORE Resource Report Resource Website 1+ mentions |
SYCAMORE (RRID:SCR_021117) | data access protocol, software resource, web service | Web browser based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Allows database supported modelling, basic model checking and estimation of unknown kinetic parameters based on protein structures. Integrates different online applications as well as locally installed software. Provides user guidance for sequence of steps associated with model building, model checking, simulation and analysis of results. | Systems biology computational analysis, modeling research environment, kinetic models analysis, kinetic models construction, kinetic models simulation, systems biology, protein structures, kinetic parameters |
has parent organization: Heidelberg Institute for Theoretical Studies; Heidelberg; Germany has parent organization: Heidelberg University; Baden-Wurttemberg; Germany |
German Ministry of Education and Research ; Klaus Tschira Foundation |
PMID:18463116 | Free, Freely available | SCR_021117 | SciCrunch Registry | SYstems biology Computational Analysis and MOdeling Research Environment | 2026-10-31 12:18:04 | 1 | |||||||
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BioSpherix: OxyCycler GT4181CN Controller Resource Report Resource Website |
BioSpherix: OxyCycler GT4181CN Controller (RRID:SCR_021113) | GT4181CN | instrument resource | Carbon Monoxide, Nitric Oxide, O2, and CO2 controller with limit control of relative humidity and monitoring of temperature conditions when used in combination with C-Chamber incubator subchamber from BioSpherix. Features secondary monitors for both Carbon Monoxide and Nitric Oxide and may be used in combination with I-Hood Incubator Hood from BioSpherix to ventilate fumes. | Carbon Monoxide, Nitric Oxide, O2, CO2, controller, instrument, equipment, USEDit | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021113.pdf | SCR_021113 | SciCrunch Registry | Carbon Monoxide, CO2, OxyCycler GT4181CN Dynamic O2, OxyCycler GT4181CN, and Nitric Oxide Subchamber Cell Culture System | 2026-10-31 12:18:06 | 0 | ||||||||
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Abricate Resource Report Resource Website 1000+ mentions |
Abricate (RRID:SCR_021093) | data analysis software, data processing software, software application, software resource | Software tool for mass screening of contigs for antimicrobial and virulence genes. Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB. | contigs mass screening, antimicrobial genes, virulence genes, antimicrobial genes contigs, virulence genes contigs, FASEB list | Free, Available for download, Freely available | SCR_021093 | SciCrunch Registry | ABRicate | 2026-10-31 12:18:10 | 1355 | ||||||||||
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PySyft Resource Report Resource Website 10+ mentions |
PySyft (RRID:SCR_021012) | software resource | Software Python library for secure and private Deep Learning. Decouples private data from model training, using Federated Learning, Differential Privacy, and Encrypted Computation and Homomorphic Encryption within main deep learning frameworks. Used for computing on data you do not own and cannot see. | Private Deep Learning, deep learning, decouples private data, unseen data computing |
is related to: PyTorch is related to: tensorflow |
Free, Available for download, Freely available | SCR_021012 | SciCrunch Registry | 2026-10-31 12:18:02 | 11 | ||||||||||
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xiNET Resource Report Resource Website 10+ mentions |
xiNET (RRID:SCR_021010) | data access protocol, data processing software, data visualization software, software application, software resource, web service | Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains. | Crosslinking mass spectrometry data visualization, linkage sites, linked peptides, crosslinking reaction product display, crosslink network maps, maps with residue resolution | Wellcome Trust | PMID:25648531 | Free, Available for download, Freely available | http://github.com/colin-combe/crosslink-viewer | SCR_021010 | SciCrunch Registry | Crosslink Network Maps With Residue Resolution | 2026-10-31 12:18:08 | 20 | |||||||
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Thermo Fisher: Applied Biosystems: QuantStudio 12K Flex RealTime PCR System Resource Report Resource Website 10+ mentions |
Thermo Fisher: Applied Biosystems: QuantStudio 12K Flex RealTime PCR System (RRID:SCR_021098) | instrument resource | System can simultaneously run up to four 3072 reaction QuantStudio 12K Flex OpenArray plates in about four hours. When combined with the QuantStudio 12K Flex OpenArray AccuFill System, can produce up to 110000 data points or more in 8 hour day. Has touch screen interface and comprehensive software analysis tools for gene expression, genotyping, and digital PCR increase productivity. Has five interchangable block formats including: OpenArray plate, TaqMan Array card, 384-well, and 96-well (0.1 and 0.2 mL). | Real Time PCR System, QuantStudio 12K Flex OpenArray, instrument, equipment, USEDit | uses: Applied Biosystems QuantStudio 12K Flex RT PCR Software | Commercially available | SCR_021098 | SciCrunch Registry | QuantStudio 12K Flex Real-Time PCR System | 2026-10-31 12:18:09 | 16 | |||||||||
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BioSpherix: ProOx C21 Controller Resource Report Resource Website 1+ mentions |
BioSpherix: ProOx C21 Controller (RRID:SCR_021131) | C21 | instrument resource | Compact O2 and CO2 Subchamber Controller used together with C-Chamber Incubator Subchamber from BioSpherix or chambers from other manufacturers. | Compact controller, Oxygen controller, CO2 controller, Subchamber Controller, BioSpherix, instrument, equipment, USEDit | Commercially Available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021131.pdf | Model_Number_ProOx C21 | SCR_021131 | SciCrunch Registry | ProOx C21, ProOx C21 Oxygen and Carbon Dioxide Subchamber Controller | 2026-10-31 12:18:11 | 1 | |||||||
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Biofactoid Resource Report Resource Website 1+ mentions |
Biofactoid (RRID:SCR_021011) | data access protocol, data or information resource, knowledge environment resource, portal, project portal, software resource, web service | Web tool for creating digital profile of scientific discoveries in article and connecting them to related research. Authors describe molecular interactions supported by their results, letting researchers explore first hand account of article findings and connect to related articles and knowledge. Web based system for scientists to compose structured representation of networks of interactions between genes, their products, and chemical compounds, represented using power of formal ontology. | Knowledge management, molecular interactions, pathway, compose network structured representation, digital profile, connect related articles, formal ontology |
is related to: Biological Pathways Exchange is related to: Biological Pathways Exchange has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard University; Cambridge; United States has parent organization: University of Oregon; Oregon; USA |
DARPA Big Mechanism ; NHGRI U41HG006623 |
Free, Freely available | SCR_021011 | SciCrunch Registry | 2026-10-31 12:18:04 | 1 | |||||||||
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Applied Biosystems QuantStudio 12K Flex RT PCR Software Resource Report Resource Website 1+ mentions |
Applied Biosystems QuantStudio 12K Flex RT PCR Software (RRID:SCR_021096) | data acquisition software, data analysis software, data processing software, software application, software resource | Software supports QuantStudio12K Flex Real Time PCR System to open and analyze experiments. Enables to set up experiments, send experiments to instrument, control thermal cycling process in instrument, collect data and analyze collected data. | control instrument thermal cycling process, data collection, data analysis, QuantStudio12K Flex Real Time PCR System support | is used by: Thermo Fisher: Applied Biosystems: QuantStudio 12K Flex RealTime PCR System | Restricted | SCR_021096 | SciCrunch Registry | QuantStudio 12K Flex Real Time PCR Software, Applied Biosystems QuantStudio 12K Flex RT PCR Software | 2026-10-31 12:18:03 | 5 | |||||||||
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BioSpherix: ProOx 360 Controller Resource Report Resource Website 1+ mentions |
BioSpherix: ProOx 360 Controller (RRID:SCR_021130) | P360 | instrument resource | Versatile high infusion rate O2 controller.Controls Oxygen and may be used with BioSpherix C-Chamber Incubator Subchamber, C-Shuttle Glove Box, I-Glove Incubator Glove Box, Xvivo System Model X3 Cytocentric Cell Incubation and Handling Platfrom, or A-Chamber Animal Chamber. Featuring capability to infuse gas over range 1-140 SCFH, may be used together with chambers which are either home built or are available from other manufacturers. | Versatile high infusion rate O2 controller, O2 controller, Oxygen controller, BioSpherix, instrument, equipment, USEDit | Commercially Available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021130.pdf | Model_Number_ProOx 360 | SCR_021130 | SciCrunch Registry | ProOx 360 High Infusion Rate O2 Controller, ProOx 360 | 2026-10-31 12:18:04 | 3 | |||||||
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ExpressionSuite Resource Report Resource Website 10+ mentions |
ExpressionSuite (RRID:SCR_021095) | data analysis software, data processing software, software application, software resource | Software tool to quantify relative gene expression across large number of genes and samples. Allows to analyze gene expression data on any current Applied Biosystems real time PCR instrument. | QuantStudio Real-Time PCR analysis, quantify relative gene expression, genes large number, analyze gene expression data, Applied Biosystems RT PCR instrument | Free, Available for download, Freely available | SCR_021095 | SciCrunch Registry | ExpressionSuite Software, ExpressionSuite v1.3 | 2026-10-31 12:18:06 | 11 | ||||||||||
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Multilayer Connectome of Caenorhabditis elegans Resource Report Resource Website |
Multilayer Connectome of Caenorhabditis elegans (RRID:SCR_021009) | data or information resource | Networks of extrasynaptic aminergic and peptidergic interactions in C. elegans | Networks, extrasynaptic aminergic interactions, peptidergic interactions, C.Elegans | DOI:10.1371/journal.pcbi.1005283 | Free, Freely available | SCR_021009 | SciCrunch Registry | 2026-10-31 12:18:08 | 0 | ||||||||||
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BioSpherix: ProOx 110 Controller Resource Report Resource Website 1+ mentions |
BioSpherix: ProOx 110 Controller (RRID:SCR_021129) | P110, ProOx 110 | instrument resource | Compact, versatile O2 controller.Controls Oxygen and may be used with either C-Chamber Incubator Subchamber or A-Chamber Animal Chamber from BioSpherix. May be used with home-built or other manufacturers chambers. | Compact O2 controller, controls Oxygen, BioSpherix, instrument, equipment, USEDit | Commercially Available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021129.pdf | Model_Number_ProOx 110 | SCR_021129 | SciCrunch Registry | BioSpherix ProOx 110 Compact O2 Controller | 2026-10-31 12:18:07 | 3 | |||||||
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xProhet Resource Report Resource Website |
xProhet (RRID:SCR_021005) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 15, 2021. Software tool for analysis of cross-linked peptides. | PMID:24356771 | THIS RESOURCE IS NO LONGER IN SERVICE | http://proteomics.ethz.ch/cgi-bin/xquest2_cgi/download.cgi | SCR_021005 | SciCrunch Registry | xQuest/xProhet | 2026-10-31 12:18:04 | 0 | |||||||||
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BioSpherix: ProCO2 120 Controller Resource Report Resource Website 1+ mentions |
BioSpherix: ProCO2 120 Controller (RRID:SCR_021127) | P120 | instrument resource | Controls CO2 levels for most physiologic concentrations and may be connected with either C-Chamber Incubator Subchambers or A-Chamber Animal Chambers from BioSpherix. May also be connected with chambers which are either home built or are available from other manufacturers. These include thermal incubators, flush boxes, culture chambers, glove boxes, and other semi sealed enclosures. | CO2 levels control, physiologic concentrations, BioSpherix, instrument, equipment, USEDit | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_021127.pdf | Model_Number_ProCO2 120 | SCR_021127 | SciCrunch Registry | ProCO2 120, ProCO2 120 Compact CO2 Controller, ProCO2 120 Compact Controller | 2026-10-31 12:18:11 | 3 | |||||||
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immuneML Resource Report Resource Website 1+ mentions |
immuneML (RRID:SCR_021004) | analysis service resource, data or information resource, portal, production service resource, service resource | Open source Python platform for machine learning based analysis and classification of adaptive immune receptors and repertoires. Supported by ELIXIR Norway. | Immune receptor, machine learning, predicting immune status, predicting antigen specificity | DOI:10.1101/2021.03.08.433891 | Free, Available for download, Freely available | SCR_021007 | https://galaxy.immuneml.uio.no/, https://github.com/uio-bmi/immuneML | SCR_021004 | SciCrunch Registry | 2026-10-31 12:18:08 | 1 | ||||||||
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HMCan Resource Report Resource Website 10+ mentions |
HMCan (RRID:SCR_010858) | HMCan | software resource | A Hidden Markov Model based software tool that is developed to detect histone modification in cancer ChIP-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:24021381 | biotools:hmcan, OMICS_00443 | https://bio.tools/hmcan | SCR_010858 | SciCrunch Registry | Histone Modification in Cancer | 2026-10-31 12:15:12 | 14 | ||||||
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DFLAT Resource Report Resource Website 1+ mentions |
DFLAT (RRID:SCR_010738) | DFLAT | data or information resource, data set, narrative resource, standard specification | We are an interdisciplinary team dedicated to annotating gene function related to human fetal development. We are contributing new functional annotation to the Gene Ontology, curating and mining gene sets suitable for the interpretation of developmental genomic data, and creating the computational tools needed to apply genomics for better understanding the molecular mechanisms of human development. Our GO annotation is in the process of being incorporated into the GOA public release. The GONE (Gene Ontology Non-Eligible) database is where we store annotations relevant to our research but that don''t quite meet GOA''s standards. Usually an annotation falls into this category because either the gene/protein described is a family of genes/proteins rather than a specific one, there is no UniProt ID to identify the gene/protein in the system, a GO term does not yet exist to describe the particular function, process, or location of the gene/protein, the species is not clearly identifiable in the paper, or the evidence is not as reliable (GO evidence codes TAS and NAS). As individual annotations these are more suspect than current GO annotation. However, for functional analysis of expression data, these gene sets can be valuable even with a certain amount of noise. We also include here a link to the supplementary data from our forthcoming PSB 2011 paper on gene set mining. | human, fetal, development | has parent organization: Tufts University; Massachusetts; USA | NICHD R01 HD058880 | PMID:21121032 | nlx_95610 | SCR_010738 | SciCrunch Registry | Developmental FunctionaL Annotation at Tufts | 2026-10-31 12:15:10 | 2 | ||||||
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TESS: Transcription Element Search System Resource Report Resource Website 100+ mentions |
TESS: Transcription Element Search System (RRID:SCR_010739) | TESS | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | TESS is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, and our CBIL-GibbsMat database. You can use TESS to search a few of your own sequences or for user-defined CRMs genome-wide near genes throughout genomes of interest. Search for CRMs Genome-wide: TESS now has the ability to search whole genomes for user defined CRMs. Try a search in the AnGEL CRM Searches section of the navigation bar.. You can search for combinations of consensus site sequences and/or PWMs from TRANSFAC or JASPAR. Search DNA for Binding Sites: TESS also lets you search through your own sequence for TFBS. You can include your own site or consensus strings and/or weight matrices in the search. Use the Combined Search under ''Site Searches'' in the menu or use the box for a quick search. TESS assigns a TESS job number to all sequence search jobs. The job results are stored on our server for a period of time specified in the search submit form. During this time you may recall the search results using the form on this page. TESS can also email results to you as a tab-delimited file suitable for loading into a spreadsheet program. Query for Transcription Factor Info: TESS also has data browsing and querying capabilities to help you learn about the factors that were predicted to bind to your sequence. Use the Query TRANSFAC or Query Matrices links above or use the search interface provided from the home page. | transcription factor, dna sequence, genome, promoter, gene regulation, FASEB list | has parent organization: University of Pennsylvania; Philadelphia; USA | PMID:18428685 | nlx_97404 | http://www.pcbi.upenn.edu/tess | SCR_010739 | SciCrunch Registry | Transcription Element Search System | 2026-10-31 12:15:08 | 191 | ||||||
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miRTar Resource Report Resource Website 50+ mentions |
miRTar (RRID:SCR_010851) | miRTar | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | An integrated web server for identifying miRNA-target interactions in human. The tool enables biologists easily to identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts. |
is listed by: OMICtools has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
OMICS_00410 | SCR_010851 | SciCrunch Registry | MicroRNA Target prediction | 2026-10-31 12:15:11 | 55 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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