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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CalcuSyn Resource Report Resource Website 50+ mentions |
CalcuSyn (RRID:SCR_020251) | software application, data processing software, data analysis software, software resource | Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools. | Biosoft, drug mixtures study, drug efficacy, dose effect, quantify synergism, quantify inhibition | is listed by: SoftCite | Restricted | SCR_020251 | CalcuSyn Version 2.0 | 2026-02-15 09:21:53 | 57 | |||||||||
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Flowlogic Resource Report Resource Website 50+ mentions |
Flowlogic (RRID:SCR_020942) | software application, data processing software, data analysis software, software resource | Software tool for flow cytometry data analysis by Miltenyi Biotec. | Flow cytometry data, data analysis, flow cytometry, Miltenyi Biotec | is listed by: SoftCite | Restricted | SCR_020942 | Flowlogic TM Software, Flowlogic Software | 2026-02-15 09:22:27 | 74 | |||||||||
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SEDFIT Resource Report Resource Website 10+ mentions |
SEDFIT (RRID:SCR_018365) | software application, data processing software, data analysis software, software resource | Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly. | Analytical ultracentrifugation, biophysical analysis, macromolecular assembly, data, analysis, National Institute of Biomedical Imaging and Bioengineering | is listed by: SoftCite | NIH | Free, Available for download, Freely available | SCR_018365 | SEDFIT version 14.7g | 2026-02-15 09:22:21 | 25 | ||||||||
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Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | software application, data processing software, data analysis software, software resource | Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. | Data matrice analysis, data matrice modification, phyloinformatics, phylogenetic tree, alignment, molecular data manipulation, data analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: NCBI |
NSF Cyberinfrastructure for Phylogenetic Research EF 0331654 | PMID:18227120 | Free, Freely available | OMICS_21687 | https://sources.debian.org/src/phyutility/ | SCR_018545 | 2026-02-15 09:22:16 | 42 | ||||||
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PROCHECK Resource Report Resource Website 50+ mentions |
PROCHECK (RRID:SCR_019043) | software application, data processing software, data analysis software, software resource | Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR. | Stereochemical quality, protein structure, plot, residue listing, protein, assessing protein quality, | is listed by: SoftCite | DOI:10.1107/S0021889892009944 | Free, Available for download | SCR_019043 | 2026-02-15 09:22:21 | 75 | |||||||||
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FCS Express Resource Report Resource Website 100+ mentions |
FCS Express (RRID:SCR_016431) | software application, data processing software, data analysis software, software resource | Software tool for flow and image cytometry data analysis by De Novo Software company. | flow, image, analysis, data, cytometry, De Novo Software, research, clinical, laboratory | is listed by: SoftCite | Commercially available, Tutorial available | SCR_016431 | 2026-02-15 09:21:52 | 488 | ||||||||||
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CTFFIND Resource Report Resource Website 100+ mentions |
CTFFIND (RRID:SCR_016732) | CTFFIND | software application, data processing software, data analysis software, software resource | Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4. |
is listed by: SoftCite is related to: Janelia Research has parent organization: MRC Laboratory of Molecular Biology |
MRC | PMID:26278980 | SCR_016732 | CTFFinding, CTFFIND4, CTFFIND2, Contrast Transfer Function Finding, Contrast Transfer FunctionFinding, CTFFIND 3 | 2026-02-15 09:21:48 | 109 | ||||||||
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CFX Manager Resource Report Resource Website 100+ mentions |
CFX Manager (RRID:SCR_017251) | software application, data processing software, data analysis software, software resource | Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | RT PCR, real time PCR, data, analysis, BioRad | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017251 | CFX Manager software | 2026-02-15 09:22:00 | 489 | |||||||||
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GeneMarker Resource Report Resource Website 1000+ mentions |
GeneMarker (RRID:SCR_015661) | software application, data processing software, data analysis software, software resource | Genotype analysis software which enhances the speed, accuracy, and ease of analysis. The software is an alternative to Applied BioSystems Genotyper®, GeneScan®, and other genotype analysis software. | genotype, gene analysis | is listed by: SoftCite | Commercially available, Trial available, Runs on Mac OS, Runs on Windows, Runs on Linux | SCR_015661 | GeneMarker: The Biologist Friendly Software | 2026-02-15 09:21:21 | 1541 | |||||||||
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MedCalc Resource Report Resource Website 10000+ mentions |
MedCalc (RRID:SCR_015044) | software application, data processing software, data analysis software, software resource | Statistical software for ROC curve analysis. MedCalc performs several statistical tests such as method comparison, method evaluation, reference intervals, and meta-analysis. | statistic, statistical analysis, roc curve, reference software | is listed by: SoftCite | Commercially available, Available for purchase, Trial available | SCR_015044 | 2026-02-15 09:21:07 | 18070 | ||||||||||
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LigandScout Resource Report Resource Website 100+ mentions |
LigandScout (RRID:SCR_014889) | software application, software resource | Software that takes a macromolecular structure containing a bound ligand and identifies the key features on the ligand which are interacting with points on a protein. Its features include: automatic interpretation of PDB ligands using geometry, dictionaries and rule; advanced handling of co-factors, ions, water molecules and covalently bound ligands; pharmacophore export to Catalyst(tm), MOE(tm) and PHASE(tm) for virtual screening; and the ability to treat co-factors and water molecules as part of the ligand or part of the macromolecule. | pharmacophore, macromolecular structure, bound ligand, pdb ligand, virtual screening, ligad based pharmacore design | is listed by: SoftCite | Available for purchase | https://www.chemistryworld.com/ligandscout/1012019.article | SCR_014889 | 2026-02-15 09:21:02 | 395 | |||||||||
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SPARTAN Resource Report Resource Website 500+ mentions |
SPARTAN (RRID:SCR_014901) | software application, software resource | Software program for determining molecular structure and calculating chemical properties. It has a graphical interface and accurate computational models that are compatible with the iPad, iPhone and iPod Touch. When combined with the Spartan'16 Parallel Suite, this enables the first fully-functional open-ended molecular modeling environment on popular mobile technology. | molecular structure, chemical properties, modeling, mobile technology, integration | is listed by: SoftCite | Commercial | SCR_014901 | 2026-02-15 09:21:02 | 534 | ||||||||||
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SQLite Resource Report Resource Website 50+ mentions |
SQLite (RRID:SCR_017672) | software application, software resource | Relational database management system contained in C library. SQLite is not client server database engine but it is embedded into the end program. | Database, management, system, C library, engine, embedded, the end program | is listed by: SoftCite | Free, Freely available | SCR_017672 | 2026-02-15 09:22:11 | 65 | ||||||||||
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Image Pro Plus Resource Report Resource Website 10000+ mentions |
Image Pro Plus (RRID:SCR_007369) | software application, data processing software, software toolkit, image acquisition software, image analysis software, software resource, data acquisition software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software package to capture, process, measure, analyze and share images and data. | morphometric, image analysis, image acquisition, automation, classification, microscope control | is listed by: SoftCite | nif-0000-00313, SCR_015803, SCR_016879 | SCR_007369 | Image-Pro Plus, Image-Pro Plus Morphometric Analysis Software | 2026-02-16 09:46:57 | 18240 | |||||||||
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FigTree Resource Report Resource Website 10000+ mentions |
FigTree (RRID:SCR_008515) | software application, data processing software, data visualization software, software resource | A graphical viewer of phylogenetic trees and a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST. | data visualization software, graphical viewer, phylogenetic tree, annotate |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Edinburgh; Scotland; United Kingdom |
OMICS_04268, nif-0000-30567 | https://sources.debian.org/src/figtree/ | SCR_008515 | FigTree | 2026-02-16 09:47:12 | 11323 | ||||||||
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Augustus Resource Report Resource Website 1000+ mentions |
Augustus (RRID:SCR_008417) | software application, data processing software, sequence analysis software, data analysis software, software resource, web application | Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes. | software, gene, prediction, eucaryotic, genomic, sequence |
is used by: BRAKER is used by: BRO_annotation is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: Gsnap2Augustus |
Deutsche Forschungsgemeinschaft (DFG) HO4545/1-1;; STA1009/6-1 ; Institute for Mathematics and Computer Science ; Ernst Moritz Arndt University of Greifswald |
PMID:23700307 DOI:10.1093/bioinformatics/btw494 |
Free, Available for download, Freely available | SCR_015981, OMICS_07777, nif-0000-30133 | https://sources.debian.org/src/autodock-vina/ | SCR_008417 | Augustus: Gene Prediction, WebAUGUSTUS, Augustus, Augustus [gene prediction] | 2026-02-16 09:47:11 | 3542 | |||||
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Research Randomizer Resource Report Resource Website 1000+ mentions |
Research Randomizer (RRID:SCR_008563) | data access protocol, software resource, web service | This site is designed for researchers and students who want a quick way to generate random numbers or assign participants to experimental conditions. Research Randomizer can be used in a wide variety of situations, including psychology experiments, medical trials, and survey research. The program uses a JavaScript random number generator to produce customized sets of random numbers. Since its release in 1997, Research Randomizer has been used to generate number sets over 10.7 million times. This service is part of Social Psychology Network and is fast, free, and runs with any recent web browser as long as JavaScript isn''t disabled. Research Randomizer is a free service offered to students and researchers interested in conducting random assignment and random sampling. By using this service, you agree to abide by the SPN User Policy and to hold Research Randomizer and its staff harmless in the event that you experience a problem with the program or its results. Although every effort has been made to develop a useful means of generating random numbers, Research Randomizer and its staff do not guarantee the quality or randomness of numbers generated. Any use to which these numbers are put remains the sole responsibility of the user who generated them. What are the system requirements needed to run Research Randomizer? This program works best with Firefox and other recent web browsers. If you''re using a browser that came with America Online, or older browsers made prior to 2003, you may experience some difficulties with Research Randomizer. You may also not be able to use Research Randomizer with some limited-function browsers that do not fully support JavaScript, such as the Opera broswer used on certain game consoles. We would suggest that you update to a fairly recent, fully- functional stand-alone browser. How do I know what browser I am using? The easiest way to find this out is to click Help on the pulldown menu at the top of the screen. One of the options should be About Mozilla Firefox, About Internet Explorer, About Netscape, or something similar. Selecting this option will open a window that displays the name, version number, and copyright date of your browser. How does Research Randomizer generate its numbers? Research Randomizer uses the Math.random method within the JavaScript programming language to generate its random numbers for all modern web browsers. If you are using an older version of Microsoft Internet Explorer or Netscape Navigator (that is prior to version 4.0 of either), Research Randomizer uses an adaptation of the Central Randomizer by Paul Houle. Note that Research Randomizer no longer supports much-older browsers by other vendors (e.g., Mosaic). Who designed Research Randomizer? The original idea and programming for Research Randomizer came from Geoffrey C. Urbaniak in 1997. Research Randomizer was then jointly developed with Scott Plous, webmaster of Social Psychology Network, and online tutorials were added to the main program. In 1999 the site was redesigned with the assistance of Mike Lestik, in 2003 Mike Lestik added the download function, and in 2007 Mike Lestik and Scott Plous redesigned the site and added new content. | is listed by: SoftCite | nif-0000-31448 | SCR_008563 | Research Randomizer | 2026-02-16 09:47:13 | 2093 | ||||||||||
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MODELLER Resource Report Resource Website 5000+ mentions |
MODELLER (RRID:SCR_008395) | software application, portal, software resource, topical portal, simulation software, data or information resource | Software tool as Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Used for homology or comparative modeling of protein three dimensional structures. User provides alignment of sequence to be modeled with known related structures and MODELLER automatically calculates model containing all non hydrogen atoms. | comparative, protein, structure, modelling, satisfaction, spatial, restrain, homology, 3D, alignment, sequence, hydrogen, atom, cluster |
is listed by: SoftCite has parent organization: University of California at San Francisco; California; USA |
Sandler Family Supporting Foundation ; NIGMS R01 GM54762; NIGMS P01 GM71790; NIH P01 A135707; NIGMS U54 GM62529; IBM ; Intel |
Restricted | nif-0000-30054 | SCR_008395 | 2026-02-16 09:47:10 | 5736 | ||||||||
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InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | software application, data processing software, web service, data analysis software, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service resource | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
European Union ; Biotechnology and Biological Sciences Research Council ; EMBL |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html https://bio.tools/interproscan_4 |
SCR_005829 | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-02-16 09:46:33 | 6936 | |||||
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UCSC Genome Browser Resource Report Resource Website 10000+ mentions Rating or validation data |
UCSC Genome Browser (RRID:SCR_005780) | project portal, database, portal, service resource, data or information resource | Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data. | Reference, sequence, assembly, collection, genome, visualize, genomic, data, ENCODE, Neanderthal, project, sequencing |
is used by: VizHub is used by: Blueprint Epigenome is used by: QmRLFS-finder is used by: International Human Epigenome Consortium Data Portal is used by: iPiG is listed by: re3data.org is listed by: OMICtools is listed by: Educational Resources in Neuroscience is listed by: SoftCite is related to: HEXEvent is related to: PicTar is related to: Phenotree is related to: Enhancer Trap Line Browser is related to: CistromeFinder is related to: ENCODE is related to: Human Epigenome Atlas is related to: ENCODE is related to: BigWig and BigBed is related to: PhenCode is related to: doRiNA is related to: ISCA Consortium is related to: WashU Epigenome Browser is related to: CRISPOR is related to: liftOver is related to: kent has parent organization: University of California at Santa Cruz; California; USA works with: TarBase |
UC BIOTEuropean UnionH ; Alfred P. Sloan Foundation ; David and Lucille Packard Foundation ; NIH ; HHMI ; CISI ; NHGRI ; DOE ; NSF DBI 9809007; NIGMS GM52848 |
PMID:12045153 PMID:22908213 PMID:23155063 |
OMICS_00926, SCR_017502, nif-0000-03603, SciEx_217, SCR_012479, r3d100010243 | http://genome.cse.ucsc.edu https://doi.org/10.17616/R3RK5C |
SCR_005780 | The Human Genome Browser at UCSC, UCSC Genome Browser Group, University of California at Santa Cruz Genome Browser, UCSC Genome Bioinformatics | 2026-02-16 09:46:41 | 10026 |
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