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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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UCSF Chimera Resource Report Resource Website 1000+ mentions |
UCSF Chimera (RRID:SCR_004097) | Chimera | software application, d visualization software, data processing software, software resource | Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials. | molecular modeling, electron microscopy, interactive visualization and analysis, molecular structures |
is used by: Structure-function linkage database is listed by: 3DVC is listed by: SoftCite is related to: Integrative Modeling Platform is related to: UCSF ChimeraX is related to: UCSF ChimeraX has parent organization: Resource for Biocomputing Visualization and Informatics |
NIGMS P41 GM103311; NCRR P41 RR001081 |
PMID:15264254 | Restricted | nlx_143560 | http://plato.cgl.ucsf.edu/chimera/ | SCR_004097 | Chimera - an Extensible Molecular Modeling System, UCSF Chimera - an Extensible Molecular Modeling System | 2026-02-15 09:18:40 | 2078 | ||||
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microRNA.org Resource Report Resource Website 1000+ mentions |
microRNA.org (RRID:SCR_006997) | microRNA.org | data or information resource, database, software resource | Database of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. This website enables users to explore: * The set of genes that are potentially regulated by a particular microRNA. * The implied cooperativity of multiple microRNAs on a particular mRNA. * MicroRNA expression profiles in various mammalian tissues. The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation. The microRNA Target Detection Software, miRanda, is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microrna, gene, expression, gene regulation, FASEB list |
is listed by: OMICtools is listed by: SoftCite |
NIGMS ; Atlantic Philanthropies ; Alfred W. Bressler Scholars Endowment Fund |
PMID:18158296 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03127, OMICS_00402 | SCR_006997 | microRNA.org - Targets and Expression | 2026-02-15 09:19:39 | 2648 | |||||
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WFU PickAtlas Resource Report Resource Website 1000+ mentions |
WFU PickAtlas (RRID:SCR_007378) | PickAtlas | software application, image processing software, data processing software, software resource | A software toolbox that provides a method for generating Region of Interest (ROI) masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy), and Tissue type. The atlases have been extended to the vertex in MNI space, and corrected for the precentral gyrus anomaly. Additional atlases (including non-human atlases) can be added without difficulty., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | neuroanatomy, cytoarchitecture, fmri, matlab, brain, brain region, talairach daemon, analyze, atlas application, matlab, microsoft, magnetic resonance, posix/unix-like, win32 (ms windows), windows, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: SoftCite is related to: Talairach Daemon has parent organization: Wake Forest School of Medicine; North Carolina; USA |
NIBIB 1R03EB008670 | PMID:12880848 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00358 | SCR_007378 | WFU_PickAtlas | 2026-02-15 09:19:34 | 1261 | |||||
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CCP4 Resource Report Resource Website 1000+ mentions |
CCP4 (RRID:SCR_007255) | CCP4 | software application, portal, data processing software, software resource, service resource, simulation software, data or information resource, data analysis software | Portal for Macromolecular X-Ray Crystallography to produce and support an integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. Used in the education and training of scientists in experimental structural biology for determination and analysis of protein structure. | macromolecular, x-ray, crystallography, biophysical, technique, structural, biology, analysis, protein, Research Complex at Harwell, computational, collaborative, project |
is used by: MoRDa is used by: PDB-REDO is listed by: SoftCite is related to: BALBES is related to: CCP4mg is related to: fragon is related to: ConPlot has parent organization: Science and Technology Facilities Council |
Science and Technology Facilities Council | Free, Available for download, Freely available, Tutorial available | SCR_016709, nif-0000-30238 | SCR_007255 | The Collaborative Computational Project Number 4 in Protein Crystallography, Collaborative Computational Project Number 4 | 2026-02-15 09:19:31 | 4740 | ||||||
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Imaris Resource Report Resource Website 10000+ mentions |
Imaris (RRID:SCR_007370) | software application, image analysis software, data processing software, software resource | Imaris provides range of capabilities for working with three dimensional images. Uses flexible editing and processing functions, such as interactive surface rendering and object slicing capabilities. And output to standard TIFF, Quicktime and AVI formats. Imaris accepts virtually all image formats that are used in confocal microscopy and many of those used in wide-field image acquisition. Imaris version 10.1 for image analysis workflows using AI trainable object detection. | Three dimensional images, 3D image, AI trainable object detection, |
is used by: Simple Assignment of Spots to Surfaces is listed by: SoftCite is related to: FilamentTracer is related to: ImarisViewer |
Restricted | nif-0000-00314 | https://imaris.oxinst.com/ https://imaris.oxinst.com/newrelease |
SCR_007370 | , Imaris 10.1, Imaris 9.7 | 2026-02-15 09:19:34 | 15762 | |||||||
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BioEdit Resource Report Resource Website 10000+ mentions |
BioEdit (RRID:SCR_007361) | software application, sequence analysis software, data processing software, software resource, alignment software, image analysis software, data analysis software | Software tool as biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7 and sequence analysis program. Provides sequence manipulation and analysis options and links to external analysis programs to view and manipulate sequences with simple point and click operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, alignment, editor, analysis, program | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156845 | SCR_007361 | 2026-02-15 09:19:34 | 13339 | |||||||||
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RMS Resource Report Resource Website 1+ mentions |
RMS (RRID:SCR_007415) | RMS | portal, training resource, job resource, data or information resource, topical portal | It is at the forefront of new ideas and developments in microscopy and imaging. The RMS is the only truly international microscopical society, drawing distinguished members from all over the world. It also serves the needs of its company members who represent all the major manufacturers and suppliers of microscopes, equipment and services. In addition to this, the Society is pursuing an initiative to encourage young microscope users who may go on to influence microscopy in years to come. The Society is dedicated to advancing science, developing careers and supporting wider understanding of science and microscopy through its Science and Society activities. In support of the above, it publishes The Journal of Microscopy and microscopy handbooks, as well as helping young scientists through bursaries. The Society is incorporated by Royal Charter. Its governing documents are its Charter and By-laws. The most recent AGM minutes, Trustees Report and Accounts are available below - 2007 AGM draft minutes Full 2007 Trustees Report and Accounts - as submitted to the Charity Commission The RMS is a member of: - the Foundation for Science and Technology - the Biosciences Federation - the International Federation of Societies for Microscopy - the European Microscopy Society training opportunities; jobs. | is listed by: SoftCite | nif-0000-00498 | SCR_007415 | The Royal Microscopical Society | 2026-02-15 09:19:35 | 6 | |||||||||
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MediaWiki Resource Report Resource Website 10+ mentions |
MediaWiki (RRID:SCR_014045) | software application, software resource, authoring tool | A server-based software wiki package written in PHP. It is a powerful, scalable software deigned for high-traffic websites. MediaWiki uses PHP to process and display data stored in a database such as MySQL. When a user submits an edit to a page, MediaWiki writes it to the database without deleting the previous versions, allowing easy reversions. MediaWiki is able to manage image and multimedia files, as well, which are stored in the filesystem. | authoring tool, software, wiki, PHP, FASEB list |
is listed by: SoftCite is related to: WorkingWiki is parent organization of: Semantic MediaWiki |
Public, Free | SCR_014045 | 2026-02-15 09:20:54 | 48 | ||||||||||
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HomeCageScan Resource Report Resource Website 10+ mentions |
HomeCageScan (RRID:SCR_014253) | software application, time-series analysis software, data processing software, software resource, data acquisition software, data analysis software | Software used for automatic high throughput analysis of unconstrained rodent behaviors in a home cage. HomeCageScan is ideal for longitudinal studies where several animals are studied and tested over long periods. Its features include twenty-four-hour recording capabilities, statistical analysis, automatic adaptation to environmental changes (including day and night changes), and a batch‐mode which allows user to run multiple videos successively without human intervention. The software can detect various behaviors ranging from feeding and urination to jumping and foraging. | automatic high throughput analysis, unconstrained rodent behavior, home cage, longitudinal study | is listed by: SoftCite | Available for purchase | SCR_014253 | 2026-02-15 09:20:51 | 29 | ||||||||||
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SlideBook Resource Report Resource Website 500+ mentions |
SlideBook (RRID:SCR_014300) | software application, image processing software, data processing software, software resource, data analysis software | Digital microscopy software for research microscopy. It comes standard with drivers to control numerous instruments in and around the microscope. When online, data is acquired in a native-3D format over time, color and specimen locations in customizable experiment protocols. Data can be analyzed by a wide variety of tools for image processing including mathematical operations, statistics functions, analysis scripting and import to/export from MATLAB. Additional modules are available for special applications ranging from deconvolution to photomanipulation to multiphoton. | digital microscopy software, research microscopy, image processing software, data analysis software | is listed by: SoftCite | Available for download, Free, Compatible with Windows 7 and Windows XP | SCR_014300 | SlideBook 6 | 2026-02-15 09:20:42 | 979 | |||||||||
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Adobe Photoshop Resource Report Resource Website 10000+ mentions |
Adobe Photoshop (RRID:SCR_014199) | software application, image processing software, data processing software, software resource, image analysis software | Software for image processing, analysis, and editing. The software includes features such as touch capabilities, a customizable toolbar, 2D and 3D image merging, and Cloud access and options. | image processing software, image analysis software, image editing, editing software, adobe |
is listed by: SoftCite is related to: Adobe Photoshop Lightroom |
SCR_014234, SCR_014298, SciRes_000161, SCR_002078 | http://www.adobe.com/products/cs6.html | SCR_014199 | Adobe Photoshop CC, Adobe Photoshop CS, Photoshop | 2026-02-15 09:20:39 | 25163 | ||||||||
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Multi Gauge Resource Report Resource Website 10+ mentions |
Multi Gauge (RRID:SCR_014299) | software application, data processing software, data analysis software, software resource | A software application for one-dimensional electrophoretic analysis of multi-labeled fluorophores. It was designed to analyze multi-channel fluorescence data from Fujifilm FLA-5000 and FLA-8000 scanning systems. The software also works with other scanners in the BAS/FLA series and with the LAS series. | data analysis software, one dimensional electrophoretic analysis, fluorophore, multi channel fluorescence data | is listed by: SoftCite | http://www.scienceimaging.se/application-info/55.html | SCR_014299 | MultiGuage | 2026-02-15 09:21:00 | 36 | |||||||||
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Origin Resource Report Resource Website 10000+ mentions |
Origin (RRID:SCR_014212) | software application, data visualization software, data processing software, software resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing. | data, analysis, software, authoring, tool, scripting, graphing, statistical, publication |
is listed by: SoftCite is related to: OriginPro |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015636 | https://www.originlab.com/index.aspx?go=PRODUCTS&PID=1834 | SCR_014212 | OriginPro | 2026-02-15 09:20:50 | 13956 | |||||||
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Refmac Resource Report Resource Website 1000+ mentions |
Refmac (RRID:SCR_014225) | software application, sequence analysis software, data processing software, software resource, data analysis software | A molecular refinement program with two main modes: REVIEW, which checks and updates the input model to establish that the geometric restraints can be properly set up, and REFINE mode, which is the standard mode and documented in keywords. In REVIEW users can: check model coordinates and write an extended output set of coordinates, find disulphide bonds and other covalent links, cis-peptides, output the sequence and REMARK records. In REFINEMENT mode users can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. Also in REFINEMENT mode, Refmac produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps. The program is supported by CCP4. | molecular refinement, data analysis software, sequence analysis software |
is used by: PDB-REDO is listed by: SoftCite |
SCR_014225 | 2026-02-15 09:20:40 | 1978 | |||||||||||
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Phenix Resource Report Resource Website 10000+ mentions |
Phenix (RRID:SCR_014224) | software application, data processing software, software resource, image analysis software, image reconstruction software | A Python-based software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Phenix includes programs for assessing data quality, experimental phasing, molecular replacement, model building, structure refinement, and validation. It also includes tools for reflection data and creating maps and models. Phenix can also be used for neutron crystallography. Tutorials and examples are available in the documentation tab. | automation, molecular structure, xray crystallography, neutron crystallography, image reconstruction software |
is listed by: SoftCite is affiliated with: Phaser is related to: MolProbity has parent organization: Lawrence Berkeley National Laboratory has parent organization: University of California at Berkeley; Berkeley; USA provides: Phenix.refine |
NIGMS | Available for download, Free for nonprofit work, Acknowledgement requested, For profit groups may access PHENIX through a Consortium agreement | https://www.phenix-online.org/documentation/ | SCR_014224 | Python-based Hierarchical ENvironment for Integrated Xtallography | 2026-02-15 09:20:58 | 10587 | |||||||
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Clocklab Resource Report Resource Website 500+ mentions |
Clocklab (RRID:SCR_014309) | software application, data processing software, software resource, standalone software, data acquisition software, data analysis software | Point and click program used to quickly analyse circadian activity data using algorithms and embedded controls to make every graph interactive and useful for data analysis. The analysis program has been used for a variety of species including mice, hamsters, rats, sheep, Drosophila, and humans. This program has three separate applications: one for data collection, one for analysis, and a chamber control program. | circadian activity data, interactive, data analysis software, data acquisition software, standalone software | is listed by: SoftCite | Pay for product, Users can order different components of ClockLab separately | SCR_014309 | 2026-02-15 09:21:00 | 546 | ||||||||||
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LabView Resource Report Resource Website 100+ mentions |
LabView (RRID:SCR_014325) | software development tool, software application, software development environment, software resource | A development environment for engineers and scientists to visualize, create, and code engineering systems. The system design software is integrated with all measurement hardware and contains signal processing IP. Other features include multithreaded execution, software deployment to hardware, and program integration into a single environment. | development environment, system design software, software development tool |
is used by: Demon Voltammetry and Analysis Software is listed by: SoftCite is related to: ZebEyeTrack is related to: ActiView |
Pay for product, Free trail is available | SCR_014325 | LabVIEW System Design Software, NI LabVIEW software, LabView System Design Software, LabVIEW | 2026-02-15 09:20:42 | 244 | |||||||||
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Mascot Resource Report Resource Website 5000+ mentions |
Mascot (RRID:SCR_014322) | software application, data processing software, software resource, standalone software, signal processing software | A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters. | server, software package, mass spectrometry, protein, identify, characterize, bio.tools |
is used by: MSQuant is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: MascotScan |
Free, Can be licensed for in-house use, Available for download | biotools:MASCOT | http://www.matrixscience.com/search_intro.html https://bio.tools/MASCOT |
SCR_014322 | Mascot Server | 2026-02-15 09:20:52 | 6896 | |||||||
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Proteome Discoverer Resource Report Resource Website 1000+ mentions |
Proteome Discoverer (RRID:SCR_014477) | software application, data processing software, software resource, workflow software, data analysis software | Software for identifying, characterizing, and quantifying proteins in biological samples. Can be used for range of proteomics workflows such as protein and peptide identification, PTM analysis, and isobaric mass tagging for quantification. Supports multiple database search algorithms and multiple dissociation techniques., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis, workflow software, proteomics, database search, FASEB list |
is used by: thermo-msf-parser is listed by: SoftCite works with: Peakjuggler works with: pepwheel |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014477 | 2026-02-15 09:20:54 | 1478 | ||||||||||
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MaxQuant Resource Report Resource Website 10000+ mentions |
MaxQuant (RRID:SCR_014485) | software application, data processing software, data analysis software, software resource | A quantitative proteomics software package for analyzing large-scale mass-spectrometric data sets. It is a set of algorithms that include peak detection and scoring of peptides, mass calibration, database searches for protein identification, protein quantification, and provides summary statistics. | mass spectrometry analysis software, proteomics software, mass calibration, protein identification, protein quantification, FASEB list | is listed by: SoftCite | PMID:19029910 PMID:25059623 |
SCR_014485 | 2026-02-15 09:20:55 | 12462 |
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