Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://www.bitplane.com/imaris/imaris
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.
Proper citation: Imaris (RRID:SCR_007370) Copy
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
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.
Proper citation: BioEdit (RRID:SCR_007361) Copy
https://www.flowjo.com/solutions/flowjo
Software for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.
Proper citation: FlowJo (RRID:SCR_008520) Copy
http://emboss.sourceforge.net/
Software analysis package for molecular biology community. Automatically copes with data in variety of formats and allows transparent retrieval of sequence data from web. Libraries are provided with package. Provides toolkit for creating bioinformatics applications or workflows. Provides set of sequence analysis programs. Provided programs cover areas such as sequence alignment, rapid database searching with sequence patterns, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, and presentation tools for publication.
Proper citation: EMBOSS (RRID:SCR_008493) Copy
Python 2D plotting library which produces publication quality figures in variety of hardcopy formats and interactive environments across platforms. Used in python scripts, web application servers, and six graphical user interface toolkits. Used to generate plots, histograms, power spectra, bar charts, error charts, scatter plots.
Proper citation: Matplotlib (RRID:SCR_008624) Copy
Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software)
Proper citation: CMAP (RRID:SCR_009034) Copy
http://www.sigmaplot.com/products/sigmaplot/sigmaplot-details.php
Software tool for data graphing and analysis by Systat Software, Inc.
Proper citation: SigmaStat (RRID:SCR_010285) Copy
http://bioinf.cs.ucl.ac.uk/psipred/
Web tool as secondary structure prediction method, incorporating two feed forward neural networks which perform analysis on output obtained from PSI-BLAST. Web server offering analyses of protein sequences.
Proper citation: PSIPRED (RRID:SCR_010246) Copy
Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals.
Proper citation: TargetScan (RRID:SCR_010845) Copy
http://lgsun.grc.nia.nih.gov/ANOVA/
Data analysis server / software designed to test statistical significance of gene microarray data, visualize the results, and provide links to clone information and gene index. Several public datasets are also available.
Proper citation: NIA Array Analysis (RRID:SCR_010948) Copy
http://ccb.jhu.edu/software/glimmer/index.shtml
A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
Proper citation: Glimmer (RRID:SCR_011931) Copy
http://mafft.cbrc.jp/alignment/server/
Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
Proper citation: MAFFT (RRID:SCR_011811) Copy
http://biomedical.materialise.com/mimics
Software for medical image processing. Use Mimics for the segmentation of 3D medical images (coming from CT, MRI, microCT, CBCT, Ultrasound, Confocal Microscopy) and the result will be highly accurate 3D models of your patient''s anatomy. You can then use these patient-specific models for a variety of engineering applications directly in Mimics or 3-matic, or export the 3D models and anatomical landmark points to 3rd party software, like statistical, CAD, or FEA packages.
Proper citation: Mimics (RRID:SCR_012153) Copy
http://sift.bii.a-star.edu.sg/
Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available.
Proper citation: SIFT (RRID:SCR_012813) Copy
https://github.com/macs3-project/MACS
Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.
Proper citation: MACS (RRID:SCR_013291) Copy
The MOBY-S system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next. The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. Sponsors: Funding was provided by Genome Prairie and Genome Alberta A Bioinformatics Platform for Genome Canada''; Canadian Institutes for Health Research; The Natural Sciences and Engineering Research Council of Canada; The Heart and Stroke Foundation for BC and Yukon; The EPSRC through the myGrid (GR/R67743/01, EP/C536444/1, EP/D044324/1, GR/T17457/01) e-Science projects; The Spanish National Institute for Bioinformatics (INB) through Fundacin Genoma Espaa; The Generation Challenge Programme (GCP; http://www.generationcp.org) of the Consultative Group for International Agricultural Research. :Keywords: Ontology, Messaging, Standard, Client, Automatically, Discovery, Biological, Data, ANalytical, Service, Model, Organism, Database, Java, Platform, Semantic, Bioinformatics,
Proper citation: BioMoby (RRID:SCR_013386) Copy
http://cleversysinc.com/?csi_products=homecagescan
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.
Proper citation: HomeCageScan (RRID:SCR_014253) Copy
https://www.intelligent-imaging.com/slidebook.php
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.
Proper citation: SlideBook (RRID:SCR_014300) Copy
https://www.adobe.com/products/photoshop.html
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.
Proper citation: Adobe Photoshop (RRID:SCR_014199) Copy
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.
Proper citation: Multi Gauge (RRID:SCR_014299) Copy
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within RRID that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
