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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
http://actimetrics.com/products/clocklab/
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.
Proper citation: Clocklab (RRID:SCR_014309) Copy
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.
Proper citation: LabView (RRID:SCR_014325) Copy
http://www.matrixscience.com/server.html
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.
Proper citation: Mascot (RRID:SCR_014322) Copy
http://darwin.uvigo.es/software/prottest_server.html
Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: ProtTest (RRID:SCR_014628) Copy
A web server which recognizes tertiary structures from an amino acid sequence based on estimated pairwise energy content. Users can input SWISS-PROT/TrEMBL identifier or accession number, or paste the amino acid sequence.
Proper citation: IUPRED (RRID:SCR_014632) Copy
Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: FATCAT (RRID:SCR_014631) Copy
Ratings or validation data are available for this resource
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
Proper citation: FastQC (RRID:SCR_014583) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET
Software tool which deletes non-brain tissue from image of the whole head and estimates both internal and external skull surfaces.
Proper citation: Brain Extraction Tool (RRID:SCR_014586) Copy
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.
Proper citation: Bowtie 2 (RRID:SCR_016368) Copy
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.
Proper citation: microRNA.org (RRID:SCR_006997) Copy
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.
Proper citation: CCP4 (RRID:SCR_007255) Copy
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.
Proper citation: RMS (RRID:SCR_007415) Copy
http://fmri.wfubmc.edu/software/PickAtlas
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.
Proper citation: WFU PickAtlas (RRID:SCR_007378) Copy
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
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