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https://www.leica-microsystems.com/products/microscope-software/details/product/leica-las-x-ls/

Software for image capture, processing and analysis with Leica fluorescence and confocal microscopes.

Proper citation: Leica Application Suite X (RRID:SCR_013673) Copy   

•   Source: SciCrunch Registry

http://www.cyto.purdue.edu/flowcyt/software/Winmdi.htm

Software to analyze flow cytometry listmode data files.

Proper citation: WinMDI Software (RRID:SCR_013745) Copy   

•   Source: SciCrunch Registry

http://animaltracker.elte.hu/

A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation.

Proper citation: AnimalTracker (RRID:SCR_014397) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.olympus-lifescience.com/en/software/cellsens/

Software suite for image acquisition and analysis. The software can be paired with high-quality cameras to maximize output quality and export it for sharing and research applications.

Proper citation: Olympus cellSens Software (RRID:SCR_014551) Copy   

•   Source: SciCrunch Registry

http://www.ccdc.cam.ac.uk/free_services/relibase_free

Web-based system for searching and analysing protein-ligand structures in the Protein Data Bank (PDB). The database provides an easily accessible web-browser interface and clear 3D structure visualisation that allows for 3D protein-ligand interaction searches, automatic superimposition and detailed analysis of related binding sites to identify protein flexibility, ligand overlap, and conserved water positions.

Proper citation: Relibase (RRID:SCR_014888) Copy   

•   Source: SciCrunch Registry

http://www.analog-electronics.eu/slicap/slicap.html

A software toolbox containing a symbolic linear circuit analysis program. It is a MATLAB application that helps set up and solve design equations of electronic circuits.

Proper citation: SLiCAP (RRID:SCR_014742) Copy   

•   Source: SciCrunch Registry

http://www2.chemie.uni-erlangen.de/software/cactvs/

Computational chemistry related-software used for the computation management, analysis and visualisation of chemical information of any defined type. This software uses a worldwide network of databases with property descriptions, computational modules, data analysis tools, visualization servers, data type handlers and I/O modules to increase the software�s capacity extensibility.

Proper citation: CACTVS System (RRID:SCR_014919) Copy   

•   Source: SciCrunch Registry

http://niag.ir/

Project to house templates used to build other projects. It is also known as the NeuroImaging and Analysis Group, which employs various physiological, functional and structural neuroimaging methodologies in both research and clinical domains.

Proper citation: Template Project (RRID:SCR_015516) Copy   

•   Source: SciCrunch Registry

http://shiny.chemgrid.org/boxplotr/

Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox.

Proper citation: BoxPlotR (RRID:SCR_015629) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.9/bioc/html/RamiGO.html

Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.

Proper citation: RamiGO (RRID:SCR_006922) Copy   

•   Source: SciCrunch Registry

http://scicrunch.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2019.

Database for those interested in the consequences of Factor VIII genetic variation at the DNA and protein level, it provides access to data on the molecular pathology of haemophilia A. The database presents a review of the structure and function of factor VIII and the molecular genetics of haemophilia A, a real time update of the biostatistics of each parameter in the database, a molecular model of the A1, A2 and A3 domains of the factor VIII protein (based on the crystal structure of caeruloplasmin) and a bulletin board for discussion of issues in the molecular biology of factor VIII. The database is completely updated with easy submission of point mutations, deletions and insertions via e-mail of custom-designed forms. A methods section devoted to mutation detection is available, highlighting issues such as choice of technique and PCR primer sequences. The FVIII structure section now includes a download of a FVIII A domain homology model in Protein Data Bank format and a multiple alignment of the FVIII amino-acid sequences from four species (human, murine, porcine and canine) in addition to the virtual reality simulations, secondary structural data and FVIII animation already available. Finally, to aid navigation across this site, a clickable roadmap of the main features provides easy access to the page desired. Their intention is that continued development and updating of the site shall provide workers in the fields of molecular and structural biology with a one-stop resource site to facilitate FVIII research and education. To submit your mutants to the Haemophilia A Mutation Database email the details. (Refer to Submission Guidelines)

Proper citation: HAMSTeRS - The Haemophilia A Mutation Structure Test and Resource Site (RRID:SCR_006883) Copy   

•   Source: SciCrunch Registry

http://geneontology.org/docs/tools-overview/

Collection of tools developed by GO Consortium and by third parties. Tools are listed by category or alphabetically and continue to be improved and expanded.

Proper citation: Gene Ontology Tools (RRID:SCR_006941) Copy   

•   Source: SciCrunch Registry

http://www.bmu.psychiatry.cam.ac.uk/software/

Suite of programs developed for fMRI analysis in a Virtual Pipeline Laboratory facilitates combining program modules from different software packages into processing pipelines to create analysis solutions which are not possible with a single software package alone. Current pipelines include fMRI analysis, statistical testing based on randomization methods and fractal spectral analysis. Pipelines are continually being added. The software is mostly written in C. This fMRI analysis package supports batch processing and comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution.

Proper citation: Cambridge Brain Activation (RRID:SCR_007109) Copy   

•   Source: SciCrunch Registry

http://weizhong-lab.ucsd.edu/cd-hit/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for clustering biological sequences with many applications in various fields such as making non-redundant databases, finding duplicates, identifying protein families, filtering sequence errors and improving sequence assembly etc. It is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU and over a dozen scripts. * CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. * CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. * CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads. * CD-HIT-OTU cluster rRNA tags into OTUs The usage of other programs and scripts can be found in CD-HIT user''s guide. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik''s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CD-HIT (RRID:SCR_007105) Copy   

•   Source: SciCrunch Registry

https://bams1.org/

Knowledge management system designed to handle neurobiological information at different levels of organization of vertebrate nervous system. Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. Handles data and metadata collated from original literature, or inserted by scientists that is associated to four levels of organization of vertebrate nervous system. Data about expressed molecules, neuron types and classes, brain regions, and networks of brain regions.

Proper citation: Brain Architecture Management System (RRID:SCR_007251) Copy   

•   Source: SciCrunch Registry

http://www.fsm.ethz.ch/publications-list/software.html

Software for tracking and analysis based on algorithms describing structural and topological features of fiber-like objects. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects.

Proper citation: FiberApp (RRID:SCR_015826) Copy   

•   Source: SciCrunch Registry

https://genome.tugraz.at/genesisclient/genesisclient_description.shtml

Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments.

Proper citation: Genesis (RRID:SCR_015775) Copy   

•   Source: SciCrunch Registry

https://github.com/DDTBOX/DDTBOX

Software toolkit for multivariate pattern analysis (MVPA) of event-related potentials. This software is written in MATLAB.

Proper citation: Decision Decoding Toolbox (RRID:SCR_015978) Copy   

•   Source: SciCrunch Registry

http://avogadro.cc/

Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

Proper citation: Avogadro (RRID:SCR_015983) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/Bio-Tradis

Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.

Proper citation: Bio-tradis (RRID:SCR_015993) Copy   

•   Source: SciCrunch Registry