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https://code.google.com/p/pride-converter-2/

Suite of software tools that allows users to convert search result files into PRIDE XML, generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra.

Proper citation: PRIDE Converter 2 (RRID:SCR_012051) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/jmzreader/

A collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML.

Proper citation: jmzReader (RRID:SCR_012050) Copy   

•   Source: SciCrunch Registry

http://insilicogenome.sourceforge.net/

A large-scale whole genome simulation tool which generates large numbers of whole genomes with known sequence characteristics based on direct sampling of experimentally known or theorized variations.

Proper citation: FIGG (RRID:SCR_012064) Copy   

•   Source: SciCrunch Registry

http://mrbayes.sourceforge.net/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.

Proper citation: MrBayes (RRID:SCR_012067) Copy   

•   Source: SciCrunch Registry

http://cat.princeton.edu/

A software package for predicting genome-wide co-binding between biological regulators such as Transcription factors (TFs).

Proper citation: CCAT (Combinatorial Code Analysis Tool) (RRID:SCR_012028) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/open-ms/

An algorithm to align LC-MS samples and to match corresponding ion species across samples.

Proper citation: OpenMS (RRID:SCR_012042) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/nailsystemsbiology/

A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use.

Proper citation: NAIL (RRID:SCR_012134) Copy   

•   Source: SciCrunch Registry

http://xmsanalyzer.sourceforge.net

A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat.

Proper citation: xMSanalyzer (RRID:SCR_012144) Copy   

•   Source: SciCrunch Registry

http://www.mathcs.emory.edu/panda/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Web-based software program for analyzing phosphorylation antibody arrays. It identifies phosphorylated antibodies in the microarray and statistically quantifies the extent of phosphorylation for these antibodies.

Proper citation: Phosphor Antibody Array Data Analysis (RRID:SCR_000633) Copy   

•   Source: SciCrunch Registry

http://datavyu.org/

Free, Java-based video coding and data visualization tool for collecting behavioral data from video. It supports all video formats that Quicktime or VLC can play, including .asf, .wmv, .avi, .flv, .mov, .mpf, .ogg, .mpg, .nsc, .wav, and .dts. It exports data in a variety of forms depending on analysis needs.

Proper citation: Datavyu (RRID:SCR_003587) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/mlgt/index.html

Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.

Proper citation: mlgt (RRID:SCR_001211) Copy   

•   Source: SciCrunch Registry

https://www.bioprocessonline.com/doc/image-processing-software-0001

Image processing software package that provides scientific image acquisition, visualization, analysis and laboratory automation in single package. Allows users to acquire grayscale and color images from most video cameras, variety of cooled CCD digital cameras and high resolution flatbed scanners. Capable of analyzing image data in seven different data types, this program can calculate integrated intensity, mean, min, and max values plus several morphometric parameters on object regions within images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: Scanalytics IPLab (RRID:SCR_002775) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/threedicsi/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Software program for multi-dimensional CSI data visualization, spectral processing, localization, quantification and multi-variate analysis.

Proper citation: 3D Interactive Chemical Shift Imaging (RRID:SCR_002581) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/valmap/

A command line voxel-wise statistical analysis software program for images. Images can be gray matter density, jacobian images, etc. The linear model is implemented, i.e. designs that can be modeled as Y=AB, where Y is a vector or matrix of dependent variables, B is a vector or matrix of parameters to be estimated, and A is a design matrix. Why use valmap? # Do not need a Matlab license to run. # Can incorporate a spatially varying independent variable (e.g., you have a perfusion map as your dependent variable, and you want to co-vary for gray matter at each voxel, so use a gray matter map as an independent variable). # Can use spatially invariant independent variables (e.g., you can have a cognitive test score as the dependent variable, and use jacobian maps as the independent variable). # Can have multiple dependent variables and do multivariate analyses (e.g., want to know the overall effect of disease on perfusion and structure, so use perfusion maps and jacobian maps as dependent variables).

Proper citation: ValMap: simple statistical mapping tool (RRID:SCR_002610) Copy   

•   Source: SciCrunch Registry

http://gmod.org/wiki/Apollo

A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses.

Proper citation: Apollo (RRID:SCR_001936) Copy   

•   Source: SciCrunch Registry

http://www.na-mic.org/Wiki/index.php/UNC_SPHARM-PDM_Tutorial

Software tool that computes point-based models using a parametric boundary description for the computing of Shape analysis. The point-based models computed with the SPHARM-PDM tool can be used in combination with the also UNC designed statistical tool shapeAnalysisMANCOVA to perform quantitative morphological assessment of structural changes at speci?c locations. Shape analysis has become of increasing interest to the medical community due to its potential to precisely locate morphological changes between healthy and pathological structures.

Proper citation: SPHARM-PDM Toolbox (RRID:SCR_002546) Copy   

•   Source: SciCrunch Registry

http://scikit-learn.org/

scikit-learn: machine learning in Python

Proper citation: scikit-learn (RRID:SCR_002577) Copy   

•   Source: SciCrunch Registry

http://www.pstnet.com/software.cfm?ID=94

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. NOTE: VR Worlds 2 is no longer available as a standalone software. Software application designed for the creation and execution of neurobehavioral studies. The VR Worlds 2 platform allows accurate, real-time data collection of the navigation and interactions within a simulated environment. You are free to design and perform custom or predefined experiments tailored to your personal research or clinical needs. Create complex environments with meaningful content using VR Worlds 2?s user-friendly, drag-and-drop interface. Include triggers to launch simple or intricate events, such as a conversation between characters or a customizable rating scale. VR Worlds 2 provides several realistic simulations to immerse your subjects in context appropriate environments, including: * Residential/Urban Area * Hotel Lobby * Medical Office * Grocery Store * Neighborhood for drug and alcohol cue extinction treatment (featured on GMA, motion capture process) * Casino for gambling addiction research (featured on Canadian Discovery Channel) * Driving simulation for mild cognitive impairment research * Phobia scenarios * Spatial navigation mazes

Proper citation: VR Worlds 2 (RRID:SCR_002608) Copy   

•   Source: SciCrunch Registry

http://psychtoolbox.org/

A free set of Matlab and GNU/Octave functions for vision research. It makes it easy to synthesize and show accurately controlled visual and auditory stimuli and interact with the observer.

Proper citation: Psychophysics Toolbox (RRID:SCR_002881) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/dnaplotter/

Software application used to generate images of circular and linear DNA maps to display regions and features of interest. The images can be inserted into a document or printed out directly. As this uses Artemis it can read in the common file formats EMBL, GenBank and GFF3.

Proper citation: DNAPlotter (RRID:SCR_005006) Copy   

•   Source: SciCrunch Registry