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http://www.dengine.org

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. Software designed to serve as a distributed computational framework to help perform mathematical simulations of muscle contraction. DEngine has a Windows PC, central controller PC and mathematical models that run as console applications on clients.

Proper citation: Distributed Computing Engine (RRID:SCR_000781) Copy   

•   Source: SciCrunch Registry

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

A Java application programming interface (API) for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data.

Proper citation: jmzIdentML API (RRID:SCR_000878) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/Pipeline

A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely.

Proper citation: LONI Pipeline Processing Environment (RRID:SCR_001161) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowWorkspace.html

Software package that facilitates comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

Proper citation: flowWorkspace (RRID:SCR_001155) Copy   

•   Source: SciCrunch Registry

http://www.genoviewer.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Open source viewer / browser software for the SAM / BAM format commonly used in the assembly tasks of Next Generation Sequencing data.

Proper citation: GenoViewer (RRID:SCR_001203) Copy   

•   Source: SciCrunch Registry

http://heim.ifi.uio.no/bioinf/Projects/CGHExplorer/

Software program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion.

Proper citation: CGH-Explorer (RRID:SCR_001283) Copy   

•   Source: SciCrunch Registry

https://apsampler.sourceforge.net/

A software tool that allows multi-locus and multi-level association analysis of genotypic and phenotypic data.

Proper citation: APSampler (RRID:SCR_000042) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/spdesigner/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa.

Proper citation: SP-Designer (RRID:SCR_000031) 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://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.html

A software package that provides functions to read raw RT-qPCR data of different platforms.

Proper citation: ReadqPCR (RRID:SCR_000030) 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.vectorfriends.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Sequence analysis software for molecular biologists.

Proper citation: VectorFriends (RRID:SCR_001230) Copy   

•   Source: SciCrunch Registry

https://github.com/neufeld/pandaseq

Software program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

Proper citation: PANDAseq (RRID:SCR_002705) Copy   

•   Source: SciCrunch Registry

http://primerdigital.com/fastpcr.html

Software tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching.

Proper citation: FastPCR (RRID:SCR_003155) Copy   

•   Source: SciCrunch Registry

http://www.geospiza.com/Products/finchtv.shtml

Chromatogram viewer that can display an entire trace in a scalable multi-pane view, allows raw data views, BLAST searching and the ability to reverse complement sequences and traces., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FinchTV (RRID:SCR_005584) Copy   

•   Source: SciCrunch Registry