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Open source application to allow the presentation of stimuli and collection of data for a wide range of neuroscience, psychology and psychophysics experiments. It is intended as a free, powerful alternative to Presentation or e-Prime.
Proper citation: PsychoPy (RRID:SCR_006571) Copy
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
http://www.softpedia.com/get/Science-CAD/BrainCSI.shtml
A tool for analysis of Magnetic Resonance Spectroscopy (MRS) data by registering it to anatomical images. BrainCSI imports LCModel results to calculate absolute metabolite concentrations using tissue water. Corrections to LCModel metabolite concentrations for partial volume of tissues are accomplished by tissue classification of the anatomical images.
Proper citation: BrainCSI (RRID:SCR_013244) Copy
http://cogent.iop.kcl.ac.uk/MaGIC.cogx
Software program to generate targeted marker sets for genome-wide association studies.
Proper citation: Marker And Gene Interpolation and Correlation (RRID:SCR_009268) Copy
http://orclinux.creighton.edu/snpp/
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. A dynamic general database management system to manage high-throughput SNP genotyping data. It provides several functions, including data importing with comparison, Mendelian inheritance check within pedigrees, data compiling and exporting. Furthermore, SNPP may generate files for repeat genotyping and transform them into files that can be executed by a liquid handling system.
Proper citation: SNPP (RRID:SCR_009404) Copy
http://www.pstnet.com/software.cfm?ID=101
Software designed to optimize E-Prime experiments for fMRI research. EEfMRI allows you to synchronize the start of your experiment with the first scanner trigger pulse along with several valuable features to enhance the control you have over your experiment. Implementing EEfMRI into your current experiments is achieved by simply dragging and dropping the correct EEfMRI package calls into the E-Prime experiment in the appropriate places. EEfMRI is designed to integrate with other PST hardware and software to increase usability for researchers while maintaining the millisecond accuracy of E-Prime.
Proper citation: E-Prime Extensions for fMRI (RRID:SCR_009568) Copy
http://www.nitrc.org/projects/fmricpca/
Constrained Principal Component Analysis (CPCA) combines regression analysis and principal component analysis into a unified framework. This method derives images of functional neural networks from singular-value decomposition of BOLD signal time series, and allows derivation of images when the analyzed BOLD signal is constrained to the scans occurring in peristimulus time, using all other scans as baseline. CPCA provides allows (1) determination of multiple functional networks involved in a task, (2) estimation of the pattern of BOLD changes associated with each functional network over peristimulus time points, (3) quantification of the degree of interaction between these multiple functional networks, and (4) a statistical test of the degree to which experimental manipulations affect each functional network. fMRI CPCA provides all results in matlab.mat file format, as well as writing images in analyze format for all components, rotated and unrotated.
Proper citation: fMRI-CPCA (RRID:SCR_009520) Copy
A workflow-oriented environment focused on biomedical image computing and simulation. The open source framework is extensible through plug-ins and is focused on building research and clinical software prototypes. Gimias has been used to develop clinical prototypes in the fields of cardiac imaging and simulation, angiography imaging and simulation, and neurology.
Proper citation: GIMIAS (RRID:SCR_009545) Copy
A software tool for post-processing diffusional kurtosis imaging (DKI) datasets. DKE consists of a suite of command-line programs along with a graphical user interface (GUI). DKE is currently supported on 32- and 64-bit Windows platforms. Given a set of diffusion-weighted images acquired following a valid DKI protocol, DKE generates a set of kurtosis (axial, mean, radial) parametric maps. DKE also generates diffusivity (axial, mean, radial) and fractional anisotropy maps using both DKI and diffusion tensor imaging signal models. DKE features include: DICOM and NIfTI format support, interactive (GUI) as well as batch mode (command-line) processing, and rigid-body motion correction. DKE implements the methods described in the following paper: Tabesh A, Jensen JH, Ardekani BA, and Helpern JA. Estimation of tensors and tensor-derived measures in diffusional kurtosis imaging. Mag Reson Med. 2011 Mar;65(3):823-36. http://www.ncbi.nlm.nih.gov/pubmed/21337412
Proper citation: Diffusional Kurtosis Estimator (RRID:SCR_009563) Copy
http://www.bioconductor.org/packages/release/bioc/html/iontree.html
Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.
Proper citation: iontree (RRID:SCR_002813) Copy
http://bmsr.usc.edu/software/lysis/
Interactive software of a set of modular programs (each performing a specific task) that provide an integrated computing environment for data analysis and system modeling. Unique capabilities of LYSIS include input-output nonlinear system modeling and the novel methodology of Principal Dynamic Modes (PDMs). LYSIS is currently available in two versions: one for LYSIS 7.1 Windows and one for LYSIS 7.2 Matlab. Early versions are also available for UNIX environments, distributed as source code that can be compiled for each UNIX implementation (e.g., Solaris, HPUX, Linux). Specific features of LYSIS that cannot be found in commercially available packages include the efficient kernel estimation using Laguerre expansions and the use of Principal Dynamic Modes (PDMs). These enable input-output modeling of dynamic nonlinear systems with relatively short data-records (even in the presence of considerable noise). System Requirements * Operating System ** Windows XP/Vista/7 ** Sun/Unix: Solaris 2.x
Proper citation: LYSIS (RRID:SCR_001385) Copy
Data analysis software for neurophysiology with a multitude of features, including: * Import of native data files created by many popular data acquisition systems * All standard histogram and raster analyses * Shift predictors in crosscorrelograms and color markers in perievent rasters * Joint PSTH, burst analysis and many more analyses of timestamped data * Spectral analysis of spike and continuous data * 3D data view and animation * Fully customizable WYSIWYG graphics * Custom analysis and batch mode processing with internal scripting language * Direct data link to Matlab and Excel * Statistical tests via direct link to R-project
Proper citation: NeuroExplorer (RRID:SCR_001818) Copy
http://www.bumc.bu.edu/cardiovascularproteomics/cpctools/strap/
Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible
Proper citation: STRAP (RRID:SCR_005675) Copy
http://www.nitrc.org/projects/jist/
A native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces. This repository maintains the current multi-institutional JIST development tree and is recommended for public use and extension. JIST was originally developed at IACL and MedIC (Johns Hopkins University) and is now also supported by MASI (Vanderbilt University).
Proper citation: JIST: Java Image Science Toolkit (RRID:SCR_008887) Copy
http://www.gtec.at/Products/Software/g.BSanalyze-Specs-Features
An interactive environment for multimodal biosignal data processing and analysis in the fields of clinical research and life sciences. It is the most comprehensive package to analyze non-invasive and invasive brain-, heart- and muscle-functions and dysfunctions. It includes many functions such as support vector machines, event-related ECG, support for P300 and SSVEP/SSSEP BCIs, zero class detection for BCIs, compressed spectral array, minimum energy, and more! g.BSanalyze consists of a base version for data import, visualization, transformation and pre-processing and has several dedicated toolboxes. The package comes with many sample biosignal data-sets, including P300, SSVEP, motor imagery, CSP BCIs, Tilt-Table, EPs, multi-unit activity, CFM, and ERD/ERS.
Proper citation: g.BSanalyze (RRID:SCR_009625) Copy
An opensource software for image analysis, processing and visualization. It provides convenient visualization tools for 2D and 3D images and it is highly extensible through its own scripting language. At visualization level, AMILab includes a 2D/3D image viewer, a 3D polygon viewer based on OpenGL, a 2D Curve viewer to visualize 2D curves, histograms and color/opacity transfer functions, and a GPU-enabled raycasting script for Volume Rendering based on VTK. The software includes an automatic C++ wrapping system which permits fast development of new visualization tools and image processing algorithms. This wrapping system currently wraps about 200 classes from wxwidgets library and about 100 classes from VTK.
Proper citation: AMILab (RRID:SCR_009525) Copy
http://ccbb.jnu.ac.in/OntoVisT.html
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. Web based ontological visualization tool for interactive visualization of any ontological hierarchy for a specific node of interest, up to the chosen level of children and/or ancestor. It takes any ontology file in OBO format as input and generates output as DAG hierarchical graph for the chosen query. To enhance the navigation capabilities of complex networks, we have embedded several features such as search criteria, zoom in/out, center focus, nearest neighbor highlights and mouse hover events. The application has been tested on all 72 data sets available in OBO format through OBO foundry. The results for few of them can be accessed through OntoVisT-Gallery.
Proper citation: OntoVisT (RRID:SCR_005674) Copy
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
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
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
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