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https://github.com/incf-nidash/XCEDE

Data management software that provides an extensive metadata hierarchy for describing and documenting research and clinical studies. The schema organizes information into five general hierarchical levels: a complete project, studies within a project, subjects involved in the studies, visits for each of the subjects, the full description of the subject's participation during each visit.

Proper citation: XCEDE Schema (RRID:SCR_002571) Copy   

•   Source: SciCrunch Registry

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

Software Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data.

Proper citation: pyxnat (RRID:SCR_002574) Copy   

•   Source: SciCrunch Registry

http://nipy.org/nipy

A complete Python environment for the analysis of structural and functional neuroimaging data. It currently has a full system for general linear modeling of functional magnetic resonance imaging (fMRI).

Proper citation: NIPY (RRID:SCR_002489) Copy   

•   Source: SciCrunch Registry

http://www.neurobs.com/

Stimulus delivery and experiment control program. Stimuli include auditory, 2D and 3D visual, and multimodal and experimental data include fMRI, ERP, MEG, psychophysics, eye movements, single neuron recording, and reaction time measures.

Proper citation: Presentation (RRID:SCR_002521) Copy   

•   Source: SciCrunch Registry

http://odr.stowers.org/websimr/

THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Open access repository of original, unprocessed data underlying work published by Stowers researchers to allow the scientific community to validate and extend the findings made by Stowers researchers. For papers first submitted for publication after November 1, 2011, the Stowers Institute requires its members to deposit original data files into the Stowers Original Data Repository or to repositories maintained by third parties at the time of publication. Access to the Stowers Original Data Repository is free, but you will be asked to register before you can download data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Stowers Original Data Repository (RRID:SCR_002640) Copy   

•   Source: SciCrunch Registry

http://www.uark.edu/

Public, co educational research university in Fayetteville, Arkansas.

Proper citation: University of Arkansas; Arkansas; USA (RRID:SCR_002515) Copy   

•   Source: SciCrunch Registry

http://www.paraview.org/

Open source, multi platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.

Proper citation: ParaView (RRID:SCR_002516) Copy   

•   Source: SciCrunch Registry

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

Software package representing Spatial Statistical Parametric Mapping that includes two tools presently: MAGEE and FADTTS. MAGEE represents the Multiscale Adaptive Generalized Estimating Equation. It was developed specifically for analyzing multivariate neuroimaging data in 3-dimensional volume (or on 2-dimensional surface) from longitudinal neuroimaging studies. FADTTS represents Functional Analysis of Diffusion Tensor Tract Statistics. The aim of this tool is to implement a functional analysis pipeline, for delineating the structure of the variability of multiple diffusion properties along major white matter fiber bundles and their association with a set of covariates of interest, in various diffusion tensor imaging studies.

Proper citation: Spatial Statistical Parametric Mapping (RRID:SCR_002592) Copy   

•   Source: SciCrunch Registry

http://theobjects.com/en/products/scientific/index.php

Software with advanced visualization techniques and state-of-the-art volume rendering provide unparalleled insight into the details and properties of neurological data acquired by CT, micro-CT, MRI, PET, SPECT, microscopy and other modalities. With data fusion tools, intramodality and multimodality registration of MR/CT or PET/CT is easily accomplished, while semi-automatic VOI delineation on fused datasets can improve analysis. Standard formats, such as DICOM, RAW, JPEG, NIFTI, Analyze are supported and 3D/4D sequences can be played. Other features include MPR, oblique, CPR, volume clipping, and surface visualization of cortex, skull, and scalp models. Also standard are easy-to-use tools for voxel-based delineation of features and the measurement of properties, including areas, volumes, counts, and intensity profiles. Present your findings by creating annotated animations or high-resolution images for posters. An SDK is also available to create plug-ins that provide new workflows or functionalities.

Proper citation: ORS Visual SI (RRID:SCR_002509) Copy   

•   Source: SciCrunch Registry

http://rubioseq.sourceforge.net/

Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments.

Proper citation: RUbioSeq (RRID:SCR_002508) Copy   

•   Source: SciCrunch Registry

http://www.openmicroscopy.org/site/products/omero

Client-server software for management, visualization, and analysis of biological microscopy images. OMERO handles images in a secure central repository where users can view, organize, analyze and share data from anywhere with internet access. Work with images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software.

Proper citation: OMERO (RRID:SCR_002629) Copy   

•   Source: SciCrunch Registry

http://sites.google.com/site/marcocongedo/software/nica

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Software program, executable under any Windows32 OS, performs Group BSS (Blind Source Separation) analysis comparing two groups of individuals and it performs NICA (Normative ICA) analysis where individuals are compared individually to a (normative) group. All analysis is performed in the frequency domain, that is, for all frequencies. The program also performs all these analysis for qEEG, that is, at the electrode level, without any BSS. The program does all computations, saves and displays results. The rationale and methods used in this program are explained in all details in the following paper: Congedo M, John ER, De Ridder D, Prichep L (2010) Group Independent Component Analysis of Resting-State EEG in Large Normative Samples International Journal of Psychophysiology 78, 89-99.

Proper citation: Normative Independent Component Analysis (RRID:SCR_002506) Copy   

•   Source: SciCrunch Registry

https://github.com/AliView

Software for aligning viewing and editing dna / aminiacid sequences, intuitive, fast and leightweight. It has been designed to meet the requirements of next generation sequencing era phylogenetic datasets.

Proper citation: AliView (RRID:SCR_002780) Copy   

•   Source: SciCrunch Registry

http://www.enzyme-database.org

Enzyme database developed as a way to access the data of the IUBMB Enzyme Nomenclature List. The data, which are stored in a MySQL database, preserve the formatting of chemical names according to IUPAC standards. A simple, easy to use, web-based query interface is provided (Search), along with an advanced search engine for more complex queries (Advanced Search). Forms are provided to submit suggestions for new enzyme entries or to report errors in existing entries. Downloads of the database are available via FTP as SQL or XML.

Proper citation: ExplorEnz (RRID:SCR_002665) Copy   

•   Source: SciCrunch Registry

http://www.cmhd.ca/genetrap/

Generate gene trap insertions using mutagenic polyA trap vectors, followed by sequence tagging to develop a library of mutagenized ES cells freely available to the scientific community. This library is searchable by sequence or key word searches including gene name or symbol, chromosome location, or Gene Ontology (GO) terms. In addition,they offer a custom email alert service in which researchers are able to submit search criteria. Researchers will receive automated e-mail notification of matching gene trap clones as they are entered into the library and database. The resource features the use of complementary second and third generation polyA trap vectors developed by the Stanford lab and the laboratory of Professor Yasumasa Ishida of the Nara Institute of Science and Technology (NAIST) in Japan to mutagenize murine embryonic stem (ES) cells. CMHD gene trap clones are distributed by the Canadian Mouse Mutant Repository(CMMR). Information about ordering, services, and pricing can be found on their web site (http://www.cmmr.ca/services/index.html)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: Centre for Modeling Human Disease Gene Trap Resource (RRID:SCR_002785) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/ExomeDepth/

Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.

Proper citation: ExomeDepth (RRID:SCR_002663) Copy   

•   Source: SciCrunch Registry

https://github.com/rcanovas/libCSAM

Contains several C++ codes for compress, decompress, and access each of the fields of any SAM format file.

Proper citation: libCSAM (RRID:SCR_002766) Copy   

•   Source: SciCrunch Registry

http://stkctr.biol.sc.edu/

The deer mouse (Peromyscus maniculatus) and congeneric species are the most common native North American mammal. Laboratory stock of both wild-type and genetically variant Peromyscus are used for investigations in which laboratory-based studies can be interfaced with those of natural populations. The major function of the Stock Center is to provide genetically characterized types of Peromyscus in limited quantities to scientific investigators. It provides a reliable source of genetically defined and virus-free animals and related materials to the scientific and educational communities. The center currently keeps nine species and more than 27 distinctive mutant and other genetically defined stocks. Included among the species maintained are P. californicus, P. leucopus, P. eremicus, P. aztecus, P. melanophrys as well as two subspecies each of P. maniculatus and P. polionotus and three inbred lines of P. leucopus. Among the mutant stocks are 17 with altered coat phenotypes, 3 with neurological symptoms, and 6 others with developmental/physiological effects. One of these is a line deficient in alcohol dehydrogenase that has been widely used in studies of alcohol metabolism. The stock center also supplies biological materials, including fresh, frozen, and preserved tissues; molecular probes, and libraries. The center functions as a clearinghouse for information regarding this genus by sponsoring an Internet database and the semi-annual Peromyscus Newsletter. The center maintains a collection of over 3,000 Peromyscus-related reprints of published articles, books, and journals-photocopies of which are available upon request. Continuation of the center is dependent upon significant external utilization, therefore potential users are encouraged to take advantage of this resource. Sufficient animals of the mutant types generally can be provided to initiate a breeding stock. Some what larger numbers, up to about 50 animals, can be provided from the wild-type stocks. A user fee of $25.00 per wild-type animal and $33.00 per mutant or other special types is charged. The user assumes the cost of air shipment. Animals lost in transit are replaced without charge. Tissues, blood, skins, etc. can also be supplied at a modest fee. Arrangements for special orders will be negotiated. :Sponsors: The peromyscus genetic stock center is supported by the University of South Carolina, :a grant from the Special Projects Program of the National Science Foundation and a P40 grant ( grant number: P40 RR014279) from the National Institutes of Health. physiological, Developmental, Biological, Animal,

Proper citation: Peromyscus Genetic Stock Center (RRID:SCR_002769) Copy   

•   Source: SciCrunch Registry

https://simtk.org

A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code.

Proper citation: Simtk.org (RRID:SCR_002680) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/simvascular

Open source software suite for cardiovascular simulation. It includes code for reading 3D images, segmenting structures, generating models and meshes, and modeling blood flow in deformable vessels. The suite also includes tools for physiologic boundary conditions, fluid structure interaction, and an accurate and efficient finite element Navier-Stokes solver. Commercial components have been used in the simulation process, and for these components, the project attempts to provide interfaces that allow substitution of open source components. The SimVascular project is derived from the ASPIRE2 software project and includes modified portions of PHASTA from RPI/SCOREC.

Proper citation: SimVascular (RRID:SCR_002686) Copy   

•   Source: SciCrunch Registry