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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Compartment Model Kinetic Analysis Tool Resource Report Resource Website |
Compartment Model Kinetic Analysis Tool (RRID:SCR_007359) | data processing software, software resource, software application | COMKAT is a software package for compartmental modeling oriented for biomedical image quantification. Free for academic research use, COMKAT has various functions for modeling and imaging analysis in both command-line function and GUIs. COMKAT is MATLAB software for compartmental modeling oriented to nuclear medicine applications (PET & SPECT). It supports models of a wide range complexity including multiple injection, receptor model with saturation. It supports many image formats, including DICOM images. Using either the command line interface or GUI, models are easily specified, solved or used to fit experimental data. Sensitivity equations are supported. No mathematical derivations are required on the part of the user. | has parent organization: Case Western Reserve University; Ohio; USA | nif-0000-00281 | http://comkat.case.edu/comkat/comkat_wiki/index.php?title=Home | SCR_007359 | COMKAT: COmpartment Model Kinetic Analysis Tool, COMKAT | 2026-08-12 10:49:36 | 0 | |||||||||
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CLEAVE Resource Report Resource Website 10+ mentions |
CLEAVE (RRID:SCR_007113) | CLEAVE | data processing software, software resource, software application | A UNIX-style command-line program which quickly computes multifactorial ANOVAs for very large data sets with minimal memory use (without loading all of the data into memory). It has been used for fMRI analysis, e.g. CLEAVE adds the following to the standard ANOVA analyses: # Unlimited numbers of factors can be analyzed. # Factor Correlation and Unequal Variance Corrections # Treatment Magnitudes: omega^2, partial eta^2, and R^2 # A convenient Ranking of Factors based upon treatment magnitudes and significance levels. # Post-Hoc Significance Tests # Post-Hoc Power Table to gauge how many subjects will be needed to achieve significance. # Allows the use of Random Factors. # A Configuration File to make the program more tunable # A Histogram and Cell Line Diagrams: which help the user to detect outliers. # Associated MATLAB functions: port CLEAVE-style data sets in or out of MATLAB. | c, console (text based), macos, microsoft, magnetic resonance, posix/unix-like, statistical operation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Davis; California; USA |
Creative Commons Attribution License | nlx_155530 | http://www.nitrc.org/projects/cleave | SCR_007113 | 2026-08-12 10:49:34 | 17 | |||||||
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COILS: Prediction of Coiled Coil Regions in Proteins Resource Report Resource Website 100+ mentions |
COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) | data processing software, software resource, software application | COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. | software, prediction, database, sequence, coil, globular, protein, probability, bio.tools, FASEB list |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1126/science.252.5009.1162 | biotools:ncoils, OMICS_07850, nif-0000-30263 | https://bio.tools/ncoils, https://sources.debian.org/src/ncoils/ | https://sources.debian.org/src/ncoils/ | SCR_008440 | COILS Server | 2026-08-12 10:49:42 | 169 | ||||||
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SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_007075) | data processing software, software resource, software application | A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options. | gene, gene expression, function, analysis, visualization, statistical analysis, windows, c#, gene function, chromosome location, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Gene Expression Omnibus |
PMID:14988116 | Free | nlx_149285, biotools:seqexpress | https://bio.tools/seqexpress | SCR_007075 | 2026-08-12 10:49:37 | 0 | |||||||
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Graphtools Resource Report Resource Website 1+ mentions |
Graphtools (RRID:SCR_009490) | Graphtools | data processing software, software resource, software application | A set of MATLAB scripts for analysis of networks derived from neuroimaging data. Some of these scripts are entirely original, while some are adapted (or just copied) from the Brain Connectivity Toolbox (https://sites.google.com/a/brain-connectivity-toolbox.net/bct) The source code is available via git: git clone ssh://user | magnetic resonance, matlab |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brain Connectivity Toolbox |
BSD License | nlx_155638 | SCR_009490 | 2026-08-12 10:49:57 | 4 | ||||||||
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OwlSim Resource Report Resource Website 1+ mentions |
OwlSim (RRID:SCR_006819) | OwlSim | data processing software, software resource, software application | Software package that provides the ability to do a number of standard semantic similarity methods and includes novel methods for combining these with dynamic selection of anonymous grouping classes. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | functional similarity, semantic similarity, ontology, phenotype, annotation, windows, mac os x, linux, unix |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Berkeley Bioinformatics Open-Source Projects has parent organization: OWLTools |
Biomedical Information Science and Technology Initiative ; National Center for Biomedical Ontology ; NHGRI U54 HG004028; NHGRI HG002659 |
PMID:19956802 | Open unspecified license - Free for academic use | nlx_149312 | SCR_006819 | 2026-08-12 10:49:34 | 5 | ||||||
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International Stroke Database/Software Resource Report Resource Website |
International Stroke Database/Software (RRID:SCR_007348) | data processing software, software resource, software application | Diffusion tensor imaging (DTI) tractography: An automated system for etiologic classification of ischemic stroke -- Causative Classification System for Ischemic Stroke DTI Task Card for Siemens systems, DTI Visualization platform independent tool kit, PWI analysis tools for bolus-tracking data |
has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; has parent organization: Harvard University; Cambridge; United States |
nif-0000-00253 | SCR_007348 | International Stroke Database/Software | 2026-08-12 10:49:42 | 0 | ||||||||||
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Brain Computer Interface 2000 Software Package Resource Report Resource Website 100+ mentions |
Brain Computer Interface 2000 Software Package (RRID:SCR_007346) | data processing software, software resource, software application | BCI2000 is a general-purpose system for brain-computer interface (BCI) and adaptive neurotechnology research. It can also be used for data acquisition, stimulus presentation, and brain monitoring applications. The mission of the BCI2000 project is to facilitate research and applications in the areas described. Their vision is that BCI2000 will become a widely used software tool for diverse areas of real-time biosignal processing. In order to achieve this vision, BCI2000 system is available for free for non-profit research and educational purposes. BCI2000 supports a variety of data acquisition systems, brain signals, and study/feedback paradigms. During operation, BCI2000 stores data in a common format (BCI2000 native or GDF), along with all relevant event markers and information about system configuration. BCI2000 also includes several tools for data import/conversion (e.g., a routine to load BCI2000 data files directly into Matlab) and export facilities into ASCII. BCI2000 also facilitates interactions with other software. For example, Matlab scripts can be executed in real-time from within BCI2000, or BCI2000 filters can be compiled to execute as stand-alone programs. Furthermore, a simple network-based interface allows for interactions with external programs written in any programming language. For example, a robotic arm application that is external to BCI2000 may be controlled in real time based on brain signals processed by BCI2000, or BCI2000 may use and store along with brain signals behavioral-based inputs such as eye-tracker coordinates. Because it is based on a framework whose services can support any BCI implementation, the use of BCI2000 provides maximum benefit to comprehensive research programs that operate multiple BCI2000 installations to collect data for a variety of studies. The most important benefits of the system in such situations are: - A Proven Solution - Facilitates Operation of Research Programs - Facilitates Deployment in Multiple Sites - Cross-Platform and Cross-Compiler Compatibility - Open Resource Sponsors: BCI2000 development is sponsored by NIH/NIBIB R01 and NIH/NINDS U24 grants. Keywords: General, Purpose, Systems, Brain, Computer, Interface, Research, Application, Brain, Diverse, Educational, Laboratory, Software, Network, Signals, Behavioral, Eye, Tracker, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institutes of Health |
NIBIB R01 EB026439; NINDS U24 NS109103; NIBIB P41 EB018783 |
nif-0000-00251 | http://www.nitrc.org/projects/bci2000, http://www.bci2000.org, https://www.neurotechcenter.org/software | SCR_007346 | BCI2000 | 2026-08-12 10:49:44 | 180 | ||||||||
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GRETNA Resource Report Resource Website 100+ mentions |
GRETNA (RRID:SCR_009487) | GRETNA | data processing software, software resource, software application | A graph theoretical network analysis toolbox which allows researchers to perform comprehensive analysis on the topology of brain connectome by integrating the most of network measures studied in current neuroscience field. | computational neuroscience, eeg, meg, electrocorticography, magnetic resonance, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: Functional Connectivity Analysis Tool for near-infrared spectroscopy data |
GNU General Public License | nlx_155634 | SCR_009487 | 2026-08-12 10:49:57 | 493 | ||||||||
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Human Brain Atlas Resource Report Resource Website 1+ mentions |
Human Brain Atlas (RRID:SCR_006131) | Human Brain Atlas | data or information resource, atlas, video resource | A labeled three-dimensional atlas of the human brain created from MRI images. In conjunction are presented anatomically labeled stained sections that correspond to the three-dimensional MRI images. The stained sections are from a different brain than the one which was scanned for the MRI images. Also available the major anatomical features of the human hypothalamus, axial sections stained for cell bodies or for nerve fibers, at six rostro-caudal levels of the human brain stem; images and Quicktime movies. The MRI subject was a 22-year-old adult male. Differing techniques used to study the anatomy of the human brain all have their advantages and disadvantages. Magnetic resonance imaging (MRI) allows for the three-dimensional viewing of the brain and structures, precise spatial relationships and some differentiation between types of tissue, however, the image resolution is somewhat limited. Stained sections, on the other hand, offer excellent resolution and the ability to see individual nuclei (cell stain) or fiber tracts (myelin stain), however, there are often spatial distortions inherent in the staining process. The nomenclature used is from Paxinos G, and Watson C. 1998. The Rat Brain in Stereotaxic Coordinates, 4th ed. Academic Press. San Diego, CA. 256 pp | human, adult, mri, fiber stain, anatomy, normal, neuroanatomy, nissl stain, image, brainstem, cell body, nerve fiber, brain, coronal, sagittal, horizontal, 3d model, montage, weil, hypothalamus |
is used by: NIF Data Federation has parent organization: Michigan State University; Michigan; USA |
NSF IBN 0131267; NSF 0131826; NSF 0131028 |
Copyrighted, Public, Request that you secure their permission, Acknowledgement required | nif-0000-00088 | SCR_006131 | MSU Brain Biodiversity Bank - Human Brain Atlas, Michigan State University Brain Biodiversity Bank - Human Brain Atlas | 2026-08-12 10:49:20 | 3 | ||||||
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RIKEN integrated database of mammals Resource Report Resource Website |
RIKEN integrated database of mammals (RRID:SCR_006890) | RIKEN integrated database of mammals | data or information resource, database, portal |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019. A database that integrates not only RIKEN''''s original large-scale mammalian databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists'''' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information. |
integration, network, standardization, biomedical, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Functional Annotation of the Mammalian Genome is related to: Cerebellar Development Transcriptome Database is related to: Ensembl is related to: Mouse Genome Informatics (MGI) is related to: OBO has parent organization: RIKEN Yokohama Institute; Kanagawa; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:21076152 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151886, biotools:riken | https://bio.tools/riken | SCR_006890 | 2026-08-12 10:49:36 | 0 | |||||
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LONI Java Image I/O Plugins Resource Report Resource Website |
LONI Java Image I/O Plugins (RRID:SCR_008277) | data processing software, software resource, software application | Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.The plugins use Java Image I/O interfaces to read and write metadata and image data and can read and write AFNI, ANALYZE 7.5, DICOM, ECAT 7.2, GE 5.0, INTERFILE (including hrrt), MINC, NIFTI, and UCLA PACS file formats. All source code is provided and usage examples are included. | plugin, MRI, software, visualization, data processing |
is related to: Laboratory of Neuro Imaging has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
Available for educational and research purposes only | nif-0000-23320 | SCR_008277 | 2026-08-12 10:49:46 | 0 | ||||||||
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Pedianet Resource Report Resource Website 10+ mentions |
Pedianet (RRID:SCR_004107) | data or information resource, database, portal | Independent network and system used to collect epidemiological information for clinical research from family paediatricians in Italy. It is based on the transmission of specific data from computerised clinical files. Such data is collected anonymously by a central server in Padua, where it is validated and elaborated. | pediatric, clinical, epidemiology, child, young human, pharmacovigilance, primary care, pediatrician | is related to: EMIF | Wellcome Glaxo | nlx_158583 | SCR_004107 | Pedianet project | 2026-08-12 10:48:55 | 18 | ||||||||
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epigenomix Resource Report Resource Website 1+ mentions |
epigenomix (RRID:SCR_006407) | epigenomix | data processing software, software resource, software application | Software package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types. | epigenetic, gene expression, microarray, histone modification, chip-seq, classification, differential expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24403540 | GNU Lesser General Public License, v3 | biotools:epigenomix, OMICS_02205 | https://bio.tools/epigenomix | SCR_006407 | epigenomix - Epigenetic and gene expression data normalization and integration with mixture models | 2026-08-12 10:49:25 | 2 | |||||
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The Surf-Hippo Neuron Simulation System Resource Report Resource Website 1+ mentions |
The Surf-Hippo Neuron Simulation System (RRID:SCR_007257) | data processing software, software resource, software application | The Surf-Hippo neuron simulator is used to investigate morphologically and biophysically detailed compartmental models of single neurons and networks of neurons. Surf-Hippo allows ready construction of cells and networks using built-in functions and various anatomical file formats (Neurolucida, NTS and others). Surf-Hippo is a public domain package, written in Lisp, and runs under Unix and Linux. | nif-0000-00170 | SCR_007257 | Surf-Hippo | 2026-08-12 10:49:43 | 1 | |||||||||||
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Cellpack Resource Report Resource Website 1+ mentions |
Cellpack (RRID:SCR_006831) | cellPack | data processing software, software resource, software application | A specialized version of autoPack designed to pack biological components together. The current version is optimized to pack molecules into cells with biologically relevant interactions to populate massive cell models with atomic or near-atomic details. Components of the algorithm pack transmembrane proteins and lipids into bilayers, globular molecules into compartments defined by the bilayers (or as exteriors), and fibrous components like microtubules, actin, and DNA. | 3d packing software, pack, molecule, cell |
is related to: Autopack has parent organization: Autopack |
QB3 at UCSF Fellowship ; NSF 07576; NCRR P41 RR08605 |
GNU Lesser General Public License | nlx_151792 | https://sites.google.com/site/autofill21/, http://code.google.com/p/autofill/ | SCR_006831 | 2026-08-12 10:49:32 | 9 | ||||||
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SOAPaligner/soap2 Resource Report Resource Website 100+ mentions |
SOAPaligner/soap2 (RRID:SCR_005503) | SOAPaligner, SOAP2 | data processing software, software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, alignment, short read, oligonucleotide, single-read, pair-end, resequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SOAP |
PMID:19497933 DOI:10.1093/bioinformatics/btn025 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:soap2 | https://bio.tools/soap2, https://sources.debian.org/src/soapaligner/ | SCR_005503 | 2026-08-12 10:49:11 | 325 | ||||||
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LONI Inspector Resource Report Resource Website 1+ mentions |
LONI Inspector (RRID:SCR_004923) | LONI Inspector | data processing software, software resource, software application | A Java application for reading, displaying, searching, comparing, and exporting metadata from medical image files: AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI. | analyze, dicom, java, minc, magnetic resonance, nifti, os independent, win32 (ms windows), workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
LONI Software License | nlx_155785 | http://www.nitrc.org/projects/inspector | http://www.loni.ucla.edu/Software/LONI-Inspector | SCR_004923 | 2026-08-12 10:49:04 | 3 | |||||
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Small-world Network Analysis and Partitioning Resource Report Resource Website |
Small-world Network Analysis and Partitioning (RRID:SCR_013662) | data processing software, software resource, software application | SNAP (Small-world Network Analysis and Partitioning) is an extensible parallel framework for exploratory analysis and partitioning of large-scale networks. SNAP is implemented in C, uses OpenMP primitives for parallelization, and targets sequential, multicore, and symmetric multiprocessor platforms. Our intent with SNAP is to provide a simple and intuitive interface for network analysis and application design, hiding the parallel programming complexity from the user. In addition to path-based, centrality, and community identification queries on large-scale graphs, we support commonly-used preprocessing kernels and quantitative measures that help understand the global network topology. The latest version of SNAP (0.4) was released in August 2010. Sponsors: This work was supported in part by NSF Grants CAREER CCF-0611589, NSF DBI-0420513, ITR EF/BIO 03-31654, IBM Faculty Fellowship and Microsoft Research grants, NASA grant NP-2005-07-375-HQ, and DARPA Contract NBCH30390004. Keywords: network, analysis, software, graph, traversal, betweenness centrality, community, identification, multicore, | has parent organization: Georgia Institute of Technology; Georgia; USA | nif-0000-00425 | SCR_013662 | SNAP | 2026-08-12 10:50:52 | 0 | ||||||||||
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TRACULA Resource Report Resource Website 10+ mentions |
TRACULA (RRID:SCR_013152) | TRACULA | data processing software, software resource, software application | Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons. | tractography, white matter tract, white matter pathway, diffusion weighted image, diffusion magnetic resonance imaging, white matter, brain, reconstruct, diffusion tensor imaging |
is related to: FreeSurfer has parent organization: Harvard Medical School; Massachusetts; USA |
Aging | NIH Blueprint for Neuroscience Research ; Ellison Medical Foundation ; NIBIB EB008129; NIMH U01-MH093765; NCRR P41-RR14075; NCRR U24-RR021382; NIBIB R01-EB006758; NIA R01-AG022381; National Center for Complementary and Alternative Medicine RC1-AT005728; NINDS R01-NS052585; NINDS R21-NS072652; NINDS R01-NS070963 |
PMID:22016733 | nlx_143919 | SCR_013152 | TRACULA - TRActs Constrained by UnderLying Anatomy, TRACULA: TRActs Constrained by UnderLying Anatomy, TRActs Constrained by UnderLying Anatomy | 2026-08-12 10:50:44 | 17 |
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