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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PRIDE Converter 2 Resource Report Resource Website 1+ mentions |
PRIDE Converter 2 (RRID:SCR_012051) | software resource | 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. | standalone software, mac os x, unix/linux, windows, java, xml, mass spectrometry, pride, ols, proteomics, psi, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Google Code |
PMID:22949509 | Apache License, v2 | biotools:pride_converter, OMICS_03344 | https://bio.tools/pride_converter | SCR_012051 | PRIDE, PRoteomics IDEntification (PRIDE) Converter 2 | 2026-09-12 12:57:44 | 1 | ||||||
|
jmzReader Resource Report Resource Website 1+ mentions |
jmzReader (RRID:SCR_012050) | software resource | 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. | standalone software, mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: Google Code |
PMID:22539430 | Apache License | OMICS_03341 | SCR_012050 | 2026-09-12 12:57:44 | 2 | ||||||||
|
FIGG Resource Report Resource Website 1+ mentions |
FIGG (RRID:SCR_012064) | software resource | 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. | standalone software, unix/linux, mac os x, windows, java, mapreduce |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24885193 | Free, Public | OMICS_04164 | SCR_012064 | Frequency-based Insilico Genome Generator | 2026-09-12 12:57:44 | 3 | |||||||
|
MrBayes Resource Report Resource Website 10000+ mentions |
MrBayes (RRID:SCR_012067) | software resource | 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. | applet, mac os x, unix/linux, windows |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:22357727 DOI:10.1093/sysbio/sys029 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04237 | https://sources.debian.org/src/mrbayes/ | SCR_012067 | 2026-09-12 12:57:44 | 10714 | |||||||
|
CCAT (Combinatorial Code Analysis Tool) Resource Report Resource Website |
CCAT (Combinatorial Code Analysis Tool) (RRID:SCR_012028) | CCAT (Combinatorial Code Analysis Tool) | software resource | A software package for predicting genome-wide co-binding between biological regulators such as Transcription factors (TFs). | windows |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
PMID:24366875 | Apache License | OMICS_02179 | SCR_012028 | 2026-09-12 12:57:43 | 0 | |||||||
|
OpenMS Resource Report Resource Website 100+ mentions |
OpenMS (RRID:SCR_012042) | software resource | An algorithm to align LC-MS samples and to match corresponding ion species across samples. | standalone software, mac os x, unix/linux, windows, c++, python, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:17646306 DOI:10.1186/1471-2105-9-163 |
GNU Lesser General Public License | biotools:openms | https://bio.tools/openms, https://sources.debian.org/src/openms/ | SCR_012042 | 2026-09-12 12:57:44 | 184 | |||||||
|
NAIL Resource Report Resource Website 1+ mentions |
NAIL (RRID:SCR_012134) | software resource | 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. | standalone software, mac os x, unix/linux, windows, matlab, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25246431 | Apache License | OMICS_05868, biotools:nail | https://bio.tools/nail | SCR_012134 | Network Analysis and Inference Library | 2026-09-12 12:57:46 | 8 | ||||||
|
xMSanalyzer Resource Report Resource Website 50+ mentions |
xMSanalyzer (RRID:SCR_012144) | software resource | 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. | software package, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23323971 | GNU General Public License | OMICS_06039 | SCR_012144 | 2026-09-12 12:57:46 | 90 | ||||||||
|
Phosphor Antibody Array Data Analysis Resource Report Resource Website |
Phosphor Antibody Array Data Analysis (RRID:SCR_000633) | PANDA | analysis service resource, data analysis service, production service resource, service resource | 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. | unix/linux, windows |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA |
PMID:18794113 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04025 | SCR_000633 | PANDA: Phosphor Antibody Array Data Analysis | 2026-09-12 01:01:20 | 0 | ||||||
|
Datavyu Resource Report Resource Website 50+ mentions |
Datavyu (RRID:SCR_003587) | Datavyu | software application, software resource, source code | 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. | windows, mac os, java, video coding, behavior, visualization |
is related to: Databrary is related to: Databrary has parent organization: New York University; New York; USA |
GNU General Public License, v3 | nlx_157734 | SCR_003587 | 2026-09-12 01:01:29 | 79 | ||||||||
|
mlgt Resource Report Resource Website |
mlgt (RRID:SCR_001211) | mlgt | data processing software, software application, software resource | 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. | roche, windows, os x, genotype, variant, allele, high throughput sequencing, locus, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Manchester; Manchester; United Kingdom |
THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:mlgt, OMICS_02131, biotools:mlgt | https://bio.tools/mlgt, https://bio.tools/mlgt, https://bio.tools/mlgt | SCR_001211 | Multi-Locus Geno-Typing, mlgt: Multi-Locus Geno-Typing | 2026-09-12 01:00:52 | 0 | ||||||
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Scanalytics IPLab Resource Report Resource Website 10+ mentions |
Scanalytics IPLab (RRID:SCR_002775) | IPLab | data processing software, software application, software resource, software toolkit | 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. | windows, macintosh | THIS RESOURCE IS NO LONGER IN SERVICE | rid_000102 | http://www.spectraservices.com/IPLAB.html | SCR_002775 | 2026-09-12 01:00:53 | 30 | ||||||||
|
3D Interactive Chemical Shift Imaging Resource Report Resource Website 1+ mentions |
3D Interactive Chemical Shift Imaging (RRID:SCR_002581) | 3DiCSI | data processing software, software application, software resource | 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. | c++, dicom, microsoft, magnetic resonance, quantification, spatial transformation, statistical operation, temporal transformation, visualization, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Columbia University; New York; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155986 | SCR_002581 | 3D Chemical Shift Imaging | 2026-09-12 01:00:53 | 1 | |||||||
|
ValMap: simple statistical mapping tool Resource Report Resource Website 1+ mentions |
ValMap: simple statistical mapping tool (RRID:SCR_002610) | ValMap | data processing software, image analysis software, software application, software resource | 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). | analyze, c, c++, java, linear, linux, microsoft, morphology, magnetic resonance, nifti, posix/unix-like, quantification, regression, statistical operation, win32 (ms windows), windows, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
Free, Available for download, Freely available | nlx_156013 | SCR_002610 | 2026-09-12 01:00:53 | 2 | ||||||||
|
Apollo Resource Report Resource Website 100+ mentions |
Apollo (RRID:SCR_001936) | Apollo | software application, software resource | 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. | java, genome annotation, genome, annotation, windows, mac os x, linux, solaris, unix, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Generic Model Organism Database Project |
PMID:19439563 PMID:12537571 DOI:10.1186/gb-2002-3-12-research0082 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11761, biotools:apollo, OMICS_01933 | https://bio.tools/apollo, https://sources.debian.org/src/aragorn/ | SCR_001936 | 2026-09-12 01:02:27 | 301 | ||||||
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SPHARM-PDM Toolbox Resource Report Resource Website |
SPHARM-PDM Toolbox (RRID:SCR_002546) | SPHARM-PDM Toolbox | software application, software resource | 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. | analyze, c++, console (text based), macos, microsoft, magnetic resonance, nifti, nrrd, posix/unix-like, quantification, quantitative shape analysis, shape analysis, shape decomposition, spherical harmonics, surface analysis, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center has parent organization: National Alliance for Medical Image Computing has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:24027625 | Free, Available for download, Freely available | nlx_155953 | http://www.nitrc.org/projects/spharm-pdm | SCR_002546 | UNC SPHARM-PDM, SPHARM-PDM UNC Toolbox | 2026-09-12 01:02:28 | 0 | |||||
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scikit-learn Resource Report Resource Website 10000+ mentions |
scikit-learn (RRID:SCR_002577) | scikit-learn | software application, software resource | scikit-learn: machine learning in Python | algorithm, discriminant analysis, independent component analysis, linear, macos, microsoft, modeling, magnetic resonance, nonlinear, posix/unix-like, principal component analysis, python, regression, statistical operation, windows, data mining, data analysis, classification, clustering, dimensionality reduction, model selection, preprocessing, machine learning | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:24600388 | Free, Available for download, Freely available | nlx_155979 | http://www.nitrc.org/projects/scikit-learn | SCR_002577 | scikit-learn: machine learning in Python | 2026-09-12 01:02:28 | 14714 | |||||
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VR Worlds 2 Resource Report Resource Website |
VR Worlds 2 (RRID:SCR_002608) | VR Worlds 2 | commercial organization, software application, software resource | 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 | eeg, meg, electrocorticography, experimental control, microsoft, magnetic resonance, win32 (ms windows), windows, windows vista, windows xp, neurobehavior, virtual environment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156011 | http://www.nitrc.org/projects/vr2 | SCR_002608 | 2026-09-12 01:02:29 | 0 | |||||||
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Psychophysics Toolbox Resource Report Resource Website 1000+ mentions |
Psychophysics Toolbox (RRID:SCR_002881) | PTB, PTB-3, PTB-2 | software resource, software toolkit | 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. | matlab, gnu/octave, vision, visual, auditory, stimuli, mac osx, linux, windows | Free, Freely available, Available for download | rid_000041 | SCR_002881 | Psychtoolbox, Psychtoolbox-3 | 2026-09-12 01:02:29 | 1139 | ||||||||
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DNAPlotter Resource Report Resource Website 100+ mentions |
DNAPlotter (RRID:SCR_005006) | DNAPlotter | software application, software resource | 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. | java, circular, linear, plot, genome, macosx, unix, windows |
is listed by: OMICtools is related to: Artemis: Genome Browser and Annotation Tool has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:18990721 | GNU General Public License | OMICS_00906, nlx_96278 | SCR_005006 | DNAPlotter: circular and linear interactive genome visualization | 2026-09-12 01:02:34 | 110 |
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