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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Ionwinze Resource Report Resource Website |
Ionwinze (RRID:SCR_012115) | software resource | Software tool to pick out ion signals that discriminate two groups of samples (e.g. diseased/healthy, resistant/susceptible) by quasi-datapoint-wise comparison using univariate statistic procedures. | standalone software, windows, c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24004415 | GNU General Public License | OMICS_05522 | SCR_012115 | 2026-09-12 12:57:45 | 0 | ||||||||
|
SketchEl Resource Report Resource Website |
SketchEl (RRID:SCR_012082) | software resource | An interactive chemical molecule sketching tool, and molecular spreadsheet data entry application. | applet, mac os x, unix/linux, windows, java, javascript |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_04982 | SCR_012082 | 2026-09-12 12:57:45 | 0 | |||||||||
|
MCDL Resource Report Resource Website 1+ mentions |
MCDL (RRID:SCR_012084) | software resource | A small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation. | applet, mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05001 | SCR_012084 | 2026-09-12 12:57:45 | 2 | ||||||||||
|
SearchGUI Resource Report Resource Website 100+ mentions |
SearchGUI (RRID:SCR_012054) | software resource | Software providing a user-friendly, lightweight and open-source graphical user interface for configuring and running the freely available OMSSA and X!Tandem search engines simultaneously. | mac os x, unix/linux, windows |
is listed by: OMICtools has parent organization: Google Code |
PMID:21337703 | Apache License | OMICS_03352 | SCR_012054 | 2026-09-12 12:57:44 | 157 | ||||||||
|
COBRApy Resource Report Resource Website 100+ mentions |
COBRApy (RRID:SCR_012096) | software resource | Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods. | software package, mac os x, unix/linux, windows, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23927696 DOI:10.1186/1752-0509-7-74 |
OMICS_05190, biotools:cobrapy | https://bio.tools/cobrapy | https://sources.debian.org/src/python3-cobra/ | SCR_012096 | COBRA for Python | 2026-09-12 12:57:45 | 341 | ||||||
|
JChemPaint Resource Report Resource Website 1+ mentions |
JChemPaint (RRID:SCR_000095) | JCP | software resource | Chemical 2D structure editor and viewer application/applet based on the Chemistry Development Kit (CDK). | applet, mac os x, unix/linux, windows, java | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_04959 | https://github.com/JChemPaint/jchempaint | SCR_000095 | 2026-09-12 12:55:03 | 1 | |||||||
|
flowCL Resource Report Resource Website |
flowCL (RRID:SCR_000046) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations. | software package, mac os x, unix/linux, windows, r, flow cytometry |
has parent organization: Bioconductor has parent organization: BC Cancer Agency |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05594 | SCR_000046 | flowCL - Semantic labelling of flow cytometric cell populations | 2026-09-12 12:55:02 | 0 | ||||||||
|
Cbrowse Resource Report Resource Website |
Cbrowse (RRID:SCR_000044) | software resource | Software providing an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. | unix/linux, mac os x, windows |
has parent organization: Google Code has parent organization: Miami University; Ohio; USA |
PMID:22789590 | Free, Available for download, Freely available | OMICS_04048 | SCR_000044 | 2026-09-12 12:55:02 | 0 | ||||||||
|
RmiR.Hs.miRNA Resource Report Resource Website |
RmiR.Hs.miRNA (RRID:SCR_000101) | software resource | Software package for various databases of microRNA Targets. | software package, unix/linux, mac os x, windows, r, annotation data, custom db schema, mirna |
is listed by: OMICtools is related to: CRAN has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05797 | SCR_000101 | RmiR.Hs.miRNA: Various databases of microRNA Targets | 2026-09-12 12:55:03 | 0 | ||||||||
|
BamView Resource Report Resource Website 10+ mentions |
BamView (RRID:SCR_004207) | BamView | software resource, source code | A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub. | bam, next-generation sequencing, java, snp calling, structural annotation, macosx, unix, windows, visualize, analyze, sequence read, reference sequence, single nucleotide polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:22253280 PMID:20071372 |
GNU General Public License | biotools:bamview, OMICS_00878, nlx_22933 | https://bio.tools/bamview | SCR_004207 | 2026-09-12 01:03:14 | 21 | ||||||
|
SigmaPlot Resource Report Resource Website 10000+ mentions |
SigmaPlot (RRID:SCR_003210) | SigmaPlot | commercial organization, software resource | Statistical analysis and scientific graphing software for Windows OS. | statistics, windows, graph, data analysis | is listed by: SoftCite | Commercial license | SciRes_000184 | SCR_003210 | sigma plot | 2026-09-12 01:03:13 | 17386 | |||||||
|
Seg3D Resource Report Resource Website 100+ mentions |
Seg3D (RRID:SCR_002552) | Seg3D | data processing software, data visualization software, image analysis software, image processing software, rendering software, segmentation software, software application, software resource | A free volume processing segmenting tool that combines a flexible manual interface with powerful image processing and segmentation algorithms. Users can explore and label image volumes using slice windows and 3D volume rendering. | analyze, c++, dicom, image display, linux, macos, microsoft, magnetic resonance, nrrd, posix/unix-like, rendering, segmentation, three dimensional display, visualization, volume rendering, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NIGMS 8 P41 GM103545-15 | PMID:29083867 | Free, Available for download, Freely available | nlx_155959 | http://www.nitrc.org/projects/seg3d | SCR_002552 | 2026-09-12 01:00:08 | 106 | |||||
|
Monte Carlo Simulation Software: tMCimg Resource Report Resource Website 1+ mentions |
Monte Carlo Simulation Software: tMCimg (RRID:SCR_002588) | tMCimg | simulation software, software application, software resource | Software application that uses a Monte Carlo algorithm to model the transport of photons through 3D volumes with spatially varying optical properties. Both highly-scattering tissues (e.g. white matter) and weakly scattering tissues (e.g. cerebral spinal fluid) are supported. Using the anatomical information provided by MRI, X-ray CT, or ultrasound, accurate solutions to the photon migration forward problems are computed in times ranging from minutes to hours, depending on the optical properties and the computing resources available. | c, computed tomography, macos, microsoft, modeling, monte carlo, magnetic resonance, optical imaging, posix/unix-like, windows, mri, x-ray ct, ultrasound, photon | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:19424345 | Free, Available for download, Freely available | nlx_155993 | http://www.nitrc.org/projects/tmcimg | SCR_002588 | Monte Carlo Photon Transport | 2026-09-12 01:00:08 | 1 | |||||
|
VisTrails Resource Report Resource Website 10+ mentions |
VisTrails (RRID:SCR_006261) | VisTrails | data processing software, software application, software resource, workflow software | Open-source scientific workflow and provenance management system that provides support for simulations, data exploration and visualization. It was designed to manage these rapidly-evolving workflows. VisTrails has a comprehensive provenance infrastructure that maintains detailed history information about the steps followed and data derived in the course of an exploratory task: VisTrails maintains provenance of data products, of the workflows that derive these products and their executions. This information is persisted as XML files or in a relational database, and it allows users to navigate workflow versions in an intuitive way, to undo changes but not lose any results, to visually compare different workflows and their results, and to examine the actions that led to a result. It also enables a series operations and user interfaces that simplify workflow design and use, including the ability to create and refine workflows by analogy and to query workflows by example. VisTrails supports the creation and execution of workflows. It allows the combination of loosely-coupled resources, specialized libraries, grid and Web services. The released version comes with support for several packages including, VTK, Image Magick, Web Services, and pylab. You can also download packages contributed by users, as well as create your own packages/modules. Workflows can be run interactively, through the VisTrails GUI, or in batch using a VisTrails server. VisTrails is written in Python and it uses the multi-platform Qt library for its user interface. It runs on Mac, Linux and Windows. Provenance-rich results derived by VisTrails can be included in LaTeX, Wiki, Microsoft Word and PowerPoint documents. | workflow, provenance, simulation, data exploration, visualization, data analysis, management system, python, mac, linux, windows |
is listed by: FORCE11 is related to: crowdLabs has parent organization: University of Utah; Utah; USA |
DOE ; IBM ; NSF IIS-0905385; NSF IIS-0844572; NSF IIS CAREER-0746500; NSF CNS-0751152; NSF IIS-0513692; NSF CCF-0401498; NSF CNS-0541560; NSF OISE-0405402; NSF OCE-0424602; NSF CNS-0524096; NSF IIS-0534628 |
Open unspecified license | nif-0000-06694 | SCR_006261 | Vis Trails | 2026-09-12 01:00:12 | 20 | ||||||
|
MoTrak Head Motion Tracking System Resource Report Resource Website 1+ mentions |
MoTrak Head Motion Tracking System (RRID:SCR_009607) | MoTrak | resource, software resource | Designed for use in an MRI simulator, MoTrak software uses Ascension Technology?s Flock of Birds. The sensor attaches to the subject?s head and determines the position of the head in space relative to the transmitter. The sensor records angular rotations as well as positional displacements from an initially calibrated position. This information is displayed and logged by the program in real-time, allowing observation of head motion in an MRI simulator. In the simulator, the participant can simultaneously be habituated to the MRI environment, while being trained to remain still via feedback from the MoTrak system. | experiment control, hardware, microsoft, magnetic resonance, training, win32 (ms windows), windows, windows vista, windows xp, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155815 | http://www.nitrc.org/projects/motrak | SCR_009607 | MoTrak - Head Motion Tracking System | 2026-09-12 01:00:14 | 3 | |||||||
|
BrainNet Viewer Resource Report Resource Website 500+ mentions |
BrainNet Viewer (RRID:SCR_009446) | BrainNet Viewer | data processing software, data visualization software, software application, software resource | Aa brain network visualization tool, which can help researchers to visualize structural and functional connectivity patterns from different levels in a quick, easy, and flexible way. | linux, macos, matlab, microsoft, magnetic resonance, posix/unix-like, visualization, win32 (ms windows), windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155589 | SCR_009446 | 2026-09-12 01:00:14 | 678 | ||||||||
|
metaMA Resource Report Resource Website |
metaMA (RRID:SCR_000408) | software resource, software toolkit | Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools is listed by: CRAN is related to: SMAGEXP |
Scottish Government Rural and Environment Research and Analysis Directorate | PMID:19628502 | Free, Available for download, Freely available | OMICS_03524 | SCR_000408 | Meta-analysis for MicroArrays, Meta analysis for MicroArrays | 2026-09-12 01:02:23 | 0 | ||||||
|
ShapeWorks Resource Report Resource Website 1+ mentions |
ShapeWorks (RRID:SCR_000424) | ShapeWorks | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2022. Software that is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results. | c++, console (text based), linux, macos, microsoft, magnetic resonance, posix/unix-like, rendering, shape analysis, surface rendering, visualization, win32 (ms windows), windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155961 | http://www.nitrc.org/projects/shapeworks | SCR_000424 | 2026-09-12 01:02:23 | 1 | ||||||
|
zmax_edf_merge_converter Resource Report Resource Website |
zmax_edf_merge_converter (RRID:SCR_022567) | software application, software resource | Software tool for comprehensive conversion of folder with Hypnodyne zmax EDF files into merged European Data Format. | hypnodyne, Zmax, converter, EDF, merge, python, windows | Free, Available for download, Freely available | SCR_022567 | 2026-09-12 01:03:01 | 0 | |||||||||||
|
BD FACSDiva Software Resource Report Resource Website 5000+ mentions |
BD FACSDiva Software (RRID:SCR_001456) | BD FACSDiva Software | commercial organization, software resource | A collection of tools for flow cytometer and application setup, data acquisition, and data analysis that help streamline flow cytometry workflows. It provides features to help users integrate flow systems into new application areas, including index sorting for stem cell and single-cell applications, as well as automation protocols for high-throughput and robotic laboratories. | flow cytometry, windows |
is used by: BD Biosciences: LSRFortessa X-20 Cell Analyzer has parent organization: BD Biosciences |
Free, Freely Available | SciRes_000115 | http://www.bdbiosciences.com/instruments/software/facsdiva/index.jsp | SCR_001456 | 2026-09-12 01:03:11 | 8327 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
