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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BVQXtools Resource Report Resource Website 10+ mentions |
BVQXtools (RRID:SCR_009532) | BVQXtools | data processing software, image processing software, software application, software resource, software toolkit | A Matlab-based toolbox for the reading, writing, and processing of BrainVoyager (QX) files in Matlab. The toolbox is freely available. | analyze, format conversion, linux, macos, matlab, microsoft, magnetic resonance, posix/unix-like, statistical operation, time domain analysis, windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainVoyager |
Free, Other/Commercial license License | nlx_155707 | SCR_009532 | 2026-09-12 12:57:13 | 11 | ||||||||
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Connectome Viewer Resource Report Resource Website 1+ mentions |
Connectome Viewer (RRID:SCR_009552) | Connectome Viewer | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | A free, open source, cross-platform Python-based software application for visualization and analysis in connectome research. Features of the software include: Connectome File Format including metadata, networks, surfaces, volumes, track files; complex network analysis toolboxes; modular plugin architecture for extensibility; Mayavi2 for 3D Scientific Visualization and Plotting; interactive data manipulation and scripting capabilities; and Neuroimaging and Diffusion in Python libraries. | animation, atlas application, c++, format conversion, gifti, image display, linux, macos, microsoft, magnetic resonance, nifti, posix/unix-like, python, rendering, software, surface rendering, three dimensional display, tractography, two dimensional display, visualization, volume rendering, win32 (ms windows), windows, connectome, connectomics, data management, multi-modal data, network analysis, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Connectome Mapping Toolkit |
PMID:21713110 | Open Source | nlx_155732 | http://www.nitrc.org/projects/cviewer | SCR_009552 | 2026-09-12 12:57:13 | 1 | ||||||
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C-mii Resource Report Resource Website 1+ mentions |
C-mii (RRID:SCR_010839) | C-mii | software resource | A software tool for plant miRNA and target identification. C-mii pipelines are based on combined steps and criteria from previous studies and also incorporated with several tools such as standalone BLAST and UNAFold and pre-installed databases including miRBase, UniProt, and Rfam. C-mii provides following distinguished features. First, it comes with graphical user interfaces of well-defined pipelines for both miRNA and target identifications with reliable results. Second, it provides a set of filters allowing users to reduce the number of results corresponding to the recently proposed constraints in plant miRNA and target biogenesis. Third, it extends the standard computational steps of miRNA target identification with miRNA-target folding module and GO annotation. Fourth, it supplies the bird eye views of the identification results with info-graphics and grouping information. Fifth, it provides helper functions for database update and auto-recovery to ease system usage and maintenance. Finally, it supports the multi-project and multi-thread management to improve the computational speed. | ubuntu linux, windows | is listed by: OMICtools | PMID:23281648 | GNU General Public License | OMICS_00394 | SCR_010839 | C-mii: A software for Computational miRNA identificaion, C-mii (A software for Computational miRNA identificaion) | 2026-09-12 12:57:24 | 4 | ||||||
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KNOSSOS Resource Report Resource Website 50+ mentions |
KNOSSOS (RRID:SCR_003582) | KNOSSOS | software resource | Software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity. By dynamically loading only data from the surround of the current view point, seamless navigation is not limited to datasets that fit into the available RAM but works with much larger dataset stored in a special format on disk. Currently, KNOSSOS is limited to 8-bit data. In addition to viewing and navigating, KNOSSOS allows efficient manual neurite annotation (''skeletonization''). KNOSSOS is being used mostly for reconstructing cell morphologies from 3D electron microscopic data generated by Serial Block-Face Electron Microscopy (SBEM), with an occasional application to 2-photon and confocal optical microscopy data. | reconstruct, neuronal morphology, connectivity, electron microscopy, windows, python, retina, neuron, morphology, serial block-face electron microscopy, visualization, annotation, 3d image | has parent organization: Max Planck Institute for Medical Research; Heidelberg; Germany | PMID:21743472 | GNU General Public License, v2 | nlx_157725 | SCR_003582 | 2026-09-12 12:56:00 | 51 | |||||||
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AliView Resource Report Resource Website 1000+ mentions |
AliView (RRID:SCR_002780) | software resource | 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. | unix/linux, mac os x, windows, java | is listed by: OMICtools | PMID:25095880 | Free, Freely available | OMICS_05209 | http://www.ormbunkar.se/aliview/ | SCR_002780 | 2026-09-12 12:55:46 | 1039 | |||||||
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NetPathMiner Resource Report Resource Website 1+ mentions |
NetPathMiner (RRID:SCR_002757) | software resource | Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths. | software package, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25075120 | Free, Freely available, Available for download | biotools:netpathminer, OMICS_05210 | https://bio.tools/netpathminer | SCR_002757 | NetPathMiner: R package for network path mining through gene expression | 2026-09-12 12:55:46 | 3 | ||||||
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Mendeley Resource Report Resource Website 1000+ mentions |
Mendeley (RRID:SCR_002750) | Mendeley | data access protocol, data or information resource, database, software resource, web service | Web application as free reference manager and academic social network to organize your research, collaborate with others online, and discover the latest research. Automatically generate bibliographies, Collaborate easily with other researchers online, Easily import papers from other research software, Find relevant papers based on what you're reading, Access your papers from anywhere online, Read papers on the go with the iPhone app. The software, Mendeley Desktop, offers: * Automatic extraction of document details * Efficient management of your papers * Sharing and synchronization of your library (or parts of it) * Additional features: A plug-in for citing your articles in Microsoft Word, OCR (image-to-text conversion, so you can full-text search all your scanned PDFs), etc The website, Mendeley Web, complements Mendeley Desktop by offering these features: * An online back up of your library * Statistics of all things interesting * A research network that allows you to keep track of your colleagues' publications, conference participations, awards etc * A recommendation engine for papers that might interest you. | journal, collaborate, organize, bibliography, mac, windows, linux |
uses: Citation Style Language is used by: Nowomics is used by: NIH Heal Project is listed by: FORCE11 is listed by: re3data.org is related to: Paper Critic is related to: ImpactStory is related to: Overleaf is parent organization of: CitationStyles is parent organization of: Mendeley Data |
Free | nif-0000-24120 | SCR_002750 | , Mendeley Data, Mendeley Research Network, Mendeley | 2026-09-12 12:55:45 | 2439 | |||||||
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CGHnormaliter Resource Report Resource Website 1+ mentions |
CGHnormaliter (RRID:SCR_002936) | software resource | Software for normalization and centralization of array comparative genomic hybridization (aCGH) data with imbalanced aberrations. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs). | standalone software, mac os x, unix/linux, windows, r, array comparative genomic hybridization, copy number alteration, microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20418341 | Free, Available for download, Freely available | OMICS_02572 | http://www.bioconductor.org/packages/release/bioc/html/CGHnormaliter.html | SCR_002936 | CGHnormaliter - Normalization of array CGH data with imbalanced aberrations. | 2026-09-12 12:55:49 | 2 | ||||||
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Chimera Resource Report Resource Website 100+ mentions |
Chimera (RRID:SCR_002959) | software resource | A Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools. The current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion, tophat-fusion-post and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the aforementioned tools. | software package, unix/linux, mac os x, windows, r, infrastructure |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
PMID:25286921 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_06335 | SCR_002959 | chimera - A package for secondary analysis of fusion products | 2026-09-12 12:55:49 | 419 | |||||||
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Gel2DE Resource Report Resource Website 1+ mentions |
Gel2DE (RRID:SCR_002977) | software resource | Software application for performing pixel-by-pixel correlation analysis on a set of gel images from two-dimensional gel electrophoresis and a set of clinical parameters for a population. The application is written in C++, and has been tested on Windows, although it in principle should compile cross platform using CMake. | windows, c++, correlation analysis, gel electrophoresis |
is listed by: OMICtools has parent organization: Google Code |
PMID:23829206 | Free, Available for download, Freely available | OMICS_02546 | SCR_002977 | gel2de - Correlation analysis of gel electrophoresis data | 2026-09-12 12:55:49 | 2 | |||||||
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EONS Resource Report Resource Website 10+ mentions |
EONS (RRID:SCR_002979) | EONS | simulation software, software application, software resource | Modeling platform to study the basic interactions between synaptic elements that allows the user to study qualitatively, and also quantitatively the relative contributions of diverse mechanisms underlying synaptic efficacy: the relevance of each and every element that comprises a synapse, the interactions between these components and their subcellular distribution, as well as the influence of synaptic geometry (presynaptic terminal, cleft and postsynaptic density). This platform consists of a graphical interface in which elements that comprise a single glutamatergic synapse (both pre- and post-synaptically), their behavior as well as the underlying synaptic geometry can be modified. For example, EONS offers the ability to study the effect of voltage-gated calcium channels density and distribution, the number and location of receptors and more. EONS is a parametric model of a generic glutamatergic synapse that takes into account pre-synaptic mechanisms, such as calcium buffering and diffusion, neurotransmitter release, diffusion and uptake in the cleft, and postsynaptic elements, such as ionotropic AMPA and NMDA receptors, their distribution and synaptic geometry, as well as metabotropic glutamate receptors. There are no complicated equations to write: all the models are predefined. This version is a great tool for first time users and students interested in learning about synapses, as well as for studying geometry and distribution hypotheses in a 2D rectangular geometry. System Requirements: EONS V1.2 is a Windows program but can be also successfully installed and run on Mac and Linux. | synapse, geometry, distribution hypothesis, 2d, synaptic modeling, synaptic, modeling, neuron, nervous system, presynaptic, postsynaptic, electromicrograph, animation, simulation, calcium channel, synaptic cleft, excitatory postsynaptic potential, potassium channel, computational neuroscience, java, macos, microsoft, windows, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Simulations Resource |
NIBIB P41-EB001978 | PMID:17946227 | Free, Available for download, Freely available | nif-0000-00504 | http://www.nitrc.org/projects/eons, http://synapticmodeling.com/ | http://www.synaptic-modeling.com | SCR_002979 | Elementary Objects of the Nervous System, EONS-The integrated synaptic modeling platform, EONS (Elementary Objects of the Nervous System) | 2026-09-12 12:55:49 | 12 | |||
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Triplex Resource Report Resource Website 10+ mentions |
Triplex (RRID:SCR_003061) | software resource | Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D. | software package, mac os x, unix/linux, windows, r, gene regulation, sequence matching, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23709494 | Free, Available for download, Freely available | OMICS_06259, biotools:triplex | http://www.fi.muni.cz/~lexa/triplex/, https://bio.tools/triplex | SCR_003061 | triplex - Search and visualize intramolecular triplex-forming sequences in DNA | 2026-09-12 12:55:51 | 10 | ||||||
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HYDEN Resource Report Resource Website 10+ mentions |
HYDEN (RRID:SCR_003126) | HYDEN | software resource | Software program for designing pairs of degenerate primers for a given set of DNA sequences. It works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp). It is a batch (i.e., command-line, as opposed to graphical interface) program, available for Windows XP (downloadable version) and Linux (upon request). | degenerate, primer, dna sequence, primer design, degenerate primer, windows, linux, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Tel Aviv University; Ramat Aviv; Israel |
PMID:17951798 | Free, Available for download, Freely available | OMICS_02338, biotools:hyden | https://bio.tools/hyden | SCR_003126 | HYDEN - A Software for Designing Degenerate Primers, HighlY DEgeNerate primers | 2026-09-12 12:55:52 | 12 | |||||
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enviPat Resource Report Resource Website 10+ mentions |
enviPat (RRID:SCR_003034) | software resource | Software for fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Freely available | OMICS_02408 | SCR_003034 | enviPat: Isotope pattern profile and centroid calculation for mass spectrometry | 2026-09-12 12:55:50 | 33 | ||||||||
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SMRT View Resource Report Resource Website 1+ mentions |
SMRT View (RRID:SCR_003029) | software resource | An open source Genome Browser that visualizes data generated by PacBio Sequencing Systems. * Users can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding. * Users can also visualize base modifications, base identification and motifs analysis results. | standalone software, unix/linux, mac os x, windows, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:smrt_view, OMICS_05137 | https://bio.tools/smrt_view | SCR_003029 | SMRT-View | 2026-09-12 12:55:50 | 9 | |||||||
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CompuCell3D Resource Report Resource Website 50+ mentions |
CompuCell3D (RRID:SCR_003052) | CC3D | simulation software, software application, software resource | Open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. It uses Cellular Potts Model to model cell behavior. | model, simulation, cellular, multi-cellular, windows, mac os x, linux, tissue, organ, organism, cell behavior | has parent organization: Indiana University; Indiana; USA | NIH ; EPA |
PMID:22482955 | Free, Available for download, Freely available | nlx_157668 | SCR_003052 | 2026-09-12 12:55:50 | 75 | ||||||
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SobekCM Resource Report Resource Website |
SobekCM (RRID:SCR_003225) | SobekCM | software resource | Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories. | archiving, resource management, metadata standard, ontology, data repository, research object, c#, windows |
is listed by: FORCE11 has parent organization: University of Florida; Florida; USA has parent organization: Google Code has parent organization: SourceForge |
NEH ; NSF ; NHPRC ; IMLS |
Free, Available for download, Freely available | nlx_157266 | SCR_003225 | SobekCM Digital Repository Software, SobekCM : Digital Content Management System, SobekCM Digital Repository | 2026-09-12 12:55:54 | 0 | ||||||
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Gemi Resource Report Resource Website 10+ mentions |
Gemi (RRID:SCR_003211) | Gemi | software resource | Automated software tool to design polymerase chain reaction (PCR) primers. It accepts multiple aligned and long sequences with degenerated nucleotides. It can be used for quantitative/real-time PCR, conventional and Sanger sequencing. Gemi accepts DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). The programs are as the following: # The first program is to design PCR primers from multiple sequence alignment. # Program to convert ClustalW format (.aln), Phylip (.phy) and (.gde) formats to Fasta format. # Reverse and/or complement program is to find the reverse and complement counterpart of single or multiple sequences. | polymerase chain reaction, primer, pcr primer design, pcr primer, dna sequence, rna sequence, c#, .net/mono, windows, probe, multiple aligned sequence |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23316117 | Free, Available for download, Freely available | OMICS_02332 | SCR_003211 | Gemi - PCR oligos / primers design from multiple sequence alignments | 2026-09-12 12:55:53 | 13 | ||||||
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MAP Software Resource Report Resource Website 10+ mentions |
MAP Software (RRID:SCR_003170) | MAP Software | commercial organization, data processing software, software application, software resource | A suite of client / server programs that control spike sorting in the Multichannel Acquisition Processor (MAP) Data Acquisition System (MAP System) and provides real-time data visualization and analysis. Plexon's original program supporting multichannel data acquisition is a suite of programs referred to as the Real-Time Acquisition System Programs for Unit Timing in Neuroscience software (RASPUTIN). This combination of software and hardware enables users to view waveforms, acquire action potential waveforms around a voltage-threshold crossing, sort them in real time according to their shape, record continuous analog signals, such as field potentials, eye position, blood pressure, as well as capture external digital-event data, such as individual TTL lines or multi-bit strobed word data. RASPUTIN utilizes a client/server architecture on a Microsoft Windows operating system. The server program runs the MAP box and distributes the data among a set of cooperating client programs. The program can record analog signals and spike and digital-event data in a single data file, and supports 16, 32, 48, 64, 96 and 128 channel configurations. RASPUTIN's operation is based on two primary programs: Sort Client and MAP Server. The Sort Client is the primary control program for the MAP System hardware and may be used to adjust the MAP operating parameters (e.g., amplification, filtering) and to set the specific sorting parameters for each channel. MAP Server is the low-level interface for configuring the MAP, which transfers commands such as gain and filter changes or parameter settings from the various clients to the MAP box. MAP Server also accumulates data coming from the MAP box in a circular buffer memory. The client programs connect to MAP Server to gain access to that data. MAP Server also mediates communication between the clients, keeping them informed of commands sent to the MAP from other clients. RASPUTIN is not sold separately, but rather arrives pre-loaded on the MAP Control Computer with the purchase of any MAP System. As the MAP System has been replaced by the advanced OmniPlex D Neural Data Acquisition System, Plexon is no longer developing the RASPUTIN software program. | electrophysiology, analysis, sort client, map server, spike sorting, windows | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000185 | SCR_003170 | Multichannel Acquisition Processor Software, RASPUTIN, Real-Time Acquisition System Programs for Unit Timing in Neuroscience, Real-Time Acquisition System Programs for Unit Timing in Neuroscience software | 2026-09-12 12:55:53 | 21 | ||||||||
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QDNAseq Resource Report Resource Website 100+ mentions |
QDNAseq (RRID:SCR_003174) | software resource | Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively. | software package, unix/linux, mac os x, windows, r, copy number variation, dna-seq, genetics, genome annotation, preprocessing, quality control, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25236618 | Free, Available for download, Freely available | OMICS_05902, biotools:qdnaseq | https://github.com/ccagc/QDNAseq, https://bio.tools/qdnaseq | SCR_003174 | QDNAseq - Quantitative DNA sequencing for chromosomal aberrations | 2026-09-12 12:55:53 | 168 |
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