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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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TriKinetics DAMSystem3 Software Resource Report Resource Website 1+ mentions |
TriKinetics DAMSystem3 Software (RRID:SCR_021809) | data processing software, software application, software resource, data acquisition software | Software tool for data collection to upload output from set of activity monitors and periodically saves it in disk files on Macintosh or Windows PC. Part of TriKinetics Drosophila Activity Monitoring System. | TriKinetics Inc USA, data collection | is related to: TriKinetics: Drosophila Activity Monitoring System | Free, Freely available, Available for download | https://www.trikinetics.com/Downloads/QuickStart%20Guide.pdf | SCR_021809 | 2026-08-14 09:28:32 | 4 | |||||||||
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PARASAIL Resource Report Resource Website 1+ mentions |
PARASAIL (RRID:SCR_021805) | image analysis software, data processing software, software application, software resource, alignment software | Software tool as multiple sequence alignement for global, local and semi global alignments. | multiple sequence alignement, global alignments, local alignments, semi global alignments, | is listed by: Debian | Pacific Northwest National Laboratory | DOI:10.1186/s12859-016-0930-z | Free, Available for download, Freely available | https://sources.debian.org/src/libparasail-dev/ | SCR_021805 | Pairwise Sequence Alignment Library | 2026-08-14 09:28:25 | 4 | ||||||
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LEON BIS Resource Report Resource Website 1+ mentions |
LEON BIS (RRID:SCR_021803) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software tool for sequence alignments evaluation. Multiple alignment evaluation of sequence neighbours using Bayesian inference system. Used to distinguish sections in multiple sequence alignments that are conserved across whole family or within subfamilies, and should be useful for automatic, high-throughput genome annotations, 2D/3D structure predictions, protein-protein interaction predictions etc. | sequence alignments evaluation, distinguish sections, multiple sequence alignments, genome annotations, 2D/3D structure predictions, protein-protein interaction predictions | PMID:27387560 | Free, Available for download, Freely available | SCR_021803 | LEON-BIS | 2026-08-14 09:28:39 | 1 | |||||||||
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LINUCS Resource Report Resource Website |
LINUCS (RRID:SCR_001571) | LINUCS | production service resource, data analysis service, software resource, source code, service resource, analysis service resource | Service that directly converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form. Input: A structure using the extended, non-graphic nomenclature (in ASCII writing) to describe complex carbohydrates as recommended by IUPAC. Output: A linear, unique notation. The source code (written in C), will be distributed so that software developers can easily implement their algorithm within their own application. LINUCS was chosen to fulfill to following conditions: * Input of extended, non-graphic nomenclature to describe carbohydrate structures. * Resulting linear code is closely related to notations and abbreviations recommended by IUPAC. * Number of additional rules to define the priority of the branches is low * Extended nomenclature of complex carbohydrates contains all information to define the hierarchy. * LINUCS is applicable to all types of carbohydrates (macrocyclic system are currently not implemented) . * Remaining unassigned linkage information are tolerated | carbohydrate, notation, structure, carbohydrate sequence, canonical description, glycodatabase, glycobioinformatics, algorithm, molecule, sequence |
is related to: sumo is related to: pdb2linucs has parent organization: glycosciences.de |
PMID:11675023 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152883 | SCR_001571 | LINUCS: LInear Notation for Unique description of Carbohydrate Sequences, LInear Notation for Unique description of Carbohydrate Sequences | 2026-08-14 09:24:20 | 0 | ||||||
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cpnDB: A Chaperonin Database Resource Report Resource Website 1+ mentions |
cpnDB: A Chaperonin Database (RRID:SCR_002263) | cpnDB | database, production service resource, data analysis service, data or information resource, service resource, analysis service resource | A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences. | chaperonin sequence, microbial ecology, phylogenetics, chaperonin, plastid, mitochondria, cytoplasm, sequence, blast, fasta, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Canadian Biotechnology Strategy ; National Research Council Genomics and Health Initiative |
PMID:15289485 | Free, Freely available | biotools:cpndb, OMICS_01511, nif-0000-02694 | https://bio.tools/cpndb | http://www.cpndb.ca/cpnDB/home.php | SCR_002263 | 2026-08-14 09:24:28 | 4 | ||||
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TrainingSpace Resource Report Resource Website 1+ mentions |
TrainingSpace (RRID:SCR_022036) | data or information resource, training resource, portal, online course | Portal that provides multimedia educational content from courses, conference lectures, and laboratory exercises from some of leading neuroscience institutes and societies to be more accessible to global neuroscience community. | Training materials resource, neuroscience multimedia educational content, neuroscience community | Free, Freely available | SCR_022036 | 2026-08-14 09:28:27 | 1 | |||||||||||
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PlaForNEA Resource Report Resource Website |
PlaForNEA (RRID:SCR_022027) | software application, simulation software, software resource | Software allows estimating growth and production at stand level of main forest species implanted in Argentine Mesopotamia such as Pino taeda, Eucalyptus grandis, Pino elliottii and Araucaria angustifolia. Areas for which models were adjusted correspond to province of Misiones, northeast of Corrientes and Concordia in province of Entre Ríos. | estimating growth and production, forest species, Argentine Mesopotamia | Free, Available for download, Freely available | https://plafornea.software.informer.com/ | SCR_022027 | PLAFORNEA | 2026-08-14 09:28:41 | 0 | |||||||||
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National Microbiome Data Collaborative Resource Report Resource Website 1+ mentions |
National Microbiome Data Collaborative (RRID:SCR_022161) | NMDC | data or information resource, portal, topical portal | Platform facilitates comprehensive discovery of and access to multidisciplinary microbiome data in order to unlock new possibilities with microbiome data science. Multi organizational effort to integrate microbiome data across diverse areas in medicine, agriculture, bioenergy, and environment. Founded to support long term advancement of microbiome science. | Microbiome data exploration and discovery, microbiome data, microbiome data science ecosystem, microbiome data, microbiome data discovery portal, FAIR, FAIRsharing | Free, Freely available | https://github.com/microbiomedata/nmdc-schema | SCR_022161 | 2026-08-14 09:28:37 | 2 | |||||||||
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MDAR Resource Report Resource Website |
MDAR (RRID:SCR_022038) | data or information resource, portal, topical portal | MDAR Framework establishes minimum set of requirements in transparent reporting applicable to studies in life sciences. MDAR checklist is tool for authors, editors and others seeking to adopt MDAR framework for transparent reporting in manuscripts and other outputs and designed to provide harmonizing principle for reporting requirements currently in use at various journals. | methods, Materials Design Analysis Reporting, requirements in transparent reporting, manuscript, journal, harmonizing principle for reporting | PMID:33893240 | Free, Freely available | https://www.incf.org/mdar, https://mfr.osf.io/render?url=https://osf.io/xfpn4/?direct%26mode=render%26action=download%26mode=render | SCR_022038 | Materials Design Analysis Reporting | 2026-08-14 09:28:42 | 0 | ||||||||
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EL MAVEN Resource Report Resource Website 10+ mentions |
EL MAVEN (RRID:SCR_022159) | data processing software, software application, data analysis software, software resource | Open source LC-MS data processing engine for simplifying metabolomics analysis. Mass spectrometry data processing engine that is optimal for isotopomer labeling and global metabolomic profiling experiments. Interactive software platform that accelerates analysis of LC-MS, GC-MS, and LC-MS/MS datasets. | Mass spectrometry data processing engine, metabolomics analysis, LC-MS data analysis, metabolomic datasets analysis, Elucidata, MAVEN | PMID:31119671 | Free, Available for download, Freely available | https://github.com/ElucidataInc/ElMaven | SCR_022159 | EL-MAVEN | 2026-08-14 09:28:42 | 10 | ||||||||
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granulator Resource Report Resource Website 1+ mentions |
granulator (RRID:SCR_022158) | data processing software, software application, data analysis software, software resource | Software R package for cell type deconvolution of heterogeneous tissues based on bulk RNAseq data or single cell RNAseq expression profiles.Provides unified testing interface to rapidly run and benchmark multiple deconvolution methods. | cell type deconvolution, heterogeneous tissues, RNAseq data, estimate cell type proportions, bulk transcriptomics data, unified testing interface | Free, Available for download, Freely available | https://github.com/xanibas/granulator | SCR_022158 | 2026-08-14 09:28:27 | 3 | ||||||||||
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SEED Resource Report Resource Website 500+ mentions |
SEED (RRID:SCR_002129) | SEED | database, production service resource, data analysis service, data or information resource, data set, service resource, analysis service resource | The SEED is a framework to support comparative analysis and annotation of genomes. The cooperative effort focuses on the development of the comparative genomics environment and, more importantly, on the development of curated genomic data. Curation of genomic data (annotation) is done via the curation of subsystems by an expert annotator across many genomes, not on a gene by gene basis. From the curated subsystems we extract a set of freely available protein families (FIGfams). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free RAST-Server (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the Metagenomics-RAST-Server freely available. We also provide a SEED-Viewer that allows read-only access to the latest curated data sets. We currently have 58 Archaea, 902 Bacteria, 562 Eukaryota, 1254 Plasmids and 1713 Viruses in our database. All tools and datasets that make up the SEED are in the public domain and can be downloaded at ftp://ftp.theseed.org | environmental genome, eukaryal, archaeal, bacterial, viral, FASEB list |
has parent organization: Fellowship for Interpretation of Genomes has parent organization: University of Chicago; Illinois; USA has parent organization: Argonne National Laboratory |
PMID:16214803 | Free, Freely Available | nif-0000-20923 | http://www.theseed.org/wiki/Main_Page | SCR_002129 | The SEED | 2026-08-14 09:24:31 | 512 | |||||
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CancerMIRNome Resource Report Resource Website 10+ mentions |
CancerMIRNome (RRID:SCR_022092) | database, web service, data or information resource, data access protocol, software resource | Web server for cancer miRNome interactive analysis and visualization based on human miRNome data of cancer types from The Cancer Genome Atlas, and public cancer circulating miRNome profiling datasets from NCBI Gene Expression Omnibus and ArrayExpress. Comprehensive database for interactive analysis and visualization of miRNA expression profiles. | cancer miRNome interactive analysis, human miRNome data, cancer data, miRNA expression profiles |
is related to: The Cancer Genome Atlas is related to: ArrayExpress |
Riverside Faculty Start-up Fund ; UC Cancer Research Coordinating Committee Competition Award ; UC Academic Senate CoR Research Grant ; United States Department of Agriculture ; National Natural Science Foundation of China ; Science and Technology Project of Guizhou Province |
DOI:10.1093/nar/gkab784 | Free, Freely available | SCR_022092 | 2026-08-14 09:28:37 | 48 | ||||||||
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Human Genetics Laboratory: WFS1 Gene Mutation and Polymorphism Database Resource Report Resource Website 1+ mentions |
Human Genetics Laboratory: WFS1 Gene Mutation and Polymorphism Database (RRID:SCR_001113) | database, data repository, storage service resource, data or information resource, service resource | This web site lists the disease causing mutations and polymorphisms found in the Wolfram syndrome (WFS1) gene. Sponsors: This resource is supported by the University of Michigan at Ann Arbor. | frequency, gene, auditory, disease, hearing, neuropathy, polymorphism, research, wolfram syndrome | has parent organization: University of Michigan; Ann Arbor; USA | nif-0000-10276 | SCR_001113 | WFS1 | 2026-08-14 09:24:13 | 3 | |||||||||
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Qvalue Resource Report Resource Website 10+ mentions |
Qvalue (RRID:SCR_001073) | data processing software, software application, data analysis software, software resource | R package that takes a list of p-values resulting from the simultaneous testing of hypotheses and estimates their q-values. It is designed to measure the proportion of false positives when a test is significant. The software is capable of generating plots for visualization. It can be applied to problems in genomics, brain imaging, astrophysics, and data mining. | p value, false positive, null hypothesis, genomics, brain imaging, astrophysics, data mining, r, visualization |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00624 | https://github.com/jdstorey/qvalue | SCR_001073 | 2026-08-14 09:24:14 | 32 | ||||||||
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eNeoTutor Resource Report Resource Website |
eNeoTutor (RRID:SCR_001590) | eNeoTutor | data or information resource, training material, software application, software resource, narrative resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. ASP.NET AJAX .NET 4, Telerik controls enabled application designed to be used with the books presented, papers and web content to help with the acceleration of learning and software development for the neurosciences. All content developed at The Cromwell Workshop is intended to accelerate the implementation of biomedical knowledge, help with EEG clinical certifications and provide the opportunity for students, software developers, neuroscientists, neurologists and neurosurgeons to collaborate globally with knowledge content. e-NeoTutor relies on a subscription model to build software components in multiple languages and access book material. Tutor designed to complement free online course content in neuroscience, work with the Society of Neuroscience, The Human Connectome Project and assist researchers with CNIM certification, biomedical informatics, neuroinformatics and neuroscience training programs. | neuroscience, curriculum, brain computer interface, eeg, tutorial, software development |
is related to: iBIOFind has parent organization: The Cromwell Workshop |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153831 | http://neuronalarchitects.com/eneotutor.html | SCR_001590 | e-NeoTutor | 2026-08-14 09:24:19 | 0 | ||||||
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ToppCluster Resource Report Resource Website 100+ mentions |
ToppCluster (RRID:SCR_001503) | ToppCluster | production service resource, data analysis service, resource, service resource, analysis service resource | A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene. | term enrichment, gene, analysis, gene enrichment analysis, connectivity, heatmap, ortholog, microarray, function, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GenitoUrinary Development Molecular Anatomy Project is related to: ToppGene Suite |
NIDDK 1U01DK70219; NIDDK P30DK078392; NCRR U54 RR025216; NIDCR U01DE020049 |
PMID:20484371 | Free | OMICS_02225, nlx_152801, biotools:toppcluster | https://bio.tools/toppcluster | SCR_001503 | ToppCluster: A multiple gene list feature analyzer for the dissection of biological systems | 2026-08-14 09:24:17 | 152 | ||||
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vIST/e Resource Report Resource Website 1+ mentions |
vIST/e (RRID:SCR_001627) | vIST/e | software toolkit, image analysis software, image processing software, data processing software, software application, software resource | Open source, platform-independent application for the visualization and analysis of complex, high-dimensional imaging data such as Diffusion Tensor Imaging (DTI) and High Angular Resolution Diffusion Imaging (HARDI). It has a plugin-based architecture which allows third parties to develop new plugins to extend the tool. Overview of the many features: * vIST/e is programmed in C++. It uses the Visualization Toolkit for visualization and pipelined data processing, as well as the cross-platform toolkit Qt Framework for an easy-to-use Graphical User Interface. * vIST/e introduces a powerful new plugin system, which allows for modular development with increased extensibility and stability. * Powerful GPU-based visualization techniques allow for smooth, real-time visualization of large data sets. Using custom ray tracing algorithms created with OpenGL, vIST/e can render DTI ellipsoids and HARDI spherical harmonics glyphs up to 4th order. The high frame rates offered by modern GPU technology allows for interactive exploration of this complex data. * Diffusion Tensor Imaging data can be visualized and interactively explored in a number of ways, including multiple cross-sections, volume rendering, and tensor glyphs. Derived scalar volumes, including various different anisotropy measures, can be computed and visualized. Data from other modalities, such as structural MRI, can be shown alongside the DTI data. * Various fiber tracking methods allow for fast and accurate reconstruction of fiber pathways. Interactively defined Regions of Interest (ROIs) can be used for seeding and filtering of fibers. Fibers are visualized either as lines, optionally using a powerful, GPU-based lighting engine, or as 3D structures such as tubes. * Scalar volumes, glyphs, and fibers can be colored using a wide array of coloring option. Customizable color loop-up tables allow for highly flexible visualization of scalar data. * Visualization and processing of various different HARDI formats is supported. HARDI data is interactively visualized using highly detailed glyphs rendered on the GPU. HARDI glyphs can be visualized in combination with DTI glyphs, for a better overview of complex diffusion data. * vIST/e includes support for NVIDIA's Compute Unified Device Architecture (CUDA), which enables highly parallel, GPU-based data processing, allowing for significant speed-up of computationally expensive algorithms. | diffusion tensor imaging, high angular resolution diffusion imaging, visualization, cross-section, volume rendering, tensor glyph, mri, fiber tracking |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion MRI of Traumatic Brain Injury has parent organization: Eindhoven University of Technology; North Brabant; Netherlands |
Free, Available for download, Freely available | nlx_153923 | http://www.nitrc.org/projects/viste | SCR_001627 | DTITool | 2026-08-14 09:24:19 | 4 | ||||||
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Sequence Tag Alignment and Consensus Knowledgebase Database Resource Report Resource Website |
Sequence Tag Alignment and Consensus Knowledgebase Database (RRID:SCR_002156) | database, data processing software, data or information resource, software application, software resource, data visualization software | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The STACKdb is knowledgebase generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACK project aims to generate a comprehensive representation of the sequence of each of the expressed genes in the human genome by extensive processing of gene fragments to make accurate alignments, highlight diversity and provide a carefully joined set of consensus sequences for each gene. The STACK project is comprised of the STACKdb human gene index, a database of virtual human transcripts, as well as stackPACK, the tools used to create the database. STACKdb is organized into 15 tissue-based categories and one disease category. STACK is a tool for detection and visualization of expressed transcript variation in the context of developmental and pathological states. The data system organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index | exonic, expressed, expressed sequence tag (est), expression, fragment, gene, alignment, alternative gene, cdna, clone, cluster, developmental, disease, diversity, genome, homo sapiens, human, isoform, knowledgebase, meta-cluster, mrna, pathological, sequence, tissue, transcript, variant, visualization | PMID:11125101 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20946 | SCR_002156 | STACKdb | 2026-08-14 09:24:28 | 0 | ||||||||
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StAMPP Resource Report Resource Website 1+ mentions |
StAMPP (RRID:SCR_022022) | data processing software, software application, data analysis software, software resource | Software R package for statistical analysis of mixed ploidy populations.Used for calculation of population structure and differentiation based on single nucleotide polymorphism genotype data from populations of any ploidy level, and/or mixed ploidy levels. | statistical analysis, mixed ploidy populations, single nucleotide polymorphism genotype data | is related to: R Project for Statistical Computing | Victorian Department of Primary Industries ; Geoffrey Gardiner Foundation ; Meat and Livestock Australia ; New Zealand Agriseeds ; Christchurch ; New Zealand ; Australian Postgraduate Award ; Dairy Futures CRC |
DOI:10.1111/1755-0998.12129 | Free, Available for download, Freely available | https://github.com/lpembleton/StAMPP | SCR_022022 | 2026-08-14 09:28:35 | 6 |
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