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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GenePattern Resource Report Resource Website 1000+ mentions |
GenePattern (RRID:SCR_003201) | GenePattern | software application, software resource, data analysis software, data processing software | A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. | gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is affiliated with: GenePattern Notebook is related to: TIGRESS has parent organization: Broad Institute |
NCI ; NIGMS |
PMID:16642009 | Free, Freely available | biotools:genepattern, OMICS_01855, nif-0000-30654 | https://bio.tools/genepattern | SCR_003201 | 2026-07-28 09:40:44 | 1078 | |||||
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Cell Image Library (CIL) Resource Report Resource Website 10+ mentions |
Cell Image Library (CIL) (RRID:SCR_003510) | CIL | service resource, data or information resource, data repository, image repository, database, storage service resource | Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment. | microscopic image repository, microscopic video repository, cell animation repository, bio.tools |
is used by: NIF Data Federation is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Cell Centered Database is related to: Cell Centered Database is related to: OME-TIFF Format is related to: Integrated Manually Extracted Annotation has parent organization: American Society for Cell Biology has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR has parent organization: University of California at San Diego; California; USA is parent organization of: Biological Imaging Methods Ontology |
NIGMS RC2 GM092708 | PMID:34218671 PMID:34218673 |
Free, Freely available | biotools:cellimagelibrary, nif-0000-37639, r3d100011601 | http://www.cellimagelibrary.org/pages/about, https://bio.tools/cellimagelibrary, https://doi.org/10.17616/R3N92J | SCR_003510 | Cell Image Library. CIL, Cell Image Library (CIL) | 2026-07-28 09:40:45 | 19 | ||||
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Proteomics Identifications (PRIDE) Resource Report Resource Website 500+ mentions |
Proteomics Identifications (PRIDE) (RRID:SCR_003411) | PRIDE | service resource, data or information resource, data repository, database, storage service resource | Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester. | proteomics, protein, peptide, mass spectrometry, annotation, standard, spectra, protein-protein interaction, amino acid, amino acid sequence, post-translational modification, biomart, bio.tools |
is used by: ProteomeXchange is used by: BioSample Database at EBI is recommended by: NIDDK Information Network (dkNET) is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: HUPO Proteomics Standards Initiative is related to: ProteomeXchange has parent organization: European Bioinformatics Institute |
Wellcome Trust WT085949MA; European Union FP7 LSHG-CT-2006-036814; European Union FP7 260558; European Union FP7 262067; European Union FP7 202272; BBSRC BB/I024204/1 |
PMID:23203882 PMID:19662629 |
Free, Available for download, Freely available | nif-0000-03336, biotools:pride, r3d100011515 | https://www.ebi.ac.uk/pride/archive/, https://bio.tools/pride, https://doi.org/10.17616/R3F330 | SCR_003411 | PRoteomics IDEntifications database, PRIDE Archive - proteomics data repository, PRIDE Archive, PRIDE, Proteomics Identifications, Proteomics Identifications (PRIDE), PRoteomics IDEntifications database (PRIDE) | 2026-07-28 09:40:42 | 642 | ||||
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Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
Ontario Research Fund ; European Molecular Biology Laboratory ; NHGRI P41 HG003751; European Union FP6 ENFIN LSHG-CT-2005-518254; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome, https://doi.org/10.17616/R3V59P | SCR_003485 | Reactome Functional Interaction Network | 2026-07-28 09:40:48 | 4282 | |||||
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L-Measure Resource Report Resource Website 10+ mentions |
L-Measure (RRID:SCR_003487) | LM | software application, service resource, software resource, data processing software, image processing software, image analysis software | A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux. | neuronal morphology, neuroinformatics, branching analysis, digital reconstruction, analysis, comparison, bio.tools |
is listed by: 3DVC is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: Computational Neuroanatomy Group |
Human Brain Project ; NINDS R01 NS39600 |
PMID:18451794 | Public | nif-0000-00003, biotools:l-measure | http://www.nitrc.org/projects/lmeasure, https://bio.tools/l-measure | SCR_003487 | 2026-07-28 09:40:44 | 30 | |||||
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eTRIKS Resource Report Resource Website 10+ mentions |
eTRIKS (RRID:SCR_003765) | eTRIKS | service resource, data or information resource, organization portal, consortium, portal | Research informatics and analytics platform for the IMI OncoTrack consortium. | data sharing, drug discovery, translational research, informatics, knowledge management, metadata standard, platform, analytics, tool development, bio.tools |
uses: tranSMART is used by: U-BIOPRED is used by: Predict-TB is used by: OncoTrack is used by: ABIRISK is used by: RA MAP is listed by: Consortia-pedia is listed by: Debian is listed by: bio.tools is related to: Roche is related to: Janssen Research and Development is related to: Merck is related to: Pfizer Animal Genetics is related to: Imperial College London; London; United Kingdom is related to: French National Center for Scientific Research is related to: Clinical Data Interchange Standards Consortium is related to: University of Luxembourg; Luxembourg; Luxembourg is related to: IDBS is related to: BioSci Consulting is related to: TraIT is related to: EMIF is related to: Open PHACTS has parent organization: Imperial College London; London; United Kingdom |
Innovative Medicines Initiative ; EFPIA |
PMID:29482119 | biotools:eTRIKS, nlx_158034 | https://bio.tools/eTRIKS | SCR_003765 | European Translational Information and Knowledge Management Services, European Translational Information & Knowledge Management Services | 2026-07-28 09:40:51 | 10 | |||||
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University of Zurich SCRM - Cell-and Tissue Biobank Resource Report Resource Website |
University of Zurich SCRM - Cell-and Tissue Biobank (RRID:SCR_004959) | SCRM-CTBB | cell repository, biomaterial supply resource, material resource | The SCRM-CTBB offers state-of-the-art infrastructure and technologies (e.g. cryogenic work bench, semiautomatic cryogenic storage system, uninterrupted cooling chain) and is structured into two areas, including research and a GMP/GCP regulated therapeutic applications. Research: For pre-clinical studies, the SCRM-CTBB provides researchers guidance regarding cell and tissue cryo-preservation, comprising registration, handling, storage and distribution. In order to ensure complete traceability on samples and belonging information all processes are controlled by a Laboratory Information Management System (LIMS) and Quality Assurance (QA) system. The SCRM Biobank is designed to create database that allows connection with other biobanks nationally and internationally. This meta-data file will enable a unique scientific resource for interdisciplinary research. For every new study a contract is established describing the study and the disposition rights. Assistance in writing Biobank Agreements (BAs) and Material Transfer Agreements (MTAs) is provided. Therapeutical applications: As a new feature, apart from research, the SCRM Biobank enables the asservation and preservation of cells and tissues under GMP conditions for later therapeutic use. A special focus will be on a conceptional combination of private and public umbilical cord blood banking (hybrid banking), which allows autologous and/or allogeneic cell applications. | cell, tissue, umbilical cord blood, blood, cryopreserved, therapy, research, clinical, frozen, transplantation |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: OMICtools has parent organization: University of Zurich; Zurich; Switzerland |
Public: The SCRM Biobank is designed to create database that allows connection with other biobanks nationally and internationally. This meta-data file will enable a unique scientific resource for interdisciplinary research. | nlx_143985, OMICS_07231 | https://sources.debian.org/src/scrm/ | SCR_004959 | University of Zurich SCRM - Cell Tissue Biobank, UZH Swiss Center for Regenerative Medicine Cell-and Tissue Biobank, University of Zurich SCRM - Cell and Tissue Biobank, UZH SCRM-CTBB, SCRM Biobank, SCRM - Cell-and Tissue Biobank (CTBB), University of Zurich Swiss Center for Regenerative Medicine Cell-and Tissue Biobank, UZH SCRM - Cell-and Tissue Biobank, SCRM - Cell- Tissue Biobank | 2026-07-27 09:32:09 | 0 | ||||||
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amide Resource Report Resource Website 100+ mentions |
amide (RRID:SCR_005940) | AMIDE | software application, image analysis software, software resource, data processing software | Software tool for viewing, analyzing, and registering volumetric medical imaging data sets. It has been written on top of GTK+ and runs on any system that supports this toolkit (Linux, Windows, Mac OS X, etc.). The program incorporates automatic non-orthogonal data reslicing, allowing multiple data set to be fused without imposed constraints on the dimensions, anisotrophy, or voxel sizes of the data. Additional features include 3D ROI (ellipses, cylinders, boxes, and isocontours), multi-slice viewing, volume rendering, and data importing through the (X)MedCon library. | volumetric medical imaging data, data analysis, data visualization, non-orthogonal data |
is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:14649056 | Free, Freely available | nif-0000-00261 | https://sources.debian.org/src/amide/ | SCR_005940 | , a medical image data examiner, A Medical Image Data Examiner | 2026-07-27 09:32:25 | 472 | |||||
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QuPath Resource Report Resource Website 1000+ mentions |
QuPath (RRID:SCR_018257) | software application, image analysis software, software resource, data processing software | Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images. | Digital pathology, image analysis, whole slide image, batch processing, tissue image, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Queens University Belfast; Ireland; United Kingdom |
Invest Northern Ireland ; Experimental Cancer Medicine Centre Network ; Sean Crummey Memorial Fund ; Tom Simms Memorial Fund ; Friends of the Cancer Centre ; Cancer Research UK Accelerator |
PMID:29203879 | Free, Available for download, Freely available | biotools:qupath | https://bio.tools/qupath | SCR_018257 | 2026-07-27 09:35:42 | 1590 | ||||||
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GeSeq Resource Report Resource Website 100+ mentions |
GeSeq (RRID:SCR_017336) | software application, service resource, software resource, data processing software | Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes. | rapid, accurate, annotation, organelle, genome, chloroplast, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Human Frontier Science Program ; Max Planck Society ; German Science Foundation |
PMID:28486635 | Free, Freely available | biotools:geseq | https://bio.tools/geseq | SCR_017336 | 2026-07-27 09:35:31 | 375 | ||||||
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SeWeR - SEquence analysis using WEb Resources Resource Report Resource Website |
SeWeR - SEquence analysis using WEb Resources (RRID:SCR_004167) | service resource, data or information resource, software resource, topical portal, portal | Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. It doesn''t require any server to host itself. The goal of SeWeR is to turn your web-browser into a powerful sequence-analysis tool. It is written entirely in JavaScript1.2. SeWeR can be downloaded and mirrored freely. The whole package is just around 300K. You can even run it from a floppy. SeWeR is not compatible with Netscape 6. SeWeR now generates graphics. Savvy is a plasmid drawing software that generates plasmid map in the revolutionary Scalable Vector Graphics format from W3C. | nucleic acid, protein, pcr, alignment, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Centre for Cellular and Molecular Biology; Hyderabad; India |
PMID:11395442 | biotools:sewer, nlx_18981 | https://bio.tools/sewer | SCR_004167 | SEquence analysis using WEb Resources, SeWeR | 2026-07-28 09:40:55 | 0 | |||||||
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BSRD Resource Report Resource Website 10+ mentions |
BSRD (RRID:SCR_004249) | BSRD | service resource, data or information resource, data repository, database, storage service resource | A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets. | srna target, srna, small regulatory non-coding rna, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23203879 | Acknowledgement requested, The community can contribute to this resource | biotools:bsrd, OMICS_01533 | https://bio.tools/bsrd | SCR_004249 | BSRD - Bacterial Small Regulatory RNA Database, Bacterial Small Regulatory RNA Database | 2026-07-28 09:40:55 | 29 | |||||
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STAR Resource Report Resource Website 10000+ mentions |
STAR (RRID:SCR_004463) | software application, software resource, data processing software, alignment software, image analysis software | Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays. | RNA-seq data, alignment, RNA-seq reads alignment, reference genome, using uncompressed suffix arrays, bio.tools |
is used by: STARsolo is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U54 HG004557 | PMID:23104886 DOI:10.1093/bioinformatics/bts635 |
biotools:star, OMICS_01254, SCR_015899 | https://github.com/alexdobin/STAR, https://bio.tools/star, https://sources.debian.org/src/rna-star/ | SCR_004463 | Spliced Transcripts Alignment to Reference, Spliced Transcripts Alignment to a Reference (STAR), rna-star, ultrafast universal RNA-seq aligner | 2026-07-28 09:41:00 | 22809 | ||||||
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TAGS Resource Report Resource Website 100+ mentions |
TAGS (RRID:SCR_004294) | TAGS | software application, data analysis software, software resource, data processing software, time-series analysis software | Software tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, enrichment analysis, time series, function, structure, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Tsinghua University; Beijing; China |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tags, nlx_31187 | https://bio.tools/tags | http://166.111.130.26/member/yliu/TAGS/ | SCR_004294 | 2026-07-28 09:40:58 | 139 | ||||||
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neurodebian Resource Report Resource Website 10+ mentions |
neurodebian (RRID:SCR_004401) | NeuroDebian | software application, data distribution software, source code, software resource, data processing software, software development environment, software development tool, software repository | Collection based on a collaborative effort of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others. It contains both unofficial or prospective packages which are not (yet) available from the main Debian archive, as well as backported or simply rebuilt packages also available elsewhere. A listing of current and planned projects is available if you want to get involved. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end, the project offers a package repository that complements the main Debian (and Ubuntu) archive. NeuroDebian is not yet another Linux distribution, but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well. With NeuroDebian, installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. There is also virtual machine to test NeuroDebian on Windows or Mac OS. If you want to see your software packaged for Debian, please drop them a note. | linux, linux distribution, virtual machine, fmri, eeg, pymvpa, python, r, debian, brain image, neuroscience, platform, afni brik, bshort, bfloat, console (text based), dicom, domain independent, freebsd, gnome, kde, linux, minc2, nifti, philips par/rec, development environment, posix/unix-like, system administrator, web environment |
lists: MRIcron is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ITK-SNAP is related to: NITRC Computational Environment is related to: PyMVPA is related to: MRtrix has parent organization: Debian has parent organization: Dartmouth College; New Hampshire; USA has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany is parent organization of: VoxBo is parent organization of: Computational Morphometry Toolkit |
PMID:23055966 | GNU General Public License v3, The community can contribute to this resource | nlx_143723 | http://www.nitrc.org/projects/neurodebian | SCR_004401 | Debian Neuroscience Repository, neuro debian | 2026-07-28 09:41:01 | 40 | |||||
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NCBI BioSystems Database Resource Report Resource Website 100+ mentions |
NCBI BioSystems Database (RRID:SCR_004690) | BioSystems | service resource, data or information resource, data repository, data analysis service, storage service resource, database, production service resource, analysis service resource | Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them. | pathway, disease, gene, protein, small molecule, literature, computation, image, biomarker, drug, structural complex, functional set, biological system, molecule, gold standard, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: NCBI Structure is related to: BioCyc is related to: EcoCyc is related to: MetaCyc is related to: Reactome is related to: Pathway Interaction Database is related to: WikiPathways is related to: Gene Ontology has parent organization: NCBI |
NIH | PMID:19854944 | r3d100011033, biotools:biosystems, nlx_69646 | https://bio.tools/biosystems, https://doi.org/10.17616/R31K80 | SCR_004690 | BioSystems Database, NCBI BioSystems | 2026-07-28 09:41:03 | 118 | |||||
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QuickGO Resource Report Resource Website 500+ mentions |
QuickGO (RRID:SCR_004608) | QuickGO | data or information resource, database, data access protocol, software resource, web service, ontology, controlled vocabulary | A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services. | gene, ontology, annotation, browser, visualization, search engine, slimmer-type tool, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, windows, mac os x, linux, unix, gold standard, bio.tools |
is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: STRAP has parent organization: European Bioinformatics Institute |
BBSRC BB/E023541/1 | PMID:19744993 PMID:20157483 |
Apache License, v2, Free for academic use | biotools:quickgo, nlx_60318, OMICS_02276 | https://bio.tools/quickgo | SCR_004608 | Quick GO | 2026-07-28 09:41:02 | 523 | ||||
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Small Molecule Pathway Database Resource Report Resource Website 50+ mentions |
Small Molecule Pathway Database (RRID:SCR_004844) | SMPDB | service resource, data or information resource, data analysis service, database, production service resource, image, analysis service resource | An interactive, visual database containing more than 350 small molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text, sequence and chemical structure searching. Users may query SMPDB with lists of metabolite names, drug names, genes / protein names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein concentration data can also be visualized through SMPDB''s mapping interface. All of SMPDB''s images, image maps, descriptions and tables are downloadable. | metabolomics, transcriptomics, proteomics, systems biology, small molecule, pathway, human, metabolic pathway, metabolic disease pathway, metabolite signaling pathway, drug-action pathway, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ConsensusPathDB has parent organization: University of Alberta; Alberta; Canada |
Genome Alberta ; Genome Canada |
PMID:19948758 | nlx_143926, biotools:smpdb, r3d100012753 | https://bio.tools/smpdb, https://doi.org/10.17616/R3TB93 | SCR_004844 | SMPDB (The Small Molecule Pathway Database), Small Molecule Pathway Database (SMPDB) | 2026-07-28 09:41:06 | 95 | |||||
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ANTS - Advanced Normalization ToolS Resource Report Resource Website 100+ mentions |
ANTS - Advanced Normalization ToolS (RRID:SCR_004757) | ANTS, ANTsX | software application, software resource, data processing software, registration software, segmentation software, image analysis software | Software package designed to enable researchers with advanced tools for brain and image mapping. Many of the ANTS registration tools are diffeomorphic*, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD). *Diffeomorphism: a differentiable map with differentiable inverse. In general, these maps are generated by integrating a time-dependent velocity field. ANTS Applications: * Gray matter morphometry based on the jacobian and/or cortical thickness. * Group and single-subject optimal templates. * Multivariate DT + T1 brain templates and group studies. * Longitudinal brain mapping -- special similarity metric options. * Neonatal and pediatric brain segmentation. * Pediatric brain mapping. * T1 brain mapping guided by tractography and connectivity. * Diffusion tensor registration based on scalar or connectivity data. * Brain mapping in the presence of lesions. * Lung and pulmonary tree registration. * User-guided hippocampus labeling, also of sub-fields. * Group studies and statistical analysis of cortical thickness, white matter volume, diffusion tensor-derived metrics such as fractional anisotropy and mean diffusion. | algorithm, atlas application, morphology, segmentation, image registration, temporal transformation, child, pediatric, normalization |
is used by: CMIND PY is used by: BICCN is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: Segmentation of Hippocampus Subfields is related to: ANTsR has parent organization: University of Pennsylvania; Philadelphia; USA |
NIBIB R01 EB006266 | PMID:20851191 PMID:33907199 |
nlx_75959 | http://www.nitrc.org/projects/ants, https://sources.debian.org/src/ants/, https://gist.github.com/ntustison/12a656a5fc2f6f9c4494c88dc09c5621 | SCR_004757 | Advanced Normalization Tools | 2026-07-28 09:41:06 | 472 | |||||
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NCBI Probe Resource Report Resource Website 10+ mentions |
NCBI Probe (RRID:SCR_004816) | NCBI Probe | service resource, data or information resource, data repository, database, storage service resource | Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications including genotyping, gene expression studies, SNP discovery, genome mapping, and gene silencing. Probe records contain information on reagent distributors, probe effectiveness, and computed sequence similarities. The database is constantly updated, with over 11,000,000 probes available. Users may deposit their data into NCBI Probe Database. | reagent, probe, registry, nucleic acid, gene expression, gene mapping, gene silencing, dna data bank, nucleic acid probe, gold standard, bio.tools |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: UniSTS has parent organization: NCBI |
Public, The community can contribute to this resource | nlx_80513, r3d100010780, biotools:ncbi_dbprobe | http://www.ncbi.nlm.nih.gov/sites/entrez?db=probe, https://bio.tools/ncbi_dbprobe, https://doi.org/10.17616/R3D041 | SCR_004816 | NCBI Probe Database, Entrez Probe Database, ProbeDB, Probe Database, dbProbe | 2026-07-28 09:41:07 | 17 |
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