Reference health
PhenoMeNal: processing and analysis of metabolomics data in the cloud
1 of 77 checkable references need attention · checked 2026-07-14
At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a publisher retraction notice. Each one is shown with the registry record that put it there.
31 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
References needing attention
does not resolve to a known work10.1093/bioinformatics/bty699/5068160
The 76 checked references that resolve
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Environmental metabolomics: a critical review and future perspectives
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Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy
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MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data
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The emergent role of metabolic phenotyping in dynamic patient stratification
resolves10.1007/s11306-007-0081-3
Proposed minimum reporting standards for data analysis in metabolomics
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Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools
resolves10.1093/bioinformatics/btu813
Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics
resolves10.1007/s11306-015-0810-y
COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access
resolves10.1093/nar/gky310
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
resolves10.1093/nar/gkw343
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
resolves10.1093/gigascience/gix099
An architecture for genomics analysis in a clinical setting using Galaxy and Docker
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Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
resolves10.1007/s11306-017-1178-y
NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics
resolves10.1021/acs.analchem.7b02795
nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data
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A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human
resolves10.1016/j.copbio.2015.02.003
A roadmap for interpreting 13C metabolite labeling patterns from cells
resolves10.1016/j.copbio.2014.12.003
How to measure metabolic fluxes: a taxonomic guide for 13C fluxomics
resolves10.1101/213603
Interoperable and scalable data analysis with microservices: Applications in Metabolomics
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MetFrag relaunched: incorporating strategies beyond in silico fragmentation
resolves10.7150/thno.26249
Integration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis
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Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses
resolves10.1038/sdata.2018.179
Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes
resolves10.1007/s11306-015-0879-3
Data standards can boost metabolomics research, and if there is a will, there is a way
resolves10.1038/nbt1346
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
resolves10.1016/j.procs.2016.08.294
Towards European Open Science Commons: The EGI Open Data Platform and the EGI DataHub
resolves10.1007/s10723-018-9453-3
INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures
resolves10.1093/bioinformatics/btq415
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level
resolves10.1089/bio.2015.0014
Sharing and Reuse of Sensitive Data and Samples: Supporting Researchers in Identifying Ethical and Legal Requirements
resolves10.1038/nrg3305
Next-generation sequencing data interpretation: enhancing reproducibility and accessibility
resolves10.1093/bioinformatics/btt199
BioBlend: automating pipeline analyses within Galaxy and CloudMan
resolves10.1186/s13321-016-0179-6
Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles
resolves10.1038/sdata.2016.18
The FAIR Guiding Principles for scientific data management and stewardship
resolves10.1016/j.future.2017.01.012
Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities
resolves10.1038/ng.3312
The European Genome-phenome Archive of human data consented for biomedical research
resolves10.1186/s13321-017-0241-z
Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application
resolves10.1007/s11306-007-0069-z
Metabolomics standards initiative: ontology working group work in progress
resolves10.1186/s12859-017-1513-3
MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes
resolves10.1038/nprot.2014.090
Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN
resolves10.3389/fmolb.2016.00026
biosigner: A New Method for the Discovery of Significant Molecular Signatures from Omics Data
resolves10.1021/ac202450g
CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets
resolves10.1073/pnas.1509788112
Searching molecular structure databases with tandem mass spectra using CSI:FingerID
resolves10.1038/nprot.2016.156
A complete workflow for high-resolution spectral-stitching nanoelectrospray direct-infusion mass-spectrometry-based metabolomics and lipidomics
resolves10.1371/journal.pcbi.1004321
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
resolves10.1186/1471-2105-15-S1-S11
The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again
resolves10.1186/1752-0509-4-135
Edelfosine-induced metabolic changes in cancer cells that precede the overproduction of reactive oxygen species and apoptosis
resolves10.1186/1471-2105-12-366
MetaboLab - advanced NMR data processing and analysis for metabolomics
resolves10.1093/bioinformatics/btq476
The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports
resolves10.1371/journal.pcbi.1005839
Metabomatching: Using genetic association to identify metabolites in proton NMR spectroscopy
resolves10.1007/s10858-013-9718-x
Nmrglue: an open source Python package for the analysis of multidimensional NMR data
resolves10.1093/bioinformatics/btw102
NMRPro: an integrated web component for interactive processing and visualization of NMR spectra
resolves10.1021/acs.analchem.6b00188
Power Analysis and Sample Size Determination in Metabolic Phenotyping
resolves10.1038/s41467-017-01318-5
Significance estimation for large scale metabolomics annotations by spectral matching
resolves10.1002/mrc.2526
rNMR: open source software for identifying and quantifying metabolites in NMR spectra
resolves10.1093/bioinformatics/btv341
JSBML 1.0: providing a smorgasbord of options to encode systems biology models
resolves10.1021/ac800795f
XCMS<sup>2</sup>: Processing Tandem Mass Spectrometry Data for Metabolite Identification and Structural Characterization
The 31 references without a DOI — listed, not checked
no DOI — not checkedFrom correlation to causation: analysis of metabolomics data using systems biology approaches
no DOI — not checkedInternational Phenome Centre Network
no DOI — not checkedFrench Ministry of Research, Higher Education and the National Agency for Science
no DOI — not checkedPhenoMeNal: The PhenoMeNal Portal
no DOI — not checkedOn the Use of Cloud Computing for Scientific Workflows. 2008 IEEE Fourth Int Conf EScience
no DOI — not checkedThe Portal App Library
no DOI — not checkedJenkins-CI, an open-source continuous integration system, as a scientific data and image-processing platform
no DOI — not checkedEGI: Advanced Computing for Research
no DOI — not checkedINtegrating Distributed data Infrastructures for Global ExplOitation
no DOI — not checkedOn-demand virtual research environments using microservices
no DOI — not checkedWiki
no DOI — not checkedGitHub Project Repository
no DOI — not checkedPhenome and Metabolome aNalysis
no DOI — not checkedPublic Galaxy Instance
no DOI — not checkedDeploy on Microsoft Azure
no DOI — not checkedDeploy on European Open Science Cloud (EOSC)
no DOI — not checkedDeploy on a local server (bare metal)
no DOI — not checked2024111706493061400_bib108
no DOI — not checkedHow to make your software tool available through PhenoMeNal
no DOI — not checkedJupyter Notebooks - a publishing format for reproducible computational workflows
no DOI — not checkedJenkins-CI Instance
no DOI — not checkedJenkins Guide
no DOI — not checked2024111706493061400_bib109
no DOI — not checkedCloudflare
no DOI — not checkedPortal Help
no DOI — not checkedInteractive Galaxy Tours
no DOI — not checkedThe PhenoMeNal YouTube page
no DOI — not checkedPeters K, Bradbury J, Bergmann S, , Supporting data for “PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud.”. GigaScience Database. 2018. 10.5524/100528.
no DOI — not checkedTerraform: Writing Infrastructure as Code
no DOI — not checkedBuilding microservices: designing fine-grained systems
no DOI — not checkedSOA with REST: principles, patterns & constraints for building enterprise solutions with REST
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