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SETUP X – A PUBLIC STUDY DESIGN DATABASE FOR METABOLOMIC PROJECTS
2006
Biocomputing 2007
Preserved Fulltext
Metabolomic databases are useless without accurate description of the biological study design and accompanying metadata reporting on the laboratory workflow from sample preparation to data processing. ...
Annotated result data files are housed by SetupX for downloads and queries. Currently, 39 users have generated 48 studies, some of which are made public. ...
public database for metabolomic studies. ...
doi:10.1142/9789812772435_0017
fatcat:ttv2x4gc6zaxbmz4tm5gma3enq
PlantMetabolomics.org: A Web Portal for Plant Metabolomics Experiments
2010
Plant Physiology
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Widespread public access to well-annotated metabolomics datasets is essential for establishing metabolomics as a functional genomics tool. ...
PlantMetabolomics.org (PM) is a web portal and database for exploring, visualizing, and downloading plant metabolomics data. ...
The initial database schema design was guided by the schema proposed in the Architecture for Metabolomics project (Jenkins et al., 2004) . ...
doi:10.1104/pp.109.151027
pmid:20147492
pmcid:PMC2850039
fatcat:6eoz5y4gxbesrhd75cvmaviboa
MASTR-MS: a web-based collaborative laboratory information management system (LIMS) for metabolomics
2016
Metabolomics
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At present, there are no Laboratory Information Management Systems (LIMS) that are specifically tailored for metabolomics laboratories that are capable of tracking samples Adam Hunter, Saravanan Dayalan ...
hundreds to thousands of individual samples per year, often over multiple projects, collaborations and sample types. ...
Conclusion MASTR-MS is a comprehensive LIMS solution specifically designed for metabolomics. ...
doi:10.1007/s11306-016-1142-2
pmid:28090199
pmcid:PMC5192047
fatcat:au6haj5ycbal7fnpkfzeqajojy
Systems View of Deconditioning During Spaceflight Simulation in the PlanHab Project: The Departure of Urine 1 H-NMR Metabolomes From Healthy State in Young Males Subjected to Bedrest Inactivity and Hypoxia
2020
Frontiers in Physiology
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altitude) for HBR and HAmb interventions, respectively. 1H-NMR metabolomes were processed using standard quantitative approaches. ...
setup (medical oversight, fluid and dietary intakes, microbial bioburden, circadian rhythm, and oxygen level). ...
data next to the experimental design and characteristics of the participants) was checked for consistency and updated with recent publications related to the PlanHab project (Debevec et al., 2014a (Debevec ...
doi:10.3389/fphys.2020.532271
pmid:33364971
pmcid:PMC7750454
fatcat:it4hkmkuj5a3foo5cxvghgaf2a
PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud
[article]
2018
bioRxiv
pre-print
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Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. ...
Findings: The PhenoMeNal (Phenome and Metabolome aNalysis) e-infrastructure provides a complete, workflow-oriented, interoperable metabolomics data analysis solution for a modern infrastructure-as-a-service ...
Terraform deploys VM setups to a number of public and private cloud providers including OpenStack, GCE and AWS. ...
doi:10.1101/409151
fatcat:ix5mbzcubvh7terrapsla3zeo4
MeltDB: a software platform for the analysis and integration of metabolomics experiment data
2008
Computer applications in the biosciences : CABIOS
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MeltDB is a web-based software platform for the analysis and annotation of datasets from metabolomics experiments. ...
the systematic storage, analysis and integration of metabolomics experiments, MeltDB was designed, implemented, and applied. ...
As a consequence, public and trial projects for the MeltDB web server can easily be established and maintained. ...
doi:10.1093/bioinformatics/btn452
pmid:18765459
fatcat:6kraieexyvaq7hcx4fikyqg5gq
A Beta-Version Of Phenomenal Integration Vmi Capable Of Proof- Of-Concept Integration With Other Vmis. Initial Services Online Supporting Phenomenal Data Standards - D5.2
2016
Zenodo
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We describe the architecture of the e-infrastructure, the workflow systems chosen, and case studies demonstrating the capabilities of integrating services. ...
This deliverable presents the PhenoMeNal VRE, which in the first 12 months of the project has reached proof-of-concept stage in terms of integration between components. ...
standards) or 2 (identified by similarity using in-house and public databases). ...
doi:10.5281/zenodo.832271
fatcat:g4j4vgsgpbfz7fmxf5cxbupq6i
Integrative Systems Biology Resources and Approaches in Disease Analytics
[chapter]
2019
Systems Biology [Working Title]
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a single database framework, instead of search and fetch a single component at time across a scatter of databases resources. ...
and/ or to provide new compound leads for drug discovery. ...
The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ...
doi:10.5772/intechopen.84834
fatcat:szdavjmg2jbwpnjl2irao6ehty
Metabolomics technologies and metabolite identification
2007
TrAC. Trends in analytical chemistry
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Metabolomics studies rely on the analysis of the multitude of small molecules (metabolites) present in a biological system. ...
Over and above large-scale analysis, a major effort is needed for unequivocal identification of metabolites. ...
Acknowledgement We acknowledge financial support from: the EU RTD project ''Capillary NMR'', a European Community-Access to Research Infrastructure action of the Improving Human Potential Program, Contract ...
doi:10.1016/j.trac.2007.08.003
fatcat:ts3h3ltberdpbl5jxi5idevwu4
Data Management and Modeling in Plant Biology
2021
Frontiers in Plant Science
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The study of plant-environment interactions is a multidisciplinary research field. ...
For this, bioinformatics and mathematics need to be combined with experimental setups in physiology, biochemistry, and molecular biology. ...
ACKNOWLEDGMENTS We thank the members of the SFB/TR175 consortium for many fruitful discussions and DFG for funding. ...
doi:10.3389/fpls.2021.717958
pmid:34539712
pmcid:PMC8446634
fatcat:t7kxxyeklfg3rc7t47ekfqc2sy
Approaches in metabolomics for regulatory toxicology applications
2021
The Analyst
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Metabolomics is progressively proving its value as an efficient strategy... ...
Innovative methodological approaches are needed to conduct human health and environmental risk assessments on a growing number of marketed chemicals. ...
Acknowledgements The authors would like to acknowledge the Swiss Centre for Applied Human Toxicology (SCAHT, Switzerland) and the Swiss National Science Foundation (grant 31003A_166658) for funding this ...
doi:10.1039/d0an02212h
pmid:33605958
fatcat:ji2ykaow4bbw7pqfjsyepyxks4
Metabolomics in the Context of Plant Natural Products Research: From Sample Preparation to Metabolite Analysis
2020
Metabolites
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Metabolomics has emerged in recent years as an indispensable tool for the analysis of thousands of metabolites from crude natural extracts, leading to a paradigm shift in natural products drug research ...
Plant-derived natural products have long been considered a valuable source of lead compounds for drug development. ...
A minimum number of 3-5 biological replicates is recommended for each condition in metabolomic studies [31] . ...
doi:10.3390/metabo10010037
pmid:31952212
pmcid:PMC7023240
fatcat:ax3jnpqshnbvdbrtagmw5eebm4
Current Challenges in Plant Eco-Metabolomics
2018
International Journal of Molecular Sciences
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Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. ...
Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. ...
to come together and discuss current challenges in Eco-Metabolomics, as well as the iDiv publication fund for covering open access costs. ...
doi:10.3390/ijms19051385
pmid:29734799
pmcid:PMC5983679
fatcat:75fv5sfenvdxfduboy32wh7av4
The metaRbolomics Toolbox in Bioconductor and beyond
2019
Metabolites
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This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation ...
Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. ...
MetNorm
[190]
CRAN
Collection of functions designed to implement,
assess, and choose a suitable normalisation method
for a given metabolomics study. ...
doi:10.3390/metabo9100200
pmid:31548506
pmcid:PMC6835268
fatcat:3b2gnq6qdrcfbcq6hewgoobdce
Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing
2019
Metabolomics
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To ensure broad use within the community such a framework also needs to be inclusive and intuitive for both computational novices and experts alike. ...
The metabolomics community has made substantial efforts to align with FAIR data standards by promoting open data formats, data repositories, online spectral libraries, and metabolite databases. ...
Data and software availability The metabolomics and metadata used in this paper were retrieved from Metabolights (https ://www.ebi. ac.uk/metab oligh ts/) study identifier: MTBLS290, and Metabolomics Workbench ...
doi:10.1007/s11306-019-1588-0
pmid:31522294
pmcid:PMC6745024
fatcat:riwra7xbxzav7cb7nz44kanpgi
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