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SETUP X – A PUBLIC STUDY DESIGN DATABASE FOR METABOLOMIC PROJECTS

MARTIN SCHOLZ, OLIVER FIEHN
2006 Biocomputing 2007  
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

P. Bais, S. M. Moon, K. He, R. Leitao, K. Dreher, T. Walk, Y. Sucaet, L. Barkan, G. Wohlgemuth, M. R. Roth, E. S. Wurtele, P. Dixon (+8 others)
2010 Plant Physiology  
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

Adam Hunter, Saravanan Dayalan, David De Souza, Brad Power, Rodney Lorrimar, Tamas Szabo, Thu Nguyen, Sean O'Callaghan, Jeremy Hack, James Pyke, Amsha Nahid, Roberto Barrero (+6 others)
2016 Metabolomics  
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

Robert Šket, Leon Deutsch, Zala Prevoršek, Igor B. Mekjavić, Janez Plavec, Joern Rittweger, Tadej Debevec, Ola Eiken, Blaz Stres
2020 Frontiers in Physiology  
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]

Kristian Peters, James Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Tim Ebbels, Carles Foguet, Robert Glen, Alejandra Gonzalez-Beltran, Ulrich Guenther, Evangelos Handakas (+44 others)
2018 bioRxiv   pre-print
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

Heiko Neuweger, Stefan P. Albaum, Michael Dondrup, Marcus Persicke, Tony Watt, Karsten Niehaus, Jens Stoye, Alexander Goesmann
2008 Computer applications in the biosciences : CABIOS  
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

PhenoMeNal Consortium
2016 Zenodo  
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]

Marco Fernandes, Holger Husi
2019 Systems Biology [Working Title]  
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

Sofia Moco, Jacques Vervoort, Sofia Moco, Raoul J. Bino, Ric C.H. De Vos, Raoul Bino
2007 TrAC. Trends in analytical chemistry  
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

Maria Krantz, David Zimmer, Stephan O. Adler, Anastasia Kitashova, Edda Klipp, Timo Mühlhaus, Thomas Nägele
2021 Frontiers in Plant Science  
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

Eulalia Olesti, Víctor González-Ruiz, Martin Wilks, Julien Boccard, Serge Rudaz
2021 The Analyst  
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

Salem, Perez de Souza, Serag, Fernie, Farag, Ezzat, Alseekh
2020 Metabolites  
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

Kristian Peters, Anja Worrich, Alexander Weinhold, Oliver Alka, Gerd Balcke, Claudia Birkemeyer, Helge Bruelheide, Onno Calf, Sophie Dietz, Kai Dührkop, Emmanuel Gaquerel, Uwe Heinig (+20 others)
2018 International Journal of Molecular Sciences  
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

Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski (+7 others)
2019 Metabolites  
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

Kevin M. Mendez, Leighton Pritchard, Stacey N. Reinke, David I. Broadhurst
2019 Metabolomics  
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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