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What is PhenoMeNal?

PhenoMeNal (Phenome and Metabolome aNalysis) is a comprehensive and standardised e-infrastructure that supports the data processing and analysis pipelines for molecular phenotype data generated by metabolomics applications. An infrastructure aimed to address the H2020 Societal Challenge in Health, Demographic Change and Wellbeing, PhenoMeNal provides services enabling computation and analysis to improve the understanding of the causes and mechanisms underlying health, healthy ageing and diseases.

Our Objectives

  • To use existing open source community standards, integrate tools, resources and methods for the management, dissemination and computational analysis of very large datasets of human metabolic phenotyping and genomic data into a secure and sustainable e-Infrastructure
  • To operate and consolidate the PhenoMeNal e-infrastructure based on existing internal and external HPC (High-performance computing), cloud, and grid resources, including the EGI and the EGI Federated Cloud, and to extend it to world-wide computational infrastructures
  • To improve and scale-up tools used within the infrastructure to cope with very large datasets
  • To establish technology for a water-tight audit trail for the processing of human metabolic phenotyping data from the raw data acquisition all the way to the generation of high-level biomedical insights (such as a medical diagnosis)
  • To establish privacy-protection methods that allow working with highly sensitive molecular phenotype data
  • To foster the worldwide adoption of PhenoMeNal through a wide range of outreach, dissemination, networking and training activities
  • To develop a model to ensure sustainability of the PhenoMeNal network

Our Services

Cloud Research Environment (CRE)

PhenoMeNal provides a Virtual Research Environment (VRE) known as the “PhenoMeNal Cloud Research Environment” (CRE), for interoperable and scalable metabolomics analysis. The main workflow system in PhenoMeNal is Galaxy, which comes with a user-friendly Graphical User Interface (GUI) for workflow authoring and execution of tools and workflows.

App Library

The PhenoMeNal App Library showcases our service catalogue listing tools that are available via Galaxy workflows through the Cloud Research Environment. Currently it includes a wide range of MS and NMR-based tools, including popular data-processing and analysis tools and packages such as XCMS, rNMR, CAMERA, BATMAN, MetFrag, univariate, and multivariate statistics.

User Support and training

The PhenoMeNal wiki provides step-by-step tutorials including technical documentations on starting a CRE on a cloud provider of choice, workflows creation and tool usage for both new and experienced users. We also host face-to-face training and workshops from time to time to provide hands-on training on PhenoMeNal resources and workflows. Follow us on twitter @PhnmlH2020 or Latest News section on our website to stay up-to-date with our activities.

Privacy and Ethics

The PhenoMeNal  e-infrastructure supports the data processing and analysis pipelines for molecular phenotype data  from the earliest time point of the data acquisition in the laboratory up to the high level medical and biological conclusions and interpretations. This includes handling of  data generated from comprehensive clinical, genotypic, ‘omics and analytic sources including medical records, electronic health records, clinical measurements, genotypic data, phenotypic data from tissue and biofluid analysis, image and pathology data. Depending on the data intended to be processed, Ethical Legal and Social Implications (ELSI) may have a strong bearing on the use and re-use of the data.

PhenoMeNal ensures patient confidentiality and prevention of identification of patients by providing a secure environment to process input data and to provide a series of data outputs for futher analysis.

See PhenoMeNal ELSI Terms of Use.

PhenoMeNal: Can I contribute?

PhenoMeNal explicitly encourages feedback and contributions from the community. The cloud-based infrastructure for metabolomics and phenomics data processing and analysis has a global scope and is not limited to Europe. Simple user feedback can be provided via the PhenoMeNal help desk. Active participation in the development can be channelled through the PhenoMeNal GitHub pages.