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MetaPlat SIGNED

Development of an Easy-to-use Metagenomics Platform for Agricultural Science

Total Cost €

0

EC-Contrib. €

0

Partnership

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Project "MetaPlat" data sheet

The following table provides information about the project.

Coordinator
UNIVERSITY OF ULSTER 

Organization address
address: CROMORE ROAD
city: COLERAINE
postcode: BT52 1SA
website: www.ulster.ac.uk

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country United Kingdom [UK]
 Project website http://www.metaplat.eu/
 Total cost 648˙000 €
 EC max contribution 648˙000 € (100%)
 Programme 1. H2020-EU.1.3.3. (Stimulating innovation by means of cross-fertilisation of knowledge)
 Code Call H2020-MSCA-RISE-2015
 Funding Scheme MSCA-RISE
 Starting year 2015
 Duration (year-month-day) from 2015-12-01   to  2019-11-30

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    UNIVERSITY OF ULSTER UK (COLERAINE) coordinator 90˙000.00
2    NSILICO LIFE SCIENCE LIMITED IE (DOUGLAS) participant 315˙000.00
3    FTK FORSCHUNGSINSTITUT FUR TELEKOMMUNIKATION UND KOOPERATION EV DE (DORTMUND) participant 135˙000.00
4    SRUC UK (EDINBURGH) participant 54˙000.00
5    UNIVERSITA DEGLI STUDI DI NAPOLI FEDERICO II IT (NAPOLI) participant 54˙000.00

Map

 Project objective

The aim of this project is to bring together experts from the academic and non-academic sectors and to create an easy-to-use integrated hardware and software platform. This will enable the rapid analysis of large metagenomic datasets. It will provide actionable insights into probiotic supplement usage, methane production and feed conversion efficiency in cattle. In the recent years, the number of projects or studies producing very large quantities of sequencing data – analysing microbial communities make-up and their interactions with the environment – has increased. Yet, the depth of analysis done is very superficial and represents an inefficient use of available information and financial resources. This project aims to address these deficiencies and will study the change within microbial communities, under various conditions in cattle guts and impacting probiotic supplement usage, methane production and feed conversion efficiency in cattle. To succeed, we propose to develop faster and more accurate analytic platforms in order to fully utilise the datasets generated. By focusing on better hardware and software platforms, better expertise and training, this project will pave the way for a more optimal usage of metagenomic datasets, thus reducing the number of animals necessary. This will ensure better and more economic animal welfare.

The Meta-Plat project objective is a mixture of innovative research, focused application and commercial awareness. The core objectives being pursued are: • Sample gut collection, from cattle, for sequencing; • Collection of publically available databases – to create a new classification of previously unclassified sequences, using machine learning algorithms; • Development of accurate classification algorithms; • Real-time or time-efficient comparison analyses; • Production of statistical and visual representations, conveying more useful information; • Platform integration; • Provide insights into probiotic supplement usage, methan

 Deliverables

List of deliverables.
Publications Documents, reports 2020-04-14 21:37:13
Public release of the meta-genomic analysis platform Other 2020-04-14 21:37:13
Technical reports and Platform Integration of WP3 pipelines Documents, reports 2020-04-14 21:37:13
Academic papers and technical reports Documents, reports 2020-04-14 21:37:13
Academic papers on changes in rumen microbial population due to chronic stress Documents, reports 2020-04-14 21:37:13
Implementation of next software platform Websites, patent fillings, videos etc. 2020-04-14 21:37:13
Academic papers & technical reports Documents, reports 2020-04-14 21:37:13
Technical reports and Platform Integration of WP4 pipelines Documents, reports 2020-04-14 21:37:13
Technical reports and Platform Integration of WP2 results and databases Documents, reports 2020-04-14 21:37:13
Academic Papers Documents, reports 2020-04-14 21:37:13
Implementation of Software platform Demonstrators, pilots, prototypes 2020-04-14 21:37:13
Submission to EBI ENA database of the raw sequence files Websites, patent fillings, videos etc. 2020-04-14 21:37:13
Current Algorithm evolution – Review/position publication Documents, reports 2020-04-14 21:37:12

Take a look to the deliverables list in detail:  detailed list of MetaPlat deliverables.

 Publications

year authors and title journal last update
List of publications.
2019 Jyotsna Talreja Wassan, Huiru Zheng, Haiying Wang, Fiona Browne, Paul Walsh, Tim Manning, Richard Dewhurst, Rainer Roehe
A Phylogeny-aware Feature Ranking for Classification of Cattle Rumen Microbiome
published pages: , ISSN: , DOI:
2019 IEEE International Conference on Bioinformatics and Biomedicine 2020-04-14
2019 Mengyuan Wang, Huiru Zheng, Haiying Wang, Richard Dewhurst, Rainer Roehe,
A knowledge driven mutual information-based analytical framework for the identification of rumen metabolites
published pages: , ISSN: , DOI:
2019 IEEE International Conference on Bioinformatics and Biomedicine 2020-04-14
2019 Timmy Manning, Miguel Somarriba, Rainer Roehe, Simon Turner, Haiying Wang, Huiru Zheng, Brian Kelly, Jennifer Lynch, Paul Walsh
Automated Object Tracking for Animal Behaviour Studies
published pages: , ISSN: , DOI:
2019 IEEE International Conference on Bioinformatics and Biomedicine 2020-04-14
2019 Binh Vu, Yanxin Wu, Haithem Afli, Paul Mc Kevitt, Paul Walsh, Felix Engel, Michael Fuchs, Matthias Hemmje
A Metagenomic Content and Knowledge Management Ecosystem Platform
published pages: , ISSN: , DOI:
2019 IEEE International Conference on Bioinformatics and Biomedicine 2020-04-14
2019 Jyotsna Talreja Wassan, Haiying Wang, Fiona Browne, Huiru Zheng
Phy-PMRFI: Phylogeny-Aware Prediction of Metagenomic Functions Using Random Forest Feature Importance
published pages: 273-282, ISSN: 1536-1241, DOI: 10.1109/tnb.2019.2912824
IEEE Transactions on NanoBioscience 18/3 2020-04-14
2018 Huiru Zheng, Haiying Wang, Richard Dewhurst, Rainer Roehe
Improving the Inference of Co-occurrence Networks in the Bovine Rumen Microbiome
published pages: 1-1, ISSN: 1545-5963, DOI: 10.1109/tcbb.2018.2879342
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2020-04-14
2017 Haiying Wang, Huiru Zheng, Fiona Browne, Rainer Roehe, Richard J. Dewhurst, Felix Engel, Matthias Hemmje, Xiangwu Lu, Paul Walsh
Integrated metagenomic analysis of the rumen microbiome of cattle reveals key biological mechanisms associated with methane traits
published pages: 108-119, ISSN: 1046-2023, DOI: 10.1016/j.ymeth.2017.05.029
Methods 124 2020-04-14
2018 Jyotsna Talreja Wassan, Haiying Wang, Fiona Browne, Huiru Zheng
A Comprehensive Study on Predicting Functional Role of Metagenomes Using Machine Learning Methods
published pages: 1-1, ISSN: 1545-5963, DOI: 10.1109/tcbb.2018.2858808
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2020-04-14
2016 Haiying Wang, Huiru Zheng, Fiona Browne, Rainer Roehe, Richard Dewhurst, Felix Engel, Matthias Hemmje, and Paul Walsh
Analysis of Rumen Microbial Community in Cattle through the Integration of Metagenomic and Network-based Approaches
published pages: , ISSN: , DOI:
Proc. of the IEEE International Conference on Bioinformatics and Biomedicine 2020-04-14

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