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Orione, a web-based framework for NGS analysis in microbiology

Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna, Andrea Sbardellati, Nicola Soranzo, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Giorgio Fotia
2014 Computer applications in the biosciences : CABIOS  
for next-generation sequencing microbiology data analysis.  ...  To overcome these limitations we present Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows  ...  To address these challenges, we developed Orione, an online framework for integrative analysis of NGS microbiology data.  ... 
doi:10.1093/bioinformatics/btu135 pmid:24618473 pmcid:PMC4071203 fatcat:5uopzyti4jalfpwpbpuftks63y

D4.17- 2nd periodic report on ongoing JIPs [article]

2021 Zenodo  
A prototype of the risk modelling framework in R shiny for quantitative microbiological risk assessment has been developed.  ...  D-JIP1-2.1 Report on requirement analysis for an "OH Knowledge Base -Epi" 12 14.01.2019 14.01.2019 ORION D-JIP1-2.2 Report on requirement analysis for an "OH Knowledge Base -NGS" 12 28.02.2019  ... 
doi:10.5281/zenodo.4897465 fatcat:p672tluybjhc7dvhbarzt6laui

D4.10- 1st periodic report on ongoing JIPs [article]

2021 Zenodo  
COHESIVE took part in the cogwheel meeting with COMPARE to look for possible connections.  ...  In this meeting the contact persons for Cohesive, Karin Johansson (ECDC) and Valentina Rizzi (EFSA), were taken part.  ...  In cooperation with EFSA and OpenAnalytics 4 , we want to work towards integrating rrisk (web-based version) into a European platform-independent framework for risk modelling.  ... 
doi:10.5281/zenodo.4897372 fatcat:gvje37vcybcothmifk5lzjr2n4

D4.3- 1st cogwheel workshop report with COMPARE [article]

2021 Zenodo  
COMPARE is a 60-month EU funded project aimed to develop an analytical framework and information sharing platform that will enable identification, containment and mitigation of emerging infectious diseases  ...  The target for the first CW activity was COMPARE (  ...  • To develop general work-flows for integration of NGS in clinical laboratory diagnostics • To develop a framework for prediction of phenotypic antimicrobial susceptibility based on the presence  ... 
doi:10.5281/zenodo.4897348 fatcat:nnafxj2fb5fcvpcvdtjt4m5v7i

D4.22- 3rd periodic report on JIPs [article]

2021 Zenodo  
WP2 -NGS JIP1-WP2-T5: Improving OH Knowledge Base -NGS (M13-M24)  With regards to the NGS handbook, the focus for the reporting period has been on building the framework for the book, and on content  ...  WP2-NGS continued to enrich the content of the web-based community NGS handbook and successfully implemented the first crosssector IRIDA ( NGS data analysis platform at the Norwegian  ...  This began in the WP4 meeting in July 2020, where a member of WP5 actively participated.  The planning on the execution of the requirement analysis for the national OH surveillance roadmaps have begun  ... 
doi:10.5281/zenodo.4897486 fatcat:zmpjf6znm5cgboh57fmrb5u3tu

Deliverable-D-JIP2-D1.4-Annual-report (COHESIVE) [article]

2020 Zenodo  
with EFSA and openanalytics 1 , we want to work towards integrating rrisk (web-based version) into a European platform-independent framework for risk modelling.  ...  implementation status of NGS methods for FBD surveillance and outbreak investigations, data gathered by ORION will be used.  ...  The annual meeting for all members of the project will be scheduled for Spring 2019. In Autumn, a workshop will be organized.  ... 
doi:10.5281/zenodo.3754248 fatcat:vqvwo7rtl5e6zd2h5afb64aouu

Deliverable JIP1-2.8 - Status report on OH Knowledge Base - NGS

Karin Lagesen, Umaer Naseer, Emily Macdonald, Lin Brandal, Olaug Taran Skjerdal, Thomas H.A. Haverkamp, Eve Zeyl Fiskebeck, Jeevan Karloss Antony Samy, Georgios Marselis, Camilla Sekse, Håkon Kaspersen, Wonhee Cha (+8 others)
2021 Zenodo  
OHEJP Project ORION  ...  At the beginning of the project, the NIPH had already established a technological framework and procedures for performing surveillance and outbreak analyses based on NGS data, while the NVI was the process  ...  The project developed a web platform that managed user access, access to data, data analysis and visualization of results, and used Nextflow for managing analysis pipelines.  ... 
doi:10.5281/zenodo.5062329 fatcat:mca5ix3ojzewzd5gyyq7g6gm5a

Integrating Microbiome Network: Establishing Linkages Between Plants, Microbes and Human Health

Suresh B. N. Krishna, Anamika Dubey, Muneer A. Malla, Richa Kothari, Chandrama P. Upadhyay, Jamila K. Adam, Ashwani Kumar
2019 Open Microbiology Journal  
This review also highlighted the potential therapies in modulating the gut microbiota and technologies for studying the microbiome.  ...  This plant microbiome has a substantial influence on human health and environment via its passage through the nasal route and digestive tract and is responsible for changing our gut microbiome.  ...  Anamika Dubey would like to thank DST for financial supports in the form of DST inspire research Fellowship.  ... 
doi:10.2174/1874285801913020330 fatcat:bc76mjzi3jfptpnfjdqvbzbzpi

Deliverable JIP1-3.3 Revised OH Harmonisation Infrastructure Hub, including lessons learned from the OH pilots

Fernanda Dórea, Taras Günther, Estíbaliz López de Abechuco, Mia Holmberg, Cecilia Jernberg, Marika Hjertkvist, Matthias Filter, Alessandro Foddai, Johanne Ellis-Iversen, Charlotte Cook, Johanna Lawes, Lesley Larkin (+5 others)
2021 Zenodo  
OHEJP Project ORION - Workpackage 3 TOWARDS AN INTEROPERABLE ONE HEALTH DATA INFRASTRUCTURE  ...  In year 1 of ORION we carried out a requirement analysis reported in the deliverable JIP1-3.1 15 .  ...  developing a formal framework for data sharing.  ... 
doi:10.5281/zenodo.5062410 fatcat:mtfo7fghs5blvizejgelkfpv4y

D1.6- Summary progress report year 2 [article]

2021 Zenodo  
JIP1-WP2-T5: Improving OH Knowledge Base -NGS (M13-M24) The focus for this task this year has been on building the basic framework for the OH NGS handbook.  ...  A prototype of the risk modeling framework in R shiny for quantitative microbiological risk assessment has been developed.  ...  Several posters and one oral presentation from the Report on requirement analysis for an "OH Knowledge Base -Integration" 12 28-02-2019 28-02-2019 The DTU ORION post doc is leaving his post before completing  ... 
doi:10.5281/zenodo.4897003 fatcat:hlxtmxmba5djfkyjcfonoug77e

BacPipe: A rapid, user-friendly whole-genome sequencing pipeline for clinical diagnostic bacteriology

Basil B. Xavier, Mohamed Mysara, Mattia Bolzan, Bruno Ribeiro-Gonçalves, Blaise T.F. Alako, Peter Harrison, Christine Lammens, Samir Kumar-Singh, Herman Goossens, João A. Carriço, Guy Cochrane, Surbhi Malhotra-Kumar
2019 iScience  
BacPipe offers a fully automated "one-stop" bacterial WGS analysis pipeline to overcome the major hurdle of WGS data analysis in hospitals and public-health and for infection control monitoring.  ...  BacPipe is integrated in EBI-SELECTA, a project-specific portal (H2020-COMPARE), and is available as an independent docker image that can be used across Windows- and Unix-based systems.  ...  Few web-based open access pipelines such as Orione ( (Cuccuru et al., 2014) and the Bacterial analysis pipeline ( (Thomsen et al., 2016) and  ... 
doi:10.1016/j.isci.2019.100769 pmid:31887656 pmcid:PMC6941874 fatcat:spyqwfdisfgnddnt4hl56fy7wa

D1.2- Summary progress report of the first year [article]

2021 Zenodo  
WP2-NGS reviewed current state-of-the art NGS-based analyses for several zoonotic agents, with the aim of discovering commonalities and key decision making points that guide the analysis process.  ...  The coordination holds monthly web meetings for the whole ORION consortium and a monthly calls for the WP leaders & deputy leaders.  ...  The PhD proposals were screened for their eligibility in alignment with the criteria listed in the G.A. Each proposal was reviewed by 2-3 reviewers, who were provided a pre-approved scoring matrix.  ... 
doi:10.5281/zenodo.4896342 fatcat:ph7nq7fiojexjnuu5ytx3h2yb4

D4.2- Report from supportive start-up meeting, 1st round [article]

2021 Zenodo  
OTHER R Dissemination level PU: Public CO: confidential, only for members of the consortium (including the Commission Services) PU Report from supportive start-up meeting for projects funded in the first  ...  One such supportive activity was the arrangement of a pre-kick-off meeting (P-KOM) for project leaders, deputy project leader or their replacements.  ...  EJP: One Health Zoonoses -Emerging Threats EU Project 773830 Procedures for Joint Research (WP3) and Integrative (WP4) Projects  ... 
doi:10.5281/zenodo.4897346 fatcat:dxjdh4swend5xgs7gpdsp7cyh4

AGINFRA PLUS D6.4 - Food Safety Risk Assessment Pilot Evaluation Report

Matthias Filter, Estíbaliz Lopez de Abechuco, Esther Sundermann
2020 Zenodo  
During all evaluation phases community experts attended hands-on workshops that allowed them to practically work with the web-based software pilots and to obtain practical experience on the advantages  ...  A detailed description of the evaluation methodology is described in the Deliverable "Food Safety Risk Assessment Community-Centred Assessment Plan (D6.3)".  ...  or a Google Form (ORION Use case).  ... 
doi:10.5281/zenodo.3634620 fatcat:h54sn4wgxjcgnmzylglem27oky

D2.1- Provisional strategic research agenda [article]

2021 Zenodo  
zoonoses monitoring data collection and analysis, as well as for BSE-TSE and microbiological risk assessment.  ...  Objectives The overall objectives will be to deploy a harmonized scheme, from sample preparation to results' analysis, for the use of the NGS technology for a more precise and rapid detection, characterization  ... 
doi:10.5281/zenodo.4897125 fatcat:vyvmidcb5fdwdbdy7u5npqtbqa
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