A student's perspective on what's required for microbiome analysis
Last week we had a requirements gathering session in Perth, where we were lucky to meet Rachele and Charlie, both students at Edith Cowan University (ECU)'s Centre for Ecosystem Management, who study the bacterial and dinoflagellate algal microbiomes that are associated with specific species of marine hosts (corals and kelps), and the similarities and differences between these microbiomes when the hosts are found in different marine environments around the country.
Being at the coal-face of research and needing to conduct informatics analysis of both amplicon and whole metagenome data almost daily meant that both Charlie and Rachele were able to provide us with really valuable insights into their current challenges and frustrations in the analysis of these data.
These range across using many disconnected tools (e.g. mothur, R, SPSS, Calypso, arb, primer-e, CytoScape) on many different systems (their own laptops, ECU's HPC etc); in several data formats (e.g. biom or not). As we heard, "...things are all over the place, ideally we would like to use one or two programs, not 50!".
Both Rachele and Charlie have also graciously agreed to be involved in iterative testing of the system we develop throughout the project and providing their feedback to help improve it and make it more fit for purpose. Thanks both!
Being at the coal-face of research and needing to conduct informatics analysis of both amplicon and whole metagenome data almost daily meant that both Charlie and Rachele were able to provide us with really valuable insights into their current challenges and frustrations in the analysis of these data.
These range across using many disconnected tools (e.g. mothur, R, SPSS, Calypso, arb, primer-e, CytoScape) on many different systems (their own laptops, ECU's HPC etc); in several data formats (e.g. biom or not). As we heard, "...things are all over the place, ideally we would like to use one or two programs, not 50!".
Both Rachele and Charlie have also graciously agreed to be involved in iterative testing of the system we develop throughout the project and providing their feedback to help improve it and make it more fit for purpose. Thanks both!
Gonistrea sp. Australian Institute of Marine Science (AIMS) CC BY-NC 3.0
Ecklonia radiata. Photography by J.M. Huisman
Image used with the permission of the Western Australian Herbarium,
Department of Biodiversity, Conservation and Attractions
Accessed on Wednesday, 18 April 2018
Comments
Post a Comment