NextGenPhenomics: Building a systems-level cloud-based platform, integrating Next Generation Sequencing and advanced real-time phenotypic quantificati
Lead Research Organisation:
Cranfield University
Department Name: School of Water, Energy and Environment
Abstract
The falling costs and the extremely high yield of genomic data from next generation sequencing (NGS) technology made it the method of choice for studying complex plant genome species. Using NGS, we are now able to produce more than one billion sequencing reads within the timeframe of a few days, which has paved the way forward for tens of thousands of biological events and environmental stress responses in parallel. In order to maximise benefit from these rapid advances in sequencing technologies, Next-generation sequencing demands next-generation phenotyping. For this reason, Cranfield University and Agri-Epi Centre have recently acquired a state-of-the-art phenotypic platform installed within a purpose-built glasshouse facility as part of a £5.5m investment. The glasshouse hosts a LemnaTec multi-sensor platform (only two other similar platforms exist worldwide) that allows for real-time assessment of crop parameters through RGB, hyperspectral, fluorescence and thermal cameras and a 3D laser scanner. This platform will allow to monitor, in real-time, the genotypic responses for various plant varieties across a number of environmental stresses and soil conditions.
Organisations
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| NE/R011265/1 | 02/10/2017 | 01/10/2022 | |||
| 1956140 | Studentship | NE/R011265/1 | 02/10/2017 | 01/04/2021 | Ewelina Sowka |
| Description | NextGenPhenomics (NGP) is a web-based platform used to automate plant phenotyping, utilising a state-of-the-art sensor-to-plant imaging system and an environmentally controlled glasshouse. The device moves in three dimensions with plants remaining static in containers. It allows automated, precise and non-invasive monitoring of plant growth and physiology under a range of soil conditions and root zone stresses; including but not limited to salinity, drought and compaction. The platform consolidates RGB, hyperspectral, fluorescence and thermal cameras and a 3D laser scanner. The glasshouse is also equipped with a large number of environmental sensors and manual phenotyping devices, including root scanners. Extensive amounts of raw data were previously stored on several servers with no user-friendly interface. Our NGP web application is developed using a JavaScript MEAN stack web framework and gathers, stores and classifies information providing users with rapid access in a structured way. The application back-end, MongoDB, detects newly added raw files and saves them automatically. Thanks to the combination of Node.js, Express and Angular, authorised users have immediate access to updated data structures. NGP allows seamless classification of measurements into their corresponding investigations and studies. Additional information, like genomic data, can be easily added to existing or new datasets. Although NGP is tailored for a site-specific system, it could be readily applied across other similar devices. |
| Exploitation Route | In further developments of the system will gain possibility to create and run analysis in cloud. Users will be able to run scripts on selected data stored in the system. Data will be added to queue, analysed and results will be returned to user. Researchers will also be able to add new methods and scripts to the system. Development will allow users to share and reuse methods of analysis and will allow to extract more results from existing datasets. Last of the planned NGP system developments is allowing user to plan and start the experiment from the webpage. Linking the NGP system directly with the glasshouse will speed up the process of metadata extraction as well as increase the amount of information extracted. Development will increase the minimum information required to start the experiment following the MIAPPE standards transferring the process of filling the gaps in the experiment setup information from the end to the beginning of the data collection processes. |
| Sectors | Agriculture, Food and Drink,Education,Environment |
| Description | DREAM CDT Challenge Week (each year) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Challenge Week is a key element in the DREAM CDT calendar for a number of reasons. Firstly, it permits the opportunity to use and apply the intellectual approaches and skillsets being developed in DREAM to real-world problems with the guidance of actual practitioners. Next, it allows to understand and articulate a challenge, and to communicate this with experts from across a range of fields and, in so doing, helps to develop skills that can aid future employability. Lastly, it helps to develop a strong cohort community, giving a great chance to get to know each young researcher and work together. The 2018 DREAM Challenge Week challenge was to design and undertake an agile prototype development of a real-time spatial hazard decision support tool for the city of Newcastle upon Tyne. Groups decide upon which hazard(s) they wish to develop the decision support tool for, evaluate the spatial impacts of these hazards and consider the adaption and interventions that would be needed to minimize disruption, economic and/or physical damage and/or risk to life. 2019 challenge was related to how best to manage the strategies, priorities and communication of the risks arising from historical landfill sites that are being exposed in coastal locations as cliff erosion takes place. A data-driven risk-based approach considering the 'Source' of contaminants, the likely 'Pathways' such contaminants might take, and the ultimate 'Eco-Receptors' affected by these contaminants can help an assessment of the impact to the 'environment', to people and society at large, and potentially to financial investments, a 'triple bottom line' approach. Challenge included a few case study sites along the Suffolk coast where. Each challenge week consists of preparation for challenge, intense week work and presentation for various interested groups. |
| Year(s) Of Engagement Activity | 2018,2019 |
| Description | DREAM Symposium on Big Data |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | DREAM CDT Symposium each year allows the researchers to communicate and discuss their work on a various levels. Getting researchers from different backgrounds involved in the projects allows to expand and polish them. Industry presence brings an applied aspect to scientific work. Each researcher not only presents their work but also takes part in various panels and discussions with involved professionals. |
| Year(s) Of Engagement Activity | 2018,2019 |
| Description | Poster presentation during 14TH INTERNATIONAL SYMPOSIUM ON INTEGRATIVE BIOINFORMATICS |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Integrative Bioinformatics aims to integrate, align, model and simulate heterogenous data to generate deep insight into complex biological systems. This symposium brings together experts in the field of bioinformatics, computational biology, computer science, systems biology and statistics. Poster presentation during Integrative Bioinformatics 2018 allowed to create connection that can be possibly used in future for project expansion and had been used as a project base (Rothamsted Research has a similar project as Cranfield University). |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.rothamsted.ac.uk/events/14th-international-symposium-integrative-bioinformatics |
| Description | Poster presentation during 17TH EUROPEAN CONFERENCE ON COMPUTATIONAL BIOLOGY |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | European Conference on Computational Biology is the main computational biology event in Europe and it welcomes scientists working in a variety of disciplines, including bioinformatics, computational biology, biology, medicine, and systems biology. Participating in ECCB 2018 is the perfect opportunity to keep pace with cutting edge research, and to network with members of ECCB community. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://eccb18.org |