Introduction to nanopore sensing
Electronics for nanopore sensing
The MinION™ device: a miniaturised sensing system
The PromethION™ system
The GridION™ system
Workflow versatility: no fixed run time
Nanopore sensing: informatics
Automatic optimisation of system performance
Analytes and applications: DNA, RNA, proteins
Fields of use
Oxford Nanopore's® informatics team is led by CTO Clive G Brown. The team includes software engineers, bioinformaticians and statisticians. The team's priority is the DNA-sequencing system, where they are working to ensure delivery of a new generation of sequencer with an improved workflow, simplified and powerful data analysis and a user-oriented interface.
The GridION™ system is designed to improve workflows and informatics of molecular analyses. For more information, please read about the system's workflow versatility, Run until... workflow design, and sample scheduling.
Monitoring, controlling and programming nodes
GridION™ nodes are equipped with on-board compute and control software, and are designed to be networked with other nodes and the host environment’s IT infrastructure. Nodes can be accessed, monitored and controlled through a web portal developed on web services APIs. The web portal provides an interface for manually starting and stopping runs, configuring nodes into federated clusters, and monitoring runtime parameters on individual and clustered nodes.
Web services APIs
The web services APIs used in developing the GridION system web portal are exposed so users can customise and automate the behaviour of nodes. With these APIs, users can develop a direct interface between one or more nodes and the host facilities’ sample tracking, LIMS, data-management systems and internal analysis pipelines. The APIs enable the creation of customised experimental workflows; permit retrieval of information about tracked entities such as cartridges, diagnostics, and aggregated data-quality statistics; and allow autonomous adjustment of run-time settings such as temperature and voltage.
GridION system runs proceed according to scripts that define experiment protocols, settings and parameters. Oxford Nanopore will provide pre-configured template scripts for a variety of different types of experiments. Template scripts can be tailored to specific experiment requirements through the modification of parameters and experimental values. Users can also create their own customised scripts.
Real-time management of experiments
With high-performance compute capabilities resident on each GridION node, data is processed in real time and made available to the user for monitoring. This creates the ability to make on-the-fly adjustments to performance settings on a single node or cluster of nodes, in response to data that has been generated. Adjustments can be made manually or automated in the experiment script to optimise for experimental success criteria. This feedback-based design enables higher efficiency experiments that can be controlled to achieve guaranteed endpoints.
Each node contains high-performance embedded electronics which perform local, application-specific data reduction. Data reduction and primary analysis are carried out in parallel as the experiment run continues. This means that the GridION™ system does not require large amounts of high-performance disk storage even with large numbers of clustered nodes. In addition, long wait times for post-run completion of primary data analysis and offloading of large volumes of data are eliminated.
Clustered nodes can co-operate to apply the same filters, share statistics and parallelise I/O.
Raw data reduction and analysis
Raw data is generated as a series of electrical signals, recorded at a rate of tens of thousands per second, that measure the degree to which ionic current through the nanopore is reduced as a result of analyte interaction with the pore. The succession of measurements produce a step wave that can be reduced to ‘events’. Each event indicates a transition between current levels resulting from the interaction between analyte and pore. These events are then interpreted relative to characteristic current changes associated with the analyte or polymer of interest. DNA and RNA base calling, protein identification and quantification, and identification and characterisation of small molecules, toxic chemicals and metal ions are all carried out in this manner.
Raw data reduction and analysis occur on the GridION node as data is generated and are completed concurrent with completion of the experiment run. The product of this primary stage of data analysis is application-centric data and quality metrics output in standard file formats.
Figure: a typical single nanopore 'trace'
The figure below shows a typical 'trace' as measured in a single nanopore experiment (this example uses only a single simple analyte, not DNA or a protein). The current is measured at very high frequency; each point on the black line represents a single measurement. As an analyte interacts with the nanopore the current is disrupted, as shown by the stepped drops in current – this is an 'event'.