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Getting started with MinION - what you need to know

How do I get started?

Will I need specialist kit?

What are the connectivity requirements?

In order to run MinKNOW (the instrument software) you will need a continuous Internet connection of a certain specification. Please also review the specification table here.

MinKNOW will upload report metrics to Oxford Nanopore so that we are better able to troubleshoot and deliver improvements. We will not receive or keep a copy of your biological results, merely diagnostic statistics on your MinION performance.

Oxford Nanopore currently provides basecalling via a cloud based service. Your MinION is configured to exploit this feature provided you have a good enough Internet connection. Again, no biological data is stored or recorded. Further analyses have been introduced in the cloud based Metrichor service, for which connectivity is required.

What applications are supported for the MinION?

MinION is provided for research use only. Some existing protocols will be provided along with the relevant sample preparation kits, these protocols include: gDNA, cDNA and PCR product/Amplicon Sequencing. However  you are encouraged to develop your own versions of these and other protocols for any application of interest to you. Some protocols have been developed by MinION users and are available in the online community or publications.nanoporetech.com.

If you wish to use MinION to explore other applications, you are encouraged to do so; however, Oxford Nanopore will provide only limited support that will initially focus on the core platform performance. The range of supported applications will expand.

Once I start using MinION, how would I get help if I have questions or problems?

As part of the Nanopore Community you will be provided with a basic support package consisting of free login to the online Nanopore community. At this site you will be able to pay the $1,000 fee, track deliveries, access support materials, ask questions of Oxford Nanopore support staff and your colleagues in the Nanopore community, enter discussions within provided community forums and organise return of used flow cells. Additional levels of paid-for support may be offered.

If you wish to use MinION to explore other applications, you are encouraged to do so; however, Oxford Nanopore will provide only limited support that will initially focus on the core platform performance. The range of supported applications will expand.

Key points:

  • We encourage use of the community site to share experiences. If you have positive experiences we would be delighted if you shared them. If you have negative feedback, we intend to listen and respond. However, you will be expected to follow an Acceptable Use policy that does not allow abusive behaviour, commercial promotion or certain other contributions
  • After notifying Oxford Nanopore that initial control experiment results meet your starter requirements, participants may wish to share their results at scientific conferences, as submissions for manuscript publications or on social media. Please refer to the publication guide for guidelines
  • If you use others' contributions in scientific presentations or publications, you are expected to acknowledge them accordingly
  • If you prefer to contribute anonymously, you can do so
  • The online community includes contributions from Oxford Nanopore support staff via the forums and Q&A with additional email support available. Oxford Nanopore will not be offering site support visits although premium support packages may be introduced.
  • Oxford Nanopore may recognise participants, who make popular or constructive contributions to online Community forums.

I work in a team, we all want to use the MinION. How does that work?

The person submitting the application is a ‘Nanopore Community leader’. This means that if you are working as a team, it is the responsibility of the Nanopore Community leader to pay the fee and track the deliveries. We invite the Nanopore Community leader to submit to us the details of others in your team (Nanopore Community participants) who will be working on the project so that we can supply the correct logins and keep everyone informed.

Can I start using my own samples straight away?

After configuration, Oxford Nanopore requires participants to conduct control experiments using a lambda sample provided by Oxford Nanopore. These are generic control experiments that Oxford Nanopore runs internally as a matter of routine. The purpose of these control runs is to enable participants to master the technology and fully understand it from end-to-end without the complication of novel biology. Importantly, participants should feel confident in the operation of the system before moving on to more complicated experiments

When conducting the control experiments you will be asked to decide whether the performance you observe is appropriate for your own purposes. If it is, you will be asked to formally notify Oxford Nanopore that you have satisfied that the outcome is suitable for your own experiments. If it is not, you have the option to repeat control experiments leveraging knowledge from the Nanopore community, or you can choose to return your MinION. You will be able to share your control results at the online community if you would like to discuss and debug your experiments with other MinION users and Oxford Nanopore's internal scientists

Will I be allowed to discuss my results?

Oxford Nanopore is happy for MinION users to share the results of their experiments and experiences. We believe that by releasing MinION device to a broad community and listening and responding to honest feedback that we will be better able to develop the product and support its full potential.

However, we ask that you do not share the results of your experiments until you have completed the control experiments and verified to Oxford Nanopore that you are happy the technology is suitable for your application. Prior to notifying us of your successful completion of the control, we ask you to treat as confidential information all technical aspects of your experience using the MinION, including workflow, data, results and performance. Subsequently you are free to discuss these publicly whether in publications, presentations or on social media, (following the guidelines in Publication Guide).

You are also required not to share your community login, Oxford Nanopore-generated material from the community or associated copyrighted materials such as software, without permission.

What bioinformatics resource/expertise do I need?

During sequencing, basecalling results are presented back to the user as .fast5 files which include the .fastq and can be in the HDF Group HDFView. The system sequences the read lengths that are presented to it and so you are able to generate very long reads.  Participants should be aware that there are a growing number of bioinformatics tools which have been optimised for working with Nanopore data, details of these can be found at in publications. Consideration should therefore be given to your bioinformatics support and custom tool development if required.

The EPI2ME platform is a cloud-based, data analysis service offered by Metrichor Ltd;  it offers different types of analyses which are presented as Applications. For example, the What's in my Pot (WIMP) class of applications allows species identification in real time.

What is the MinION Mk 1B?

The MinION Mk 1B is the new iteration of the MinION, and is released in May 2016.  It follows the Mk 1 that was released in May 2015.  

MinION Mk 1B is designed for novel flow cell chemistries being developed by Oxford Nanopore Technologies. It is based on its predecessor (the Mk 1) so is compatible with all the Mk 1 Flow Cells currently available from the Nanopore store. For an experiment running at a baseline speed of 70bases per second the impact of improved electromagnetic shielding will be very minimal but as we begin to turn up the dial on speed - for example with R9 - we have found this electromagnetic shield provides a significant boost in accuracy.

All attendees of London Calling 2016 who have a Nanopore account are taking one home with them as a replacement for their current MinION.
The Mk 1B will become available to the wider community a few weeks later and users will be given the opportunity to upgrade their MinIONs for the Mk 1B as flow cell deliveries are shipped.
There will be no charge for upgrading to the Mk 1B however Oxford Nanopore will require users to return their old MinIONs to complete the account upgrade process

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