CZI-CABANA Microbiome Bioinformatics with QIIME 2 Workshop (our first-ever online QIIME 2 workshop!)

Overview

Members of the QIIME 2 team will teach a five-day online workshop on bioinformatics tools for microbiome science. The workshop will include lectures covering QIIME 2 usage and theory, and interactive work with QIIME 2 to perform microbiome analysis from raw sequence data through publication-quality statistics and visualizations. This workshop will also feature several opportunities for attendees to network with other researchers in the field, as well as with QIIME 2 developers and other experts.

Topics will include:

  • Introduction to QIIME 2
  • Core concepts
  • QIIME 2 types, formats, and metadata
  • Demultiplexing and quality control
  • Phylogenetic reconstruction
  • Measuring alpha and beta diversity
  • Importing and exporting data
  • Taxonomic analysis
  • Differential abundance
  • QIIME 2 plugin highlights
  • And more!

Registration Information:

General registration will be available no later than September 15th, 2020 - please watch this page (link) for more details.

Registration details now available (please see below: CZI-CABANA Microbiome Bioinformatics with QIIME 2 Workshop (our first-ever online QIIME 2 workshop!)). In the meantime, please save the dates for:

  • October 5th - October 9th, 2020
  • Sessions will begin at 8a and end at 2p daily, UTC-7 (3p-9p UTC+0)
  • Registration with be $50 (US) per participant (see below for purchasing power parity discounts)

Purchasing Power Discounts

Purchasing power discounts are no longer available for this workshop.

Logistics

This online course will comprise a blend of pre-recorded and live lectures. Pre-recorded lectures will be made available prior to each day of the workshop, that way attendees with schedule conflicts can stay caught up with the material. There will also be interactive command-line based tutorial sessions, where attendees will perform microbiome analyses using QIIME 2, online. We will also host many live question-and-answer sessions, as well as general discussion sessions.

Required software

Before the workshop, please install the latest version of the Google Chrome web browser. If you don’t have Google Chrome installed, get it here.

If you already have Google Chrome installed, make sure it is the latest version by following these instructions.

Next, install the Secure Shell app for Google Chrome.

After that, try opening this page to ensure that your browser is configured correctly to view Emperor plots. If you get a notice that the page cannot be opened, follow the instructions provided on that page and try the link again.

Preparing for the workshop

Students will use the Linux command line extensively during the hands-on portion of the workshop. We will not cover command-line usage in this workshop and thus it is strongly encouraged that you become familiar with the command line prior to the workshop.

The following resources are recommended to learn the command line. Depending on previous experience with the command line and level of technical expertise, it may take anywhere from a few hours to a few days to get comfortable using the command line. Thus, we recommend that students start working through this material as soon as possible, including the accompanying exercises.

  • Our cheat-sheet of command-line basics: The minimum working knowledge necessary for working with QIIME 2 on the command line.
  • Udacity Linux command line course (free): This course is pretty comprehensive and will take a few days to complete. Additionally, it shows users how to set up a virtual machine to run Linux commands in (this step is required for Windows users but can also be performed by Mac OS X and Linux users).
  • Software Carpentry Unix Shell introduction (free): This course is shorter than the Udacity course above, taking about 1.5 hours to complete. If you are on Windows, you will need access to a Linux machine (or virtual machine) to execute commands in. The Udacity course above will show you how to do this, or you can try out a Linux command line emulator (there are emulators available online). If you are using Mac OS X or Linux, you can alternatively use the Terminal program included with your operating system to execute commands in.

See https://workshops.qiime2.org/microbiome-bioinformatics-qiime-2-online-2020-10-0/ for the latest updates for this workshop. Hope to see you there!

46 Likes

Hi Matthew,

I was looking forward to such a course for a long time! Unfortunately I cannot find a link to registration/payment!
Also, I appreciate your special consideration for those who might not be able to afford this course.

Kinds,
Farhad

5 Likes

Hi @thermokarst,

Thank you for providing this course! This is amazing.
I agree with @farhad1990 if there is an opportunity to provide a subsidy or scholarship to attend this course. 70 CAD is quite a big amount :sweat_smile:

Thanks,
Anirban

1 Like

It will be a great workshop!

Will the workshop be recorded? Due to differences in time zones, I may have problems with participation in the endings of sessions.

2 Likes

Hi @farhad1990!

Please see this part of the announcement above:

Registration won’t be live until September 15th. Stay tuned though, in case we start registration sooner!

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Hi @anirban.mcgill!

Did you see this part of the announcement?

Just send us an email with your suggested price (cc @farhad1990, you were asking about this, too).

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Hi @jakub.ruszkowski!

Please check out this part of the announcement for details:

Hope that answers your question!

2 Likes

Could you please clarify further. Will the workshops/tutorials and live lectures themselves be recorded? I live in NZ, and due to the timezone differences will find it impossible to attend any of the live sessions. If all the material is going to be recorded and accessible, I would love to enroll.

3 Likes

Hi @ChrisKav! The tutorials will be recorded, but it is undecided at the moment if the live Q&A and discussion sessions will be recorded. I think even if you aren’t able to make it to the live sessions, you will hopefully have a complete experience with the pre-recorded material (we are planning on supporting asynchronous question-and-answers throughout the workshop, too, so if you get stuck we will hopefully still be able to connect). I should also note - this is our first-ever online QIIME 2 workshop, so there are many unknowns for us still, we appreciate your patience as we figure it out!

:heart_eyes: I always waiting for this workshop.

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This is great, will like to attend

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I will attend. I believe the workshop will be very useful.

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Can’t wait to start! :tada:

2 Likes

Awesome, I would like to attend absolutely. How do I get an notification when the registration starts?

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Will the pre-recorded sessions be available after the workshop for future reference?

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Can’t wait to join and start! :smiley:

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Highly interested :slightly_smiling_face:

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Will these be recorded, by chance? Say we want to attend and can go forward with the registration fee, but can’t join for all of the time slots.

Many thanks for organizing!

2 Likes