Getting ready for @JasonWilliamsNY #biome20 workshop in 5, 4....
Let's get this party started!! @JasonWilliamsNY presenting on Genomics Education Alliance at #biome20 
#biome20 is the re-incarnated Summer Workshop presented by @qubeshub and @BioQUESTed - it's in person incarnation is a lot like a summer camp for folks interested in teaching math and biology - and this year we are focusing on engaging students in research!
While the workshops are not available to non-registered participants, we are providing resource links and tweeting as a bit of a #biome20 backchannel! Follow @qubeshub and @BioQUESTed for updates!
For this session, you can find many of the resources presented here at the Genomics Education Alliance qubeshub.org/community/grou…
Intros around - Three words that describe you (the participant) - to get a feel for why you are in the room today - I like that!! I am wearing a @qubeshub "staff" hat, so my three are Twitter, QUBES, and community!
Some of the words shared are commensal bacteria, microbiome, bioinformatics, interdisciplinarity, education, fun, viruses, gene expression, curiosity, visualization, classroom, high-throughput, and undergraduate research.
As Jason says "You are the most important resource."
As Jason says "You are the most important resource."
Jason is walking us through a what a lesson looks like …seq-lesson-dev.readthedocs-hosted.com/en/latest/inde… #biome20
He is also advertising a Faculty Mentoring Network - where you can work with others every week until November on using @CyVerseOrg for bioinformatics in your classes. cyverse.org/fossonline
There is still time for folks to register for that workshop - the launch is today though, so hurry up!!! #biome20
Walking through how to launch @ProjectJupyter from @CyVerseOrg
Also showing that you can launch a command line version. Though Jupyter notebook excels at communication as the goal. #biome20
Jason says that Jupyter notebooks are particularly good for creating lessons that do a lot of explaining of commands for students, then backing off a little and getting students to try some commands and variations in a template-like environment. #biome20
Talking now about the command line - old fashioned maybe, but definitely here to stay... timeless? :) #biome20 - try the command line tutorial here: …seq-lesson-dev.readthedocs-hosted.com/en/latest/sect…
And now on to biology - A look at the RNA-seq experiment - full data set directly from a paper looking at leptin and Wnt from mice colon samples.
#biome20
…seq-lesson-dev.readthedocs-hosted.com/en/latest/sect…
#biome20
…seq-lesson-dev.readthedocs-hosted.com/en/latest/sect…
The big question - are these different? - This particular lesson is an introduction that your students can see, yes they are different "by eye" through the visualization, but does not include the robust statistical analysis. #biome20
The lesson does give student the opportunity to walk through the process of download and using data from the Sequence Read Archive. #biome20 ncbi.nlm.nih.gov/sra
The @CyVerseOrg tutorial gives all of the needed commands in one place for your students with some practice in using commands like head and cut to handle the data being retrieved. #biome20
Some helpful links: Getting started with the SRA - ncbi.nlm.nih.gov/sra/docs/
Explain shell - explainshell.com
#biome20
Explain shell - explainshell.com
#biome20
This tutorial also introduces the FastQ file format for students. #biome20 …seq-lesson-dev.readthedocs-hosted.com/en/latest/sect…
Jason is pointing out the benefits of using Jupyter notebooks to turn "type this into your command-line" into a rich lesson with explanations for WHY students are using particular commands in text instead of just verbal instructions from you. #biome20
The end of the notebook includes exercises so that students can write their own code/modify previous code to run different, but similar analyses #biome20
Participant Q around storage, access, etc. A: @CyVerseOrg is funded through multiple sources which gives longevity - each user is allocated 100GB for free, and more can be requested. #biome20
Jason is advertising lots of opportunities with GEA to try out new lessons, implemented in your class, and they have an ability to "dockerize" it - freeze framed, so that the software/data interaction are stable through time. #biome20
Q: Accessibility A: Please give feedback and ask/upvote particular concerns. @CyVerseOrg is really interested in improving its offerings. #biome20
Q: What are the characteristics of the datasets which balance realistic, but not too long to run an analysis. A: This is why we used a paper, because we know it is realistic, and did iterations of how small a sample you can do to be meaningful. #biome20
