New tutorial video

[odetomyday]

Hello. I work at North Carolina State University in the Biotechnology program. We use Qiime in our metagenomics class. The students requested that I record a tutorial on installing Qiime using VirtualBox, so I did. The link is here: https://www.youtube.com/watch?v=ZDEF3gtS7cE

It's only part 1 of 3 so far, but I thought you all might be interested in knowing it exists.

[colinbrislawn]

That video looks like a great place for students to start.

I googled 'NC State supercomputing' and found that you have a solid compute center. Have you considered installing qiime on your supercomputing cluster? Amplicon studies are a lot smaller than most other types of metagenomics so, a supercomputer will really let you lab churn through large data sets.

Colin Brislawn

[odetomyday]

It's not my lab, I only maintain the equipment, but I passed that message along to the PI. I completed the tutorial series -- you all are free to link to it on your tutorial pages if you think people would find it useful. Most of our students have never used a command line interface before, so it goes very step-by-step.

Part 2 https://www.youtube.com/watch?v=njw31zxnPtI Part 3 https://www.youtube.com/watch?v=jcGiIDJGYL8

[colinbrislawn]

I just watched parts two and three and they are excellent! Qiime is used by lots of microbiologists who have never used linux of Python before, so these are a great place to start. Would you be comfortable with us mentioning these or linking to a NC State page with these videos?

[odetomyday]

You are welcome to link to or embed the videos anywhere you want! So long as you're not pulling it off Youtube and re-uploading, we are fine with you putting them anywhere online. (Actually, people were excited that they might end up on the website.)

I have the green light to keep producing QIIME tutorials, are there any topics which people seem to especially struggle with? I will make sure to tell you when new ones are online in case you want to link to them in y'alls tutorials section. And is this thread the best way to reach you?

[colinbrislawn]

Cool. I'll look into adding these somewhere. I'll have to check with the PIs about a good place for them. Maybe a new section of the Qiime tutorials? @gregcaporaso, advice appreciated.

A general linux tutorial with a focused scope would be helpful. Many people have never used a Linux terminal before and that's more of a challenge than the qiime scripts themselves. Existing linux tutorials get too complicated too fast, so one tailored for qiime use could be perfect. It would include an overview of the very basic linux commands like:

cd
ls
ls -alh
pwd
cp
mv 
mkdir
rm
rm -rf

If you could have a folder up next to the terminal while running these, people could see the results of each command. This helps 'close the loop' conceptually, which is hard at first in the terminal.

Mention using the tab key to autocomplete linux paths!!! That's so helpful.

Mention using the activity monitor in the qiime VM to check on RAM and CPU usage to identify bottlenecks. I have a super old post about that, but including it in the video would be nice.

Let's communicate on github because it's easy, public, and let's other folks 'qiime in.' Would you be interested in contributing some of these changes to the project? I don't want to steal your thunder if you want to have your name on the Pull Requests.

[odetomyday]

Great idea! I have also been asked to make a file mapping tutorial, I expect to be done with both within a week, other responsibilities permitting. Our funding for captioning the videos only lasts 6 months, and we're hoping to get as many done as possible before June 1.

I am still not used to the Git system, so you're welcome to contribute the changes yourself if you have time. Also, I brought up supercomputing again with the instructor of the Metagenomics class, and after doing some research we decided to apply for some space at one of the facilities here-- thanks for the tip.

[colinbrislawn]

Oh yeah, a mapping file tutorial would be great. Building the file, running validate_mapping_file.py and fixing the errors always gives people problems.

I'm totally fine with making the changes you suggest. Making suggestions and opening issues is a great way to contribute. Let me know how I can help!

[colinbrislawn]

Here is a great Linux tutorial that is a good fit for using qiime. http://linuxcommand.org/

[gregcaporaso]

Thanks for the great videos @odetomyday, and for providing all of the input @colinbrislawn! What I'd suggest here is that you create a YouTube channel for all of your QIIME videos. This will let you customize the layout, and highlight any acknowledgements, etc that you'd like to make. Once you've done that, we can link to your channel.

I think what I'll end up doing is creating a new wiki page for videos, and have videos.qiime.org point there (it currently just goes directly to YouTube). We can then list your channel as well as other relevant videos there. Does that sound like a good plan?

Regarding Linux tutorials/etc, I generally point to the Software Carpentry materials these days. I think they do a good job of this.

A mapping file video would be great too. I would highly recommend highlighting Keemei (pre-print here) in this video, rather than validate_mapping_file.py, as we're moving toward the Keemei-style validation (and validation doesn't require that QIIME be installed, which is a big bonus!). The ideal situation might be to coordinate with @jairideout on this - we have an open issue to create a Keemei video here, and if you cover the points that he wants to cover he'd probably be open to linking your video from the Keemei website. If this sounds interesting to you, I'd follow up on that issue.

[odetomyday]

The videos that I make need to be kept on the NCSU BIT Youtube channel, which will eventually have a variety of content, not all of it QIIME related. The playlist function on Youtube might work for what you are saying -- there is space for a description, and the manager of the playlist can reorder the videos as well. I have already made one for our QIIME videos: https://www.youtube.com/playlist?list=PLGpKV7oOe22rVUduGQ-xSCOl9ADfidg2k -- does that work?

As for a landing page, a wiki could be nice, or whoever runs qiimeHelp could create a tutorial video playlist on that channel. It might be really interesting to find one sample data set and stick with it through all of the QIIME tutorials. Do you already have one somewhere? That way, a viewer could do things along with me in the videos.

[colinbrislawn]

Playlists work great. We can definitely use the one you posted. Software carpendary is very good: http://swcarpentry.github.io/shell-novice/ Validation with Keemei is also good, especially for first time users.

The illumina overview tutorial uses the Moving Pictures data set: ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_tutorial-1.9.0.tgz

[gregcaporaso]

Playlist is a great idea, thanks! (Sorry for the slow reply, was at a meeting last week.)

On Mon, Feb 15, 2016 at 10:46 AM, Colin Brislawn notifications@github.com wrote:

Playlists work great. We can definitely use the one you posted. Software carpendary is very good: http://swcarpentry.github.io/shell-novice/ Validation with Keemei is also good, especially for first time users.

The illumina overview tutorial http://nbviewer.jupyter.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/illumina_overview_tutorial.ipynb uses the Moving Pictures data set: ftp://ftp.microbio.me/qiime/tutorial_files/moving_pictures_tutorial-1.9.0.tgz

— Reply to this email directly or view it on GitHub https://github.com/biocore/qiime/issues/2129#issuecomment-184321879.

[odetomyday]

Great-- I have already added the videos from Qiime Help to the playlist linked above. I have successfully recorded the linux command tutorial video, which is actually going to be more of a lecture (uncut length is over an hour). I haven't gotten a chance to record the Keemei video yet, but that is next on the list.

[odetomyday]

By the way -- I finished the two Linux tutorials https://www.youtube.com/watch?v=P0KeDt-GuEI https://www.youtube.com/watch?v=uDvJ5KhqT5A

as well as a tutorial about how to log into an image of QIIME hosted by one of the NC State supercomputers (only available for students and faculty at North Carolina public schools as well as a few partner institutions) https://www.youtube.com/watch?v=oOw-lGoJcYE