I’m a bioinformatics technician that has been working primarily with Qiime 1.9 and am now switching our lab over to Qiime 2. I have a few quick suggestions that may improve the ease of access for students and researchers that don’t necessarily know the jargon or might be transitioning as well.
1. An easy-to-follow road map for a general analysis.
Create a flow chart for every common data type that shows which plugins would be used at which steps for a general, all-around analysis. In my mind this wouldn’t be as much a tutorial (no example data/code) but more of a guide as to where you can go from each step with branches when options are present. This may be a somewhat complex flow chart but it could still appear clean with just the plugin names hyperlinking to their description pages.
2. The relations of Qiime 1.9 scripts -> Qiime 2 plugins.
One of the more difficult aspects of transitioning from 1.9 to 2 is the change of name/usage going from scripts to plugins. I realize that some things have changed completely and some steps which may have been multiple python scripts have been combined into single plugins, however, a quick mention of which Qiime 1.9 scripts relate to each plugin (or how a plugin may have taken somethings place) would greatly assist the folks that are transitioning.
3. A full explanation of what plugins are doing.
This may be a little too much, but what I have in mind is a way to more easily introduce people to Qiime or better yet, make it accessible to those without someone guiding them. The idea isn’t to explain the code in depth but to explain the operations it’s performing to your data and why that’s a good thing. It may not even need to be a written explanation but a simple link to a guide or Wikipedia page regarding the subject.
Hi @Willis! These are all great ideas, thanks for sharing them with us! I was planning to tackle some of this for the upcoming 2017.12 release, but ran out of time. Hopefully we will implement these ideas in early 2018, though I can't provide specific time estimates. We'll follow up here as progress is made!
We have some open issues tracking these ideas, and I've cross-referenced your forum post on those issues. Specifically:
The Moving Pictures tutorial aims to provide an end-to-end "general" microbiome analysis, but a wizard/flowchart/roadmap would be a nice complement to the tutorials. We have an open issue tracking progress on that.
We have a spreadsheet that's incomplete and in need of some cleanup, with open issues (1, 2) to fix that and turn it into proper documentation.
This one doesn't have an associated issue. Our recommendation is for plugin developers to write tutorials covering whatever is relevant to their plugin (e.g. theory, example data, usage). Plugin developers can add their tutorials to the forum's Community Tutorials (there are already several there!), or host the docs wherever they want to. Community Tutorials may be transitioned into "official" tutorials (i.e. hosted on https://docs.qiime2.org), but either location is a good spot to look for details about plugins, what they do, and how to use them.
Are there specific topics and/or plugins that you think would benefit from the expanded docs you described? That'll help us prioritize what gets documented.
Also, the type of info you're requesting may exist in some of the tutorials already (the Moving Pictures tutorial includes some explanation about why you'd perform certain analyses, though it's certainly not complete). There's a new community tutorial on alpha/beta diversity analyses that may be interesting to you as well.
Thanks for the feedback, we appreciate it! Happy QIIMEing!
Good job so far with Qiime 2 devs!