my comments and Satra answers to the lessons 1-3 (copy of the email conversation)

[djarecka]

Lesson 1: Core concept
General:
- you're saying at the beginning that the lesson use the Simple Workflow, but it's not clear to me how specific parts are related to the repo. I would expect much more guidance.

can you suggest what kind of guidance?

Element 1:
- are you planning to "convert" the JSON file (that is missing for now) to the two standards you mention? It would me very useful IMO.

we should revise this. NIDM-E is not set in stone, so if we release we should have some confirmation of a NIDM-E version.

Element 2:
- don't understand the first sentence, "...when a different dataset containing the same data or a slightly different workflow is used."

i don't see this sentence here: http://www.reproducibleimaging.org/module-dataprocessing/02-concepts/

Lesson 2: Annotate..

General:

• there are no "elements"

elements were conceptual pieces in the concepts lesson - we can refer back to those elements, but don't expect elements to be in everything (i think).

Links don't work:

• metadata editor: http://data.wu.ac.at/csvengine/csvm/editor
• BIDS: http://www.reproducibleimaging.org/module-dataprocessing/03-data/bids.neuroimaging.io

http://data.wu.ac.at/csvengine/csvm
the second looks like a markdown typo.

Data and Metadata

• not sure what is the main point here, convincing people to submit data to archives? A few sentences of intro might be nice. When do you use NDA and when NeuroVault for sharing?

yes, and introductory statement would be good there.

Lesson3: Create and...
General:
- there are no "elements"
- IMO a general motivation when to use VM, when Docker or Singularity, in scientific application, is missing. You have it in your presentation, but not here.
- as I mentioned, it might be useful to work on the final version of the videos so they are easier to use.

we should update things here with respect to the presentation.

Docker
- I know you mention Bids-App, but it could be useful to point to some Python or Nipype images, so they don't have to install everything to run Nipype workflow.

sure - the current nipype dockerfile has most things necessary.

Singularity

• I don't see any "smooth transition" to Vagrant. I understand that Vagrant is needed when one uses OSX or when has to create an image on a machine without sudo (since she/he is a root in VM), but it's not obvious IMO.

we should point out a few more things here, but there are a few places in the web we can draw from.

[djarecka]

@satra

• re the Simple Workflow and guidance:
  I can try to create a PR, but I'm not sure if I actually understand what you expect people to do (we can talk about it). For example in the element 2, do you want to point to environmental.yml file from the SimpleWorkflow? If yes, that should be clearly written. Moreover, according to the README the file is used to create a conda environment, so your comment "The script itself does not care if these installs conflict with your existing software environment." is not so relevant.
  If you think more about creating requirements.txt file, an example can be useful.
  The same about element 4, which file people should read?
  If you don't want to point to anything from the SimpleWorkflow repo in this lesson, but just give an introduction and motivation, you might want to change the first sentence "This lesson uses the Simple Workflow Github".

• Sorry, the sentence "Once the data and environment are setup appropriately and the analysis is run, it would be good to know if the same results are obtained when a different dataset containing the same data or a slightly different workflow is used." is in the element 4

• talking about conda: shouldn't be included in the lesson 3?