Specific changes to the manuscript

[cwehmeyer]

There are several small points to address:

• [x] Page 1: "distances. (see [10]" -> remove period.
• [x] "By assessing how well the approximated transition probability matrix adheres to the CK property," Should include a link to citation discussing the criteria?
• [x] In Theory section, provide specific references to not only the original scientific papers citing them the different methods and concepts, but mention specific chapters / articles that are the best to learn about them. The HMM section is particuarly terse wirth a lot of definitions, and could use specific recommended citations with more details (not just the original ones). You don't need to explain all of the details (this is a tutorial) but should show people where to get the details. There are other places where this occurs, for example, the description of multiensemble Markov Models. Again, since it's not a review, you don't have to explain everything, but explicitly state recommendations for where to look for more information if you bring up new concepts that are not covered in the tutorial.
• [x] Figure 4: Make it easier to interpret alone. We would suggest saying what the conclusions the data demonstrate, in addition to describing the data. Figures 3, 5 and 6 are good examples of more self-contained figures with conclusions included.
• [x] Page 9: "make use of the specific Jupyter notebooks distributed with PyEMMA." For the methods you discuss, specify which notebooks address those features and where to find them.
• [x] "Additional technical challenges for large systems include high demands on memory and computation time; we explain how to deal with those in the tutorials." Say where in the tutorials this is done.

[marscher]

I think the last point is covered very briefly in nb01: http://www.emma-project.org/vdevel/generated/01-data-io-and-featurization.html#load-versus-source

But the concept itself although it super useful is not used, since not needed for the small test systems, throughout the notebooks. It is not clear to me whether the reviewer wants to tip finger on this shortage or just wants a single reference.

I think the discretization part would be most useful to demonstrate the feature (eg. performing everything without a single get_output(), load() etc.).

[franknoe]

Acknowledgements need to be completed (please check in the future that funding for all authors is there. SFBs must specify the project number).

TH acknowledges financial support from Deutsche Forschungsgemeinschaft (SFB/TRR 186, Project A12). FN and BEH acknowledge funding from European Commission (ERC CoG 772230 "ScaleCell"). FN acknowledges funding from Deutsche Forschungsgemeinschaft (SFB 1114, Projects A04 and C03, NO 825/2-2). SO acknowledges a postdoctoral fellowship from the Alexander von Humboldt Foundation.

[brookehus]

I will look at item 3 (citation stuff) either this afternoon or first thing tomorrow morning

[thempel]

@brookehus I did some restructuring of the HMM section in branch details. Maybe you want togo on with this branch or merge into your branch.

[brookehus]

I will PR to your branch!

[brookehus]

Item 3 done in #176

[thempel]

Item 5 done by @cwehmeyer by 040c423

[franknoe]

Please add as a second affiliation for me:

Rice University, Department of Chemistry, Houston, Texas 77005, United States

[thempel]

@franknoe could you provide a street address?

[brookehus]

Online it says 6100 Main St., Houston, TX 77005 for the chem dept

[franknoe]

thanks, right