CMK-1 ms plan of attack

[ttimbers]

@eardiel @troymcdiarmid - here's what we need to do:

task	person
remove prob data from figures	Evan
upload good copies of all old figures to results dir on Github	Evan
find new data (Troy's rescue exps & Tiff & Evan's double exp)	Troy
reformat manuscript for genetics (incl reformat refs)	Troy
write scripts to do analysis and make plots for new data	Tiff
run scripts on new data	Troy
make final figures of new data after scripts are run	Evan
incorporate stats and new data into manuscript	Troy

[ttimbers]

@troymcdiarmid - I got the code working up to creating the file you need to do stats and making figs. Read the README in src for dependencies, how Choreography must be installed and how to run scripts. Try running on some data to test that you can get a nice .csv with the columns: plate, group, id, time, and rev_dist

After that, you and I can work together on rev_stats.R (I say you and I because I can't work on this again for another few days and I could have my baby and day - so this could fall to you...)

[ttimbers]

@eardiel @troymcdiarmid - OK, I think I have now finished the code, getting it to work from Nachos to Cheesecake (stole that phrase from Jenny Bryan :wink:) - meaning from MWT folders/zip files to a .csv of the summary stats (p-values from Tukey's HSD) and a .pdf figure of the habituation reversal distance (that should look very similar to the ones I made previously in Matlab).

Please try it out and let me know if it works. Follow the docs in the README in src to see what dependencies to install and how to call the 3 scripts. note - the way I have written the code will not work on a Windows machine. If you must run it on Windows, let me know and I can set-up a Docker image for you to do this.

[troymcdiarmid]

Got it I will try this ideally today if not then tomorrow!

[ttimbers]

That is what I would expect if I just type Chore and everything is installed correctly.

[troymcdiarmid]

Works! Figure made! Should I upload the results to github? :)

[ttimbers]

Well done and yes please! Put the figs and stats .csv in the results directory.

On Feb 19, 2017 2:48 PM, "troymcdiarmid" notifications@github.com wrote:

Works! Figure made! Should I upload the results to github? :)

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[troymcdiarmid]

Uploaded!

[troymcdiarmid]

The data that is uploaded shows that we can dissociate the initial response and final habituation level phenotypes as PY1589 cmk-1(oy21) putative null showed higher initial response and final habituation level while the GN244 cmk-1(pg58) showed higher initial response but lower final habituation level. Pg58 lacks a nuclear export sequence and accumulates in the nucleus, suggesting cytoplasmic function of cmk-1 is necessary for normal initial response but not final habituation level.

I am now working on formatting the MS for genetics and including the stats for this data!

[troymcdiarmid]

Also while reading the GENETICS guide for authors their second paragraph explicitly states we can submit in any format (see below) and then if accepted we will reformat it. I will update the MS to include line numbers and update references but this is fairly clear we can submit essentially as is.

Initial Submission in Any Format return to top GENETICS accepts manuscripts in any format, including figures, tables, and references (e.g. it may be formatted according to another journal’s guidelines or a format of your preference). For the review process, please include line numbers and page numbers if possible. You may also upload your manuscript as a PDF file. If your manuscript is accepted for publication, we'll ask you then to format the files for publication according to the guidelines below and provide the non-pdf files.

[ttimbers]

OK, @troymcdiarmid - so sounds like we don't need to focus too much on the formatting. Let's get the writing and figure parts done first.

[ttimbers]

@eardiel - I have uploaded what I "think" is the most recent Figure 5 in this commit: 0c20b1ef1b722af42fcf0de09bff7f7745eedce4

[ttimbers]

Thanks for Fig S3 @eardiel! I've uploaded it to the results dir using the upload files button (there are several ways to get things in this Github repo, any way you do it is fine with me :wink:). I only see the white box @troymcdiarmid mentioned when I view the file on Github, not when I download it, so I think its fine.

[troymcdiarmid]

I just uploaded the new MS with everything updated (see doc section of repository). I am converting Evan's new figure 6 to .eps from .pdf.

After that, I think we have completed all of the tasks on this plan of attack!

[ttimbers]

@troymcdiarmid @eardiel - great news!

FYI - In this final stage of pregnancy, although the baby has not yet arrived, I am experiencing early/prodromal labour that is quite painful and uncomfortable. Thus, I will likely not be able to work on this with you for a while. So I give @eardiel my complete trust and authority to make any necessary final decisions regarding the manuscript for submission to Genetics and bioRxiv. Note - you should submit to bioRxiv at the same time as Genetics (or just shortly after) as accepted manuscripts cannot be put on bioRxiv.

Let me know once you submit to bioRxiv and I will make this repo public so readers can access the src code we link to in the methods.

Thanks to you both for all your hard work on this!

[ttimbers]

I see this is now submitted to Genetics & BioRxiv, nice work team!