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New files (and fixes) for Tom #1

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dmzuckerman opened this issue Apr 19, 2018 · 29 comments
Open

New files (and fixes) for Tom #1

dmzuckerman opened this issue Apr 19, 2018 · 29 comments

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@dmzuckerman
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Tom, for the first go-around, I created a directory 'for_tom_w' where I put the files you will need. (Otherwise it would be hard to figure out what was new.)

Please list the new page in two places:
under 'Physical/Molecular Processes', call it "Diffusion FAQ: The basics"
under 'Cell Biology Phenomena', call it "Diffusion basics: Single-particle tracking etc."

Thank you. --Dan
@wheelercreek
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This is completed. I've also run some security updates that needed to be done.

@dmzuckerman
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@wheelercreek thanks. I made a small edit to the diffusion html file ... which you can now find easily in the main directory by what's been updated. (There was a mistake in the first paragraph - of course!) I moved the 'for_tom_w' directory to 'older' because we shouldn't need to use that anymore.

A couple of other things for the Diffusion page:

  • The References and Exercises did not get the right heading level ... they're too small
  • Can you make the equations a bit smaller? The font in the equations should be only a little larger than the regular font.

Thank you! --Dan

@wheelercreek
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wheelercreek commented Apr 24, 2018 via email •
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@dmzuckerman
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The headings themselves are actually in the HTML template which is used on all pages. So I can make them bigger, but it would be site-wide.

Please do it site-wide. Thank you.

@wheelercreek
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Completed. Let me know if there's any other issues..

@dmzuckerman
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Looks good. Thank you.

@dmzuckerman
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I updated the steady page - use the file with 'mod' in the title.
Please check equations sizes are right.
Thanks a lot. --Dan

@wheelercreek
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wheelercreek commented May 9, 2018 via email

@dmzuckerman
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Two of the equations got messed up on my end - I replaced the files if you can update them.
Thanks a lot.

@dmzuckerman dmzuckerman changed the title New files for Tom New files (and fixes) for Tom Jun 11, 2018
@dmzuckerman
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Some adjustments needed on the 'conformational statistical mechanics' page http://www.physicallensonthecell.org/chemical-physics/conformational-statistical-mechanics

  • Equation sizes should be adjusted to avoid some of the giant fonts
  • Equation numbers should be right-justified.

Thanks.

@wheelercreek
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wheelercreek commented Jun 12, 2018 via email

@dmzuckerman
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I added a new page on Advanced Diffusion (files named fokker*). This should be placed in the 'Under the Hood' subsection of Chemical Physics. Be sure to check equations sizes.

Hope you had a great trip. --Dan

@wheelercreek
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wheelercreek commented Jun 19, 2018 via email

@dmzuckerman
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I made a new folder called 'corrections' for changes to older files via commented pdfs (because my versions of these files were converted to traditional html/drupal by others). Thanks.

@dmzuckerman
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Tom, two additional things (beyond my update to file) for 'Advanced Diffusion':

  • Please change the title of the page (on the contents bar) to 'Advanced Diffusion and the Fokker-Planck Picture'
  • A reference to Eq (10) that precedes Eq (11) seems to have gotten corrupted: it looks ok in my file

Thank you.

@dmzuckerman
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BTW 'advanced diffusion' file is called 'fokker ...'

@wheelercreek
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Hi Daniel, I believe we've got these done for you!

@dmzuckerman
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Tom, thanks. There are a few changes to the 'Advanced Diffusion' (fokker) page that were not done. Please see above and the repo. Also I just noticed that the advanced diffusion page does not appear on the category contents page.

@wheelercreek
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wheelercreek commented Jul 18, 2018 via email

@dmzuckerman
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Two more items

  • You missed this one: Please change the title of the page (on the contents bar) to 'Advanced Diffusion and the Fokker-Planck Picture'
  • In the 'fokker' file itself, I forgot that I needed to change the equation number manually in my cross-reference: see latest push

Thanks a lot.

@wheelercreek
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wheelercreek commented Jul 18, 2018 via email

@dmzuckerman
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I guess I mean the menu (the blue spectrum bar at the top of each page). And yes, the contents page should match. Thank you. --Dan

@wheelercreek
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wheelercreek commented Jul 18, 2018 via email

@dmzuckerman
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thanks

@dmzuckerman
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Tom, minor additions to Basic Diffusion and Active/Kinetic Proofreading pages - see today's commits. For the Proofreading page, you only need to look at the most recent commit; prior commit was just to bring my html up to date with what you had already corrected manually on the site. Thank you.

@dmzuckerman
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Tom, regarding kineticProof page

  • A couple of typos fixed - see recent commit
  • Acknowledgement heading should be same as other major headings - i.e., font size
  • You missed the new reference added in last commit

Thank you!

@wheelercreek
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Sorry about that - these are completed now.

@dmzuckerman
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thanks

@dmzuckerman
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Files added for Discrete Kinetics. (I got an error - 'try again later' - trying to add directly to Drupal site.)
See if my file "discreteKinetics.html_drupal.html" is properly formatted for you.
Please list the page under Chemical Physics/Under the Hood
Call the page "Discrete-state kinetics and Markov models"
Thanks a lot.

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@wheelercreek @dmzuckerman