New files (and fixes) for Tom

[dmzuckerman]

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]

This is completed. I've also run some security updates that needed to be done.

[dmzuckerman]

@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]

I'll make the text & equations adjustments. Regarding the References and Exercises headings.. the way this is set up, you have a couple of separate text boxes that I dropped in the reference and exercises (apart from the rest of the page):

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.

I left the larger h3 heading for acknowledgements in the body of the page, so that's why they changed position also.

Tom

On Mon, Apr 23, 2018 at 5:03 PM, dmzuckerman notifications@github.com wrote:

@wheelercreek https://github.com/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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dmzuckerman/PhysicalLensOnTheCell/issues/1#issuecomment-383760433, or mute the thread https://github.com/notifications/unsubscribe-auth/AA84JlX-KO8nJShUQrbv9M-aJmNvSPYVks5trmvigaJpZM4TcfPh .

-- Tom Wheeler President / Lead Drupal Developer Wheelercreek Studio Inc. http://wheelercreek.com ph. 360-326-5076

[dmzuckerman]

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]

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

[dmzuckerman]

Looks good. Thank you.

[dmzuckerman]

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

[wheelercreek]

Hi Dan, completed this - you can take a look and let me know if I missed anything.

Tom

On Tue, May 8, 2018 at 7:33 AM, dmzuckerman notifications@github.com wrote:

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

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-- Tom Wheeler President / Lead Drupal Developer Wheelercreek Studio Inc. http://wheelercreek.com ph. 360-326-5076

[dmzuckerman]

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

[dmzuckerman]

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]

Okay will do - currently I'm out of the country (Africa) on a vacation trip

• be back to work on Monday the 18th.

Tom

On Mon, Jun 11, 2018 at 3:17 PM, dmzuckerman notifications@github.com wrote:

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.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dmzuckerman/PhysicalLensOnTheCell/issues/1#issuecomment-396259326, or mute the thread https://github.com/notifications/unsubscribe-auth/AA84JoRGVo1NzTOi0Z72DSQnIEkzC5Diks5t7nvsgaJpZM4TcfPh .

-- Tom Wheeler President / Lead Drupal Developer Wheelercreek Studio Inc. http://wheelercreek.com ph. 360-326-5076

[dmzuckerman]

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]

These recent changes and Advanced Diffusion page are complete & ready for you to check.

On Fri, Jun 15, 2018 at 3:54 PM, dmzuckerman notifications@github.com wrote:

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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dmzuckerman/PhysicalLensOnTheCell/issues/1#issuecomment-397761905, or mute the thread https://github.com/notifications/unsubscribe-auth/AA84JrVcCCe3CSZmO1UBPc41K5DHrUKKks5t9DsZgaJpZM4TcfPh .

-- Tom Wheeler President / Lead Drupal Developer Wheelercreek Studio Inc. http://wheelercreek.com ph. 360-326-5076

[dmzuckerman]

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]

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]

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

[wheelercreek]

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

[dmzuckerman]

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]

Sorry about that - I think we've found them all now.

Tom

On Tue, Jul 17, 2018 at 11:15 AM, dmzuckerman notifications@github.com wrote:

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 http://www.physicallensonthecell.org/physical-lens-cell/chemical-physics .

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-- Tom Wheeler President / Lead Drupal Developer Wheelercreek Studio Inc. http://wheelercreek.com ph. 360-326-5076

[dmzuckerman]

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]

What do you mean "on the contents bar"? Do you mean the contents page? And do you also want it changed in the menu?

The equation number is corrected.

Tom

On Wed, Jul 18, 2018 at 10:07 AM, dmzuckerman notifications@github.com wrote:

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.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dmzuckerman/PhysicalLensOnTheCell/issues/1#issuecomment-406005323, or mute the thread https://github.com/notifications/unsubscribe-auth/AA84JgUKjeagvkh8tu1B5OHUMSUhgaziks5uH2tlgaJpZM4TcfPh .

-- Tom Wheeler President / Lead Drupal Developer Wheelercreek Studio Inc. http://wheelercreek.com ph. 360-326-5076

[dmzuckerman]

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]

Okay got it.. yeah sorry the terminology can get confusing sometimes. This is completed.

On Wed, Jul 18, 2018 at 11:45 AM, dmzuckerman notifications@github.com wrote:

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

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-- Tom Wheeler President / Lead Drupal Developer Wheelercreek Studio Inc. http://wheelercreek.com ph. 360-326-5076

[dmzuckerman]

thanks

[dmzuckerman]

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]

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]

Sorry about that - these are completed now.

[dmzuckerman]

thanks

[dmzuckerman]

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.