Streamlining Draft Flow - Revision history

Mbg: /* Comments on Parts of the Draft */

2021-09-07T14:17:41Z

Comments on Parts of the Draft

← Older revision		Revision as of 14:17, 7 September 2021
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	** Way to List [[Affiliation]] for Mark Gerstein on papers		** Way to List [[Affiliation]] for Mark Gerstein on papers

	* [[Affiliation for postdocs]]		* Affiliation for postdocs
	** Postdocs whose primary appointment is the "MB&B Department" are also affiliated to the "Program in Computational Biology & Bioinformatics" (CBB)		** Postdocs whose primary appointment is the "MB&B Department" are also affiliated to the "Program in Computational Biology & Bioinformatics" (CBB)
	** Hence, they can list both the affiliations. Mark would prefer CBB be listed first, but if they want MB&B can be listed first.		** Hence, they can list both the affiliations. Mark would prefer CBB be listed first, but if they want MB&B can be listed first.

Mbg: /* Comments on Parts of the Draft */

2021-09-07T14:17:18Z

Comments on Parts of the Draft

← Older revision		Revision as of 14:17, 7 September 2021
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	* [[Affiliation]]		* [[Affiliation]]
	** Way to List ~~Affiliations~~ for Mark Gerstein on papers		** Way to List [[Affiliation]] for Mark Gerstein on papers
	** Mark B. Gerstein 1,2,3
	** 1 Program in Computational Biology and Bioinformatics, 2 Department of Molecular Biophysics and Biochemistry, and 3 Department of Computer Science, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520 (Mark.Gerstein (at) Yale.edu)

	* [[Affiliation for postdocs]]		* [[Affiliation for postdocs]]

Mbg at 10:46, 29 June 2018

2018-06-29T10:46:32Z

← Older revision		Revision as of 10:46, 29 June 2018
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	rather than		rather than
	http://meetings.gersteinlab.org/2017/12.17/privaseq3-GG-121717-diff.pdf		http://meetings.gersteinlab.org/2017/12.17/privaseq3-GG-121717-diff.pdf

	~~== Submission and Dealing with the Journal ==~~
	* Use the pi address for the corresponding author.
	** Deprecated: Do NOT use [[xxmg at gersteinlab.org \| xxmg@gersteinlab.org]] for the correct address to use for paper correspondence.
	* Use templates (at http://wiki.gersteinlab.org/labinfo/index.php/Templates) for the submission letter and response to the referees

	== Comments on Parts of the Draft ==		== Comments on Parts of the Draft ==
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	** All my papers in draft form should just start off acknowledging funding from the "NIH or NSF and from the AL Williams Professorship Funds". We will fill in a specific grant number or other agency as appropriate at the very end, usually in proof stage. If a journal asks where the open access charges come from, again, one should just say "the NIH". Do not put in grant numbers!		** All my papers in draft form should just start off acknowledging funding from the "NIH or NSF and from the AL Williams Professorship Funds". We will fill in a specific grant number or other agency as appropriate at the very end, usually in proof stage. If a journal asks where the open access charges come from, again, one should just say "the NIH". Do not put in grant numbers!
	** I suggest the following boilerplate: "We acknowledge support from the NIH and from the AL Williams Professorship funds."		** I suggest the following boilerplate: "We acknowledge support from the NIH and from the AL Williams Professorship funds."

			== Submission and Dealing with the Journal ==
			* Use the pi address for the corresponding author.
			** Deprecated: Do NOT use [[xxmg at gersteinlab.org \| xxmg@gersteinlab.org]] for the correct address to use for paper correspondence.
			* Use templates (at http://wiki.gersteinlab.org/labinfo/index.php/Templates) for the submission letter and response to the referees

	== [[Proof Stage Pointers]] ==		== [[Proof Stage Pointers]] ==

Mbg at 10:44, 29 June 2018

2018-06-29T10:44:52Z

← Older revision		Revision as of 10:44, 29 June 2018
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	* there's a number of commericial proofreading servies such as Edit My English or grammarly.		* there's a number of commericial proofreading servies such as Edit My English or grammarly.
	* I'm willing to pay for a professional editor as well.		* I'm willing to pay for a professional editor as well.

	~~== Update Apr. '14 ==~~

	~~Ideas on [[File Presentation for Revised Drafts]]~~

	== Revisions ==		== Revisions ==

	The one thing that annoys me in revising a document is when I make extensive suggestions for changes, particularly on paper in some print out format, and then on the next version none of the suggestions have been incorporated or responded to. I think it's important when I look at a version of the document I have some indication of what the suggested changes are. Either my marked up corrections (via digital send of this) or a all-changes-file or something similar. It doesn't matter if you don't want to put in the changes I suggest. I'd at least like to have them acknowledged and not have to repeat them over and over again.		The one thing that annoys me in revising a document is when I make extensive suggestions for changes, particularly on paper in some print out format, and then on the next version none of the suggestions have been incorporated or responded to. I think it's important when I look at a version of the document I have some indication of what the suggested changes are. Either my marked up corrections (via digital send of this) or a all-changes-file or something similar. It doesn't matter if you don't want to put in the changes I suggest. I'd at least like to have them acknowledged and not have to repeat them over and over again.

	''' Track Changes'''		''' Track Changes'''

	When looking at many versions of a document, particularly at the final stages, it's very useful to use track changes so one can focus on just the changes.		When looking at many versions of a document, particularly at the final stages, it's very useful to use track changes so one can focus on just the changes.
	This can be done in several ways		This can be done in several ways

Mbg: /* IDs & File conventions */

2018-06-29T10:44:13Z

IDs & File conventions

← Older revision		Revision as of 10:44, 29 June 2018
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	* Word & PDF		* Word & PDF
	Use MS Word (or HTML) over latex. If you need to use latex for equations, embed them in the word file as GIFs. If you send me a PDF with equations, please try to make sure they come out OK on windows. In connection with this, [ftp://selab.janelia.org/pub/publications/Eddy01b/Eddy01b-techreport.pdf] might be a useful link~~. Also, please use "doc" in preference to docx as the later doesn't work with all readers~~. Best to send a PDF & a doc of just the maintext (without figures & supplement). Figures can be kept in a separate PDF or ppt file as necessary.		Use MS Word (or HTML) over latex. If you need to use latex for equations, embed them in the word file as GIFs. If you send me a PDF with equations, please try to make sure they come out OK on windows. In connection with this, [ftp://selab.janelia.org/pub/publications/Eddy01b/Eddy01b-techreport.pdf] might be a useful link. Best to send a PDF & a doc of just the maintext (without figures & supplement). Figures can be kept in a separate PDF or ppt file as necessary (see below).

	* Lab ID		* Lab ID
	When working on a draft, people should try and develop a one or two word lab ID -- e.g. "sandy" or "pseudopiped". This is useful in terms of organizing correspondence about the document and quickly referring to it. Later on, we will use this lab ID in the framework on the [http://wiki.gersteinlab.org/labinfo/index.php/Papers_page_and_e-print_directory papers page]. Try to separate this ID with a dash or dot ("-" or "."), not an underscore ("_"), as this helps with searching.		When working on a draft, people should try and develop a one or two-word lab ID -- e.g. "sandy" or "pseudopiped". This is useful in terms of organizing correspondence about the document and quickly referring to it. Later on, we will use this lab ID in the framework on the [http://wiki.gersteinlab.org/labinfo/index.php/Papers_page_and_e-print_directory papers page]. Try to separate this ID with a dash or dot ("-" or "."), not an underscore ("_"), as this helps with searching.

	* ~~Use dropbox for the file exchange~~		* LabDropbox
	Use the lab dropbox for the exchange of the drafts. If you want to show me multiple files, create a folder with the lab ID of the project and put all of your files into that folder. Check the link of the folder on the meetings page and send me the web address of the folder.		Use the lab dropbox for the exchange of the drafts. If you want to show me multiple files, create a folder with the lab ID of the project and put all of your files into that folder. Check the link of the folder on the meetings page and send me the web address of the folder.

			== Optimal Situation and Example Format ==
			The best situation is to segregate the figures from the text and put everything in lab dropbox. Then send me a link to both the doc and pdf files of the text (showing track changes if appropriate) and then a link to the figures (as a PPT or PDF).
			Here's the format currently preferred for drafts of papers and some parts of grants :

			* Word doc with the current version
			** saved in the sync dropbox & send a link to this on lab archive (http://archive.gersteinlab.org/meetings/s/...). (Don't use the actual archive server anymore!)
			*** Please use a "meetings" url not a link to a "homes" outbox or google drive
			** Please do NOT put figures into this . Keep the text "clean".
			** Use an ID convention & version date the filename

			* email a PDF diff doc with track changes from the last edited version to the last one and also put into sync
			** You can use compare documents to generate this.
			** This should only be maintext changes v. the previous version.

			* Put a PPT (preferred) or PDF of the figures saved in the sync dropbox
			** (send link to this via archive as in #1)
			** Also put the supplement and other associated files in the sync too.

			* For the response to referees documents use the same approach as the maintext -- ie doc in the dropbox with email link + track change PDF attached
			** Do this even if you using a gdoc for the response

	* Unique names in drobbox		* Unique names in drobbox
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	Then you update this. Please use a link like		Then you update this. Please use a link like

	http://meetings.gersteinlab.org/2017/12.17/privaseq3-GG-121717-diff-v2.pdf		http://meetings.gersteinlab.org/2017/12.17/privaseq3-GG-121717-diff-v2.pdf
	rather than		rather than

	http://meetings.gersteinlab.org/2017/12.17/privaseq3-GG-121717-diff.pdf		http://meetings.gersteinlab.org/2017/12.17/privaseq3-GG-121717-diff.pdf

	* Optimal Situation

	The best situation is to segregate the figures from the text and put everything in lab dropbox. Then send me a link to both the doc and pdf files of the text (showing track changes if appropriate) and then a link to the the figures (as a PPT or PDF).
	.

	== Submission and Dealing with the Journal ==		== Submission and Dealing with the Journal ==

Mbg: /* IDs & File conventions */

2018-06-26T23:42:20Z

IDs & File conventions

← Older revision		Revision as of 23:42, 26 June 2018
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	* Use dropbox for the file exchange		* Use dropbox for the file exchange
	Use the lab dropbox for the exchange of the drafts. If you want to show me multiple files, create a folder with the lab ID of the project and put all of your files into that folder. Check the link of the folder on the meetings page and send me the web address of the folder.		Use the lab dropbox for the exchange of the drafts. If you want to show me multiple files, create a folder with the lab ID of the project and put all of your files into that folder. Check the link of the folder on the meetings page and send me the web address of the folder.


	* Unique names in drobbox		* Unique names in drobbox

Mbg: /* Submission and Dealing with the Journal */

2018-06-26T23:41:56Z

Submission and Dealing with the Journal

← Older revision		Revision as of 23:41, 26 June 2018
Line 79:		Line 79:

	== Submission and Dealing with the Journal ==		== Submission and Dealing with the Journal ==
	* Deprecated: See [[xxmg at gersteinlab.org \| xxmg@gersteinlab.org]] for correct address to use for paper correspondence.
	* Use the pi address for the corresponding author.		* Use the pi address for the corresponding author.
			** Deprecated: Do NOT use [[xxmg at gersteinlab.org \| xxmg@gersteinlab.org]] for the correct address to use for paper correspondence.
	* Use templates (at http://wiki.gersteinlab.org/labinfo/index.php/Templates) for the submission letter and response to the referees		* Use templates (at http://wiki.gersteinlab.org/labinfo/index.php/Templates) for the submission letter and response to the referees

Mbg: /* IDs & File conventions */

2018-06-26T23:41:06Z

IDs & File conventions

← Older revision		Revision as of 23:41, 26 June 2018
Line 50:		Line 50:

	* Word & PDF		* Word & PDF
	Use MS Word (or HTML) over latex. If you need to use latex for equations, embed them in the word file as GIFs. If you send me a PDF with equations, please try to make sure they come out OK on windows. In connection with this, [ftp://selab.janelia.org/pub/publications/Eddy01b/Eddy01b-techreport.pdf] might be a useful link. Also, please use "doc" in preference to docx as the later doesn't work with all readers.		Use MS Word (or HTML) over latex. If you need to use latex for equations, embed them in the word file as GIFs. If you send me a PDF with equations, please try to make sure they come out OK on windows. In connection with this, [ftp://selab.janelia.org/pub/publications/Eddy01b/Eddy01b-techreport.pdf] might be a useful link. Also, please use "doc" in preference to docx as the later doesn't work with all readers. Best to send a PDF & a doc of just the maintext (without figures & supplement). Figures can be kept in a separate PDF or ppt file as necessary.

	* Lab ID		* Lab ID

Public: /* IDs & File conventions */

2017-12-18T17:42:13Z

IDs & File conventions

← Older revision		Revision as of 17:42, 18 December 2017
Line 55:		Line 55:
	When working on a draft, people should try and develop a one or two word lab ID -- e.g. "sandy" or "pseudopiped". This is useful in terms of organizing correspondence about the document and quickly referring to it. Later on, we will use this lab ID in the framework on the [http://wiki.gersteinlab.org/labinfo/index.php/Papers_page_and_e-print_directory papers page]. Try to separate this ID with a dash or dot ("-" or "."), not an underscore ("_"), as this helps with searching.		When working on a draft, people should try and develop a one or two word lab ID -- e.g. "sandy" or "pseudopiped". This is useful in terms of organizing correspondence about the document and quickly referring to it. Later on, we will use this lab ID in the framework on the [http://wiki.gersteinlab.org/labinfo/index.php/Papers_page_and_e-print_directory papers page]. Try to separate this ID with a dash or dot ("-" or "."), not an underscore ("_"), as this helps with searching.

	* ~~Email small files and Outbox links to bigger things~~		* Use dropbox for the file exchange
	~~If you want to go~~ for ~~email, try to keep~~ the ~~size~~ of the ~~emailed file less than 1 Mb~~. If you want to ~~go to bigger~~ files, ~~send~~ a ~~link. If you send a big message to my normal email, it will fill up a number~~ of ~~my mailboxes~~ and ~~cause messages to be bounced~~. ~~If we are working~~ on ~~a big document, you can either~~ send ~~just~~ the ~~section you changed as an attachment or send a link to whole edited file~~.		Use the lab dropbox for the exchange of the drafts. If you want to show me multiple files, create a folder with the lab ID of the project and put all of your files into that folder. Check the link of the folder on the meetings page and send me the web address of the folder.

	* Unique names in ~~outboxes~~
	when sending me links to files in ~~your~~ "~~outbox~~" . I'd appreciate if this link be		* Unique names in drobbox
			when sending me links to files in "meetings". I'd appreciate if this link be
	unique and that you don't overwrite files with the same name. I have my own		unique and that you don't overwrite files with the same name. I have my own
	internal file system (for "inboxes") that gets confused when you overwrite names. In particular, if you send me something like this:		internal file system (for "inboxes") that gets confused when you overwrite names. In particular, if you send me something like this:

	http://~~homes~~.gersteinlab.org/~~people~~/~~joelabmember/outbox/proj1~~/~~mypaper~~.~~doc~~		http://meetings.gersteinlab.org/2017/12.17/privaseq3-GG-121717-diff.pdf

	Then you update this. Please use a link like		Then you update this. Please use a link like

	http://~~homes~~.gersteinlab.org/~~people~~/~~joelabmember/outbox/proj1~~/~~mypaper2~~.~~doc~~		http://meetings.gersteinlab.org/2017/12.17/privaseq3-GG-121717-diff-v2.pdf

	rather than		rather than

	http://~~homes~~.gersteinlab.org/~~people~~/~~joelabmember/outbox/proj1~~/~~mypaper~~.~~doc~~		http://meetings.gersteinlab.org/2017/12.17/privaseq3-GG-121717-diff.pdf

	* Optimal Situation		* Optimal Situation

	The best situation is to segregate the figures from the text and put everything in ~~an outbox~~. Then send me a link to both the doc and pdf files of the text (showing track changes if appropriate) and then a link to the the figures (as a PPT or PDF).		The best situation is to segregate the figures from the text and put everything in lab dropbox. Then send me a link to both the doc and pdf files of the text (showing track changes if appropriate) and then a link to the the figures (as a PPT or PDF).
	.		.

Public: /* Revisions */

2017-12-18T17:37:17Z

Revisions

← Older revision		Revision as of 17:37, 18 December 2017
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	The one thing that annoys me in revising a document is when I make extensive suggestions for changes, particularly on paper in some print out format, and then on the next version none of the suggestions have been incorporated or responded to. I think it's important when I look at a version of the document I have some indication of what the suggested changes are. Either my marked up corrections (via digital send of this) or a all-changes-file or something similar. It doesn't matter if you don't want to put in the changes I suggest. I'd at least like to have them acknowledged and not have to repeat them over and over again.		The one thing that annoys me in revising a document is when I make extensive suggestions for changes, particularly on paper in some print out format, and then on the next version none of the suggestions have been incorporated or responded to. I think it's important when I look at a version of the document I have some indication of what the suggested changes are. Either my marked up corrections (via digital send of this) or a all-changes-file or something similar. It doesn't matter if you don't want to put in the changes I suggest. I'd at least like to have them acknowledged and not have to repeat them over and over again.

	* Track Changes		''' Track Changes'''
	~~When looking at many versions of a document, particularly at the final stages, it~~'s very useful to use track changes so one can focus on just the changes. This can work with latex by just giving me the track changed version of the source file and a PDF of the formatted version (without changes). One should try to do track changes relative to the ''~~'last~~''' ~~edit, not to the original version of the manuscript. This can be achieved by accepting all the changes after an edit discussion and then starting afresh.~~

	It's ~~also possible~~ just ~~to highlight (eg with "yellow")~~ the ~~changed bits~~.		When looking at many versions of a document, particularly at the final stages, it's very useful to use track changes so one can focus on just the changes.
			This can be done in several ways

	* Revision History		* Do the track changes on the word document and create a pdf file that has the track changes. Add "-diff" to the title of this file, so I know it has the changes relative to the previous version.
	One should maintain a rough revision history of the document, that is each draft should be given a kind of draft number and some indication~~, maybe at~~ the ~~head of~~ the draft ~~or in an e-mail, should be given as to which drafts were sent to which people~~. We can use this information to decide on other people to send the draft to in the lab and also to get a sense of how many times it's been turning over. If we are working on a document in response to referee's comments, best to always send draft with at least a rough response to referees. (See below for format.)		* If you're using latex, make sure to highlight your changes. You can highlight with yellow. If you want to show me what you delete, you can strike the sentences that are deleted. Again, name this file with a tag "-diff" and send me the pdf version.


			''' Revision History'''

			One should maintain a rough revision history of the document, that is each draft should be given a kind of draft number and some indication. The easiest way is naming the draft with the date tag and the authors' initials in case there are more than one person editing the draft.

			We can use this information to decide on other people to send the draft to in the lab and also to get a sense of how many times it's been turning over. If we are working on a document in response to referee's comments, best to always send draft with at least a rough response to referees. (See below for format.)

	== IDs & File conventions ==		== IDs & File conventions ==