Proof Stage Checklist

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* Corresponding author
+
==Short version==
-
** CHANGE corresponding email to mark ((at)) gersteinlab.org from pi ((at)) gersteinlab.org
+
* Get grant right!
 +
* correct MG email + ORCID
 +
* papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github
 +
* github should have a license/permissions
 +
* lab homepage image
 +
* tweet
 +
* slide deck
 +
 
 +
(see '''<code>Proofsx57m</code>''' tag on correspondence)
 +
 
 +
==Long version of checklist==
 +
 
 +
* Press & PR
 +
** If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.
 +
 
 +
* MG affiliation and Corresponding author
** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719
** Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719
 +
** Check that MG's [[Affiliation]] is accurate
* Funding
* Funding
-
** remember to add funding acknowledgments with precise grant number, so paper goes into PMC (see below)
+
** Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)
-
*** This needs to be updated on the papers page entry
+
*** We should usually acknowledge grant XXX and ALW
-
** discuss with the Mark the grant for the page/reprint charges (not necessarily the same as the PMC)
+
** Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this.
 +
*** We might have to do a justification for this. Here is some sample text: , noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)
 +
** Funding is usually applicable when MG is the last author.
 +
 
 +
*** There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &lab in the middle -someone else handles.
 +
 
 +
*PMC & License
 +
** For license, go for open access for non-commercial use unless prohibitively expensive.
 +
** Need to make sure paper comes out in PMC when paper comes out https://guides.library.yale.edu/nihpolicy/how-to-comply. or slides [https://docs.google.com/presentation/d/1wU2VG-6k3cOaARRSJlrix2j6SdYnmOJaNW6bLT4DeC4/edit?slide=id.g23e716205a8_0_0#slide=id.g23e716205a8_0_0]
 +
** JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/
 +
** If there are problems, don't write to the editor. Write to the publishing people. "production people"
 +
** Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)
* Papers Page (papers.gersteinlab.org)
* Papers Page (papers.gersteinlab.org)
-
** Get a lab ID for the paper from Mark (eg lab "ID=cmptxn"). Occasionally, we can use the pubmed ID here, but normally this is the ID that has been used internally the project pre-publication.
+
** Get a lab ID for the paper from Mark (eg, lab "ID=cmptxn"). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.
 +
*** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.
 +
*** Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint.
 +
** Many of the grant abbreviations are visible via http://papers.gersteinlab.org/subject or http://info.gersteinlab.org/Summaries. For additional ones, work with the lab asst. on the correct abbreviation. If the grant abbreviation is not on the papers page, please create on via the papers page maintainers.  
** Do a papers page rebuild, requires lab ID & website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code
** Do a papers page rebuild, requires lab ID & website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code
 +
*** Send the following information to whoever is in charge of rebuilding the papers page:
 +
**** PubMed ID or doi of the preprint
 +
**** A link to the paper
 +
**** A link to the tools or resources (see "Tools & Resources" section below)
 +
**** Appropriate tags and topics, e.g. http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources (a full list can be obtained from http://papers.gersteinlab.org/subject/). You may propose new tags if they don't appear.
 +
**** Any additional information such as co-first authorship
*** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources
*** Make sure paper is appropriately tagged on the papers -- eg tag with http://papers.gersteinlab.org/subject/coretools or http://papers.gersteinlab.org/subject/resources
*** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv
*** Note the rebuild can be done before the paper comes out with a PMID, using just a biorxiv
 +
** Co-first and co-corresponding authors can be indicated with the footnote field
 +
** Use the link field to directly link the journal site (particularly if there is no pubmed)
* Tools & Resources
* Tools & Resources
 +
**  Website
 +
*** All papers should have the Gersteinlab URL - github.gersteinlab.org/ABCDE
 +
*** Best is where the paper ID is what, eg, ABCDE
 +
*** Try to use the GitHub standard for code data
 +
*** Ask MF about the lab GitHub
** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) & in the lab github (https://github.gersteinlab.org)
** Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) & in the lab github (https://github.gersteinlab.org)
** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball  
** Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball  
 +
** Make sure you software links the permissions statement & has a license (MIT)
** Make sure you have a final URL for website/github materials from above and enter it into the papers page   
** Make sure you have a final URL for website/github materials from above and enter it into the papers page   
-
** Make sure you use long-term email addresses for software contacts and a link to the lab FAQ
+
** Make sure you use long-term email addresses for software contacts (use or mkar@gersteinlab.org) and a link to the lab FAQ
-
** Make sure you have proper, long-term links for all files (files.gersteinlab.org, no dropbox or personal homepage links)
+
** Make sure you have proper, long-term links for all files ('''files.gersteinlab.org''', no dropbox or personal homepage links)
 +
** You can use the "website" field on the papers page to link your github site.
-
* PMC & reprints
+
* Preprints
-
** make sure journal publishes in PubMed Central (send email to editor to confirm this)
+
** Do a biorxiv submission (or another equiv. preprint server)  
-
** Do a preprint as a public lab doc or a biorxiv submission if your paper won't go into PMC -- use *pi@gersteinlab.org*
+
** use pi at gersteinlab.org for bioxriv submission
*** Link this from the papers page
*** Link this from the papers page
*** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ).  
*** Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ).  
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* Slides & Images
* Slides & Images
** Make sure Mark has "slide packs" for the paper
** Make sure Mark has "slide packs" for the paper
-
*** Try to use a current slide pack template  
+
*** Try to use a current slide pack template - a recent lecture at http://lectures.gersteinlab.org
** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .
** Do a homepage image, pad with white space to fill out to exact specifications, viz http://info.gersteinlab.org/Homepage_image_gallery .
* Tweet
* Tweet
-
**Tweet a ~200 char tweet on the paper and mention Mark (@MarkGerstein), including bits of the title; you can include an image too. Mark will retweet.
+
**Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.
 +
**You can use the lab twitter (@GersteinLab)
**Some recent examples:
**Some recent examples:
  https://twitter.com/markgerstein/status/789117961843900417  
  https://twitter.com/markgerstein/status/789117961843900417  

Latest revision as of 21:37, 9 September 2025

Short version

  • Get grant right!
  • correct MG email + ORCID
  • papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github
  • github should have a license/permissions
  • lab homepage image
  • tweet
  • slide deck

(see Proofsx57m tag on correspondence)

Long version of checklist

  • Press & PR
    • If appropriate, we should contact Yale PR (currently Karen Guzman) to discuss a possible press release. We can offer to draft a summary and provide the paper.
  • Funding
    • Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)
      • We should usually acknowledge grant XXX and ALW
    • Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC). You may need to ask the lab financial person (e.g. Janine) if there's enough money on the listed grant for publication charges. The lab admin can help with this.
      • We might have to do a justification for this. Here is some sample text: , noting that most of the work was funded by source XXX, while YYY supported only the components related to the final figure. (This is for Yale internal use, not for the paper’s acknowledgments section.)
    • Funding is usually applicable when MG is the last author.
      • There are 3 categories- MG last-we're responsible for; MG co-correspond-we're responsible for some stuff- publicize, nice lab ID; MG &lab in the middle -someone else handles.
  • PMC & License
    • For license, go for open access for non-commercial use unless prohibitively expensive.
    • Need to make sure paper comes out in PMC when paper comes out https://guides.library.yale.edu/nihpolicy/how-to-comply. or slides [1]
    • JIST website (searchable journal compliance) https://openpolicyfinder.jisc.ac.uk/
    • If there are problems, don't write to the editor. Write to the publishing people. "production people"
    • Make sure the journal publishes in PubMed Central (send an email to the editor to confirm this)
  • Papers Page (papers.gersteinlab.org)
    • Get a lab ID for the paper from Mark (eg, lab "ID=cmptxn"). Occasionally, we can use the PubMed ID here, but normally, this is the ID that has been used internally during the project pre-publication.
      • This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioRxiv.
      • Bioxriv needs to be uploaded with not the final version, before final acceptance - this should be linked to the papers' preprint.
    • Many of the grant abbreviations are visible via http://papers.gersteinlab.org/subject or http://info.gersteinlab.org/Summaries. For additional ones, work with the lab asst. on the correct abbreviation. If the grant abbreviation is not on the papers page, please create on via the papers page maintainers.
    • Do a papers page rebuild, requires lab ID & website from above + (hopefully) the PubMed ID - ie http://info.gersteinlab.org/Papers_Page_Code
    • Co-first and co-corresponding authors can be indicated with the footnote field
    • Use the link field to directly link the journal site (particularly if there is no pubmed)
  • Tools & Resources
    • Website
      • All papers should have the Gersteinlab URL - github.gersteinlab.org/ABCDE
      • Best is where the paper ID is what, eg, ABCDE
      • Try to use the GitHub standard for code data
      • Ask MF about the lab GitHub
    • Software from the paper should be listed on the lab tools page (http://info.gersteinlab.org/Resources) & in the lab github (https://github.gersteinlab.org)
    • Make sure there exists a minimal and maximally durable distribution of code and key data as a simple tarball
    • Make sure you software links the permissions statement & has a license (MIT)
    • Make sure you have a final URL for website/github materials from above and enter it into the papers page
    • Make sure you use long-term email addresses for software contacts (use or mkar@gersteinlab.org) and a link to the lab FAQ
    • Make sure you have proper, long-term links for all files (files.gersteinlab.org, no dropbox or personal homepage links)
    • You can use the "website" field on the papers page to link your github site.
  • Preprints
    • Do a biorxiv submission (or another equiv. preprint server)
    • use pi at gersteinlab.org for bioxriv submission
      • Link this from the papers page
      • Update bioRxiv preprint when the paper is published (wait 2-3 weeks before contacting bioRxiv - bioRxiv should automatically link it ).
  • Tweet
    • Tweet a ~200 char tweet on the paper and mention MG (@MarkGerstein), including bits of the title; you can include an image too. He will retweet.
    • You can use the lab twitter (@GersteinLab)
    • Some recent examples: 
https://twitter.com/markgerstein/status/789117961843900417 
https://twitter.com/markgerstein/status/851125314264715267
https://twitter.com/markgerstein/status/813772503063609344
  • Wikipedia
    • Try to link your paper to a relevant article on Wikipedia and edit that entry as appropriate
Retrieved from "http://info.gersteinlab.org/Proof_Stage_Checklist"
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