Proof Stage Checklist

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==Short version==
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* Get grant right!
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* correct MG email + Orcid
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* papers page update with correct labid, tags, and correct grant + links to bioxriv and website/github
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* github should have a license/permissions
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* lab homepage image
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* tweet
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* slide deck
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(see '''<code>Proofsx57m</code>''' tag on correspondence)
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==Long version of checklist==
* MG affiliation and Corresponding author
* MG affiliation and Corresponding author
** CHANGE corresponding email to mark ((at)) gersteinlab.org from pi ((at)) gersteinlab.org
** CHANGE corresponding email to mark ((at)) gersteinlab.org from pi ((at)) gersteinlab.org
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** Check that MG's [[Affiliation]] is accurate  
** Check that MG's [[Affiliation]] is accurate  
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* Funding
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* Funding + License
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** remember to add funding acknowledgments with precise grant number, so paper goes into PMC (see below)
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** 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 (see below) and can be done as soon as there is a bioxriv.   
*** This needs to be updated on the papers page entry (see below) and can be done as soon as there is a bioxriv.   
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** Discuss with MG the grant for the page/reprint charges (not necessarily the same as the PMC)
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*** 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.
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** 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.
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** For license, go for open access for non-commercial use unless prohibitively expensive
* Papers Page (papers.gersteinlab.org)
* Papers Page (papers.gersteinlab.org)
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** 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.
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** 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.
** 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
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*** Send the following information to whoever is in charge of rebuilding the papers page:
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**** PubMed ID or doi of the preprint
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**** A link to the paper
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**** A link to the tools or resources (see "Tools & Resources" section below)
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**** 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.
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**** 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
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** co-first and co-corresponding authors can be indicated with the footnote field
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** 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)
** Use the link field to directly link the journal site (particularly if there is no pubmed)
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** 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  
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** 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 and a link to the lab FAQ

Latest revision as of 21:22, 21 September 2024

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

  • MG affiliation and Corresponding author
  • Funding + License
    • Remember to add funding acknowledgments with precise grant numbers, so the paper goes into PMC (see below)
    • 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.
    • For license, go for open access for non-commercial use unless prohibitively expensive
  • Tools & Resources
    • 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 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.
  • PMC & preprints
    • make sure journal publishes in PubMed Central (send email to editor to confirm this)
    • 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
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