Proof Stage Checklist

From GersteinInfo

• MG affiliation and Corresponding author
  • CHANGE corresponding email to mark ((at)) gersteinlab.org from pi ((at)) gersteinlab.org
  • Make sure Mark's Orcid ID is used, viz: http://orcid.org/0000-0002-9746-3719
  • Check that MG's Affiliation is accurate

• Funding
  • 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.
    • 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.
  • Discuss with MG the grant for the page/reprint charges (usually but not necessarily the same as the PMC)

• 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.
  • 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
    • 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
  • 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 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 ).

• Slides & Images
  • Make sure Mark has "slide packs" for the paper
    • 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 .

• 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

• Tag for this page
  • Proofsx57m
  • Linked from Streamlining_Draft_Flow = x57m