BioHackrXiv

In this group we will work on the mini-publications infrastructure for the BioHackathons.

Coordinator:

• Pjotr Prins

Participants:

• Erick Antezana
• Leyla Garcia
• Ben Busby
• Ali Haider Bangash (hhaider4@gmail.com)
• Toshiaki Katayama

Communication

We communicate mostly by E-mail.

Topics

• Author instructions
  • Shall we limit only to accept Markdown?
    • Pros:
      • We can have control over the contents (incl. automatic translation, text mining, statistics).
      • Also we can apply consistent design to the generated PDF files.
    • Cons:
      • The current OSF submission system doesn't accept Markdown by default
        • For the time being, authors need to use our own PDF generator command (or our web service) before the submission
        • Or editors take a look on the Markdown files submitted to our own registry (where?) then generate a PDF and authors (by themselves) or editors (on behalf) can submit it to the BioHackrXiv at OSF
      • Authors not familiar with Markdown might hesitate to submit
      • Authors might need LaTeX for the math markup
• Submission guidelines. See JOSS as an example
  • Please make it generic and put it at https://github.com/biohackrxiv/biohackrxiv.github.io/blob/master/submission_guidelines.md (to be created)
• Journal policies.
  • Please put it at https://github.com/biohackrxiv/biohackrxiv.github.io/blob/master/journal_policies.md (to be created)
• Editor acceptance check list
  • most importantly, reporting original work (derived from BioHackathons and similar events)
  • fit within the scope
  • well-formatted by following the submission templates (only Markdown accepted?)
  • clearly written in English
  • all necessary information (e.g., references, figures and supplemental materials if any) are provided
• Fix web-based PDF generator
  • We can host it at http://preview.biohackrxiv.org/ or similar (under the subdomain)

Submission process

Plan A:

• BioHackrXiv provides templates for Markdown, Word, and LaTeX
• Author generates a PDF file (how?)
• Author submits the PDF to the BioHackrXiv

Plan B:

• BioHackrXiv only accept Markdown
• Author generates a PDF file (how?)
• Author submits the PDF to the BioHackrXiv

Plan C:

• BioHackrXiv only accept Markdown
• Author submits the Markdown to a repository (where?)
• Author notify the editors (how?)
• Editor reviews and generate a PDF file (how?)
• Editor submits the PDF to the BioHackrXiv on behalf

Plan D:

• BioHackrXiv only accept Markdown
• Authors submits the Markdown to a repository (where?)
• Author notify the editors (how?)
• Editor reviews and generate a PDF file (how?)
• Editor returns the PDF to authors (how?)
• Author submits the PDF to the BioHackrXiv

Plan A might be the simplest. Plan D might be best for now if we consider making use of the Markdown for text processing in the near future, such as text mining (to extract topics, evaluate trends, show statistics) or automatic language translation (e.g., to Japanese).

How to generate Markdown (Word, LaTeX) to PDF

• Markdown -> PDF (generated through the command or our service)
  • Run https://github.com/biohackrxiv/bhxiv-gen-pdf by author
  • Use the service at http://preview.biohackrxiv.org/ or somewhere else
• Word -> PDF
• LaTex -> PDF

Where to put the Markdown draft and how to notify the editors?

• One ad hoc idea is:
  • Author puts the materials at our repository GitHub or author's own Git repo at anywhere
  • Inform editors where the repository is by submitting empty PDF only with URL of the above repo to BioHackrXiv.