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codeinpapers.md

Publishers and code in papers

  • F1000

    • F1000 Research
      • doi: 10.12688/f1000research.2-191.v1 (taxize paper) here
        • html: text blocks as .gif images, syntax highlighting,
        • pdf: you can copy text from code blocks, but all formatting lost
        • xml: embeds a gif image of code block wrapped in p tags like <p><graphic xlink:href="f1000research-2-2227-g0006.gif"/></p>
    • communication: They heard from Ethan White, Carl Boettiger, and Scott Chamberlain about improving presentation of code, and they are working with their typesetters to include the code in xml

  • Wiley

    • Methods in Ecology and Evolution:
      • doi: 10.1111/j.2041-210X.2011.00169.x here
        • pdf: plain text, indented 1 tab, no syntax highlighting
        • html: same
        • xml: none available
        • with prompts
      • doi: 10.1111/2041-210X.12065 here
        • pdf: plain text, indented a few tabs, no syntax highlighting
        • html: same
        • xml: none available
        • with prompts and "+" to fold code to next line (not good)
    • communication: not contacted yet

  • BioMed Central

    • BMC Bioinformatics
      • doi: 10.1186/1471-2105-14-75 here
        • pdf: plain text, indented 1 tab, no syntax highlighting
        • html: same
        • xml: full code avail. wrapped in p tags, e.g., <p>&gt; GSE23402 &lt;&#8722; getGEO("GSE23402")</p>
        • with prompts ">"
    • communication: not contacted yet

  • PeerJ

    • doi: 10.7717/peerj.80 here
      • html: png images, with line numbers
      • pdf: can copy code blocks, but formatting lost, and line numbers get in the way
      • xml: code blocks in xml, wrapped in monospace tags (line numbers gone in the xml code) <monospace>Geometry.geometry()</monospace>
      • code blocks have line numbers, and are images (.png), minimal syntax highlighting
    • communication: did get response from @invisiblecomma that he would look at a solution, and if it was easy enough, would implement it

  • Springer

    • asdf
    • communication: not contacted yet

  • PLOS

    • asdf
    • communication: not contacted yet
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