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TemplateJournalsbiologymedicine

bioRxiv Preprint

HenriquesLab two-column bioRxiv preprint class, a popular community template for life-science preprints on bioRxiv.

GPL-3.0

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What’s inside

  • Starter files
  • main.tex1.7 KB
    % Trimmed from the HenriquesLab bioRxiv template,
% https://github.com/HenriquesLab/HenriquesLab-BioRxiv-template
\documentclass[times, twoside]{zHenriquesLab-StyleBioRxiv}

\leadauthor{Author}

\begin{document}

\title{Your Preprint Title Here}
\shorttitle{Short running title}

\author[1,\Letter]{First Author}
\author[2]{Second Author}
\affil[1]{Department of Cell Biology, Example University, City, Country}
\affil[2]{Example Institute for Biomedical Research, City, Country}

\maketitle

\begin{abstract}
Replace this abstract with a short summary of your preprint. Keep it self-contained; bioRxiv shows it on the preprint's landing page.
\end{abstract}

\begin{keywords}
keyword one | keyword two | keyword three
\end{keywords}

\begin{corrauthor}
first.author\at example.edu
\end{corrauthor}

\section*{Introduction}

Introduce the problem and cite prior work \cite{watson1953,fire1998}. Sections are unnumbered; the layout is two-column with dropped capitals available via \verb|\lettrine|.

\section*{Results}

Display equations are numbered:
\begin{equation}
  v = \frac{V_{\max}\,[S]}{K_m + [S]}.
  \label{eq:mm}
\end{equation}
Column-wide figures use \verb|figure|, full-width ones \verb|figure*|, and side-captioned ones \verb|SCfigure*|; \cref{eq:mm} style references come from cleveref.

\section*{Discussion}

Summarize the findings. Ask the agent in the chat to draft sections, tighten the abstract, or format your reference list for you.

\section*{Methods}

Methods typically follow the discussion in bioRxiv preprints.

\begin{acknowledgements}
Funding sources and thanks go here.
\end{acknowledgements}

\section*{Bibliography}
\bibliography{references}

\end{document}
  • Libraries and docs
  • references.bib692 B
    @article{watson1953,
  author  = {Watson, J. D. and Crick, F. H. C.},
  title   = {Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid},
  journal = {Nature},
  volume  = {171},
  number  = {4356},
  pages   = {737--738},
  year    = {1953},
  doi     = {10.1038/171737a0}
}

@article{fire1998,
  author  = {Fire, Andrew and Xu, SiQun and Montgomery, Mary K. and Kostas, Steven A. and Driver, Samuel E. and Mello, Craig C.},
  title   = {Potent and Specific Genetic Interference by Double-Stranded RNA in Caenorhabditis elegans},
  journal = {Nature},
  volume  = {391},
  number  = {6669},
  pages   = {806--811},
  year    = {1998},
  doi     = {10.1038/35888}
}
  • zHenriquesLab-StyleBib.bst24 KB
    %% File: `unsrtnat.bst'
%% A modification of `unsrt.bst' for use with natbib package 
%%
%% Copyright 1993-2007 Patrick W Daly
%% Max-Planck-Institut f\"ur Sonnensystemforschung
%% Max-Planck-Str. 2
%% D-37191 Katlenburg-Lindau
%% Germany
%% E-mail: daly@mps.mpg.de
%%
%% This program can be redistributed and/or modified under the terms
%% of the LaTeX Project Public License Distributed from CTAN
%% archives in directory macros/latex/base/lppl.txt; either
%% version 1 of the License, or any later version.
%%
 % Version and source file information:
 % \ProvidesFile{natbst.mbs}[2007/11/26 1.93 (PWD)]
 %
 % BibTeX `plainnat' family
 %   version 0.99b for BibTeX versions 0.99a or later,
 %   for LaTeX versions 2.09 and 2e.
 %
 % For use with the `natbib.sty' package; emulates the corresponding
 %   member of the `plain' family, but with author-year citations.
 %
 % With version 6.0 of `natbib.sty', it may also be used for numerical
 %   citations, while retaining the commands \citeauthor, \citefullauthor,
 %   and \citeyear to print the corresponding information.
 %
 % For version 7.0 of `natbib.sty', the KEY field replaces missing
 %   authors/editors, and the date is left blank in \bibitem.
 %
 % Includes field EID for the sequence/citation number of electronic journals
 %  which is used instead of page numbers.
 %
 % Includes fields ISBN and ISSN.
 %
 % Includes field URL for Internet addresses.
 %
 % Includes field DOI for Digital Object Idenfifiers.
 %
 % Works best with the url.sty package of Donald Arseneau.
 %
 % Works with identical authors and year are further sorted by
 %    title text, as in the standard plain.bst etc.
 %
ENTRY
  { address
    author
    booktitle
    chapter
    doi
    eid
    edition
    editor
    howpublished
    institution
    isbn
    issn
    journal
    key
    month
    note
    number
    organization
    pages
    publisher
    school
    series
    title
    type
    url
    volume
    year
  }
  {}
  { label extra.label sort.label short.list }

INTEGERS { output.state before.all mid.sentence after.sentence after.block }

FUNCTION {init.state.consts}
{ #0 'before.all :=
  #1 'mid.sentence :=
  #2 'after.sentence :=
  #3 'after.block :=
}

STRINGS { s t }

FUNCTION {output.nonnull}
{ 's :=
  output.state mid.sentence =
    { ", " * write$ }
    { output.state after.block =
        { add.period$ write$
          newline$
          "\newblock " write$
        }
        { output.state before.all =
            'write$
            { add.period$ " " * write$ }
          if$
        }
      if$
      mid.sentence 'output.state :=
    }
  if$
  s
}

FUNCTION {output}
{ duplicate$ empty$
    'pop$
    'output.nonnull
  if$
}

FUNCTION {output.check}
{ 't :=
  duplicate$ empty$
    { pop$ "empty " t * " in " * cite$ * warning$ }
    'output.nonnull
  if$
}

FUNCTION {fin.entry}
{ add.period$
  write$
  newline$
}

FUNCTION {new.block}
{ output.state before.all =
    'skip$
    { after.block 'output.state := }
  if$
}

FUNCTION {new.sentence}
{ output.state after.block =
    'skip$
    { output.state before.all =
        'skip$
        { after.sentence 'output.state := }
      if$
    }
  if$
}

FUNCTION {not}
{   { #0 }
    { #1 }
  if$
}

FUNCTION {and}
{   'skip$
    { pop$ #0 }
  if$
}

FUNCTION {or}
{   { pop$ #1 }
    'skip$
  if$
}

FUNCTION {new.block.checka}
{ empty$
    'skip$
    'new.block
  if$
}

FUNCTION {new.block.checkb}
{ empty$
  swap$ empty$
  and
    'skip$
    'new.block
  if$
}

FUNCTION {new.sentence.checka}
{ empty$
    'skip$
    'new.sentence
  if$
}

FUNCTION {new.sentence.checkb}
{ empty$
  swap$ empty$
  and
    'skip$
    'new.sentence
  if$
}

FUNCTION {field.or.null}
{ duplicate$ empty$
    { pop$ "" }
    'skip$
  if$
}

FUNCTION {emphasize}
{ duplicate$ empty$
    { pop$ "" }
    { "\emph{" swap$ * "}" * }
  if$
}

INTEGERS { nameptr namesleft numnames }

FUNCTION {format.names}
{ 's :=
  #1 'nameptr :=
  s num.names$ 'numnames :=
  numnames 'namesleft :=
    { namesleft #0 > }
    { s nameptr "{ff~}{vv~}{ll}{, jj}" format.name$ 't :=
      nameptr #1 >
        { namesleft #1 >
            { ", " * t * }
            { numnames #2 >
                { "," * }
                'skip$
              if$
              t "others" =
                { " et~al." * }
                { " and " * t * }
              if$
            }
          if$
        }
        't
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
}

FUNCTION {format.key}
{ empty$
    { key field.or.null }
    { "" }
  if$
}

FUNCTION {format.authors}
{ author empty$
    { "" }
    { author format.names }
  if$
}

FUNCTION {format.editors}
{ editor empty$
    { "" }
    { editor format.names
      editor num.names$ #1 >
        { ", editors" * }
        { ", editor" * }
      if$
    }
  if$
}

FUNCTION {format.isbn}
{ isbn empty$
    { "" }
    { new.block "ISBN " isbn * }
  if$
}

FUNCTION {format.issn}
{ issn empty$
    { "" }
    { new.block "ISSN " issn * }
  if$
}

FUNCTION {format.url}
{ url empty$
    { "" }
    { "" }
  if$
}

FUNCTION {format.doi}
{ doi empty$
    { "" }
    { new.block "\doi{" doi * "}" * }
  if$
}

FUNCTION {format.title}
{ title empty$
    { "" }
    { title "t" change.case$ }
  if$
}

FUNCTION {format.full.names}
{'s :=
  #1 'nameptr :=
  s num.names$ 'numnames :=
  numnames 'namesleft :=
    { namesleft #0 > }
    { s nameptr
      "{vv~}{ll}" format.name$ 't :=
      nameptr #1 >
        {
          namesleft #1 >
            { ", " * t * }
            {
              numnames #2 >
                { "," * }
                'skip$
              if$
              t "others" =
                { " et~al." * }
                { " and " * t * }
              if$
            }
          if$
        }
        't
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
}

FUNCTION {author.editor.full}
{ author empty$
    { editor empty$
        { "" }
        { editor format.full.names }
      if$
    }
    { author format.full.names }
  if$
}

FUNCTION {author.full}
{ author empty$
    { "" }
    { author format.full.names }
  if$
}

FUNCTION {editor.full}
{ editor empty$
    { "" }
    { editor format.full.names }
  if$
}

FUNCTION {make.full.names}
{ type$ "book" =
  type$ "inbook" =
  or
    'author.editor.full
    { type$ "proceedings" =
        'editor.full
        'author.full
      if$
    }
  if$
}

FUNCTION {output.bibitem}
{ newline$
  "\bibitem[" write$
  label write$
  ")" make.full.names duplicate$ short.list =
     { pop$ }
     { * }
   if$
  "]{" * write$
  cite$ write$
  "}" write$
  newline$
  ""
  before.all 'output.state :=
}

FUNCTION {n.dashify}
{ 't :=
  ""
    { t empty$ not }
    { t #1 #1 substring$ "-" =
        { t #1 #2 substring$ "--" = not
            { "--" *
              t #2 global.max$ substring$ 't :=
            }
            {   { t #1 #1 substring$ "-" = }
                { "-" *
                  t #2 global.max$ substring$ 't :=
                }
              while$
            }
          if$
        }
        { t #1 #1 substring$ *
          t #2 global.max$ substring$ 't :=
        }
      if$
    }
  while$
}

FUNCTION {format.date}
{ year duplicate$ empty$
    { "empty year in " cite$ * warning$
       pop$ "" }
    'skip$
  if$
  month empty$
    'skip$
    { month
      " " * swap$ *
    }
  if$
  extra.label *
}

FUNCTION {format.btitle}
{ title emphasize
}

FUNCTION {tie.or.space.connect}
{ duplicate$ text.length$ #3 <
    { "~" }
    { " " }
  if$
  swap$ * *
}

FUNCTION {either.or.check}
{ empty$
    'pop$
    { "can't use both " swap$ * " fields in " * cite$ * warning$ }
  if$
}

FUNCTION {format.bvolume}
{ volume empty$
    { "" }
    { "volume" volume tie.or.space.connect
      series empty$
        'skip$
        { " of " * series emphasize * }
      if$
      "volume and number" number either.or.check
    }
  if$
}

FUNCTION {format.number.series}
{ volume empty$
    { number empty$
        { series field.or.null }
        { output.state mid.sentence =
            { "number" }
            { "Number" }
          if$
          number tie.or.space.connect
          series empty$
            { "there's a number but no series in " cite$ * warning$ }
            { " in " * series * }
          if$
        }
      if$
    }
    { "" }
  if$
}

FUNCTION {format.edition}
{ edition empty$
    { "" }
    { output.state mid.sentence =
        { edition "l" change.case$ " edition" * }
        { edition "t" change.case$ " edition" * }
      if$
    }
  if$
}

INTEGERS { multiresult }

FUNCTION {multi.page.check}
{ 't :=
  #0 'multiresult :=
    { multiresult not
      t empty$ not
      and
    }
    { t #1 #1 substring$
      duplicate$ "-" =
      swap$ duplicate$ "," =
      swap$ "+" =
      or or
        { #1 'multiresult := }
        { t #2 global.max$ substring$ 't := }
      if$
    }
  while$
  multiresult
}

FUNCTION {format.pages}
{ pages empty$
    { "" }
    { pages multi.page.check
        { "pages" pages n.dashify tie.or.space.connect }
        { "page" pages tie.or.space.connect }
      if$
    }
  if$
}

FUNCTION {format.eid}
{ eid empty$
    { "" }
    { "art." eid tie.or.space.connect }
  if$
}

FUNCTION {format.vol.num.pages}
{ volume field.or.null
  number empty$
    'skip$
    { "\penalty0 (" number * ")" * *
      volume empty$
        { "there's a number but no volume in " cite$ * warning$ }
        'skip$
      if$
    }
  if$
  pages empty$
    'skip$
    { duplicate$ empty$
        { pop$ format.pages }
        { ":\penalty0 " * pages n.dashify * }
      if$
    }
  if$
}

FUNCTION {format.vol.num.eid}
{ volume field.or.null
  number empty$
    'skip$
    { "\penalty0 (" number * ")" * *
      volume empty$
        { "there's a number but no volume in " cite$ * warning$ }
        'skip$
      if$
    }
  if$
  eid empty$
    'skip$
    { duplicate$ empty$
        { pop$ format.eid }
        { ":\penalty0 " * eid * }
      if$
    }
  if$
}

FUNCTION {format.chapter.pages}
{ chapter empty$
    'format.pages
    { type empty$
        { "chapter" }
        { type "l" change.case$ }
      if$
      chapter tie.or.space.connect
      pages empty$
        'skip$
        { ", " * format.pages * }
      if$
    }
  if$
}

FUNCTION {format.in.ed.booktitle}
{ booktitle empty$
    { "" }
    { editor empty$
        { "In " booktitle emphasize * }
        { "In " format.editors * ", " * booktitle emphasize * }
      if$
    }
  if$
}

FUNCTION {empty.misc.check}
{ author empty$ title empty$ howpublished empty$
  month empty$ year empty$ note empty$
  and and and and and
  key empty$ not and
    { "all relevant fields are empty in " cite$ * warning$ }
    'skip$
  if$
}

FUNCTION {format.thesis.type}
{ type empty$
    'skip$
    { pop$
      type "t" change.case$
    }
  if$
}

FUNCTION {format.tr.number}
{ type empty$
    { "Technical Report" }
    'type
  if$
  number empty$
    { "t" change.case$ }
    { number tie.or.space.connect }
  if$
}

FUNCTION {format.article.crossref}
{ key empty$
    { journal empty$
        { "need key or journal for " cite$ * " to crossref " * crossref *
          warning$
          ""
        }
        { "In \emph{" journal * "}" * }
      if$
    }
    { "In " }
  if$
  " \citet{" * crossref * "}" *
}

FUNCTION {format.book.crossref}
{ volume empty$
    { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
      "In "
    }
    { "Volume" volume tie.or.space.connect
      " of " *
    }
  if$
  editor empty$
  editor field.or.null author field.or.null =
  or
    { key empty$
        { series empty$
            { "need editor, key, or series for " cite$ * " to crossref " *
              crossref * warning$
              "" *
            }
            { "\emph{" * series * "}" * }
          if$
        }
        'skip$
      if$
    }
    'skip$
  if$
  " \citet{" * crossref * "}" *
}

FUNCTION {format.incoll.inproc.crossref}
{ editor empty$
  editor field.or.null author field.or.null =
  or
    { key empty$
        { booktitle empty$
            { "need editor, key, or booktitle for " cite$ * " to crossref " *
              crossref * warning$
              ""
            }
            { "In \emph{" booktitle * "}" * }
          if$
        }
        { "In " }
      if$
    }
    { "In " }
  if$
  " \citet{" * crossref * "}" *
}

FUNCTION {article}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  new.block
  format.title "title" output.check
  new.block
  crossref missing$
    { journal emphasize "journal" output.check
      eid empty$
        { format.vol.num.pages output }
        { format.vol.num.eid output }
      if$
      format.date "year" output.check
    }
    { format.article.crossref output.nonnull
      eid empty$
        { format.pages output }
        { format.eid output }
      if$
    }
  if$
  format.issn output
  format.doi output
  new.block
  note output
  fin.entry
}

FUNCTION {book}
{ output.bibitem
  author empty$
    { format.editors "author and editor" output.check
      editor format.key output
    }
    { format.authors output.nonnull
      crossref missing$
        { "author and editor" editor either.or.check }
        'skip$
      if$
    }
  if$
  new.block
  format.btitle "title" output.check
  crossref missing$
    { format.bvolume output
      new.block
      format.number.series output
      new.sentence
      publisher "publisher" output.check
      address output
    }
    { new.block
      format.book.crossref output.nonnull
    }
  if$
  format.edition output
  format.date "year" output.check
  format.isbn output
  format.doi output
  new.block
  note output
  fin.entry
}

FUNCTION {booklet}
{ output.bibitem
  format.authors output
  author format.key output
  new.block
  format.title "title" output.check
  howpublished address new.block.checkb
  howpublished output
  address output
  format.date output
  format.isbn output
  format.doi output
  new.block
  note output
  fin.entry
}

FUNCTION {inbook}
{ output.bibitem
  author empty$
    { format.editors "author and editor" output.check
      editor format.key output
    }
    { format.authors output.nonnull
      crossref missing$
        { "author and editor" editor either.or.check }
        'skip$
      if$
    }
  if$
  new.block
  format.btitle "title" output.check
  crossref missing$
    { format.bvolume output
      format.chapter.pages "chapter and pages" output.check
      new.block
      format.number.series output
      new.sentence
      publisher "publisher" output.check
      address output
    }
    { format.chapter.pages "chapter and pages" output.check
      new.block
      format.book.crossref output.nonnull
    }
  if$
  format.edition output
  format.date "year" output.check
  format.isbn output
  format.doi output
  new.block
  note output
  fin.entry
}

FUNCTION {incollection}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  new.block
  format.title "title" output.check
  new.block
  crossref missing$
    { format.in.ed.booktitle "booktitle" output.check
      format.bvolume output
      format.number.series output
      format.chapter.pages output
      new.sentence
      publisher "publisher" output.check
      address output
      format.edition output
      format.date "year" output.check
    }
    { format.incoll.inproc.crossref output.nonnull
      format.chapter.pages output
    }
  if$
  format.isbn output
  format.doi output
  new.block
  note output
  fin.entry
}

FUNCTION {inproceedings}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  new.block
  format.title "title" output.check
  new.block
  crossref missing$
    { format.in.ed.booktitle "booktitle" output.check
      format.bvolume output
      format.number.series output
      format.pages output
      address empty$
        { organization publisher new.sentence.checkb
          organization output
          publisher output
          format.date "year" output.check
        }
        { address output.nonnull
          format.date "year" output.check
          new.sentence
          organization output
          publisher output
        }
      if$
    }
    { format.incoll.inproc.crossref output.nonnull
      format.pages output
    }
  if$
  format.isbn output
  format.doi output
  new.block
  note output
  fin.entry
}

FUNCTION {conference} { inproceedings }

FUNCTION {manual}
{ output.bibitem
  format.authors output
  author format.key output
  new.block
  format.btitle "title" output.check
  organization address new.block.checkb
  organization output
  address output
  format.edition output
  format.date output
  new.block
  note output
  fin.entry
}

FUNCTION {mastersthesis}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  new.block
  format.title "title" output.check
  new.block
  "Master's thesis" format.thesis.type output.nonnull
  school "school" output.check
  address output
  format.date "year" output.check
  new.block
  note output
  fin.entry
}

FUNCTION {misc}
{ output.bibitem
  format.authors output
  author format.key output
  title howpublished new.block.checkb
  format.title output
  howpublished new.block.checka
  howpublished output
  format.date output
  format.issn output
  new.block
  note output
  fin.entry
  empty.misc.check
}

FUNCTION {phdthesis}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  new.block
  format.btitle "title" output.check
  new.block
  "PhD thesis" format.thesis.type output.nonnull
  school "school" output.check
  address output
  format.date "year" output.check
  new.block
  note output
  fin.entry
}

FUNCTION {proceedings}
{ output.bibitem
  format.editors output
  editor format.key output
  new.block
  format.btitle "title" output.check
  format.bvolume output
  format.number.series output
  address output
  format.date "year" output.check
  new.sentence
  organization output
  publisher output
  format.isbn output
  format.doi output
  new.block
  note output
  fin.entry
}

FUNCTION {techreport}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  new.block
  format.title "title" output.check
  new.block
  format.tr.number output.nonnull
  institution "institution" output.check
  address output
  format.date "year" output.check
  new.block
  note output
  fin.entry
}

FUNCTION {unpublished}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  new.block
  format.title "title" output.check
  new.block
  note "note" output.check
  format.date output
  fin.entry
}

FUNCTION {default.type} { misc }


MACRO {jan} {"January"}

MACRO {feb} {"February"}

MACRO {mar} {"March"}

MACRO {apr} {"April"}

MACRO {may} {"May"}

MACRO {jun} {"June"}

MACRO {jul} {"July"}

MACRO {aug} {"August"}

MACRO {sep} {"September"}

MACRO {oct} {"October"}

MACRO {nov} {"November"}

MACRO {dec} {"December"}



MACRO {acmcs} {"ACM Computing Surveys"}

MACRO {acta} {"Acta Informatica"}

MACRO {cacm} {"Communications of the ACM"}

MACRO {ibmjrd} {"IBM Journal of Research and Development"}

MACRO {ibmsj} {"IBM Systems Journal"}

MACRO {ieeese} {"IEEE Transactions on Software Engineering"}

MACRO {ieeetc} {"IEEE Transactions on Computers"}

MACRO {ieeetcad}
 {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"}

MACRO {ipl} {"Information Processing Letters"}

MACRO {jacm} {"Journal of the ACM"}

MACRO {jcss} {"Journal of Computer and System Sciences"}

MACRO {scp} {"Science of Computer Programming"}

MACRO {sicomp} {"SIAM Journal on Computing"}

MACRO {tocs} {"ACM Transactions on Computer Systems"}

MACRO {tods} {"ACM Transactions on Database Systems"}

MACRO {tog} {"ACM Transactions on Graphics"}

MACRO {toms} {"ACM Transactions on Mathematical Software"}

MACRO {toois} {"ACM Transactions on Office Information Systems"}

MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"}

MACRO {tcs} {"Theoretical Computer Science"}


READ

FUNCTION {sortify}
{ purify$
  "l" change.case$
}

INTEGERS { len }

FUNCTION {chop.word}
{ 's :=
  'len :=
  s #1 len substring$ =
    { s len #1 + global.max$ substring$ }
    's
  if$
}

FUNCTION {format.lab.names}
{ 's :=
  s #1 "{vv~}{ll}" format.name$
  s num.names$ duplicate$
  #2 >
    { pop$ " et~al." * }
    { #2 <
        'skip$
        { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =
            { " et~al." * }
            { " and " * s #2 "{vv~}{ll}" format.name$ * }
          if$
        }
      if$
    }
  if$
}

FUNCTION {author.key.label}
{ author empty$
    { key empty$
        { cite$ #1 #3 substring$ }
        'key
      if$
    }
    { author format.lab.names }
  if$
}

FUNCTION {author.editor.key.label}
{ author empty$
    { editor empty$
        { key empty$
            { cite$ #1 #3 substring$ }
            'key
          if$
        }
        { editor format.lab.names }
      if$
    }
    { author format.lab.names }
  if$
}

FUNCTION {author.key.organization.label}
{ author empty$
    { key empty$
        { organization empty$
            { cite$ #1 #3 substring$ }
            { "The " #4 organization chop.word #3 text.prefix$ }
          if$
        }
        'key
      if$
    }
    { author format.lab.names }
  if$
}

FUNCTION {editor.key.organization.label}
{ editor empty$
    { key empty$
        { organization empty$
            { cite$ #1 #3 substring$ }
            { "The " #4 organization chop.word #3 text.prefix$ }
          if$
        }
        'key
      if$
    }
    { editor format.lab.names }
  if$
}

FUNCTION {calc.short.authors}
{ type$ "book" =
  type$ "inbook" =
  or
    'author.editor.key.label
    { type$ "proceedings" =
        'editor.key.organization.label
        { type$ "manual" =
            'author.key.organization.label
            'author.key.label
          if$
        }
      if$
    }
  if$
  'short.list :=
}

FUNCTION {calc.label}
{ calc.short.authors
  short.list
  "("
  *
  year duplicate$ empty$
  short.list key field.or.null = or
     { pop$ "" }
     'skip$
  if$
  *
  'label :=
}

INTEGERS { seq.num }

FUNCTION {init.seq}
{ #0 'seq.num :=}

EXECUTE {init.seq}

FUNCTION {int.to.fix}
{ "000000000" swap$ int.to.str$ *
  #-1 #10 substring$
}


FUNCTION {presort}
{ calc.label
  label sortify
  "    "
  *
  seq.num #1 + 'seq.num :=
  seq.num  int.to.fix
  'sort.label :=
  sort.label *
  #1 entry.max$ substring$
  'sort.key$ :=
}

ITERATE {presort}

SORT

STRINGS { longest.label last.label next.extra }

INTEGERS { longest.label.width last.extra.num number.label }

FUNCTION {initialize.longest.label}
{ "" 'longest.label :=
  #0 int.to.chr$ 'last.label :=
  "" 'next.extra :=
  #0 'longest.label.width :=
  #0 'last.extra.num :=
  #0 'number.label :=
}

FUNCTION {forward.pass}
{ last.label label =
    { last.extra.num #1 + 'last.extra.num :=
      last.extra.num int.to.chr$ 'extra.label :=
    }
    { "a" chr.to.int$ 'last.extra.num :=
      "" 'extra.label :=
      label 'last.label :=
    }
  if$
  number.label #1 + 'number.label :=
}

FUNCTION {reverse.pass}
{ next.extra "b" =
    { "a" 'extra.label := }
    'skip$
  if$
  extra.label 'next.extra :=
  extra.label
  duplicate$ empty$
    'skip$
    { "{\natexlab{" swap$ * "}}" * }
  if$
  'extra.label :=
  label extra.label * 'label :=
}

EXECUTE {initialize.longest.label}

ITERATE {forward.pass}

REVERSE {reverse.pass}

FUNCTION {bib.sort.order}
{ sort.label  'sort.key$ :=
}

ITERATE {bib.sort.order}

SORT

FUNCTION {begin.bib}
{   preamble$ empty$
    'skip$
    { preamble$ write$ newline$ }
  if$
  "\begin{thebibliography}{" number.label int.to.str$ * "}" *
  write$ newline$
  "\providecommand{\natexlab}[1]{#1}"
  write$ newline$
  "\providecommand{\url}[1]{\texttt{#1}}"
  write$ newline$
  "\expandafter\ifx\csname urlstyle\endcsname\relax"
  write$ newline$
  "  \providecommand{\doi}[1]{doi: #1}\else"
  write$ newline$
  "  \providecommand{\doi}{doi: \begingroup \urlstyle{rm}\Url}\fi"
  write$ newline$
}

EXECUTE {begin.bib}

EXECUTE {init.state.consts}

ITERATE {call.type$}

FUNCTION {end.bib}
{ newline$
  "\end{thebibliography}" write$ newline$
}

EXECUTE {end.bib}
  • zHenriquesLab-StyleBioRxiv.cls15 KB
    %%
%% This is file `zHenriquesLab-StyleBioRxiv.cls',
%%
%% Class files for pre-print servers such as BioRXiv
%%
%% Copyright (C) Ricardo Henriques <r.henriques@ucl.ac.uk>
%% 
\typeout{Document Class `HenriquesLab' <18-April-2018>.}
\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{zHenriquesLab-StyleBioRxiv}
  [2018/04/18 revision by RH]

%% Load base class
\LoadClass[a4paper]{article}

%% define new needed boolean variables
\newif\if@tmptwocolumn  \@tmptwocolumnfalse
\newif\if@times         \@timesfalse

%% Options
\newif\ifbfabstract     \bfabstracttrue
\DeclareOption{rmabstract}{\bfabstractfalse}
\newif\ifbibskip        \bibskipfalse
\DeclareOption{bibskip}{\bibskiptrue}
\newif\ifwatermark        \watermarkfalse
\DeclareOption{watermark}{\watermarktrue}

\DeclareOption{draft}{\PassOptionsToClass{draft}{article}}
\DeclareOption{times}{\@timestrue}
\DeclareOption{twoside}{\@twosidetrue}
\DeclareOption{twocolumn}{\@tmptwocolumntrue}
\DeclareOption{onecolumn}{\@tmptwocolumnfalse}
%\DeclareOption{watermark}{\@displaywatermark}

\ExecuteOptions{times,twoside,twocolumn}
\ProcessOptions

%% and math support and fonts
\RequirePackage{amsmath,amsfonts,amssymb}
\RequirePackage{mathptmx}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Henriques lab dependencies - Start %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\RequirePackage{xcolor}
\RequirePackage{authblk}
\RequirePackage[latin1,utf8]{inputenc}
\RequirePackage[english]{babel}
\RequirePackage{lmodern}
\RequirePackage{siunitx}
\RequirePackage{textgreek}
% [Sundial vendoring patch] early cleveref load removed; cleveref is loaded after hyperref below (required by current cleveref)
\RequirePackage{gensymb}
\RequirePackage{textcomp}
\RequirePackage[version=4]{mhchem}
\RequirePackage[scaled]{helvet}
\RequirePackage[T1]{fontenc}
\RequirePackage{lettrine} % For dropped capitals
\RequirePackage[rightcaption]{sidecap} % For sidecaptions
\RequirePackage[misc]{ifsym} % For the \Letter symbol
\RequirePackage{bbding} % For the \Envelope symbol
\RequirePackage[twoside,%
				letterpaper,includeheadfoot,%
				layoutsize={8.125in,10.875in},%
                layouthoffset=0.1875in,%
                layoutvoffset=0.0625in,%
                left=38.5pt,%
                right=43pt,%
                top=43pt,% 10pt provided by headsep
                bottom=32pt,%
                headheight=0pt,% No Header
                headsep=10pt,%
                footskip=25pt]{geometry}
\RequirePackage[labelfont={bf,sf},%
                labelsep=period,%
                figurename=Fig.]{caption}

\DeclareUnicodeCharacter{00B0}{\degree}

%% Hyperlinking
\RequirePackage[colorlinks=true, allcolors=blue]{hyperref}

%% Ref to Sup
\RequirePackage{nameref}
\RequirePackage{cleveref}
\crefname{equation}{Eq. S}{equations}
\crefname{figure}{Fig.}{figures}
\crefname{section}{Sup. Note}{notes}
% \crefname{chapter}{Chapter}{Chapters}
% \crefname{section}{Section}{Sections}
% \crefname{subsection}{Section}{Sections}
% \crefname{subsubsection}{Section}{Sections}
% \crefname{figure}{Figure}{Figures}
% \crefname{table}{Table}{Tables}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Henriques lab dependencies - End %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% Fonts

\if@times\RequirePackage{times}\fi



%% sizes and margins
\topmargin      -16.0mm
%\oddsidemargin  -11.0mm
%\evensidemargin -11.0mm
%\textwidth        175mm
\textheight       243mm
\columnsep          7mm
\headsep          6.3mm
\headheight        12pt
\lineskip           1pt
\normallineskip     1pt
\def\baselinestretch{1}

\marginparsep      10pt
\marginparwidth    20pt
\marginparpush     25pt

\partopsep          \z@
\topsep           1.3ex
\parsep             \z@
\itemsep            \z@

%%
\abovedisplayskip       0pt plus2pt minus5pt%
\belowdisplayskip       \abovedisplayskip
\abovedisplayshortskip  0pt plus3pt%
\belowdisplayshortskip  0pt plus3pt minus3pt%

\arraycolsep     5pt
\tabcolsep       6pt
\arrayrulewidth .4pt
\doublerulesep   2pt
\tabbingsep\labelsep

%% footnotes
\skip\footins 10pt plus 4pt minus 2pt
\footnotesep 7pt
\footskip 10mm
\skip\@mpfootins = \skip\footins
\fboxsep = 3pt \fboxrule = .4pt
\long\def\@makefntext#1{\parindent .8em\indent$^{\@thefnmark}$#1}
\def\footnoterule{}


\newdimen\@maxsep
\newdimen\@dblmaxsep
%% Definitions for floats
%%
%% Normal Floats                      %% Double Column Floats
\floatsep 12pt plus 2pt minus 2pt     \dblfloatsep 12pt plus 2pt minus 2pt
\textfloatsep 20pt plus 2pt minus 4pt \dbltextfloatsep 20pt plus 2pt minus 4pt
\@maxsep 20pt                         \@dblmaxsep 20pt
\@fptop 0pt plus 1fil                 \@dblfptop 0pt plus 1fil
\@fpsep 8pt plus 2fil                 \@dblfpsep 8pt plus 2fil
\@fpbot 0pt plus 1fil                 \@dblfpbot 0pt plus 1fil
\def\topfraction{1.0}                 \def\dbltopfraction{1.0}
\def\floatpagefraction{0.8}           \def\dblfloatpagefraction{0.8}
\setcounter{topnumber}{2}             \setcounter{dbltopnumber}{4}
\intextsep 12pt plus 2pt minus 2pt
\setcounter{bottomnumber}{2}
\def\bottomfraction{.1}
\setcounter{totalnumber}{4}
\def\textfraction{.1}
\setlength{\belowcaptionskip}{-10pt} % reduces spacing between figure legend and text

\renewcommand{\topfraction}{0.99}
\renewcommand{\floatpagefraction}{0.5}
\renewcommand{\bottomfraction}{0.99}
\renewcommand{\textfraction}{0.01}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%
%% Henriques lab parts adapted from PNAS %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\newcommand{\shorttitle}[1]{\def\@shorttitle{#1}}
\newcommand{\leadauthor}[1]{\def\@leadauthor{#1}}
%\newcommand{\headerfont}{\normalfont\sffamily\fontsize{7}{9} \selectfont}
\newcommand{\footerfont}{\normalfont\sffamily\fontsize{7}{9} \selectfont}
\newcommand{\titlefont}{\fontfamily{lmss}\bfseries\fontsize{22pt}{24pt}\selectfont}
\newcommand{\dropcapfont}{\fontfamily{lmss}\bfseries\fontsize{26pt}{28pt}\selectfont}
\newcommand{\datesfont}{\normalfont\sffamily\fontsize{7}{8}\selectfont}
\newcommand{\absfont}{\normalfont\sffamily\bfseries\fontsize{8}{11}\selectfont}
\newcommand{\keywordsfont}{\normalfont\rmfamily\fontsize{7}{10}\selectfont}
\newcommand{\copyrightfont}{\normalfont\rmfamily\fontsize{6}{8}\selectfont}

%% Set document color scheme
\definecolor{black50}{gray}{0.5} % 50% black for hrules
\definecolor{color0}{RGB}{0,0,0} % Base
\definecolor{color1}{RGB}{59,90,198} % author email, doi
\definecolor{color2}{RGB}{16,131,16} %

%% Author and affiliation
\setlength{\affilsep}{8.5pt} % 16.5pts between base of author line and base of affil line
\renewcommand\Authfont{\color{color0}\normalfont\sffamily\bfseries\fontsize{9}{11}\selectfont}
\renewcommand\Affilfont{\color{color0}\normalfont\sffamily\fontsize{7}{8}\selectfont}
\makeatletter
\renewcommand\Authands{, and }

%% Section/subsection/paragraph set-up
\RequirePackage[explicit]{titlesec}
\renewcommand{\thesubsection}{\Alph{subsection}}

%\usepackage[explicit]{titlesec}
% \titleformat{<command>}[<shape>]{<format>}{<label>}{<sep>}{<before>}[<after>]
% \titleformat{\section}[hang]{\normalfont\Large\bfseries}%
%     {\thechapter.}{4pt}%
%     {#1 \arabic{section}.}
% \makeatletter
% \renewcommand\thesection{}
% \renewcommand\thesubsection{\@arabic\c@section.\@arabic\c@subsection}
% \makeatother
% \titleformat{\section}[hang]
%   {\large\sffamily\bfseries}
%   {\thesection.}
%   {0.5em}
%   {#1.}
%   []

\titleformat{\section}
  {\large\sffamily\bfseries}
  {}
  {0em}
  {Supplementary Note \thesection: #1}
  []
\titleformat{name=\section,numberless}
  {\large\sffamily\bfseries}
  {}
  {0em}
  {#1}
  []  
\titleformat{\subsection}[runin]
  {\sffamily\bfseries}
  {\thesubsection.}
  {0.5em}
  {#1. }
  []
\titleformat{\subsubsection}[runin]
  {\sffamily\small\bfseries\itshape}
  {\thesubsubsection.}
  {0.5em}
  {#1. }
  []    
\titleformat{\paragraph}[runin]
  {\sffamily\small\bfseries}
  {}
  {0em}
  {#1} 
\titlespacing*{\section}{0pc}{3ex \@plus4pt \@minus3pt}{5pt}
\titlespacing*{\subsection}{0pc}{2.5ex \@plus3pt \@minus2pt}{2pt}
\titlespacing*{\subsubsection}{0pc}{2ex \@plus2.5pt \@minus1.5pt}{2pt}
\titlespacing*{\paragraph}{0pc}{1.5ex \@plus2pt \@minus1pt}{12pt}

%% Figure caption style
\DeclareCaptionFormat{smallformat}{\normalfont\sffamily\fontsize{7}{9}\selectfont#1#2#3}
\DeclareCaptionFormat{largeformat}{\normalfont\sffamily\fontsize{9}{12}\selectfont#1#2#3}
\captionsetup*{format=smallformat}

% %% Watermark 
\usepackage[printwatermark]{xwatermark}
\AtBeginDocument{%
  \ifwatermark%
  \newwatermark[allpages,color=gray!20,angle=45,scale=3,xpos=0,ypos=0]{DRAFT}
  \fi
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Henriques lab parts adapted from PNAS - END %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Henriques lab parts to count words - Start %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\RequirePackage{verbatim} 

%% You can pass in your own texcount params, e.g. -chinese to turn on Chinese mode, or -char to do a character count instead (which does NOT include spaces!)
%%% http://app.uio.no/ifi/texcount/documentation.html
\newcommand{\detailtexcount}{%
  \immediate\write18{texcount -merge -sum -incbib -dir \jobname.tex > \jobname.wcdetail }%
  \verbatiminput{\jobname.wcdetail}%
}

\newcommand{\quickwordcount}{%
  \immediate\write18{texcount -1 -sum -merge \jobname.tex > \jobname-words.sum }%
  \input{\jobname-words.sum} words%
}

\newcommand{\quickcharcount}{%
  \immediate\write18{texcount -1 -sum -merge -char \jobname.tex > \jobname-chars.sum }%
  \input{\jobname-chars.sum} characters (not including spaces)%
}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Henriques lab parts to count words - End %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% marks
\def\markboth#1#2{\def\leftmark{#1}\def\rightmark{#2}}
\def\footernote#1{\markboth{#1}{#1}}

% %% bibliography
\RequirePackage{chapterbib}
\RequirePackage[sectionbib,numbers,sort&compress,merge,round]{natbib}
\setlength{\bibsep}{0.0pt}
\bibliographystyle{zHenriquesLab-StyleBib}
\renewcommand{\bibsection}{} % Remove header
\renewcommand\bibfont{\normalfont\sffamily\fontsize{6}{8}\selectfont} % set font to be sans serif

\makeatletter 
\renewcommand\@biblabel[1]{ #1.} % Remove brackets from label
\def\tagform@#1{\maketag@@@{\bfseries(\ignorespaces#1\unskip\@@italiccorr)}}
\renewcommand{\eqref}[1]{\textup{{\normalfont Eq.~(\ref{#1}}\normalfont)}}
% \makeatother

%% Title
\def\maketitle{\par
  \begingroup
  \def\thefootnote{} % the \thanks{} mark type is empty
\if@tmptwocolumn
  \twocolumn[\@maketitle]
\else
  \@maketitle
\fi
  \thispagestyle{plain}\@thanks
  \endgroup
  \setcounter{footnote}{0}\let\maketitle\relax\let\@maketitle\relax
  \gdef\@thanks{}\gdef\@author{}\gdef\@title{}\let\thanks\relax
}

\def\@maketitle{\newpage
  \begin{center}
    \vskip0.2em{\Huge\bfseries\@title\par}\vskip1.0em%
    {\lineskip.5em\large\@author\par}
  \end{center}\par\vskip 1.4em}

%% Abstract and keywords
\def\abstract{%\vspace{-.3em}
  \ifbfabstract\small\bfseries\else\footnotesize\fi}

\def\endabstract{\vspace{1.0em}\par\normalsize}

% \def\keywords{%\vspace{-.3em}
% \noindent\ifbfabstract\Affilfont\bfseries\itshape\else\footnotesize\fi  Keywords --- }
% \def\endkeywords{\vspace{0.3em}\par\normalsize}

% \newcommand{\at}{\makeatletter @\makeatother}
% \def\corrauthor{%\vspace{-.3em}
% \noindent\ifbfabstract\Affilfont\bfseries\itshape\else\footnotesize\fi  Correspondence --- }
% \def\endcorrauthor{\vspace{0.3em}\par\normalsize}

\def\keywords{%\vspace{-.3em}
\ifbfabstract\Affilfont\bfseries\else\footnotesize\fi}
\def\endkeywords{\vspace{0.3em}\par\normalsize}

\newcommand{\at}{\makeatletter @\makeatother}
\def\corrauthor{%\vspace{-.3em}
\noindent\ifbfabstract\Affilfont\bfseries\else\footnotesize\fi  Correspondence:\itshape}
\def\endcorrauthor{\vspace{0.3em}\par\normalsize}

\def\acknowledgements{\vspace{1em}
\Affilfont\bfseries ACKNOWLEDGEMENTS\par\mdseries}
\def\endacknowledgements{\vspace{0.3em}\par\normalsize}

\def\contributions{\vspace{.3em}
\Affilfont\bfseries AUTHOR CONTRIBUTIONS\par\mdseries}
\def\endcontributions{\vspace{0.3em}\par\normalsize}

\def\interests{\vspace{.3em}
\Affilfont\bfseries COMPETING FINANCIAL INTERESTS\par\mdseries}
\def\endinterests{\vspace{0.3em}\par\normalsize}

%% environemts
\newdimen\tmpitemindent
\def\QED{\mbox{\rule[0pt]{1.5ex}{1.5ex}}}
\def\proof{\noindent\hspace{2em}{\it Proof: }}
\def\endproof{\hspace*{\fill}~\QED\par\endtrivlist\unskip}
\def\@begintheorem#1#2{\tmpitemindent\itemindent\topsep 0pt\rm\trivlist
    \item[\hskip \labelsep{\indent\it #1\ #2:}]\itemindent\tmpitemindent}
\def\@opargbegintheorem#1#2#3{\tmpitemindent\itemindent\topsep 0pt\rm \trivlist
    \item[\hskip\labelsep{\indent\it #1\ #2\ \rm(#3)}]\itemindent\tmpitemindent}
\def\@endtheorem{\endtrivlist\unskip}

\newtheorem{theorem}{Theorem}
\newtheorem{definition}{Definition}
\newtheorem{corollary}{Corollary}

\twocolumn \sloppy \flushbottom

%% Units
\DeclareSIUnit\molar{\mole\per\cubic\deci\metre}
\DeclareSIUnit\Molar{\textsc{m}}


%% Allows to enter BIOGRAPHY leaving place for picture
%%
\newenvironment{biography}[1]{%
\footnotesize\unitlength 1mm\bigskip\bigskip\bigskip\parskip=0pt\par%
\rule{0pt}{39mm}\vspace{-39mm}\par%   garantees correct page breaking
\noindent\setbox0\hbox{\framebox(25,32){}}%   box containing the frame
\ht0=37mm\count10=\ht0\divide\count10 by\baselineskip%  calculates lines
\global\hangindent29mm\global\hangafter-\count10%
\hskip-28.5mm\setbox0\hbox to 28.5mm {\raise-30.5mm\box0\hss}%
\dp0=0mm\ht0=0mm\box0\noindent\bf#1\rm}{
\par\rm\normalsize}

%% Default rules for including pictures
\RequirePackage{graphicx}
\RequirePackage{color}
\DeclareGraphicsRule{*}{eps}{*}{}

%% Page headers and footers
%%
\RequirePackage{fancyhdr} % Custom headers/footers
\RequirePackage{lastpage} % Number of pages in the document
\pagestyle{fancy}		  % Enables the custom headers/footers

\def\aBioRXiv{{\footnotesize
    \footerfont \@leadauthor\ifnum \value{authors} > 1\hspace{2pt}\textit{et al.}\fi\hspace{7pt}|\hspace{7pt}bio\textcolor{red}{R}$\chi$iv\hspace{7pt}|\hspace{7pt}\today\hspace{7pt}|\hspace{7pt}\thepage\textendash\pageref{LastPage}
  }}

\def\bBioRXiv{{\footnotesize
    \footerfont \thepage\hspace{7pt}|\hspace{7pt}bio\textcolor{red}{R}$\chi$iv
  }}
  
\def\cBioRXiv{{\footnotesize
    \footerfont bio\textcolor{red}{R}$\chi$iv\hspace{7pt}|\hspace{7pt}\thepage
  }}
   
\def\dBioRXiv{{\footnotesize
    \footerfont \@leadauthor\ifnum \value{authors} > 1\hspace{2pt}\textit{et al.}\fi\hspace{7pt}|\hspace{7pt}\@shorttitle
  }}

\lfoot[\bBioRXiv]{\dBioRXiv}
\rfoot[\dBioRXiv]{\cBioRXiv}

\rhead[]{\footnotesize\rightmark}
\lhead[\footnotesize\leftmark]{}
\cfoot{}
\renewcommand{\headrulewidth}{0pt}

\fancypagestyle{plain}{
\fancyhf{}
\fancyfoot[RE]{}
\fancyfoot[LO]{}
\fancyfoot[LE]{}
\fancyfoot[RO]{\aBioRXiv}}

\def\sectionmark#1{\relax}

\parindent=0pt
\endinput
  • main.pdfprebuilt · 123 KBReplaced by the first recompile.

    Binary file, seeded as-is.

  • main.synctex.gzprebuilt · 7.8 KBReplaced by the first recompile.

    Binary file, seeded as-is.