ISMB2001 - The 9th International Conference on Intelligent Systems for Molecular Biology, Tivoli Gardens, Copenhagen, Denmark, July 22 - 25, 2001
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PAPER FORMATTING INSTRUCTIONS
ACCEPTED PAPERS PAPER FORMAT INSTRUCTIONS

Dear corresponding author,

  • The deadline for submitting revised manuscripts is April 2
  • The formatted manuscript should be no longer than 9 pages
  • You are required to assign copyright using this PRINTABLE FORM
As mentioned previously, we here at CBS will be ultimately responsible for typesetting the proceedings. This will be done using the LaTeX typesetting system. Your job is first and foremost to revise your manuscript taking into account the comments of the referees. However, we ask that you nevertheless format your paper according to the present guidelines so that (1) you can check that the paper is at most 9 pages long, and (2) so that our job will perhaps be easier in the end.

The ISMB proceedings will be published as a supplementary issue of Bioinformatics, and the papers will be formatted in accordance with the ordinary style of that journal.

We prefer submissions in Latex but any wordprocessing format will do. Below you will find instructions specific to Word-users and to Latex-users. All submissions should be sent to gorm@cbs.dtu.dk (Anders Gorm Pedersen). The manuscript number should be clearly stated, and all relevant files (text, bibliography, figures, etc.) should be attached to the same email. Please note that the proceedings will not include colorfigures.

Please feel free to contact Anders Gorm Pedersen if you have any further questions regarding paper formatting or submission.

On behalf of the organizing committee,

Best regards,
Anders Gorm Pedersen

Word

Authors who submit in Word, can use the following template document to check whether the formatted manuscript meets the length limitations of max 9 pages.

If you submit in Word then please also send us any figures as separate files (preferably in encapsulated postscript, but other picture formats can also be used).

Latex

Here is a collection of files that you should use when formatting your paper: 

Style and class-files:


The bioinformatics logo:


Empty Latex-file ready to be filled in:


An example of a finished manuscript:


An encapsulated postscript file used in example.tex:


An example bibliography file that is used in example.tex:

You may already have some of the .sty and .bst files in your Latex-distribution.

Instructions

Simply cut'n'paste your manuscript into the empty template-file "template.tex", adding information to the empty braces (names and adresses of authors, email, name of bibliography file, etc. ). Note that instead of the standard "article" class, we use the special "gen-bioinformatics" class. The corresponding class-file ("gen-bioinformatics.cls") has a few special tags in the title and abstract. The use of these should be relatively clear from the example latex file ("example.tex"), but a brief explanation is also included below. The class file contains all necessary information about margins, paper size, column width etc. so you do not need to set any of these parameters yourself.

You can test the functionality of the latex files by saving all of them to one directory and then executing: 

latex example
bibtex example
latex example
dvips example

This should result in creation of a postscript file with the name 

example.ps
formatted according to the Bioinformatics guidelines.

(The text in "example.tex" is by Charles Darwin and Alfred Wallace from the Journal of the Proceedings of the Linnean Society, Zoology 3: 45-62. 20 Aug 1858, and was stolen from this excellent website: http://www.inform.umd.edu/PBIO/darwin/darwin01.html).

Submitting latex files

Please submit the following files:

  • .tex (the manuscript)
  • .bib (any bibliography files)
  • .bbl (processed bibliography)
  • .ps (your formatted manuscript)
  • .eps (figures - preferably in encapsulated postscript)

Please submit your final manuscript to gorm@cbs.dtu.dk (Anders Gorm Pedersen). The manuscript number should be clearly stated, and all relevant files (text, bibliography, figures, etc.) should be attached to the same email.

Special tags used with the bioinformatics class:

 
\Sup{1}
Explanation: \Sup{1} turns on superscripts for contact information. \Sup{0} turns them off. 

 
\verso{C.R.Darwin \etal}
Explanation: name of first author for header 

 
\recto{Natural Selection}
Explanation: running title for header 

 
\author[1]{\pfnm{Charles}  \pinit{R.}  \psnm{Darwin}}
Explanation: first name, middle initial, and surname of author number one. (The number in brackets will appear as a superscript, if superscripts are turned on with \Sup{1}). 

 
\address[1]{\porgdiv{Evolutionary Biology Group}
 \porgname{Linnean Society of London}
 \pstreet{Down House, Luxted Road}
 \pcity{Downe}
 \postcode{BR6}
 \pcnty{UK}}
Explanation: organization name and address for author number one. 

 
\begin{subabstract}[Contact]
\email{darwin@evolution.ac.uk}
\end{subabstract}
Explanation: email of corresponding author.

Inserting graphics

To insert encapsulated postscript files you must do two things:

  1. add the command "\usepackage{graphics}" in the document preamble.
  2. use the command "\includegraphics{filename}" to insert the eps-file.

The "graphics" package was released with LaTeX2e in 1994. It is a replacement for older TeX macros, and the latex packages "epsf", "psfig", and "epsfig". It also includes commands for scaling, rotation etc. More information can be found here:

Graphics are usually used within figure environments. The following example will include the eps file "darwin.eps", resized to have the width of a single column and a proportionally resized height: 


\begin{figure}
  \resizebox{\columnwidth}{!}{
     \includegraphics{darwin.eps}
  }   
  \caption{Charles Darwin (1809-1882)}
\end{figure}

Tables: do not use vertical separators

Bioinformatics (like many other journals) render tables entirely without vertical lines. Moreover, only three horizontal separators are usually used: one at the top of the table, one just below the column headings, and one at the bottom of the table. If you attempt to use vertical separators with the Bioinformatics class file they will appear as broken "dashes".

We suggest that you prepare the table with no vertical separators. (You can have a look at a recent issue of Bioinformatics if you want to see their table-style).

Here's an example of a table that spans two columns, fills the entire page, and uses only three horizontal separators: 


\begin{table*}
\caption{Correlation between trinucleotide scales}\label{tricorr}
\begin{tabular*}{\textwidth}{lccccc} 
\hline
     & B     & NP    & PNP    & SBS    & PBS   \\ 
\hline
B    & 1     & 0.272 &-0.0079 & -0.025 & 0.022 \\ 
NP   &       &  1    & 0.161  & -0.766 & 0.753 \\ 
PNP  &       &       & 1      & -0.123 & 0.186 \\ 
SBS  &       &       &        &    1   &-0.985 \\         
PBS  &       &       &        &        & 1     \\ 
\hline   
\end{tabular*}
\end{table*}
Note the use of "starred" environments. The \begin{table*} environment makes the table span two columns. The \begin{tabular*} environment adds an extra optional parameter specifying the width of the table. In this example the parameter is set to the value \textwidth, meaning the table will take up the entire width of the page.

Online resources for LaTeX:

This page has been created by Anders Gorm Pedersen and Johanne Keiding.
It is maintained by Anders Gorm Pedersen
gorm@cbs.dtu.dk   Phone: +45 45 25 24 84   Fax: +45 45 93 15 85

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