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Accepted Papers
Submission Guidelines for Accepted Papers

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Bioinformatics Journal
SIGSIM: Systems Biology of E.coli

Detailed ACCEPTED Paper Submission and Formatting Guidelines
Please Note - The following instructions are ONLY for papers ACCEPTED for inclusion in OUP's ISMB 2003 Proceedings.

Submission Guidelines

When to submit

  • Final version of accepted manuscripts: March 6, 2003
  • You will receive page proofs: by April 11, 2003
  • You will return page proofs: by April 13, 2003
How to submit
  • You will submit the final version of your accepted paper using CyberChairPro.
  • You will return your corrected page proofs by express post (preferred) or fax to the address below. Or you may scan your corrected proofs and send them by email as a JPEG file. At the same time, you will also express mail the ORIGINAL of your completed copyright form to the address given below.
    Timothy Bailey
    Mathematics Department
    Bldg. 69, room 720
    University of Queensland
    Brisbane, Qld 4072
    Email:; Tel: +61 7 3365 7570; FAX: +61 7 3365 6136
What to submit
You will need to submit:
  • The compiled version of your paper--postscript or PDF file--and,
  • The source files for your paper:
    • MSWord file and all figure files (.eps files), or
    • all LaTex source files and figure files (.tex,.eps, etc) needed to compile your paper, tar-ed into one file.
Formatting Guidelines

LaTeX style sheets for submissions

Download the files as a tar file here. Download the files as a bin-hex file here. Please Note - Because the LaTeX style sheets use proprietary fonts, you will see many non-fatal warnings when you compile your document. In our experience, you may safely ignore these font-related warnings.

MS Word template for submissions
Download an MSWord Sample Document here (.doc file) and an MSWord Document Template here (.dot file). To download the files in zipped formats, please select one of the following files (based on your OS zip preferences):, template.sit.hqx, or template.sit. Please Note: Some users have had problems downloading the MSWord template using Netscape. Please try downloading it using Internet Explorer if you experience difficulties.

Title Page
The title should be short, specific and informative, avoiding if possible version number and the words: tool, package, application, software (and similar). The surname and initials of each author should be followed by his/her department, Institution, city with postal code and country. Any changes of address may be added to the footnotes. The author to whom offprint requests are to be sent should be indicated by an asterisk and the footnote 'To whom correspondence should be addressed'. Please provide a running head of not more than 50 characters. Up to five key words should be supplied to assist with the compilation of the annual Subject Index.

Structured Abstract
Abstracts are structured with a standard layout such that the text is divided into sub-sections under the following five headings: Motivation, Results, Availability, Contact and Supplementary Information. In cases where authors feel the headings inappropriate, some flexibility is allowed. The abstracts should be succinct and contain only material relevant to the headings. A maximum of 150 words is recommended. If internet hyperlinks are available for any part of the abstract, then this should be given in the form of 'clickable text', i.e.{{http://www...}}. (See recent issues of Bioinformatics for examples.)
  • Motivation
    This section should specifically state the scientific question within the context of the field of study.

  • Results
    This section should summarize the scientific advance or novel results of the study, and its impact on computational biology.

  • Availability
    This section should state software availability (academic or commercial) if the paper focuses mainly on software development or on the implementation of an algorithm. Examples are: free availability over the internet on WWW or ftp server; available on request from the authors; or available as a commercial package. The complete address (URL) should be given. In the electronic version of the journal, URLs will appear as active hyperlinks. Software that is the main focus of the paper should also be available to the referees. Where possible authors are encouraged to place their academic software on the EMBL file server (send E-mail to or the Indiana University software repository (

  • Contact
    Full electronic mail address to be given.

  • Supplementary Information
    Links to figures/data on web pages or to files located on the Oxford University Press server. These links can point to specialised details that are of interest to small audiences.

Introduction, Systems and Methods, Algorithm, Implementation, Discussion and Conclusion
These should conform to standard scientific reporting style. Previous work in the field should be mentioned. Sufficient information should be given so that an application can be re-implemented. A test data set and results must be provided (where appropriate).

Authors are responsible for the accuracy of the References. Published articles and those in press (state the journal which has accepted them) may be included. In the text, a reference should be cited by author and date; not more than 2 authors may be cited per reference; if there are more than 2 authors use et al. References must NOT be numbered. At the end of the manuscript, the citations should be given in alphabetical order, with the authors surname followed by the initial. References should include in the following order: author name(s), year, paper title, journal title, volume number, inclusive page numbers. The name of the journal should be abbreviated according to the World List of Scientific Periodicals. Book references should also include the editors and the name and address of the publisher. References should therefore be listed as follows:

Bryce,C.F.A. (1982) Rapid nucleic acid sequencing methods - alternative approaches to facilitating learning. J. Biol. Educ., 16, 275-280.
Soll,D. and Roberts,R.J. (1984) The Applications of Computers to Research on Nucleic Acids II Part 2. IRL Press, Oxford.
Lonsdale,D.M., Hodge,T.P. and Stoehr,P.J. (1984) A computer program for the management of small cosmid banks. In Soll,D. and Roberts,R.J. (eds), The Applications of Computers to Research on Nucleic Acids II Part 2. IRL Press, Oxford, pp. 429-436.

Personal communications (J.Smith, personal communication) should be authorized by those involved in writing, and unpublished data should be cited as (unpublished data). Both should be used as sparingly as possible and only when the unpublished data referred to is peripheral rather than central to the discussion. References to manuscripts submitted but not yet accepted should be included in the list of references.

These should be included at the end of the text and not in footnotes.

Tables should be placed in the text where you want them to appear be be numbered consecutively. Tables should be self-explanatory and include a brief descriptive title. Footnotes to tables should be indicated by lower case letters but should not include extensive experimental detail.

Figures should be placed in the text where you want them to appear be be numbered consecutively. All figures should be referred to in the text as Figure 1 etc. Where available, the figures should be submitted in electronic form e.g. as an encapsulated postscript (EPS) file.

Web Screen Dumps
These should have a white background to increase the contrast between the illustration and the background, so that the figure is easy to read.

Line illustrations
These must be of sufficient quality for publication as submitted, i.e. clear, sharp, clean and of even density. Figures will NOT be redrawn or relabeled. Any lettering or text should be in proportion with the rest of the figure.

These must be of sufficient quality with respect to detail, contrast, and fineness of grain to withstand the unavoidable loss of contrast inherent in the printing process.

Colour plates
The online version of the paper will be in colour. Inclusion of colour plates in the printed version is subject to a special charge. Contact the Production Editor for details:

Production Editor (Bioinformatics)
Oxford University Press
Journals Department
Academic Division
Great Clarendon Street
Oxford OX2 6DP>
Tel: +1865 556767; Fax: +1865 267773

In general, submitted papers should follow the conventions of the CBE Style Manual(Council of Biology Editors, Bethesda, MD, 1983, 5th edition). Follow Chemical Abstracts and its indices for chemical names. For guidance in the use of biochemical terminology follow the recommendations issued by the IUPAC-IUB Commission on Biochemical Nomenclature, as given in Biochemical Nomenclature and Related Documents, published by the Biochemical Society, UK. For enzymes, use the recommended name assigned by the IUPAC-IUB Committee on Biochemical Nomenclature, 1978, as given in Enzyme Nomenclature, published by Academic Press, New York, 1980. Where possible, use the recommended SI units. Genotypes should be italicized. Phenotypes should not be italicized. For bacterial agents nomenclature follow Demerc et al. (1966) Genetics, 54, 61-76.

Page Charge
Page charges are NOT levied.

Authors of accepted papers will be sent page proofs. Page proofs will be sent by email to the contact author as a PDF file. These should be printed out and checked immediately. Mark any typographical or layout errors on the printed copy and send it to the address given above. Please Note - Authors must restrict changes at this stage to correction of typographical and layout errors. A charge is made to authors who insist on amendment within the text at the page proof stage.

It is a condition of publication in Bioinformatics that authors assign copyright. A completed copyright form must be returned with the proofs. This ensures that requests from third parties to reproduce articles are handled efficiently and consistently and will also allow the article to be as widely disseminated as possible. In assigning copyright, authors may use their own material in other publications provided that Bioinformatics is acknowledged as the original place of publication.