Instructions for Authors, ISMB02 Proceedings


When accepted by the editors, authors should send the files of the final copy to the Proceedings Production office at the ftp site link on the Paper Submission page . If it is necessary we may request one hard copy of the manuscript and figures. The files are used for typesetting, and most Macintosh or PC-based word processing packages, including LATEX, are acceptable (with images printed to a postscript file). Authors are also required to complete and submit a signed copyright transfere form, see link to PDF file on


Authors please note that software should be available for a full TWO YEARS after publication of the manuscript.

Manuscript Length

In contrast to what we wrote to you in our acceptance letter, we do NOT need the camera-ready version.  Instead, we need the manuscript in on of the formats
specified below.  The final publication must occupy no more that 9 journal pages, including all text, figures and tables.  Submission in LaTex using the templates supplied at  will give you an excellent estimate.  If you are submitting in another format, Word for example, the rule of thumb is that 2 journal pages will hold 1400 words or one figure plus 1000 words.  If you need to submit in some format other than LaTex or Word, contact to discuss the submission.  When submitting, please send copies fo all figures as individual EPS format files in addition to the mansucript.  If submitting as a LaTex file, please include an ASCII text file with the text of the manuscript as well as .tex, .dvi. and a PDF or PS view of the final paper.  Please direct all questions regarding submission to

Sections of the manuscript

Please subdivide manuscripts into the following sequence of sections:

Title page, Abstract, Introduction, System and methods, Algorithm, Implementation, Discussion, References.

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.

Structured Abstract (see recent issues of journal for examples)

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...}}.

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. Papers will not be accepted if the software is not freely available. 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, preferably an institution e-mail address.

Supplementary Information: Links to figures/data on web pages or to files located on the OUP 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 reimplemented. 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 and enclosed by round brackets; 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 author's 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:
Myasnikova,E., Samsonova,A., Kozlov,K., Samsonova,M. and Reinitz,J. (2000) Registration of the expression patterns of Drosophila segmentation genes by two independent methods, Bioinformatics, 17 ,3-12.
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.
A maxium of 10 authors' names should be included in the citation; if there are more than ten authors, replace those names with "et al."

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 included separately from the text and 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.


All figures should be referred to in the text as Figure 1 etc. They should follow the main body of the text and their approximate final positions indicated in the margin of the text. Where available, the figures should be submitted in electronic form e.g. as a PDF file. Please label figures lightly on the back with number, first author and manuscript title. An arrow should be used to indicate the top of the figure. All figures should be formatted to fit into, or be reduced to, a single (86 mm) or double (178 mm) column width. Figure legends should appear on a separate page.

Web screen dumps: Authors are encouraged to avoid screen dumps as figures, unless really necessary - a table or figure is much preferred by the editors. All figures 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 relabelled. Any lettering or text should be in proportion with the rest of the figure.

Photographs: 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: Inclusion of colour plates is subject to a special charge of £750. The online version of the paper will be in colour.


In general, the journal follows 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 Demarc et al. (1966) Genetics,54, 61-76.


TEX-based manuscripts should be produced using the LATEX article style format only. The document style options used must indicate two-column text with 86 mm column widths. The final version should be supplied containing .tex, .dvi, .ps and ascii files (Templates can be downloaded from Hard copies of both text and figures should be supplied in the conventional way. Authors will receive proofs.

Page charges

Page charges are NOT levied.


Authors are sent page proofs. These should be checked immediately and returned to the ISMB02 Proceedings Production Staff by express post, telephone or fax, to:
Warren Gallin
ISMB02 Proceedings Production
Department of Biological Sciences
University of Alberta
Alberta    T6G 2E9
Tel: 780-492-1285; Fax: 780-492-9234
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.


There are no free reprints from the Proceedings.  The Proceedings will be mounted for public access on the web site fo the journal Bioinformatics.  Reprints can be ordered by the authors when they return final page proofs.  A pricing schedule will be mounted soon.