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ISMB/ECCB 2004: SUBMISSION GUIDELINES AND FORMATTING INSTRUCTIONS FOR ACCEPTED LONG PAPERS
The following instructions are ONLY for papers ACCEPTED for inclusion in OUP’s ISMB/ECCB 2004 Proceedings.
WHEN TO SUBMIT
  • Final version of accepted manuscripts: MONDAY MARCH 15, 2004, 12:00 Midnight Hawaii-Aleutian Standard Time (see www.timeanddate.com/worldclock/ to find out how this compares to your local time)
  • You will receive page proofs: between MONDAY 3 MAY AND MONDAY 10 MAY
  • You will return page proofs: WITHIN 48 HOURS OF RECEIPT (EXCLUDING WEEKENDS). IF YOU DO NOT RETURN YOUR PROOF CORRECTIONS WITHIN 48 HOURS YOUR PAPER WILL BE PRINTED AS IS.
HOW TO SUBMIT

You will submit the final version of your accepted paper using CyberChair Pro at http://www.ismbconf.org/papers/submit/

You will return your corrected page proofs by fax to the number below. Alternatively you may scan your corrected proofs and send them by email as a JPEG or a PDF file.

Veena Krishnan
NewGen Imaging Systems
Chennai 600041, India
Tel: (00 9144) 2445 2041/2443 0996/24430676 (India)
Fax: +44 (0)870 705 3303 (UK number) OR (001) 646 349 3845 (US number)
email: bioinformatics@newgenimaging.com

You will also express mail the ORIGINAL of your completed copyright form, click here to download the form as a pdf, to:

Production Editor (Bioinformatics)
Oxford University Press
Journals Department
Academic Division
Great Clarendon Street
Oxford OX2 6DP
UK

Tel: +44(0)1865 556767
Fax: +44(0)1865 353332

email: bioinformatics@oupjournals.org

WHAT TO SUBMIT

You will need to submit:

  • The compiled version of your paper – as a PDF file – AND
  • The source files for your paper: EITHER 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.
CONDITIONS OF ACCEPTANCE
  • Publication status
    Submission of a paper implies that it reports unpublished work, that is not under consideration for publication elsewhere and that, if accepted, it will not be published elsewhere in the same form, either in English or in any other language, without the consent of the publisher.
  • Revisions to original submission
    Authors must not significantly alter the content or scope of their initial submission except to address the reviewers' comments or to improve the English.
  • Quality and length
    Papers must be clearly and concisely written in English and within the recommended length – i.e. NO MORE THAN 8 PAGES USING THE TEMPLATES PROVIDED (this is equivalent to 10 pages of single-spaced 12-point text). In the interests of speed, manuscripts are not extensively copyedited and authors are requested to check their texts carefully before submitting them so that proofs will require only correction of typographical errors.
  • Copyright permissions
    If previously published tables, illustrations or more than 200 words of text are to be included, then the copyright holder's written permission must be obtained. WE CANNOT ACCEPT YOUR PAPER UNLESS SUCH PERMISSIONS ARE RECEIVED BY 1 APRIL 2004. Send copies of any such permission letters to:

    Production Editor (Bioinformatics)
    Oxford University Press
    Journals Department
    Academic Division
    Great Clarendon Street
    Oxford OX2 6DP
    UK
    Tel: +44(0)1865 556767
    Fax: +44(0)1865 353332
  • Copyright license agreement
    A licence to publish must be completed by the authors and this is handled by the publisher. RECEIPT OF A COMPLETED COPYRIGHT LICENSE FORM BY 1 APRIL 2004 IS A CONDITION OF FINAL ACCEPTANCE. Send the ORIGINAL signed copyright license form (click here to download the form as a pdf) to:

    Production Editor (Bioinformatics)
    Oxford University Press
    Journals Department
    Academic Division
    Great Clarendon Street
    Oxford OX2 6DP
    UK

    Tel: +44(0)1865 556767
    Fax: +44(0)1865 353332
FORMATTING GUIDELINES

LaTeX style sheets for submissions

You must use one of the templates provided to format your paper; failure to do so will prevent use from accepting your paper. Questions and issues regarding these templates should be directed to bioinformatics@newgenimaging.com.

Download the files as a .rar file here
Download the files as a .zip file here
Download the files as a .bin.hex file here

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 document template (.dot file) click here to download
View the document template as a pdf click here to download

To download the files in zipped formats, please select one of the following files (based on the zip preferences of your operating system):
Word_template.zip
Word_template.tar
Word_template.sit.hqx

NOTE: Some users have had problems downloading the MSWord template using Netscape. Please try downloading it using Internet Explorer or another browser if you experience difficulties.

First 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 Software@embl-ebi.ac.uk) or the Indiana University software repository (ftp://iubio.bio.indiana.edu/).

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 specialized 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).

References
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.

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

Tables
Tables should be placed in the text where you want them to appear and should 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
All figures should be referred to in the text as Figure 1 etc. If you use the LaTeX template supplied, figures should be placed in the main text in their approximate final positions. If you use the MSWord template supplied, please indicate the approximate positions in the text where your figures should be inserted and supply your figures separately. Where available, the figures should be submitted in electronic form as encapsulated postscript files. Hard copies of figures should be sent only as a last resort. If you must do this, 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, and send them by express mail to:

Veena Krishnan
NewGen Imaging Systems
Chennai 600041, India
Tel: (00 9144) 2445 2041/2443 0996/24430676 (India)
Fax: +44 (0)870 705 3303 (UK number) OR (001) 646 349 3845 (US number)
email: bioinformatics@newgenimaging.com

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: Tables or figures are preferable to web screen dumps. All screen dumps 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. A minimum screen resolution of 300 dpi at the printed size is recommended for bitmap files; vector files (e.g. .eps) are preferable. Figures will NOT be redrawn or relabeled. 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. A minimum screen resolution of 1200 dpi at the printed size is recommended.

Colour plates
The online version of the paper will be in colour.
NOTE: OUP levies a charge of US $655 for any figures printed in colour. If you wish to have any figures printed in colour, you MUST pay these charges. Authors may pay for colour plates via credit card at: https://www.iscb.org/ismb_color.php. ANY AUTHOR WHO HASN’T PAID THEIR COLOUR CHARGES BY 9 APRIL WILL HAVE THEIR FIGURES PRINTED IN BLACK AND WHITE.

If for any reason you are unable to pay by credit card over the Internet, please fax your completed order form with credit card information to 001 619 374 2890.

Conventions
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.

Proofs
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.

Copyright
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.

Offprint orders
Authors may order offprints of their papers from OUP. Click here to download the Offprint Order Form as a pdf.