ALL ARTICLES MUST BE SUBMITTED ONLINE. Once you have prepared your manuscript according to the Instructions below please visit the online submission website. Instructions on submitting your manuscript online can be viewed here.
If you wish to submit a revised version of a manuscript that was originally submitted before 9th July 2003, when Bioinformatics started using an online submission system, please submit it in the normal way at http://bioinformatics.manuscriptcentral.com. Please include a covering letter stating that the manuscript is a revised version of an existing submission, giving the original title of your manuscript (if changed), and detailing your responses to the reviewers comments. If possible, please also quote the reference number from your original submission.
Please read these instructions carefully and follow them strictly, so that the publication process is efficient and as rapid as possible. The Editors reserve the right to return submissions that are not prepared in accordance with the following instructions.
Scope
Bioinformatics provides a forum for the exchange of information in the fields of computational molecular biology and post-genome bioinformatics, with emphasis on the documentation of new algorithms and databases that allows the progress of bioinformatics and biomedical research in a significant manner. The following categories of paper may be submitted for publication.
Papers (3-8 pages) Original papers that describe new research developments in computational molecular biology, for example: models, algorithms, software involving new methods, biological databases and network information services, and their impact on molecular biology or computer science. Actual biological data, as opposed to purely simulated data, must be used.
Paper Sections (3-8 pages) Sets of papers on a specific subject, e.g. `Policy' and `Ontology' are published in a section. Policy papers cover a broad range of issues related to funding or education. Ontology covers the design and implementation of ontologies in bioinformatics. Sections may also include selected papers from a conference, usually handled by guest editors.
Reviews (3-8 pages) Most review papers are commissioned, although the editors welcome suggestions from prospective authors who should in the first instance submit a draft.
Discovery Notes (4 pages maximum) Discovery notes are papers intended for the reporting of biologically interesting discoveries using computational techniques. Topics may include sequence motif detection, structural similarities, gene structure prediction, comparative genomics, biomolecular networks and other aspects of computational molecular biology.
Application Notes (2 pages maximum) Applications Notes are short descriptions about novel software or new algorithm implementations, databases and network services (web servers, and interfaces), strictly limited to 2 printed pages (approx. 1400 words or 1000 words plus one figure). The software or data should be freely available. Because two pages is too short to contain all the information on the topic of the Application Note, authors are advised to post a more detailed description on their web page.
If describing a server, the server should function well at the time of refereeing, and be capable of working well for at least 2 years after publication. If describing software, the software should run well, and should not be exclusively for Windows 95 or 98 with excell 3.1 and netscape 4.6.5, but should run under nearly all conditions on a wide range of machines. Additionally, there should be some relevance.
The difference between Applications Notes and regular papers is that the former are notes about applications and are almost exclusively an `exercise in software development', the latter is about research. The `Availability' is an important aspect of Application Notes, more so than for research articles, which often explain an idea or principle which might, or might not have been worked out in a program or webserver, etc.
Page charges
For Original articles - ?00/$165 per excess page (over 8 published pages)
For Discovery notes - ?00/$165 per excess page (over 4 published pages)
For Application notes - ?00/$165 per excess page (over 2 published pages)
Preparation of manuscripts
The Executive Editor, associate editors and 'guest' editors, in conjunction with the editorial board and other invited referees, handle the full editorial process.
Submission
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. 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. Enclose copies of any such permission letters with your paper.
Papers must be clearly and concisely written in English and within the recommended length. 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.
Pre-screening
Papers received in the Bioinformatics office undergo a pre-screening process to increase the efficiency of the publication process. Papers that are considered to be of minor importance to the readership of the journal are not reviewed.
Refereeing
The papers are sent out to two (or three/four) referees, who agree to undertake the refereeing within a short period. Authors should normally carry out the revision within three weeks. An interactive reviewing form for referees is available at http://bioinformatics.manuscriptcentral.com as part of the journals online submission site
Acceptance
When accepted by the editors, authors may be asked to send the files of the final copy to the editorial office.
These files are used for typesetting and should be either
- a text (most Macintosh or PC-based word processing) and a .pdf file or
- LaTeX files (including the postscript file) with the images printed to a postscript file and a .pdf file.
- A licence to publish is required to be completed by the authors and this is handled by the publisher.
Software
Authors please note that software should be available for a full 2YEARS after publication of the manuscript.
Sections of the manuscript
Please subdivide manuscripts into the following sequence of sections, according to the type of paper:
Original papers: Title page, Structured Abstract, Introduction, System and methods, Algorithm, Implementation, Discussion, References.
Reviews: May be in a format best suited to subject matter, but should include Title page, Structured Abstract, Text, References. For clarity the main body of text should be sub-divided into sections.
Applications notes: Title page, Short Structured Abstract, Text.
Discovery notes: The description of the analysis can be up to 4 pages long (2000 words) including one/two figures. An abstract is not required. Sequences must be freely available in the database and the results of the analyses should not have been published elsewhere.
Please ensure that the URL (ftp and www address) conforms to the standard, e.g. http://www.ebi.ac.uk/ and ftp://iubio.bio.indiana.edu.
Authors are advised that specialized details in papers that are of interest to small audiences should be put on to the author’s web page and linked to the supplementary information section in the structured abstract.
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)
Original papers
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 Software@embl-ebi.ac.uk) or the Indiana University software repository (ftp://iubio.bio.indiana.edu/).
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.
Applications Notes
Abstracts for Applications Notes are much shorter than those for an Original paper. They are structured with four headings: Summary, Availability, Contact and Supplementary Information.
Summary: This section should summarize the purpose/novel features of the program in 1 or 2 sentences.
Availability: Availability of software and URL (ftp or WWW address) for internet access to be stated.
Contact: Full E-mail address to be supplied, preferably an institution 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).
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 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.
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 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.
Figures
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 postscript 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: The editors prefer tables or figures instead of web screen dumps. 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 figures: Inclusion of colour figures is subject to a special charge (?00/US$650 to print a figure in colour).
Online only colour figures: Colour figures can be uploaded as Supplementary Data at no extra charge. Please contact the Production Editor (Saraswathy Rajagopalan, saraswathy.rajagopalan@oupjournals.org) at OUP for details.
Conventions
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.
LATEX
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, .ps and ascii files. Hard copies of both text and figures should be supplied in the conventional way. Authors will receive proofs.
Proofs
Authors are sent page proofs. These should be checked immediately and returned to the Publishers by express post, telephone or fax, 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
A charge is made to authors who insist on amendment within the text at the page proof stage.
Licence to Publish
It is a condition of publication in Bioinformatics that authors grant an exclusive licence to Oxford University Press. 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. As part of the licence agreement, Authors may use their own material in other publications provided that Bioinformatics is acknowledged as the original place of publication and Oxford University Press as the Publisher
Offprints
Authors will receive electronic access to their paper free of charge. Printed offprints may be purchased in multiples of 100. Rates are indicated on the order form which must be returned with the proofs. Orders for printed offprints received after the deadline will be subject to a 100% surcharge.
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