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# Bioinformatics

# Instructions to Authors

OPEN ACCESS OPTION FOR AUTHORS

Open access

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, along with the compulsory Word and LaTex* templates, are available. [*If you use bibtex, please use the bibliography style named natbib.bst]. Help with inserting figures into the templates may be found at http://office.microsoft.com/en-gb/assistance/HA010547971033.aspx.

Please read these instructions carefully and follow them strictly so that the publication process is efficient and as rapid as possible. The Editors and the Editorial Office 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.
Upon submission you will be asked to provisionally select one of the following categories for your manuscript:

- Genome analysis
- Sequence analysis
- Phylogenetics
- Structural bioinformatics
- Gene expression
- Genetic and population analysis
- Systems biology
- Data and text mining
- Databases and ontologies

Detailed Scope Guidelines are also available for the above categories.

## TYPES OF MANUSCRIPT

The following types of paper may be submitted for publication.
Original Papers (up to 7 pages; this is approx. 5000 words - in response to a rapid increase in submissions and papers published the Bioinformatics page layout has been updated in February 2005 resulting in considerable space savings).
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.

Discovery Notes(up to 4 pages, this is approx. 3000 words)
Discovery notes report biologically interesting discoveries using computational techniques. Topics may include sequence motif detection, definition of new domains, structural similarities, gene structure prediction, comparative genomics, biomolecular networks and other aspects of computational molecular biology.
The results presented should present new discoveries, bringing insight to a relevant biological problem, and not be the simple extension of current knowledge. The results are expected to proceed from the specialized use of tools, methods, and databases. The inclusion of experimental results is considered very positively.

Application Notes (up to 2 pages; this is approx. 1300 words or 1000 words plus one figure)
Applications Notes are short descriptions of novel software or new algorithm implementations, databases and network services (web servers, and interfaces). Software or data must be freely available to non-commercial users. Availability must be clearly stated in the article. Authors must also ensure that the software is available for a full TWO YEARS following publication. Web services should not require mandatory registration by the user. Additional Supplementary data can be published online-only by the journal, or may be provided on the author's web site. This supplementary material should be referred to in the abstract of the Application Note.
If describing software, the software should run under nearly all conditions on a wide range of machines.

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.

Letters to the Editor
Bioinformatics publishes "letters to the editors" on the broad range of topics covered by the journal, including political, technical and scientific analyses of issues related to bioinformatics and computational biology. The letters can also include the discussion of papers published by the journal.

Conference Papers
Bioinformatics considers proposals for publishing conference proceeding papers, as supplementary issues or as special sections of the journal. Please be sure to include the following information in your proposal:

- What is the theme of the conference and submitted papers?
- What numbers of papers are expected to be submitted and published?
- What peer review process will be put in place by the conference organisers to recommend papers for publication in the journal?
- How many delegates are expected to attend the conference?
- Assurance that the papers proposed for publication have not and will not be published elsewhere prior to publication in Bioinformatics, or afterwards without the permission of the journal’s publisher.

## PAGE CHARGES

The journal strongly discourages authors from exceeding the page limits. Manuscripts exceeding the recommended limits may be rejected without review - for example manuscripts that exceed the limit by 20% or more are usually returned by the Editorial Office immediately. In the event that a manuscript does exceed the page limits we make the following charges:

- Original papers: £100/$190 per excess page (over 7 published pages)
- Discovery notes: £100/$190 per excess page (over 4 published pages)
- Application notes: £100/$190 per excess page (over 2 published pages)

To help you estimate the page length of your manuscript, please use the provided Word and LaTex author templates for submissions.

## GENERAL POLICIES

Previous publication
Submission of a manuscript implies that it reports unpublished work, that it 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. Authors should provide the references of similar work that they have already published, or which is currently under consideration by another journal. If the work has previously been presented at a conference, authors should provide details in the covering letter. The journal will consider publication of work that has previously been presented as either a short abstract or poster at a conference, but not as a full paper. 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. Include copies of any such permission letters with your paper.

Authorship
All persons designated as authors should qualify for authorship. Each author should have participated sufficiently in the work to take public responsibility for the content. Authorship credit should be based on substantial contribution to conception and design, execution, or analysis and interpretation of data. All authors should be involved in drafting the article or revising it critically for important intellectual content, and must have read and approved the final version of the manuscript.

Other than in exceptional circumstances the Journal does not allow addition or removal of author names after submission. A satisfactory explanation for any proposed changes in authorship will be required. We will also require a letter of consent from any person whose name has been removed indicating that they agree to the removal of their name from the author list. Owing to the complexity of these rules we strongly advise authors to fix the author list before submission and not to attempt to make changes later.

Conflicts of Interest
At the point of submission, Bioinformatics policy requires that each author reveal any financial interests or connections, direct or indirect, or other situations that might raise the question of bias in the work reported or the conclusions, implications, or opinions stated - including pertinent commercial or other sources of funding for the individual author(s) or for the associated department(s) or organization(s), personal relationships, or direct academic competition. When considering whether you should declare a conflicting interest or connection please consider the conflict of interest test: Is there any arrangement that would embarrass you or any of your co-authors if it was to emerge after publication and you had not declared it?

As an integral part of the online submission process, Corresponding authors are required to confirm whether they or their co-authors have any conflicts of interest to declare, and to provide details of these. If the Corresponding author is unable to confirm this information on behalf of all co-authors, the authors in question will then be required to submit a completed Conflict of Interest form to the Editorial Office. It is the Corresponding author’s responsibility to ensure that all authors adhere to this policy.
If the manuscript is published, Conflict of Interest information will be communicated in a statement in the published paper.

Software
If the manuscript describes new software tools or the implementation of novel algorithms the software must be freely available to non-commercial users at the time of submission. Availability must be clearly stated in the article. Authors must also ensure that the software is available for a full TWO YEARS following publication. The editors of Bioinformatics encourage authors to make their source code available and, if possible, to provide access through an open source license (see www.opensource.org for examples). Authors should make every effort to use URLs that will remain stable.

Supporting Data
All data on which the conclusions given in the publication are based must be publicly available. Bioinformatics fully supports the recommendations of the National Academies regarding data sharing (see Board on Life Sciences, Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences. Available at www.nap.edu/books/0309088593/html). If the analysis is based on new datasets, authors are encouraged to submit these to appropriate public repositories. In particular, microarray data should be submitted to one of the recognized public repositories in a MIAME compliant way (see C. A. Ball et al., Submission of Microarray Data to Public Repositories. PLoS Biology, 2, e317). In any event, all data should be made available to the journal for the purpose of peer review. If your manuscript describes a three-dimensional model of a protein that has been manually built, you should deposit it in the PMDB database (http://www.caspur.it/PMDB, see also NAR 34, 306-309). The database will return a unique identifier which you can include in your manuscript, thereby allowing readers to have access to your model.

Supplementary Data
Only directly relevant material should be included in the full text of manuscripts. Supporting materials and Appendices which are not essential for inclusion in the full text, but would nevertheless benefit the reader, can be published as online-only Supplementary Data. Supplementary Data should be submitted for review, in a separate file from the manuscript. Authors should ensure that the Supplementary Data is referred to in the main manuscript at an appropriate point in the text. It cannot be altered or replaced after the paper has been accepted for publication. For the purpose of long-term preservation of this information, we require supplementary material to be published and stored on our website. It is acceptable for authors to post supplementary material on their own website in addition to this, but not in place of this.

Pre-screening
At present the journal accepts 20% of manuscripts that are submitted.
Therefore, to increase the efficiency of the publication process, manuscripts received in the Bioinformatics office undergo a pre-screening process.
Papers that are considered to be of low significance to the readership of the journal are returned without review.

The review process
At least four recommended reviewers must be provided by the author at the submission stage. A manuscript will not be assigned to an Associate Editor until this information has been provided. Manuscripts that pass the pre-screening phase are sent to two or more referees, who agree to undertake the refereeing within a short period. Authors should normally carry out any revision within four weeks. Revisions that are not received within 90 days will be treated as new submissions.

Acceptance
When accepted by the editors, authors may be asked to send the files of the final manuscript 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 Gen-bioinformatics.cls., bib, .bst and .ps files) 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.

Because accepted manuscripts are published online following acceptance, it is important that the final version of the manuscript supplied by the author contains no information regarding the citation information (volume, issue, year) or a copyright line as this will mislead readers.

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. Information about the New Creative Commons licence can be found here.

Author Self-Archiving/Public Access policy from May 2005
For information about this journal's policy, please visit our Author Self-Archiving policy page

Scientific Misconduct
When dealing with potential cases of misconduct the journal follows the guidelines provided by the Committee on Publication Ethics (COPE).

Bioinformatics Advance Access
Bioinformatics Advance Access is the journal's system for the early online publication of articles ahead of the printed issue. Manuscripts will be published online as soon as possible after they have been accepted, with updates on a weekly basis. In order to achieve this rapid publication time, the accepted manuscript is published online before copyediting and formatting has been carried out. Appearance in Advance Access constitutes official publication, and the Advance Access version can be cited by a unique DOI (Digital Object Identifier). The accepted manuscript is then copyedited and typeset as normal, before print and online publication of the final version. Both versions of the paper continue to be accessible and citable.

## OPEN ACCESS OPTION FOR AUTHORS

Bioinformatics authors have the option, at an additional charge, to make their paper freely available online immediately upon publication, under the
Oxford Open initiative. After your manuscript is accepted, as part of the mandatory licence form required of all corresponding authors, you will be asked to indicate whether or not you wish to pay to have your paper made freely available immediately. If you do not select the Open Access option, your paper will be published with standard subscription-based access and you will not be charged.

For those selecting the Open Access option, the charges for Bioinformatics vary depending on the institution at which the Corresponding author is based (see below). Charges also vary depending on whether the paper is an Original Paper or an Application Note. Discovery Notes are charged at the same rate as Application Notes (please select Application Note on the online charge form for the purposes of Open Access).

ORIGINAL PAPERS - optional Oxford Open charges:
For a Corresponding author based at an institution with an online subscription to Bioinformatics:
Regular charge per paper - £800 / $1500
List B developing country charge* - £400 / $750
List A developing country charge* - £0 / $0
For a Corresponding author based at an institution that does not subscribe to the online journal:
Regular charge per paper - £1500 / $2800
List B developing country charge* - £750 / $1400
List A developing country charge* - £0 / $0

APPLICATION NOTES - optional Oxford Open charges:
For a Corresponding author based at an institution with an online subscription to Bioinformatics:
Regular charge per paper - £400 / $750
List B developing country charge* - £200 / $375
List A developing country charge* - £0 / $0
For a Corresponding author based at an institution that does not subscribe to the online journal:
Regular charge per paper - £750 / $1400
List B developing country charge* - £375 / $700
List A developing country charge* - £0 / $0
*Visit http://www.oxfordjournals.org/jnls/devel/ for list of qualifying countries

The above Open Access charges are in addition to any page charges and colour charges that might apply.
Orders from UK will be subject to a 17.5% VAT charge. For orders from the rest of the EU, we will assume that the service is provided for business purposes, please provide a VAT number for yourself or your institution and ensure you account for your own local VAT correctly.

If you choose the Open Access option you will also be asked to complete an Open Access charge form online. You will be automatically directed to the appropriate version of the form depending on whether you are based at an institution with an online subscription to Bioinformatics. Therefore please make sure that you are using an institutional computer when accessing the form. To check whether you are based at a subscribing institution please use the Subscriber Test link for Bioinformatics.

## MANUSCRIPT PREPARATION

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.

How to prepare text and figures

For guidelines on the types of documents that can be uploaded to the online submission system, please click here. Please note: This journal does not accept Microsoft Word 2007 documents at this time. Please use Word's "Save As" option to save your document as an older (.doc) file type.

Prepare your figures at publication quality resolution, using applications capable of generating high-resolution .tif files (1200 d.p.i. for line drawings and 300 d.p.i. for colour and half-tone artwork). The printing process requires your figures to be in this format if your paper is accepted and printed. For useful information on preparing your figures for publication, go to http://cpc.cadmus.com/da. For online submission, please also prepare a second version of your figures at low-resolution for use in the review process; these versions of the figures can be saved in .jpg, .gif, .tif or .eps format. For INITIAL submission, it is preferable that you insert the low-resolution versions of the figures and tables into the word processing but you can also upload these versions as separate files.

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 four pages long including one or two figures. Please include an abstract. Sequences must be freely available in the database and the results of the analyses should not have been published elsewhere.

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 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. If the manuscript describes new software tools or the implementation of novel algorithms the software must be freely available to non-commercial users. Authors must also ensure that the software is available for a full TWO YEARS following publication. The editors of Bioinformatics encourage authors to make their source code available and, if possible, to provide access through an open source license (see www.opensource.org for examples.
- Contact:Full email address to be given, preferably an institution email address.
- Supplementary information: Links to additional figures/data available on a web site, pr reference to online-only supplementary data available at the journal's web site.

Applications Notes
Abstracts for Applications Notes are much shorter than those for an Original Paper. They are structured with four headings: Summary, Availability, Copntact and Supplementary Information.

- Summary: This section should summarize the purpose/novel features of the program in one or two 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 additional figures/data available on a web site, or reference to online-only Supplementary data available at the journal's web site.

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 and enclosed by round brackets; not more than two authors may be cited per reference; if there are more than two 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, 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. et al. (2000) Registration of the expression patterns of Drosophila segmentation genes by two independent methods. Bioinformatics, 17, 3-12.
- Schäfer,J. and Strimmer,K. (2005) An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics, 21, 754-764.
- 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. Personal communications, unpublished results, manuscripts submitted or in preparation, statistical packages, computer programs and web sites should be cited in the text only, NOT included in the References section. References to manuscripts accepted for publication but not yet published should be included in the reference list as 'in press'.

Funding
Details of all funding sources for the work in question should be given in a separate section entitled 'Funding'. This should appear before the 'Acknowledgements' section. The following rules should be followed: the full official funding agency name should be given, i.e. ‘National Institutes of Health’, not ‘NIH’; grant numbers should be given in brackets; multiple grant numbers should be separated by a comma; agencies should be separated by a semi-colon; no extra wording like 'Funding for this work was provided by ...' should be used; where individuals need to be specified for certain sources of funding the following text should be added after the relevant agency or grant number 'to [author initials]'. An example is given here: ‘National Institutes of Health (CB5453961 to C.S., DB645473 to M.H.); Funding Agency (hfygr667789).’

Acknowledgements
These should be included at the end of the text and not in footnotes. Please ensure you acknowledge all sources of funding, see funding section above.

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. 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 (£350/US$600 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 bioinformatics@oxfordjournals.org 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.

Proofs
Authors are sent page proofs by email. These should be checked immediately and returned to the publishers by email or fax (further details are supplied with the proof). A charge may be made to authors who insist on amendment within the text at the page proof stage.

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.

## The Journal

- About this journal
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- Dispatch date of the next issue

### Impact factor: 4.894

### Editors-in-Chief

#### A Bateman

#### A Valencia

- View full editorial board

## For Authors

- Instructions to authors
- Online submission
- Submit Now!
- Self-archiving policy

Open access options for authors - visit Oxford Open

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