# Instructions to Authors

Please note that the journal now encourages authors to complete their copyright licence to publish form online. Upon receipt of accepted manuscripts at Oxford Journals authors will be invited to complete an online copyright licence to publish form.

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 here.

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
• Bioimage informatics

Detailed Scope Guidelines are also available for the above categories.

## TYPES OF MANUSCRIPT

The following types of paper may be submitted for publication. Please note the page limits for each type of paper.

Original Papers (up to 7 pages; this is approx. 5000 words) 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 and Implementation 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 must not require mandatory registration by the user. Additional Supplementary data can be published online-only by the journal. 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. Web servers should not be browser specific. Application Notes must not describe trivial utilities, nor involve significant investment of time for the user to install. The name of the application should be included in the title.

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 or abstract/summary no longer than a page.

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*) Orders from the UK will be subject to the current UK VAT charge. For orders from elsewhere in the EU you or your institution should account for VAT by way of a reverse charge. Please provide us with your or your institution’s VAT number. * Please note that the Word and LaTex author templates used for submission to Manuscript Central (ScholarOne) are not an exact reflection of the final typeset article, and therefore cannot be used to estimate exactly how many published pages your final typeset article will be. Please use the following word count guidelines for a more accurate indication: Original papers: up to 7 pages, this is approx. 5000 words, Discovery notes: up to 4 pages, this is approx. 3000 words, Application notes: up to 2 pages; this is approx. 1300 words or 1000 words plus one figure. ## 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. Please note that if considered appropriate, plagiarism checking software may be applied to your manuscript during the editorial review process. Authors retain the right to make a preprint version of the article available on their own personal website and/or that of their employer and/or in free public servers of preprints and/or articles in their subject area. Authors making their manuscripts available in this way must clearly note this in their submission. Once the manuscript has been accepted the authors must acknowledge that the article has been accepted for publication as follows: "This article has been accepted for publication in [Journal Title] ©: [year] [owner as specified on the article]Published by Oxford University Press [on behalf of xxxxxx]. All rights reserved." Please read the full policy on self-archiving here: www.oxfordjournals.org/access_purchase/self-archiving_policyb.html 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, and appropriate test data should be made available. Availability must be clearly stated in the article. Authors must also ensure that the software and test data 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. At the minimum, authors must provide one of: webserver, source code or binary. The name of the software should be included in the title of the paper wherever possible. 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 (https://bioinformatics.cineca.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 or files from the manuscript. Authors should make sure that all additional text, figures and tables are presented in a single file to minimise the number of files. 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 30% 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 Word or LaTex files. 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 Advanced Access articles are initially published in their 'Accepted Manuscript' form as soon as possible post acceptance. Subsequently, a copyedited, typeset, corrected version of the 'Corrected Proof' is also published on the Advanced Access page. More information, including how to cite Advance Access papers, can be found on the Advance Access Page. Complimentary ISCB memberships for authors Bioinformatics is an official journal of the ISCB and as part of our partnership with the Society we have 200 complimentary ISCB memberships to offer our authors each year. If you are the corresponding author of a Bioinformatics paper then the ISCB will be in touch after your article has been published. ## 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. Oxford Open articles are published under Creative Commons licences. Authors publishing in Bioinformatics can use the following Creative Commons licences for their articles: • Creative Commons Attribution licence (CC BY) • Creative Commons Non-Commercial licence (CC BY-NC) Please click here for more information about the Creative Commons licences. Charges also vary depending on the manuscript category. Please see below for details: Original Paper/Review/Special issue article - optional Oxford Open charges: Regular charge - £1850/$3000 / €2450
Reduced Rate Developing country charge* - £925 / $1500 / €1225 Free Developing country charge * - £0 /$0 / €0

Application Note/Letter to the Editor/Message from ISCB/Discovery Note
– optional Oxford Open charges:
Regular charge - £900 / $1600 / €1350 Reduced Rate Developing country charge* - £450 /$800 / €675
Free Developing country charge* - £0 / $0 / €0 * Visit our Developing Countries page for a list of qualifying countries. The above Open Access charges are in addition to any page charges and colour charges that might apply. Orders from the UK will be subject to the current UK 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. You can pay Open Access charges using our Author Services site. This will enable you to pay online with a credit/debit card, or request an invoice by email or post. Third-Party Content in Open Access papers If you will be publishing your paper under an Open Access licence but it contains material for which you do not have Open Access re-use permissions, please state this clearly by supplying the following credit line alongside the material: Title of content Author, Original publication, year of original publication, by permission of [rights holder] This image/content is not covered by the terms of the Creative Commons licence of this publication. For permission to reuse, please contact the rights holder. ## 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. Prepare your figures at publication quality resolution, using applications capable of generating high-resolution .tif files (1200 d.p.i. for line drawings and 350 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, please click here. 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). If novel software is being described, the name of the software should be included in the title. 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 and Implementation, 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 and Implementation: This section should state software availability if the paper focuses mainly on software development or on the implementation of an algorithm. Examples are: 'Freely available on the web at http://www.example_url.org.' Website implemented in Perl, MySQL and Apache, with all major browsers supported'; or 'Source code and binaries freely available for download at URL, implemented in C++ and supported on linux and MS Windows'. 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 and Implementation, Contact and Supplementary Information. • Summary: This section should summarize the purpose/novel features of the program in one or two sentences. • Availability and Implementation: See above for advice and examples for this section. • 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. 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 below. 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. Funding information The following rules should be followed: • The sentence should begin: ‘This work was supported by …’ • The full official funding agency name should be given, i.e. ‘National Institutes of Health’, not ‘NIH’ (full RIN-approved list of UK funding agencies) Grant numbers should be given in brackets as follows: ‘[grant number xxxx]’ • Multiple grant numbers should be separated by a comma as follows: ‘[grant numbers xxxx, yyyy]’ • Agencies should be separated by a semi-colon (plus ‘and’ before the last funding agency) • 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: ‘This work was supported by the National Institutes of Health [AA123456 to C.S., BB765432 to M.H.]; and the Alcohol & Education Research Council [hfygr667789].’ Oxford Journals will deposit all NIH-funded articles in PubMed Central. See Depositing articles in repositories – information for authors for details. Authors must ensure that manuscripts are clearly indicated as NIH-funded using the guidelines above. Crossref Funding Data Registry In order to meet your funding requirements authors are required to name their funding sources, or state if there are none, during the submission process. For further information on this process or to find out more about the CHORUS initiative please click here. References 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 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: 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'. Examples are given here: • 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. Tables Tables should be embedded within the main document file 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 embedded within the text inside the main document file and referred to in the text as Figure 1 etc. 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 adjacent to the relevant figure. • 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/€525 to print a figure in colour). Online colour figures are free of charge. Orders from the UK will be subject to the current UK VAT charge. For orders from elsewhere in the EU you or your institution should account for VAT by way of a reverse charge. Please provide us with your or your institution’s VAT number.

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.

English Language Editing

Language editing, if your first language is not English, to ensure that the academic content of your paper is fully understood by journal editors and reviewers is optional. Language editing does not guarantee that your manuscript will be accepted for publication. For further information on this service, please click here. Several specialist language editing companies offer similar services and you can also use any of these. Authors are liable for all costs associated with such services.

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

A URL providing free access to the online version of the article will be e-mailed to the corresponding author. This link may then be distributed to interested parties. Paper offprints may be ordered during production of your paper using the Author Services site. Orders from the UK will be subject to the current UK VAT charge. For orders from elsewhere in the EU you or your institution should account for VAT by way of a reverse charge. Please provide us with your or your institution’s VAT number.

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