Instructions for Genome Biology authors

General information

Genome Biology serves the biological research community as an international forum for the dissemination, discussion and critical review of information about all areas of biology informed by genomic research. Key objectives are to provide a guide to the rapidly developing resources and technology in genomics and its impact on biological research, to publish large datasets and extensive results that are not readily accommodated in traditional journals, and to help establish new standards and nomenclature for post-genomic biology. Genome Biology publishes articles from the full spectrum of biology. Subjects covered include any aspect of molecular, cellular, organismal or population biology studied from a genomic perspective, as well as genomics, proteomics, bioinformatics, genomic methods (including structure prediction), computational biology, sequence analysis (including large-scale and cross-genome analyses), comparative biology and evolution.

If you wish to make a presubmission enquiry about the suitability of your article, please e-mail the editors, who will respond to your enquiry within two working days.

Online submission process

To facilitate rapid publication and to minimize administrative costs, Genome Biology prefers online submission. The submission process is compatible with version 3.0 or later of Internet Explorer and Netscape Navigator, and with most other modern web browsers. It can be used from PC, Mac, or Unix platforms.

Files can be submitted as a batch, or one by one. The submission process can be interrupted at any time - when users return to the site, they can carry on where they left off.

See below for examples of acceptable word processor and graphics file formats. Additional files of any type, such as movies, animations, or original data files, can also be submitted as part of the publication.

During submission you will be asked to provide a cover letter. Please use this to explain why your manuscript should be published in the journal, to elaborate on any issues relating to our editorial policies detailed in the instructions for authors, and to declare any potential competing interests.

Assistance with the process of manuscript preparation and submission is available from the editorial office (editorial@genomebiology.com)

Article-processing charges

Genome Biology levies an article-processing charge for every accepted article, to cover the costs incurred by open access publication. In 2008 the article-processing charge is £1350 (€1700, US$2700). Generally, if the submitting author's institution is a BioMed Central member the cost of the article processing charge is covered by the membership, and no further charge is payable. In the case of authors whose institutions are supporter members of BioMed Central, however, a discounted article processing charge is payable by the author. Please click here to check if your institution is a BioMed Central member. We offer a £30 discount for manuscripts formatted with EndNote 5 (or later versions) or Reference Manager 10 or created using Publicon. We routinely waive charges for authors from low-income countries. For further details, see more information about article-processing charges.

Policies

Any manuscript , or substantial parts of it, submitted to the journal must not be under consideration by any other journal although it may have been deposited on a preprint server. The manuscript should not have already been published in any journal or other citable form, with the exception that the journal is willing to consider peer-reviewing manuscripts that are translations of articles originally published in another language. In this case, the consent of the journal in which the article was originally published must be obtained and the fact that the article has already been published must be made clear on submission and stated in the abstract. Authors are required to ensure that no material submitted as part of a manuscript infringes existing copyrights, or the rights of a third party. Authors who publish in Genome Biology retain copyright to their work (more information). The authors are understood to give Genome Biology permission to reproduce the article or portions of it for print and online distribution; advertisements may be included to help defray the costs of handling and distribution. Correspondence concerning articles published in Genome Biology is encouraged . Correspondence containing data or scientific argument is subject to peer-review.

Submission of a manuscript to Genome Biology implies that all authors have read and agreed to its content, and that any experimental research that is reported in the manuscript has been performed with the approval of an appropriate ethics committee. Research carried out on humans must be in compliance with the Helsinki Declaration, and any experimental research on animals must follow internationally recognized guidelines. A statement to this effect must appear in the Methods section of the manuscript, including the name of the body which gave approval, with a reference number where appropriate. Informed consent must also be documented. Manuscripts may be rejected if the editorial office considers that the research has not been carried out within an ethical framework, e.g. if the severity of the experimental procedure is not justified by the value of the knowledge gained.

Generic drug names should generally be used. When proprietary brands are used in research, include the brand names in parentheses in the Methods section.

Genome Biology requires authors to declare any competing financial or other interest in relation to their work. If any author has a competing interest, it should be declared in the covering letter.

Any 'in press' articles cited within the references and necessary for the reviewers' assessment of the manuscript should be made available if requested by the editorial office.

Submission of a manuscript to Genome Biology implies that readily reproducible materials described in the manuscript, including all relevant raw data, will be freely available to any scientist wishing to use them for non-commercial purposes. Nucleic acid sequences, protein sequences, and atomic coordinates should be deposited in an appropriate database in time for the accession number to be included in the published article. In computational studies where the sequence information is unacceptable for inclusion in databases because of lack of experimental validation, the sequences must be published as an additional file with the article.

Any 'in press' articles cited within the references and necessary for the reviewers' assessment of the manuscript should be made available if requested by the editorial office.

Nucleotide sequences

Nucleotide sequences can be deposited with the DNA Data Bank of Japan (DDBJ), European Molecular Biology Laboratory (EMBL/EBI) Nucleotide Sequence Database, or GenBank (National Center for Biotechnology Information).

Protein sequences

Protein sequences can be deposited with SwissProt or the Protein Information Resource (PIR).

Structures

Protein structures can be deposited with one of the members of the Worldwide Protein Data Bank. Nucleic Acids structures can be deposited with the Nucleic Acid Database at Rutgers. Crystal structures of organic compounds can be deposited with the Cambridge Crystallographic Data Centre.

Chemical structures and assays

Structures of chemical substances can be deposited with PubChem Substance. Bioactivity screens of chemical substances can be deposited with PubChem BioAssay.

Microarray data

Where appropriate, authors should adhere to the standards proposed by the Microarray Gene Expression Data Society and must deposit microarray data in one of the public repositories, such as ArrayExpress, Gene Expression Omnibus (GEO) or the Center for Information Biology Gene Expression Database (CIBEX).

Computional modeling

We encourage authors to prepare models of biochemical reaction networks using the Systems Biology Markup Language and to deposit the model with the BioModels database, as well as submitting it as an additional file with the manuscript.

Plasmids

We encourage authors to deposit copies of their plasmids as DNA or bacterial stocks with Addgene, a non-profit repository, or PlasmID, the Plasmid Information Database at Harvard.

BioMed Central is a member of the Committee on Publication Ethics (COPE). Authors who have appealed against a rejection but remain concerned about the editorial process can refer their case to COPE. For more information, visit www.publicationethics.org.uk.

BioMed Central endorses the World Association of Medical Editors (WAME) Policy Statement on Geopolitical Intrusion on Editorial Decisions.

Immediate publication on acceptance

Once an original research article is accepted, it is published in Genome Biology immediately as a provisional PDF file, with a final citation, and will be included in PubMed. The article will subsequently be copyedited and published in both a fully browseable web form and as a formatted PDF; the article will then be available through Genome Biology , BioMed Central and PubMed Central.

Preparing main manuscript text

File formats

The following word processor file formats are acceptable for the main manuscript document:

• Microsoft Word (version 2 and above)
• Rich text format (RTF)
• Portable document format (PDF)
• TeX/LaTeX (use BioMed Central's TeX template)

Users of other word processing packages should save or convert their files to RTF before uploading. Many free tools are available which ease this process.

TeX/LaTeX users: We recommend using BioMed Central's TeX template and BibTeX stylefile. If you use this standard format, you can submit your manuscript in TeX format (after you submit your TEX file, you will be prompted to submit your BBL file). If you have used another template for your manuscript, or if you do not wish to use BibTeX, then please submit your manuscript as an RTF file.

Publicon users: Information about Publicon and instructions for authoring in Publicon are available.

Note that figures must be submitted as separate image files, not as part of the submitted DOC/ PDF/TEX file.

Article types

When submitting your manuscript, you will be asked to assign one of the following types to your article:

Please read the descriptions of each of the article types, choose which is appropriate for your article and structure it accordingly. If in doubt, your manuscript should be classified as Research, the structure for which is described below.

Microsoft Word template

Although we can accept manuscripts prepared as Microsoft Word, Word Perfect or RTF files, we have designed a Microsoft Word template that can be used to generate a standard style and format for your article. It can be used if you have not yet started to write your paper, or if it is already written and needs to be put into Genome Biology style.

Download the template (Mac and Windows compatible Word 1998/2000) from our site, and save it to your hard drive. Double click the template to open it.

How to use the Genome Biology template

The template consists of a standard set of headings that make up a Genome Biology Research article manuscript, along with dummy fragments of body text. Follow these steps to create your manuscript in the standard format:

• Replace the dummy text for Title, Author details, Institutional affiliations, and the other sections of the manuscript with your own text (either by entering the text directly or by cutting and pasting from your own manuscript document).
• If there are sections which you do not need, delete them (but check the rest of the Instructions for Authors to see which sections are compulsory).
• If you need an additional copy of a heading (e.g. for additional figure legends) just copy and paste.
• For the references, you may either manually enter the references using the reference style given, or use bibliographic software to insert them automatically. We provide style files for End Note and Reference Manager.

For extra convenience, you can use the template as one of your standard Word templates. To do this, put a copy of the template file in Word's 'Templates' folder, normally C:\Program Files\Microsoft Office\Templates on a PC. The next time you create a new document in Word using the File menu, the template will appear as one of the available choices for a new document.

Note - From version 6, EndNote includes a full set of structured article templates for BioMed Central journals. Users of EndNote are encouraged to upgrade if necessary and make use of these templates. More information is available here.

Preparing illustrations and figures

Figures should be provided as separate files. Each figure should comprise only a single file. There is no charge for the use of color.

Please read our figure preparation guidelines for detailed instructions on maximising the quality of your figures. , for further information please contact the Editorial Office

Formats

The following file formats can be accepted. Detailed information for each file type can be found by clicking on individual links.

• EPS (suitable for diagrams and/or images)
• PDF (suitable for diagrams and/or images)
• Microsoft Word (suitable for diagrams and/or images, figures must be a single page)
• PowerPoint (suitable for diagrams and/or images, figures must be a single page)
• TIFF (suitable for images)
• JPEG (suitable for photographic images, less suitable for graphical images)
• PNG (suitable for images)
• BMP (suitable for images)

Genome Biology will edit all figures supplied by the author. For this reason it is especially important that authors should supply figures in vector form, to facilitate such editing.

Figure legends

The legends should be included in the main manuscript text file immediately following the references, rather than being a part of the figure file. For each figure, the following information should be provided: Figure number (in sequence, using Arabic numerals - i.e. Figure 1, 2, 3 etc); short title of figure (maximum 15 words); detailed legend, up to 300 words.

Please note that it is the responsibility of the author(s) to obtain permission from the copyright holder to reproduce figures or tables that have previously been published elsewhere.

Preparing tables

Each table should be numbered in sequence using Arabic numerals (i.e. Table 1, 2, 3 etc.). Tables should also have a title that summarizes the whole table, maximum 15 words. Detailed legends may then follow, but should be concise.

Tables integral to the manuscript can be pasted into the end of the document text file, in portrait format (note that tables on a landscape page must be reformatted onto a portrait page or submitted as additional files). These will be typeset and displayed in the final published form of the article. Such tables should be formatted using the 'Table object' in a word processing program to ensure that columns of data are kept aligned when the file is sent electronically for review; this will not always be the case if columns are generated by simply using tabs to separate text. Commas should not be used to indicate numerical values. Color and shading should not be used.

Larger datasets can be uploaded separately as additional files. Additional files will not be displayed in the final, published form of the article, but a link will be provided to the files as supplied by the author.

Tabular data provided as additional files can be uploaded as an Excel spreadsheet (.xls) or comma separated values (.csv). As with all files, please use the standard file extensions.

Preparing additional files

Web-only material

If there is necessary material that cannot be provided in the PDF version, such as large datasets or movies, we will make it available on the Genome Biology website with the electronic edition of the article.

Additional files

If additional files are provided (e.g. movie files, original datafiles), each should be described in this section of the manuscript, providing the following information:

• file name
• file format (including name and URL link of appropriate viewer if format is unusual)
• title of this dataset
• description of this dataset.

Additional data files may be referenced generically within the body of the article. e.g. "See additional data file 1 for the original data used to perform this analysis". Additional files are considered integral to articles published by Genome Biology . There is no distinction between the main article and 'supplementary material'. Files will be virus-scanned on submission.

File formats

Files should not be platform-specific, and should be viewable using free or widely available tools. The following are examples of suitable formats:

• additional documentation - PDF (Adobe Acrobat) or TXT (plain text)
• animations - SWF (Shockwave Flash)
• movies - MOV (Quicktime) and MPG (MPEG)
• tabular data - XLS (Excel spreadsheet) and CSV (Comma Separated Values)

File extensions

It is recommended that files be given the appropriate standard three letter file extension for their file type (e.g. spreadsheet.xls or table.csv). This is especially important for Macintosh users, since the Macintosh operating system does not enforce the use of standard extensions.

Mini-websites

Small self-contained websites can be submitted as additional files, in such a way that they will be browsable from within the full text HTML version of the article. In order to do this, please follow these instructions:

1. Create a folder containing a starting file called index.html (or index.htm) in the root
2. Put all files necessary for viewing the mini-website within the folder, or sub-folders
3. Ensure that all links are relative (ie "images/picture.jpg" rather than "/images/picture.jpg" or "http://yourdomain.net/images/picture.jpg" or "C:\Documents and Settings\username\My Documents\mini-website\images\picture.jpg") and no link is longer than 255 characters
4. Access the index.html file and browse around the mini-website, to ensure that the most commonly used browsers (Internet Explorer and Firefox) are able to view all parts of the mini-website without problems, it is ideal to check this on a different machine
5. Compress the folder into a ZIP, check the file size is under 20 MB, ensure that index.html is in the root of the ZIP, and that the file has .zip extension, then submit as an additional file with your article

Proofs and reprints

Edited versions will be sent by email. Corrections should be returned within 2 days, preferably by fax or courier if sending corrections on paper. Please provide a typed list of corrections clearly indicating where the corrections should be made and please send this list by e-mail. Any substantial additions must be in the form of a note added in proof.

Reprints may be purchased for articles published. Prices are available from the Editorial Office.

Style and language

General

Currently, Genome Biology can only accept manuscripts written in English. Spelling should be US English .

Gene names should be in italic, but protein products should be in plain type.

There is no explicit limit on the length of articles submitted, but authors are encouraged to be concise. There is no restriction on the number of figures, tables or additional files that can be included with each article online. Authors should include all relevant supporting data with each article.

Help and advice on scientific writing

Tim Albert has produced for BioMed Central a list of tips for writing a scientific manuscript. MedBioWorld also provides a list of resources for science writing.

Abbreviations

Abbreviations should be used as sparingly as possible. They should be defined when first used and a list of abbreviations should be provided preceding the acknowledgements and references.

• Please use double line spacing.
• Type the text unjustified, without hyphenating words at line breaks.
• Use hard returns only to end headings and paragraphs, not to rearrange lines.
• Capitalize only the first word, and proper nouns, in the title.
• All pages should be numbered.
• Use the Genome Biology reference format.
• Footnotes to text should not be used.
• Greek and other special characters may be included. If you are unable to reproduce a particular special character, please type out the name of the symbol in full.
  
  Please ensure that all special characters used are embedded in the text, otherwise they will be lost during conversion to PDF.

Units

SI Units should be used throughout (liter and molar are permitted, however).

Last revised: 3 October 2005