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  Instructions for /Genome *Biology*/ authors

General information <#h1general>
Manuscript text <#h1text>
Illustrations and figures <#h1figures>
Tables <#h1tables>
Additional files <#h1data>
Proofs and reprints <#h1proofs>
Style and language <#h1style>
	


  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
<mailto:editorial@genomebiology.com>, 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
</manuscript/default.asp?txt_jou_id=3001>. 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
<mailto: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 (?1795,
US$2645). Generally, if the submitting author's institution is a BioMed
Central member <http://www.biomedcentral.com/info/about/instmembership>
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
<http://www.biomedcentral.com/info/about/supportersmembership> of BioMed
Central, however, a discounted article processing charge is payable by
the author. Please click here <http://www.biomedcentral.com/inst/> to
check if your institution is a BioMed Central member. We offer a £30
discount for manuscripts formatted with EndNote 5
<http://www.biomedcentral.com/info/ifora/endnote> (or later versions) or
Reference Manager 10 <http://www.biomedcentral.com/info/ifora/refman> or
created using Publicon
<http://www.biomedcentral.com/info/ifora/publicon>. We routinely waive
charges for authors from low-income countries. For further details, see
more information about article-processing charges </info/faq/apcfaq.asp>.

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
<http://www.biomedcentral.com/info/authors/license> ). 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, that readily replaceable
material described in the article will be freely distributed to academic
colleagues, 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 <http://www.wma.net/e/policy/b3.htm>, 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.

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 article. Where appropriate, authors should adhere
to the standards proposed by the Microarray Gene Expression Data Society
(http://www.mged.org) and must deposit microarray data in one of the
public repositories, such as ArrayExpress
(http://www.ebi.ac.uk/arrayexpress), Gene Expression Omnibus (GEO;
http://www.ncbi.nlm.nih.gov/projects/geo/) or the Center for Information
Biology Gene Expression Database (CIBEX; http://cibex.nig.ac.jp).

/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.

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
<http://www.publicationethics.org.uk>.

BioMed Central endorses the World Association of Medical Editors (WAME)
Policy Statement on Geopolitical Intrusion on Editorial Decisions
<http://www.wame.org/wamestmt.htm#geopolitical>.

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.

	return to top <#top>
General information <#h1general>
Manuscript text <#h1text>
Illustrations and figures <#h1figures>
Tables <#h1tables>
Additional files <#h1data>
Proofs and reprints <#h1proofs>
Style and language <#h1style>
	


  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)
    * TeX/LaTeX (use BioMed Central's TeX template)
      <http://www.biomedcentral.com/info/ifora/tex>

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 <http://www.biomedcentral.com/info/ifora/tex>. 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
<http://www.biomedcentral.com/info/ifora/publicon> and instructions for
authoring in Publicon
<http://www.biomedcentral.com/info/ifora/publiconinstructions> are
available.

Note that figures <#h1figures> must be submitted as separate image
files, not as part of the submitted DOC/ TEX file.

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

Research <#defaulttype>

Commentary/Editorial <?txt_jou_id=3001&txt_mst_id=3021>

Interaction <?txt_jou_id=3001&txt_mst_id=3023>

Method <?txt_jou_id=3001&txt_mst_id=3015>

Review <?txt_jou_id=3001&txt_mst_id=3016>

Software <?txt_jou_id=3001&txt_mst_id=3014>

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.

Manuscript sections for Research articles
Manuscripts for Research articles submitted to /Genome *Biology* /
should be divided into the following sections:

    * Title page <#title>
    * Abstract <#abstract>
    * Background <#background>
    * Results <#results>
    * Discussion <#discussion>
    * Conclusions <#conclusions>
    * Materials and Methods <#mandm>
    * List of abbreviations used <#abbreviations> (if any)
    * Authors' contributions <#authorscon>
    * Acknowledgements <#acknowledgements>
    * References <#references>
    * Figure legends <#legends> (if any)
    * Tables and captions <#h1tables> (if any)
    * Description of additional data files <#h1data> (if any)

The *Accession Numbers* of any nucleic acid sequences, protein sequences
or atomic coordinates cited in the manuscript should be provided, in
square brackets and include the corresponding database name; for
example, [EMBL:AB026295, EMBL:AC137000, DDBJ:AE000812, GenBank:U49845,
PDB:1BFM, Swiss-Prot:Q96KQ7, PIR:S66116].

The databases for which we can provide direct links are: EMBL Nucleotide
Sequence Database (EMBL <http://www.ebi.ac.uk/embl/>), DNA Data Bank of
Japan (DDBJ <http://www.ddbj.nig.ac.jp> ), GenBank at the NCBI (GenBank
<http://www.ncbi.nlm.nih.gov/Genbank/index.html>), Protein Data Bank
(PDB <http://www.rcsb.org/pdb/>), Protein Information Resource (PIR
<http://pir.georgetown.edu/>) and the Swiss-Prot Protein Database
(Swiss-Prot <http://us.expasy.org/sprot/>).

*Title page*
This should list the title of the article, the full names, institutional
addresses, and e-mail addresses for all authors. The corresponding
author should also be indicated.

*Abstract*
The abstract of the manuscript should not exceed 250 words and must be
structured into three separate sections: *Background*, the context and
purpose of the study; *Results*, the main findings; *Conclusions*, brief
summary and potential implications. Please minimize the use of
abbreviations and do not cite references in the abstract.

*Background*
The background section should be written from the standpoint of
researchers without specialist knowledge in that area and must clearly
state - and, if helpful, illustrate - the background to the research and
its aims. The section should end with a very brief statement of what is
being reported in the article.

*Results and Discussion*
The Results and Discussion may be combined into a single section or
presented separately. They may also be broken into subsections with
short, informative headings.

*Conclusions*
This should state clearly the main conclusions of the research and give
a clear explanation of their importance and relevance. Summary
illustrations may be included.

*Materials and methods*
This should be divided into subsections if several methods are described.

*List of abbreviations*
If abbreviations are used in the text they should be defined in the text
where first used and a list of abbreviations should be provided.

*Acknowledgements*
Please acknowledge anyone who contributed towards the study by making
substantial contributions to conception, design, acquisition of data, or
analysis and interpretation of data, or who was involved in drafting the
manuscript or revising it critically for important intellectual content,
but who does not meet the criteria for authorship. Please also include
their source(s) of funding. Please also acknowledge anyone who
contributed materials essential for the study.

Authors should obtain permission to acknowledge from all those mentioned
in the Acknowledgements.

Please list the source(s) of funding for the study, for each author, and
for the manuscript preparation in the acknowledgements section. Authors
must describe the role of the funding body, if any, in study design; in
the collection, analysis, and interpretation of data; in the writing of
the manuscript; and in the decision to submit the manuscript for
publication.

*References*
All references must be numbered consecutively, in square brackets, in
the order in which they are cited in the text, followed by any in tables
or legends. Reference citations should not appear in titles or headings.
Each reference must have an individual reference number. Please avoid
excessive referencing. If automatic numbering systems are used, the
reference numbers must be finalized and the bibliography must be fully
formatted before submission.

Only articles and abstracts that have been published or are in press, or
are available through public e-print/preprint servers, may be cited;
unpublished abstracts, unpublished data and personal communications
should not be included in the reference list, but may be included in the
text. Notes/footnotes are not allowed. Obtaining permission to quote
personal communications and unpublished data from the cited author(s) is
the responsibility of the author. Journal abbreviations follow Index
Medicus/MEDLINE. For each reference, name all authors unless there are
more than ten, in which case name the first ten followed by /et al./

We encourage authors to use a recent version of EndNote (version 5 and
above) or Reference Manager (version 10) when formatting their reference
list, as this allows references to be automatically extracted. Authors
submitting articles in EndNote 5 or higher or Reference Manager 10
format will save £30 on the £1350 (?1795, US$2645) article processing
charge. In order to obtain this discount, you should upload the
manuscript file containing your EndNote or Reference Manager-formatted
bibliography as a .doc file. Please ensure you do not convert to another
format (e.g. RTF or PDF). On upload, the discount will be automatically
granted and you will receive a confirmation on-screen and by email. You
will also be able to preview an HTML version of the extracted references
during submission, and we urge authors to check this. EndNote or
Reference Manager users should also make sure that any changes made to
the reference list are done within their reference management program,
rather than by manually editing the formatted bibliography. This is
because manually introduced changes will not be picked up in the
automatically extracted list.

Further details about EndNote
<http://www.biomedcentral.com/info/endnote.asp> and Reference Manager
<http://www.biomedcentral.com/info/ifora/refman> are available on the
BioMed Central site, including style files that conform to the BioMed
Central style and information about how to upgrade. Users of other
reference management programs should be able to select other journal
styles that output a numeric list styled similarly to the guide below.

For EndNote users, we provide a detailed technical guide
<http://www.biomedcentral.com/info/ifora/endnote/#technicalhelp> to help
with resolving problems that are encountered with the automated
reference extraction process. Please check that your reference
extraction is accurate after uploading the manuscript text file.

We are also working towards integrating data from RefWorks referencing
software. We are working in partnership with the development team of
RefWorks <http://www.refworks.com/> to produce a high quality extraction
process.

Examples of the /Genome *Biology* / reference style are shown below.
Please take care to follow the reference style precisely; references not
in the correct style may be retyped, necessitating tedious proofreading.

Links
Web links and URLs should be included in the reference list. They should
be provided in full, including both the title of the site and the URL,
in the following format: *The Mouse Tumor Biology Database*
[http://tumor.informatics.jax.org/cancer_links.html]

/Genome *Biology* / reference style

/Article within a journal/
1. Koonin EV, Altschul SF, Bork P: *BRCA1 protein products: functional
motifs.* /Nat Genet/ 1996, *13:*266-267.

/Article within a journal supplement /
2. Orengo CA, Bray JE, Hubbard T, LoConte L, Sillitoe I: *Analysis and
assessment of ab initio three-dimensional prediction, secondary
structure, and contacts prediction.* /Proteins/ 1999, *Suppl 3:*149-170.

/In press article/
3. Kharitonov SA, Barnes PJ: *Clinical aspects of exhaled nitric
oxide.* /Eur Respir J/, in press.

/Published abstract/
4. Zvaifler NJ, Burger JA, Marinova-Mutafchieva L, Taylor P, Maini RN:
*Mesenchymal cells, stromal derived factor-1 and rheumatoid arthritis
[abstract].* /Arthritis Rheum/ 1999, *42:*s250.

/Article within conference proceedings/
5. Jones X: *Zeolites and synthetic mechanisms.* In /Proceedings of the
First National Conference on Porous Sieves: 27-30 June 1996; Baltimore./
Edited by Smith Y. Stoneham: Butterworth-Heinemann; 1996:16-27.

/Book chapter, or article within a book/
6. Schnepf E: *From prey via endosymbiont to plastids: comparative
studies in dinoflagellates.* In /Origins of Plastids. Volume 2./ 2nd
edition. Edited by Lewin RA. New York: Chapman and Hall; 1993:53-76.

/Whole issue of journal/
7. Ponder B, Johnston S, Chodosh L (Eds): *Innovative oncology.* In
/Breast Cancer Res/ 1998, *10:*1-72.

/Whole conference proceedings/
8. Smith Y (Ed): /Proceedings of the First National Conference on Porous
Sieves: 27-30 June 1996; Baltimore./ Stoneham: Butterworth-Heinemann; 1996.

/Complete book/
9. Margulis L: /Origin of Eukaryotic Cells./ New Haven: Yale University
Press; 1970.

/Monograph or book in a series/
10. Hunninghake GW, Gadek JE: *The alveolar macrophage.* In /Cultured
Human Cells and Tissues./ Edited by Harris TJR. New York: Academic
Press; 1995:54-56. [Stoner G (Series Editor): /Methods and Perspectives
in Cell Biology,/ vol 1.]

/Book with institutional author/
11. Advisory Committee on Genetic Modification: /Annual Report./ London;
1999.

/PhD thesis/
12. Kohavi R: *Wrappers for performance enhancement and oblivious
decision graphs.* /PhD thesis./ Stanford University, Computer Science
Department; 1995.

/Link / URL/
13. *The Mouse Tumor Biology Database*
[http://tumor.informatics.jax.org/cancer_links.html]

	return to top <#top>
	

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 </information/instructions/GBresearchtemplate.doc>
(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 <#reflist> given, or use bibliographic
      software to insert them automatically. We provide style files
      <#stylefile> 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
<http://www.biomedcentral.com/info/ifora/endnote>.


General information <#h1general>
Manuscript text <#h1text>
Illustrations and figures <#h1figures>
Tables <#h1tables>
Additional files <#h1data>
Proofs and reprints <#h1proofs>
Style and language <#h1style>
	


  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
<http://www.biomedcentral.com/info/ifora/figures> for detailed
instructions on maximising the quality of your figures
<http://www.biomedcentral.com/info/ifora/figuretypes> , for further
information please contact the Editorial Office < mailto:
editorial@genomebiology.com> .

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
<http://www.biomedcentral.com/info/ifora/figures#bitmapvector>, to
facilitate such editing.

Figure legends
All figure legends should start with a single sentence that acts as the
figure's title. 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.

	return to top <#top>
General information <#h1general>
Manuscript text <#h1text>
Illustrations and figures <#h1figures>
Tables <#h1tables>
Additional files <#h1data>
Proofs and reprints <#h1proofs>
Style and language <#h1style>
	


  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.

	return to top <#top>
General information <#h1general>
Manuscript text <#h1text>
Illustrations and figures <#h1figures>
Tables <#h1tables>
Additional files <#h1data>
Proofs and reprints <#h1proofs>
Style and language <#h1style>
	


  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

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