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*Editor-in-Chief*
Melissa Norton, MD <mailto: bmcserieseditor@biomedcentral.com>

*Biology Editor*
Penelope Webb, PhD <mailto: bmcserieseditor@biomedcentral.com>

*In-house Editor*
Matt Hodgkinson <mailto: editorial@biomedcentral.com?subject=FAO: Matt
Hodgkinson, BMC Bioinformatics>


	
BMC  Instructions for /BMC Bioinformatics/ authors

General information <#h1general>
Preparing main manuscript text <#h1text>
Preparing illustrations and figures <#h1figures>
Preparing tables <#h1tables>
Preparing additional files <#h1data>
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  General information

You are advised also to read About this journal
</bmcbioinformatics/about>, which includes other relevant information.

Submission process

Manuscripts must be submitted by one of the authors of the manuscript,
and should not be submitted by anyone on their behalf. The submitting
author takes responsibility for the article during submission and peer
review.

To facilitate rapid publication and to minimize administrative costs,
/BMC Bioinformatics/ accepts only online submission
</manuscript/default.asp?txt_jou_id=1002>. 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 customer support team (info@biomedcentral.com
<mailto:info@biomedcentral.com>).

We also provide a collection of links to useful tools and resources for
scientific authors, on our Tools for Authors
<http://www.biomedcentral.com/info/authors/authortools> page.

Publication and peer review processes
Submitted manuscripts will be sent to peer reviewers, unless they are
either out of scope or below threshold for the journal, or the
presentation or written English is of an unacceptably low standard. They
will generally be reviewed by two experts with the aim of reaching a
first decision as soon as possible. Reviewers do not have to sign their
reports but are welcome to do so. They are asked to declare any
competing interests.

We ask all authors to provide the contact details (including e-mail
addresses) of at least four potential peer reviewers for their
manuscript. These should be experts in their field of study, who will be
able to provide an objective assessment of the manuscript. Any suggested
peer reviewers should not have published with any of the authors of the
manuscript within the past five years and should not be members of the
same research institution . Members of the Editorial Board of the
journal can be nominated. Suggested reviewers will be considered
alongside potential reviewers identified by their publication record or
recommended by Editorial Board members.

Reviewers are asked whether the manuscript is scientifically sound and
coherent, how interesting it is and whether the quality of the writing
is acceptable. Where possible, the final decision is made on the basis
that the peer reviewers are in accordance with one another, or that at
least there is no strong dissenting view. In cases where there is strong
disagreement either among peer reviewers or between the authors and peer
reviewers, advice is sought from a member of the journal's Editorial
Board. The journal allows a maximum of two revisions of any manuscripts.
All appeals should be directed to the Biology Editor. The ultimate
responsibility for editorial decisions lies with the Editor-in-Chief.

Reviewers are also asked to indicate which articles they consider to be
especially interesting or significant. These articles may be given
greater prominence and greater external publicity, and the authors may
be asked if they would prefer to have the manuscript published in /BMC
Biology/ .

Once an article is accepted, it is published in /BMC Bioinformatics/
immediately as a provisional PDF file. The paper will subsequently be
published in both fully browseable web form, and as a formatted PDF; the
article will then be available through /BMC Bioinformatics/, BioMed
Central and PubMed Central, and will also be included in PubMed.

Authors will be able to check the progress of their paper through the
submission system at any time by logging into My *BioMed Central*
</my/manuscripts>, a personalized section of the site.

Article-processing charges
/BMC Bioinformatics/ 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 £950 (?1265,
US$1860). 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
<http://www.biomedcentral.com/info/about/apcfaq>.

Editorial 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 that
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 who publish in /BMC Bioinformatics/
retain copyright to their work ( more information
<http://www.biomedcentral.com/info/authors/license> ). Correspondence
concerning articles published in /BMC Bioinformatics/ is encouraged.

Submission of a manuscript to /BMC Bioinformatics/ 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
<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.

/BMC Bioinformatics/ 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.

Submission of a manuscript to /BMC Bioinformatics/ 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
<http://www.ddbj.nig.ac.jp/> (DDBJ), European Molecular Biology
Laboratory (EMBL/EBI) Nucleotide Sequence Database
<http://www.ebi.ac.uk/>, or GenBank <http://www.ncbi.nlm.nih.gov/>
(National Center for Biotechnology Information).

*Protein sequences*
Protein sequences can be deposited with SwissProt
<http://www.expasy.org/sprot/> or the Protein Information Resource
<http://pir.georgetown.edu/> (PIR).

*Structures*
Protein structures can be deposited with one of the members of the
Worldwide Protein Data Bank <http://www.wwpdb.org/>. Nucleic Acids
structures can be deposited with the Nucleic Acid Database
<http://ndbserver.rutgers.edu/> at Rutgers. Crystal structures of
organic compounds can be deposited with the Cambridge Crystallographic
Data Centre <http://www.ccdc.cam.ac.uk/products/csd/deposit/>.

*Chemical structures and assays*
Structures of chemical substances can be deposited with PubChem
Substance <http://pubchem.ncbi.nlm.nih.gov/>. Bioactivity screens of
chemical substances can be deposited with PubChem BioAssay
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pcassay>.

*Microarray data*
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 <http://www.ncbi.nlm.nih.gov/projects/geo/> (GEO) or the Center
for Information Biology Gene Expression Database
<http://cibex.nig.ac.jp/> (CIBEX).

*Computional modeling*
We encourage authors to prepare models of biochemical reaction networks
using the Systems Biology Markup Language <http://sbml.org/> and to
deposit the model with the BioModels database
<http://www.ebi.ac.uk/biomodels/>, 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 <http://www.addgene.org/>, a non-profit
repository, or PlasmID <http://plasmid.hms.harvard.edu/>, 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
<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>.

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  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)
    * WordPerfect (version 5 and above)
    * Rich text format (RTF)
    * Portable document format (PDF)
    * TeX/LaTeX (use BioMed Central's TeX template)
      <http://www.biomedcentral.com/info/ifora/tex>
    * DeVice Independent format (DVI)
    * Publicon Document (NB)

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 a DVI
file. We do not recommend converting to RTF.

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/ PDF/TEX/DVI file.

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

Research article <#defaulttype>

Database <?txt_jou_id=1002&txt_mst_id=1008>

Methodology article <?txt_jou_id=1002&txt_mst_id=1002>

Software <?txt_jou_id=1002&txt_mst_id=1009>

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 a Research article , the
structure for which is described below.

Manuscript sections for Research articles
Manuscripts for Research articles submitted to /BMC Bioinformatics/
should be divided into the following sections:

    * Title page <#title>
    * Abstract <#abstract>
    * Background <#background>
    * Results <#results>
    * Discussion <#discussion>
    * Conclusions <#conclusions>
    * Methods <#mandm> (can also be placed after Background)
    * 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)

You can download a template
<http://biomedcentral.com/download/templates/BMC153n.dot> (Mac and
Windows compatible; Microsoft Word 98/2000) for your article. For
instructions on use, see below <#template>.

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, which should include an
accurate, clear and concise description of the reported work, avoiding
abbreviations; and 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 350 words and must be
structured into 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. *Trial Registration*, if your
research article reports the results of a controlled health care
intervention, please list your trial registry, along with the unique
identifying number, e.g. *Trial registration*: Current Controlled Trials
ISRCTN73824458. Please note that there should be no space between the
letters and numbers of your trial registration number.

*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.

*Methods* (can also be placed after Background)
This should include the design of the study, the setting, the type of
participants or materials involved, a clear description of all
interventions and comparisons, and the type of analysis used, including
a power calculation if appropriate.

*List of abbreviations*
If abbreviations are used in the text either they should be defined in
the text where first used, or a list of abbreviations can be provided,
which should precede the authors' contributions and acknowledgements.

*Authors' contributions*
In order to give appropriate credit to each author of a paper, the
individual contributions of authors to the manuscript should be
specified in this section.

An "author" is generally considered to be someone who has made
substantive intellectual contributions to a published study. To qualify
as an author one should 1) have made substantial contributions to
conception and design, or acquisition of data, or analysis and
interpretation of data; 2) have been involved in drafting the manuscript
or revising it critically for important intellectual content; and 3)
have given final approval of the version to be published. Each author
should have participated sufficiently in the work to take public
responsibility for appropriate portions of the content. Acquisition of
funding, collection of data, or general supervision of the research
group, alone, does not justify authorship.

We suggest the following kind of format (please use initials to refer to
each author's contribution): AB carried out the molecular genetic
studies, participated in the sequence alignment and drafted the
manuscript. JY carried out the immunoassays. MT participated in the
sequence alignment. ES participated in the design of the study and
performed the statistical analysis. FG conceived of the study, and
participated in its design and coordination and helped to draft the
manuscript. All authors read and approved the final manuscript.

All contributors who do not meet the criteria for authorship should be
listed in an acknowledgements section. Examples of those who might be
acknowledged include a person who provided purely technical help,
writing assistance, or a department chair who provided only general support.

*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. Citations in the reference list should contain all
named authors, regardless of how many there are.

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 £950 (?1265, US$1860) 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 /BMC Bioinformatics/ 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]

/BMC Bioinformatics/ 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]

Microsoft Word template
Although we can accept manuscripts prepared as Microsoft Word, Word
Perfect, RTF or PDF 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 /BMC
Bioinformatics/ style.

Download the template
<http://www.biomedcentral.com/download/templates/BMC153n.dot> (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 /BMC Bioinformatics/ template
The template consists of a standard set of headings that make up a /BMC
Bioinformatics/ 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>.

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  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> .

Formats
The following file formats can be accepted:

    * *EPS* (preferred format for diagrams)
    * *PDF* (also especially suitable for diagrams)
    * *PNG* (preferred format for photos or images)
    * Microsoft Word (version 5 and above; figures must be a single page)
    * PowerPoint (figures must be a single page)
    * TIFF
    * JPEG
    * BMP
    * CDX (ChemDraw)
    * TGF (ISIS/Draw)

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.

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  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.

Smaller tables considered to be 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. Columns and rows of data should be
made visibly distinct by ensuring the borders of each cell display as
black lines. Commas should not be used to indicate numerical values.
Colour 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.

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  Preparing additional files

Although /BMC Bioinformatics/ does not restrict the length and quantity
of data in a paper, there may still be occasions where an author wishes
to provide data sets, tables, movie files, or other information as
additional information. These files can be uploaded using the
'Additional Material files' button in the manuscript submission process.

The maximum file size for additional files is 20 MB each, and files will
be virus-scanned on submission.

Any additional files will be linked into the final published article in
the form supplied by the author, but will not be displayed within the
paper. They will be made available in exactly the same form as
originally provided.

If additional material is provided, please list the following
information in a separate section of the manuscript text, immediately
following the tables (if any):

    * File name
    * File format (including name and a URL of an appropriate viewer if
      format is unusual)
    * Title of data
    * Description of data

Additional datafiles should be referenced explicitly by file name within
the body of the article, e.g. 'See additional file 1: Movie1 for the
original data used to perform this analysis'.

Formats and uploading
Ideally, file formats for additional 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
          o PDF (Adobe Acrobat)
    * Animations
          o SWF (Shockwave Flash)
    * Movies
          o MOV (QuickTime)
          o MPG (MPEG)
    * Tabular data
          o XLS (Excel spreadsheet)
          o CSV (Comma separated values)

As with figure files, files should be given the standard file
extensions. This is especially important for Macintosh users, since the
Mac OS does not enforce the use of standard extensions. Please also make
sure that each additional file is a single table, figure or movie
(please do not upload linked worksheets or PDF files larger than one sheet).

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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  Style and language

General
Currently, /BMC Bioinformatics/ can only accept manuscripts written in
English. Spelling should be US English or British English, but not a
mixture .

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 also no restriction on
the number of figures, tables or additional files that can be included
with each article online. Figures and tables should be sequentially
referenced. Authors should include all relevant supporting data with
each article.

/BMC Bioinformatics/ will not edit submitted manuscripts for style or
language; reviewers may advise rejection of a manuscript if it is
compromised by grammatical errors. Authors are advised to write clearly
and simply, and to have their article checked by colleagues before
submission. In-house copyediting will be minimal. Non-native speakers of
English may choose to make use of a copyediting service.

Help and advice on scientific writing
The abstract is one of the most important parts of a manuscript. For
guidance, please visit our page on "Writing titles and abstracts for
scientific articles" <http://www.biomedcentral.com/info/ifora/abstracts>
Tim Albert has produced for BioMed Central a list of tips
<http://www.biomedcentral.com/info/ifora/report> for writing a
scientific manuscript. MedBioWorld
<http://www.medbioworld.com/advice/presenting.html> also provides a list
of resources for science writing.

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

Typography

    * 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.
    * Capitalise only the first word, and proper nouns, in the title.
    * All pages should be numbered.
    * Use the /BMC Bioinformatics/ 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 (litre and molar are permitted,
however).

Last revised: 3 October 2005

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