Instructions for preparation of manuscripts for publication in a supplement

The supplement organizer is responsible for all communications with authors submitting manuscripts for publication in the Supplement. We ask that all manuscripts accepted for publication are prepared according to the 'Instructions for preparation of manuscripts for publication in a supplement'.

General information
Manuscript preparation
Style and language
Manuscript sections

General information

Publication
Manuscripts accepted by the supplement organizers will be published online in both fully browseable web form and as a formatted PDF file. Articles will then be available through BioMed Central and submitted for inclusion in PubMed and PubMed Central.

Editorial policies
Submission of a manuscript for publication in a supplement published by BioMed Central implies that all authors have read and agreed to its content, and that readily reproducible materials described in the manuscript 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 paper. Where appropriate, authors are encouraged to adhere to the standards proposed by the Microarray Gene Expression Data Society and to deposit microarray data in one of the public repositories.

Authors are required to ensure that no material submitted as part of a manuscript infringes existing copyrights, or the rights of a third party. The manuscript should not already have been published in a journal and should not be under consideration by any other journal, but it can already have been deposited on a preprint server.

Submission of a manuscript reporting experimental research on humans or animals implies that authors have obtained approval for their research from the appropriate ethics committee or government body regulating animal or human research. A statement to this effect must be included in the Methods section of your manuscript.

Style and language
BioMed Central will not edit submitted manuscripts for style or language; although we may request the revision 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. Non-native speakers of English may choose to make use of a copyediting service.

Copyright
Copyright on articles published in supplements to journals published by BioMed Central will be retained by the author(s). Authors grant BioMed Central a license to publish the article and identify itself as the original publisher. Authors also grant any third party the right to use the article freely as long as its integrity is maintained and its original authors, citation details and publisher are identified. The BioMed Central Copyright and License Agreement formalizes these and other terms and conditions of publishing articles in the supplement.

Manuscript preparation

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)

Users of other word processing packages should save or convert their files to RTF before submission.

Note that figures must be submitted as separate image files, not as part of the main manuscript.

Microsoft Word template
Although we can accept any manuscript prepared as Microsoft Word, Word Perfect or RTF file, 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 journal style.

How to use the BMC journal template
The template consists of a standard set of headings that make up an 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 that 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.
• Enter the references using the reference style given.

Preparing figures
Illustrations should be provided as separate files, not embedded in the text file. Each figure should include a single illustration, which should be submitted as a separate graphics file. Figures may be submitted in color. Each figure should be closely cropped to minimize the amount of white space surrounding the illustration. Our figure cropping guidelines may be of help.

If a figure consists of separate parts, it is important that a single composite illustration file should be submitted which contains all parts of the figure.

Photographs should be provided with a scale bar if appropriate, as well as high-resolution component files.

Scaling/resolution
Illustrations should be designed such that all information is legible when scaled to a horizontal width of 600 pixels, since this is the default size for a BMC journal (and PubMed Central) illustration on the web. High-quality versions of figures will also be generated and stored by BioMed Central, however, so image files should be submitted at a resolution of 300 dpi or greater if possible.

Text within figures should use either Arial or Helvetica fonts, although Courier may also be used if a monospaced font is required. Text too should be designed to be legible when the illustration is scaled to a width of 600 pixels.

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 A4 portrait, single page only)
• PowerPoint (figures must be a single page)
• TIFF
• JPEG
• BMP

BioMed Central is not able to process figures submitted in GIF format.

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.

If the large size of TIFF or EPS figures is an obstacle to submission, authors may find that conversion to JPEG format results in significantly reduced file size, while retaining acceptable quality. JPEG is a 'lossy' format, however. In order to maintain acceptable image quality, it is recommended that JPEG files are saved at High or Maximum quality.

Files should not be compressed with tools such as Zipit or Stuffit prior to submission. These tools will in any case produce negligible file-size savings for JPEGs and TIFFs which are already compressed.

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.

Small tables which are integral to the manuscript should be pasted into the end of the document text file. 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; 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.

Tables should not include shading or colour.

Style and language

General
Currently, BioMed Central 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 to supplements, unless otherwise instructed by the supplement organizers, but authors are encouraged to be concise. There is also no restriction on the number of figures or tables, but note that these should be limited to a reasonable number for the length of the article. Figures and tables should be sequentially referenced. Authors should include all relevant supporting data with each article.

BioMed Central will not edit submitted manuscripts for style or language.

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.
• All pages should be numbered.
• Use the BioMed Central 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 may be lost during conversion to PDF.

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

Manuscript sections

Note that all articles must be structured and include a title page and abstract. Manuscripts should be divided into sections as appropriate to the article. The following sections must be included:

Title page
Abstract
Background
Main text
Conclusions
List of abbreviations used (if any)
Acknowledgements
References
Figure legends (if any)
Tables and captions (if any)

Research articles must additionally include Methods and Results sections, with an optional Discussion section.

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
This should not exceed 250 words and, where appropriate, should be structured into separate sections headed Background, Results and Conclusions. Please do not use abbreviations or cite references, figures or tables in the abstract.

Background
The background section should clearly state the background to the article and its aims. The section should end with a very brief statement of what is being reported in the article.

Main text
Main text should be arranged under appropriate subheadings. The supplement organizers should specify the order of these sections, which may include:

Methods
This should be divided into subsections if several methods are described. [NB. The Methods section may be placed after the Conclusion if this is specified by the supplement organizers.]

Results (where included)
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 and give a clear explanation of their importance and relevance.

List of abbreviations used (if any)
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 acknowledgements. Acknowledgements
These should be kept to a minimum. Authors should obtain permission to acknowledge from all those mentioned in the acknowledgements.

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 figure legends. Each reference must have an individual reference number. Please avoid excessive referencing.

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 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 published 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. There should usually be no more than 50 references per article.

Examples of the BMC journal reference style are shown below. Please take care to follow the reference style precisely; references not in the correct style may result in manuscripts being returned to the supplement organizers for correction, delaying publication of the supplement.

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 3:149-70.

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. Mouse Tumor Biology Database [http://tumor.informatics.jax.org/cancer_links.html]

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

Tables and captions (if any)
Tables which are integral to the manuscript should be included at the end of the document text file.

Preparing additional files
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 BMC journals. 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.

Although BMC journals do 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 10 MB, 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

PDF (Adobe Acrobat)

Animations

SWF (Shockwave Flash)

Movies

MOV (QuickTime)

MPG (MPEG)

Tabular data

XLS (Excel spreadsheet)

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 send linked worksheets or PDF files larger than one sheet).

It is important that authors are provided with the authors presubmission checklist to ensure that the manuscript is formatted correctly. This is provided in the document, supplement organizers submission checklist.