The following instructions are adapted from BMC Bioinformatics.
The following word processor file formats are acceptable for the main manuscript document:
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. 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 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/DVI 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 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:
You can download a template (Mac and Windows compatible; Microsoft Word 98/2000) for your article. For instructions on use, see below.
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), DNA Data Bank of Japan (DDBJ ), GenBank at the NCBI (GenBank), Protein Data Bank (PDB), Protein Information Resource (PIR) and the Swiss-Prot Protein Database (Swiss-Prot).
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
This should be divided into subsections if several methods are described.
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 £850 (€1250, US$1685) 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 and Reference Manager are available on the BioMed Central site, including information about how to upgrade.
Style files that conform to the BioMed Central style are available for EndNote and Reference Manager. 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.
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 (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:
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.
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.
Formats
The following file
formats can be accepted:
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.
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. 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.
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 10 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):
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.
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).
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"
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 can be
defined when first used or a list of abbreviations can be provided preceding the
acknowledgements and references.
Units
SI Units should be
used throughout (litre and molar are permitted, however).