期刊名称：BMC BIOINFORMATICS
 期刊简介(About the journal)
投稿须知(Instructions to Authors)
编辑部信息(Editorial Board)
About the journal
About BMC Bioinformatics
BMC Bioinformatics (ISSN 1471-2105) is an online journal publishing research articles after full peer review. All articles are published, without barriers to access, immediately upon acceptance. The journal is published by BioMed Central Ltd, Floor 6, 236 Gray's Inn Road, London, WC1X 8HL, United Kingdom.
Scope
BMC Bioinformatics is an Open Access, peer-reviewed journal that considers articles on all aspects of computational methods used in the analysis and annotation of sequences and structures, as well as all other areas of computational biology.
Criteria for publication
Publication of research articles by BMC Bioinformatics is dependent primarily on their validity and coherence , as judged by peer reviewers, who are also asked whether the writing is comprehensible and how interesting they consider the article to be. If an article is of broad interest, the authors may be asked if they would prefer it to be published in BMC Biology, and the article may be highlighted in a variety of ways as a service to our readers and contributors.
Speed of publication
BMC Bioinformatics offers a very fast publication schedule while maintaining rigorous peer review; all articles must be submitted online, and peer review is managed fully electronically (articles are distributed in PDF form, which is automatically generated from the submitted files). Articles will be published electronically in manuscript form immediately upon acceptance. A fully structured web version, and accompanying laid out PDF, will be published within a few weeks of acceptance.
Flexibility
As an electronic-only journal, BMC Bioinformatics gives authors the opportunity to publish large data sets, large numbers of illustrations and moving pictures, to display data in a form that can be read directly by other software packages so as to allow readers to manipulate the data for themselves, and to create all relevant links (for example, to PubMed, to sequence and other databases, and to other papers).
Submission of manuscripts
Manuscripts must be submitted to BMC Bioinformatics electronically using the online submission system. Full details of how to submit a manuscript are given in the instructions for authors.
Indexing and archiving
Following publication in BMC Bioinformatics, the full text of each article is immediately and permanently archived in PubMed Central, the US National Library of Medicine's full-text repository of life science literature, and also in repositories at the University of Potsdam in Germany, at INIST in France and in e-Depot, the National Library of the Netherlands' digital archive of all electronic publications. BMC Bioinformatics is indexed/tracked/covered by PubMed, MEDLINE, BIOSIS, CAS, Scopus, EMBASE and Google Scholar.
BMC Bioinformatics is included in Thomson Reuters Web of Science and other products. It has an Impact Factor of 3.49.
Copyright
The authors are the copyright holders for all articles in BMC Bioinformatics and have granted to any third party, in advance and in perpetuity, the right to use, reproduce or disseminate the article, according to the BioMed Central copyright and license rules.
Citing papers in the journal
Articles in BMC Bioinformatics should be cited in the same way as articles in a traditional journal, with one exception. Because articles in this journal are not printed, they do not have page numbers. Instead, they have a unique article number.
The following citation:
BMC Bioinformatics 2000, 1:2
refers to article 2 from volume 1 of the journal.
As an online journal, BMC Bioinformatics does not have issue numbers. Each volume corresponds to a calendar year.
Contacting BMC Bioinformatics
Queries about content, submissions, or the review process should be directed to editorial@biomedcentral.com. All other enquiries should be directed to info@biomedcentral.com.
Instructions to Authors
Instructions for BMC Bioinformatics authors
General information
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Style and language
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General information
You are advised also to read About this journal, 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. 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).
We also provide a collection of links to useful tools and resources for scientific authors, on our Tools for Authors 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.
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 manuscript. 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 , their 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 2009 the article-processing charge is ?025/US$1515/€1130. Generally, if the submitting author's institution is a BioMed Central member the cost of the article processing charge is covered by the membership, and no further charge is payable. In the case of authors whose institutions are supporter members of BioMed Central, however, a discounted article processing charge is payable by the author. Please click here to check if your institution is a BioMed Central member. We offer a ?0 discount for manuscripts formatted with EndNote 5 (or later versions) or Reference Manager 10 or created using Publicon. We routinely waive charges for authors from low-income countries. For further details, see more information about article-processing charges.
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 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 who publish in BMC Bioinformatics retain copyright to their work (more information). Correspondence concerning articles published in BMC Bioinformatics is encouraged through the online comment system.
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, 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.
Any 'in press' articles cited within the references and necessary for the reviewers' assessment of the manuscript should be made available if requested by the editorial office.
Submission of a manuscript to 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.
BMC Bioinformatics also supports initiatives aimed at improving the reporting of biomedical research. We recommend authors refer to the MIBBI Portal for prescriptive checklists for reporting biological and biomedical research where applicable.
Nucleotide sequences
Nucleotide sequences can be deposited with the DNA Data Bank of Japan (DDBJ), European Molecular Biology Laboratory (EMBL/EBI) Nucleotide Sequence Database, or GenBank (National Center for Biotechnology Information).
Protein sequences
Protein sequences can be deposited with SwissProt or the Protein Information Resource (PIR).
Structures
Protein structures can be deposited with one of the members of the Worldwide Protein Data Bank. Nucleic Acids structures can be deposited with the Nucleic Acid Database at Rutgers. Crystal structures of organic compounds can be deposited with the Cambridge Crystallographic Data Centre.
Chemical structures and assays
Structures of chemical substances can be deposited with PubChem Substance. Bioactivity screens of chemical substances can be deposited with PubChem BioAssay.
Microarray data
Where appropriate, authors should adhere to the standards proposed by the Microarray Gene Expression Data Society and must deposit microarray data in one of the public repositories, such as ArrayExpress, Gene Expression Omnibus (GEO) or the Center for Information Biology Gene Expression Database (CIBEX).
Computional modeling
We encourage authors to prepare models of biochemical reaction networks using the Systems Biology Markup Language and to deposit the model with the BioModels database, as well as submitting it as an additional file with the manuscript.
Plasmids
We encourage authors to deposit copies of their plasmids as DNA or bacterial stocks with Addgene, a non-profit repository, or PlasmID, the Plasmid Information Database at Harvard.
BioMed Central is a member of the Committee on Publication Ethics (COPE). Authors who have appealed against a rejection but remain concerned about the editorial process can refer their case to COPE. For more information, visit www.publicationethics.org.uk.
BioMed Central endorses the World Association of Medical Editors (WAME) Policy Statement on Geopolitical Intrusion on Editorial Decisions.
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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)
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. 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 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:
Research article
Database
Methodology article
Software
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
Abstract
Background
Results
Discussion
Conclusions
Methods (can also be placed after Background)
List of abbreviations used(if any)
Authors' contributions
Authors' information (if any)
Acknowledgements
References
Figure legends (if any)
Tables and captions (if any)
Description of additional data files (if any)
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.
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.
Authors' information
You may choose to use this section to include any relevant information about the author(s) that may aid the reader’s interpretation of the article, and understand the standpoint of the author(s). This may include details about the authors' qualifications, current positions they hold at institutions or societies, or any other relevant background information. Please refer to authors using their initials. Note this section should not be used to describe any competing interests.
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 ?0 on the ?025/US$1515/€1130 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 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 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 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, 43(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:
Replace the dummy text for Title, Author details, Institutional affiliations, and the other sections of the manuscript with your own text (either by entering the text directly or by cutting and pasting from your own manuscript document).
If there are sections which you do not need, delete them (but check the rest of the Instructions for Authors to see which sections are compulsory).
If you need an additional copy of a heading (e.g. for additional figure legends) just copy and paste.
For the references, you may either manually enter the references using the reference style given, or use bibliographic software to insert them automatically. We provide style files for End Note and Reference Manager.
For extra convenience, you can use the template as one of your standard Word templates. To do this, put a copy of the template file in Word's 'Templates' folder, normally C:\Program Files\Microsoft Office\Templates on a PC. The next time you create a new document in Word using the File menu, the template will appear as one of the available choices for a new document.
Note - From version 6, EndNote includes a full set of structured article templates for BioMed Central journals. Users of EndNote are encouraged to upgrade if necessary and make use of these templates. More information is available here.
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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 for detailed instructions on maximising the quality of your figures,
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. 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.
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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
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 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:
Create a folder containing a starting file called index.html (or index.htm) in the root
Put all files necessary for viewing the mini-website within the folder, or sub-folders
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
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
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 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.
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.
Capitalize 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 (liter and molar are permitted, however).
Last revised: 3 October 2005
Editorial Board
BMC Bioinformatics Editorial Board Members
Timothy Aitman Imperial College London, UK
Adam Arkin Lawrence Berkley National Laboratory, USA
Peer Bork European Molecular Biology Laboratory, Germany
Michael R Brent Washington University, St. Louis, USA
Roger Bumgarner University of Washington, USA
Ting Chen University of Southern California, USA
George M Church Harvard Medical School, USA
Kevin R Coombes University of Texas M.D. Anderson Cancer Center, USA
Richard Copley Wellcome Trust Centre For Human Genetics, UK
Joaquin Dopazo Centro de Investigación Príncipe Felipe, Spain
Richard Durbin Wellcome Trust Sanger Institute, UK
Sean Eddy Janelia Farm Research Campus, USA
Janan T Eppig The Jackson Laboratory, USA
Olivier Gascuel LIRMM-CNRS, France
Mikhail Gelfand Russian Academy of Science, Russian Federation
Mark Gerstein Yale University, USA
Winston Hide University of the Western Cape, South Africa
Des G Higgins University College Dublin, Ireland
Liisa Holm University of Helsinki, Finland
Frank Holstege University Medical Center Utrecht, Netherlands
Rafael Irizarry Johns Hopkins University, USA
Bernard Jacq IBDM, France
Tao Jiang University of California, Riverside, USA
Minoru Kanehisa Institute for Chemical Research, Kyoto University, Japan
Peter D Karp SRI International, USA
Steen Knudsen Medical Prognosis Institute, Denmark
Isaac Kohane Harvard Medical School, USA
Burkhard Morgenstern University of Goettingen, Germany
B F Francis Ouellette Institute for Cancer Research MaRS Centre, Canada
Jonathan Pevsner Kennedy Krieger Institute, USA
Pavel A Pevzner University of California, San Diego, USA
J. Sunil Rao Case Western Reserve University, USA
Steven Salzberg University of Maryland, USA
Colin Semple MRC Human Genetics Unit, UK
Donna Slonim Tufts University, USA
Berend Snel Radboud University Nijmegen Medical Centre , Netherlands
Toshihisa Takagi University of Tokyo, Japan
Masaru Tomita Keio University, Japan
Martin Vingron Max-Planck-Institut fur Molekulare Genetik, Germany
Michael S. Waterman University of Southern California, USA
BMC Bioinformatics Associate Editors
Fatima Al-Shahrour Centro de Investigación Príncipe Felipe, Spain
Marcella Attimonelli Universit?degli Studi di Bari, Italy
Emmanuel Barillot U900 INSERM Institut Curie, France
Rita Casadio University of Bologna, Italy
Duccio Cavalieri University of Florence, Italy
Matthew J Chalmers University of Glasgow, UK
Zhuchu Chen Xiangya School of Medicine, China
Thomas Dandekar University of Wurzburg, Germany
Jean-Jacques Daudin AgroParisTech, France
Eytan Domany Weizmann Institute of Science, Israel
Werner Dubitzky University of Ulster, UK
Sandrine Dudoit University of California, Berkeley, USA
Daniel Gautheret INSERM ERM-206 , France
Debashis Ghosh University of Michigan, USA
Raffaele Giancarlo University of Palermo, Italy
J Peter Gogarten University of Connecticut, USA
Stavros Hamodrakas University of Athens, Greece
Ze-Guang Han Chinese National Human Genome Center at Shanghai, China
Eivind Hovig The Norwegian Radium Hospital, Norway
Hsien-Da Huang National Chiao Tung University, Taiwan
Igor Jurisica Ontario Cancer Institute, Canada
Pandjassarame Kangueane Biomedical Informatics, India
Ina Koch Max Planck Institute for Molecular Genetics, Germany
Anders Krogh University of Copenhagen, Denmark
Deepak Kumar University of the District of Columbia, USA
Luhua Lai Peking University, China
Yixue Li Chinese Academy of Sciences, China
Jingchu Luo Peking University, China
Baldo Oliva Universitat Pompeu Fabra, Spain
Ivan Ovcharenko National Center for Biotechnology Information (NCBI), USA
Ivan Ovcharenko National Center for Biotechnology Information (NCBI), USA
Magnus Palmblad Leiden University Medical Center, Netherlands
Peter J Park Harvard University, USA
Anton Peeters Utrecht University, Netherlands
Graziano Pesole University of Milan, Italy
Mihai Pop University of Maryland, USA
Teresa M. Przytycka NCBI / NLM / NIH, USA
Ping Qiu Schering-Plough Research Institute, USA
Shoba Ranganathan Macquarie University, Australia
Jaques Reifman US Army Medical Research and Materiel Command, USA
Eric Rivals LIRMM, France
David M Rocke University of California, Davis, USA
Paolo Romano Instituto Nazionale per la Ricerca sul Cancro, Italy
Marie France Sagot Universite Claude Bernard, France
Kevin Sanbonmatsu Los Alamos National Laboratory, USA
Jacques Schrenzel Geneva University Hospitals, Switzerland
Denis C Shields UCD Conway Institute, Ireland
Richard Simon National Cancer Institute, USA
Thomas Simonson Ecole Polytechnique, France
Peter F Stadler University Leipzig, Germany
Stanislas Tomavo Universite des Sciences et Technologies de Lille, France
Chang-Shung Tung Los Alamos National Laboratory, USA
Gabriel Valiente Technical University of Catalonia, Spain
Mark P Wachowiak Nipissing University, Canada
Zhiping Weng Boston University, USA
Shoshana Wodak University of Toronto, Canada
Zhu Xiaoyan Tsinghua University, China
Zheng Rong Yang University of Exeter, UK
Mohammed Yeasin University of Memphis, USA
Michael Zhang Cold Spring Harbour Laboratory, USA
Xuegong Zhang Tsinghua University, China
Yang Zhong Fudan University, China
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