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Aims and scope of journal

Molecular Systems Biology is an integrative discipline that seeks to explain the properties and behaviour of complex biological systems in terms of their molecular components and their interactions. Molecular Systems Biology publishes reviews and relevant, high-quality research in the evolving fields of systems biology, bioinformatics, genomics and proteomics, microbial and eukaryotic cell and tissue systems, cell signaling and computational networks. The Editors will select those manuscripts that merit urgent publication because they report novel findings of wide biological significance. An additional criterion for acceptance will be the extent to which the work reported leads to the integration of large datasets both with each other and with theory, with a goal to better understand the dynamic and complex nature of living systems. Reports of new experimental methods and manuscripts that put forward proposals of metrics for the quality and validation of complex datasets will also be considered in the context of this policy. Articles addressing topics in mathematical biology will be accepted only if they are firmly grounded in experimental biological data. Although the primary emphasis of the journal will be on molecular components and their interactions, systems studies at the organ level may also be considered.

Papers should be intelligible to as wide an audience as possible. Particular attention should be paid to the Abstract, Extended Synopsis, Introduction and Discussion sections, which should clearly draw attention to the novelty and significance of the data reported. Failure to do this may result in delays to publication or rejection of the paper.

Submission of a paper implies that it reports unpublished work and that it is not under consideration for publication elsewhere. Molecular Systems Biology allows and encourages prior publication on recognized community preprint servers for review by other scientists in the field before formal submission to the journal. The details of the preprint server concerned and any accession numbers should be included in the cover letter accompanying submission of the manuscript. This policy does not extend to preprints that are publicised outside the scientific community before or during the submission and consideration process at Molecular Systems Biology.

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Prior to submission

To avoid unnecessary delays in the review process, please consider the following policies carefully before you submit your manuscript.

Availability of published material, data and software

The following guidelines were inspired, in part, by the recommendations formulated by the Board on Life Sciences from the National Academies Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences (National Academies Press, 2003). It is understood that by publishing their work in Molecular Systems Biology, authors agree to the disclosure of their findings and the release of their data, reagents and methods to enable colleagues in academic research to verify, reproduce and build on the published work. The guidelines below should be interpreted in this spirit.

• Organisms, viruses, cells, nucleic acids, antibodies, and other reagents that were used in the research reported and that are not available from commercial suppliers should be freely available to colleagues in academic research.
• Datasets obtained by experimentation, computation or data mining, should be made freely available, without restriction. This holds without exception to data that are central and integral to the findings reported in the paper and it is strongly recommended for any remaining associated data.
• Software should be described in sufficient detail to allow reproduction of the underlying algorithms by others. This may be achieved by providing the appropriate narrative or mathematical description, pseudocode and, possibly but not obligatorily, the source code. If a specific implementation is the focus of the study, it is strongly recommended that non-commercial users are granted free access to this implementation.
• If a piece of software is central to the study, it is strongly recommended that it provides appropriate mechanisms (eg data import and export functionalities) for a reasonable integration in other workflows.
• Databases represent a combination of software (formulations of queries) and structured data (definitions and content of tables). As such, the two components of databases should be treated according to the guidelines above on data and software sharing.
• Any restrictions on the availability or on the use of included data, software and databases should be clearly specified in the paper. These restrictions may detract from the overall impact of a study, in particular when datasets, software or databases are central to the findings reported, and, therefore, will be taken into account in the final editorial decision.

Deposition of data that cannot be published together with the manuscript itself should preferably be in one of the public databases (see Submission to public databases below). To avoid delays in publication of the manuscript, we encourage authors to deposit such data prior to submission. The authors may request that the data be stored in a confidential section of the database, in which they can request passwords from the database administrators, and these should be passed on the Editorial Office to allow the editors and referees to anonymously access the information during the review process. Accession codes must be provided at the time a revised manuscript is returned to the Editorial Office. Data for which no suitable public database yet exists may be submitted to the journal archive site for interim storage.

Conflicts of interest

In the interests of transparency and to help reviewers assess any potential bias, Molecular Systems Biology requires authors of original research papers to declare any competing commercial interests in relation to the submitted work. Referees are also asked to indicate any potential conflict they might have reviewing a particular paper. Please refer to the 'Guide for Referees' for details.

Electronic manipulation of images

Digital image enhancement is acceptable practice, although it can result in the presentation of quite unrepresentative data as well as in the loss of meaningful signals. During manipulation of images a positive relationship between the original data and the resulting electronic image must be maintained. If a figure has been subjected to significant electronic manipulation, the specific nature of the enhancements must be noted in the figure legend or in the 'Materials and methods' section. The Editors reserve the right to request original versions of figures from the authors of a paper under consideration. Digital files should be submitted in a transparent format.

Related articles and supplementary information for the editors and the reviewers

Any manuscripts under review or accepted for publication elsewhere should accompany the submission if they are relevant to its scientific assessment. Authors should also provide upon submission any kind of supplementary material that will aid the review process. This may include access to appropriate software tools to allow editors and referees independently assess the methods used for data analysis.

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Submission

The Editors reserve the right to return manuscripts that are not in accordance with the following instructions.

Manuscripts must be written in clear and concise English and be intelligible to a broad readership.

Authors should include the names of 4 potential reviewers when submitting their manuscript. After consultation with the Senior Editors, the Editor based at EMBO in Heidelberg will select appropriate referees. The decision concerning publication, revision or rejection is taken based on their reports and recommendations. Papers may, however, be returned to authors without review if in the judgement of the Editors and the Editorial Advisory Board, they fall out of scope of the Journal, fail to meet the criteria of wide biological significance and novelty, or if they are considered too preliminary.

We will acknowledge receipt of a submitted manuscript by e-mail as soon as a Senior Editor has been assigned to the paper. All further correspondence will also be by e-mail.

Original research articles

Molecular Systems Biology publishes original research in two main formats: Articles and Reports.

Articles

Articles are full-length original research papers and should be divided into the following sections:

• Title page
• Abstract
• Extended Synopsis
• Introduction
• Results
• Discussion
• Materials and methods
• Acknowledgements
• References
• Figure legends
• Figures
• Tables
• Supplementary information

The total character count (including spaces) for an Article, excluding the Extended Synopsis, Methods section, tables and supplementary material, but including title page, abstract, figure legends and references should not exceed 60,000 characters (the exact character count to be stated on the title page). Articles have typically 6-8 Figures. Manuscripts exceeding this limit at submission may be returned to the authors for amendment. Please consider including a Supplementary information section (see below) if your manuscript exceeds the above limitations.

Reports

Reports are short publications focusing on a particularly provocative and novel aspect of a study. Reports do not have a Synopsis, but they should have an Abstract phrased in terms that are comprehensible to readers outside the discipline. Results and Discussion sections should be combined. The remaining sections are organized as described above for Articles.

The total character count (including spaces) for Reports, excluding the Methods section, tables and supplementary material, but including title page, abstract, figure legends and references should not exceed 22,000 characters (the exact character count to be stated on the title page). Reports have in principle a maximum of 3 Figures. Manuscripts exceeding this limit at submission may be returned to the authors for amendment. Please consider including a Supplementary information section (see below) if your manuscript exceeds the above limitations.

Title Page

The title should be short and informative, and should not contain any abbreviations. The total length of the title should not exceed 100 characters (including spaces). Serial titles are not accepted.

The full name of each author should be given. Numbers in superscript should be used to indicate the department, institution, city with postal code and country, for each author. Any changes of address may also be given in numbered footnotes. It is possible to name more than one author as the correspondent of a published article; at the time of submission, however, it is important to indicate only a single author to whom all correspondence is to be addressed, together with an e-mail address, telephone and fax numbers.

The title page must also state the precise character count of the manuscript.

Please provide a running title of no more than 50 characters including spaces.

Up to five keywords, which may or may not appear in the title, should be given in alphabetical order, below the abstract, each separated by a slash (/).

Subject Categories are used to structure the current and archived online content of Molecular Systems Biology, and to help readers interested in particular areas of molecular biology find relevant information more easily. Subject Categories are also indicated in the table of contents and on the title page of the published article.

Authors should suggest appropriate Subject Categories for the submitted manuscript. One or two categories may be selected from the following list:

• Bioinformatics
• Proteomics
• Functional genomics
• Structural genomics
• Metabolic and regulatory networks
• Synthetic biology
• Computational methods
• Simulation and data analysis
• Development
• Immunology
• Neuroscience
• Plant Biology
• Structural Biology
• Genome Stability & Dynamics
• Chromatin & Transcription
• RNA
• Proteins
• Cellular Metabolism
• Signal Transduction
• Cell Cycle
• Differentiation & Death
• Membranes & Transport
• Cell & Tissue Architecture
• Microbiology & Pathogens
• Molecular Biology of Disease

Abstract

This should be a single paragraph not exceeding 175 words. The Abstract should be comprehensible to readers before they have read the paper, and abbreviations should be avoided. Reference citations within the abstract are not permitted.

Extended Synopsis (Article format only)

Authors should provide an extended synopsis of their report. The style and format should be appropriate to a wider readership that may not necessarily be interested in (or able to follow) the complexities of mathematical modeling etc. The total length of this section should not exceed 1000 words and it may contain up to two of the original article figures. Where necessary, the Editor and NPG will provide support to create this section of the manuscript, once the original article has been accepted. Authors will approve the final proofs.

The extended synopsis does not need to be included in the initial submission but should be submitted at revision stage. The synopsis text should be saved in a separate file and submitted as such together with the other parts of the manuscript.

Introduction

The Introduction should be succinct and provide only the necessary background information, rather than a comprehensive review of the specific field. It should not contain subheadings.

Results and Discussion

These sections should be combined in the Report format. In articles, each section should be divided by subheadings and may be combined into one section if appropriate.

Materials and methods

This section should contain sufficient detail so that all experimental procedures can be repeated by others, in conjunction with cited references. Authors should also provide clear and complete descriptions of the metrics applied for quality assessment and validation of their datasets and the computational tools used for data analysis. Molecular Systems Biology encourages detailed descriptions of methodology or additional materials to be included as Supplementary information. This information should, however, not be of immediate importance for the understanding of the manuscript.

Acknowledgements

These should be placed at the end of the text and not in footnotes. Personal acknowledgements should precede those of institutions or agencies.

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Other article types

Reviews

Review articles aim to provide accessible, authoritative overviews of a field or topic. Reviews should communicate a sense of enthusiasm, weaving background information with the latest advances, and placing both of these elements in the context of the rest of the field. The readership of Molecular Systems Biology encompasses a wide range – from advanced undergraduate and graduate students to group leaders and professors. Technical terms and specialist jargon should be avoided or clearly defined.

Reviews are usually commissioned but can also be submitted. After submission, all articles are refereed.

The main text should be about 5,000 words. References should be limited to ~100 for a long Review concentrating on significant original research papers.

Perspectives

Perspective papers provide a platform to expose hypotheses and concepts that open up new avenues in Systems and Synthetic Biology. A Perspective paper has a more focused scope than a Review in the sense that it may highlight the work of a single laboratory and may present a particular viewpoint on a field.

This format can also accommodate proposals, in which existing knowledge is used to delineate the plan of an ambitious project that would provide decisive and novel insight in the fields of Systems and Synthetic Biology. The proposed goal has to be highly original and of broad interest to the community. A proposal should detail the various aspects of the project such as its objectives, main concrete steps and milestones, utility and implications while in development and after completion.

Perspectives are usually commissioned but can also be submitted. After submission, all articles are refereed.

The main text should be about 5,000 words. References should be limited to ~100.

News & Views

Molecular Systems Biology's News & Views section provides a forum in which scientific news can be communicated to a wide audience spanning the varied disciplines covered in systems biology.

News & Views articles are short (usually 800-900 words), and have as much in common with journalistic news reports as the formal scientific literature. They should therefore make clear the news and opinions being discussed, and communicate a sense of excitement, yet provide a critical evaluation of the research or approach concerned.

Blog

The Seven Stones is the blog of Molecular Systems Biology. It provides a forum for open discussions and an exchange platform for all scientists interested in the fields of Systems and Synthetic Biology. The topics covered include all aspects of Systems and Synthetic Biology, including technical matters, general scientific issues and societal aspects. The blog is seeded by the Editors of the journal, but suggestions for posts can be sent to msbforum@embo.org

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General Guidelines

Text

The Editorial Office will only accept text files in LaTeX, RTF or MS Word format. The final character count must be clearly indicated on the title page of the revised manuscript. Manuscripts that do not comply with the formatting guidelines above, or exceed the length restrictions, will not be considered and returned to the authors for amendment. Please submit the full text (including figure legends, tables, and references) as an MS Word or RTF file, named "<5-digit manuscript number>.doc" or "<5-digit manuscript number>.rtf" (eg "48000.doc" or "48000.rtf").

Please use 'Times' font at 10 or 12 point size for all text pages, 'Symbol' font for non–Latin characters, and 'Helvetica' font for lettering on figures. 'Courier' font may be used for sequence data. Number each page at the bottom (Title page is 1).

Saving files with Microsoft Office 2007

Microsoft Office 2007 saves files in an XML format by default (file extensions .docx, .pptx and xlsx). Files saved in this format cannot be accepted for publication.

Save Word documents using the file extension .doc

• Select the Office Button in the upper left corner of the Word 2007 Window and choose "Save As"
• Select "Word 97-2003 Document"
• Enter a file name and select "Save"

These instructions also apply for the new versions of Excel and PowerPoint.

Equations in Word must be created using Equation Editor 3.0

Equations created using the new equation editor in Word 2007 and saved as a "Word 97–2003 Document" (.doc) are converted to graphics and can no longer be edited. To insert or change an equation with the previous equation editor:

• Select "Object" on the "Text" section of the "Insert" tab
• In the drop-down menu – select "Equation Editor 3.0"

Do not use the "Equation" button in the "Symbols" section of the "Insert" tab.

Non–Native Speakers of English

Authors who are not native speakers of English who submit manuscripts to international journals often receive negative comments from referees or editors about the English–language usage in their manuscripts, and these problems can contribute to a decision to reject a paper. To help reduce the possibility of such problems, we strongly encourage such authors to take at least one of the following steps:

• Have your manuscript reviewed for clarity by a colleague whose native language is English.
• Use a service such as one of those listed below.

An editor will improve the English to ensure that your meaning is clear and identify problems that require your review. Note that the use of such a service is at the author's own expense and risk and does not guarantee that the article will be accepted. Nature Publishing Group accepts no responsibility for the interaction between the author and the service provider or for the quality of the work performed.

• American Journal Experts
• Inter-Biotec
• Inter-Biotec also provides a free online writing course to help biomedical scientists whose first language is not English to write and publish their papers in English-language journals.
• SPI Professional Editing Services
• Write Science Right

References

Authors are responsible for the accuracy of the references. Published articles as well as those in press (please state the name of the journal and enclose a copy of the manuscript) may be included. In the text of the manuscript, a reference should be cited by author and year of publication; no more than two authors may be cited per reference; 'et al' should be used if there are more than two authors (Ferrier & Lunkes, 2003; Wiersdorff et al, 2000).

In the reference list, citations should be listed in alphabetical order and then chronologically, with the authors' surnames and initials inverted; et al should be used after the 20th author if there are more than 20 authors. Publications by the same author(s) in the same year should be identified with a, b, c after the year of publication.

The name of each journal should be abbreviated according to Index Medicus and italicized. References should therefore be listed (and will subsequently appear in print) as follows:

Wendland J (2003) Analysis of the landmark protein Bud3 of Ashbya gossypii reveals a novel role in septum construction. EMBO rep 4: 200-204

a) example of book chapter:

Price SR, Oubridge C, Varani G, Nagai K (1998) Preparation of RNA-protein complexes for X-ray crystallography and NMR. In RNA-Protein Interaction: Practical Approach, Smith C (ed) pp 37-74. Oxford: Oxford University Press

b) example of book:

Sambrook J, Fritsch E & Maniatis T (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbour Press, Cold Spring Harbour, New York, USA

Citations to articles in press or only published online at the time of submission should be made as follows:

c) example of article in press without doi:

Lim E-K, Ashford DA, Hou B, Jackson RG, Bowles DJ (2004) Arabidopsis glycosyltransferases as biocatalysts in fermentation for regioselective synthesis of diverse quercetin glucosides. Biotech Bioeng, (in press)

d) example of article in press with doi:

Eng-Kiat Lim and Dianna J Bowles, A class of plant glycosyltransferases involved in cellular homeostasis, The EMBO Journal advance online publication 8 July 2004; doi: 10.1038/sj.emboj.7600295

Personal communications (J Doe, personal communication, 2001) should be authorized in writing by those involved, and unpublished data should be cited as (J Smith and D Jones, unpublished data, 2001). References to manuscripts in preparation or submitted, but not yet accepted, should be cited in the text as (C Lee and N Jones, in preparation), not as (C Lee and N Jones, submitted), and should not be included in the list of references.

Web–based resources or manuscripts posted on non peer–reviewed pre–print servers should not be included in the list of references but should be cited directly in the text by providing the appropriate URL (http://www.example.net) or Digital Object Identifier (J Doe, 2007, doi:10.5555/npre.2007.223.1).

Citing articles published in Molecular Systems Biology

As Molecular Systems Biology is an online-only journal, articles are published on a rolling basis. Articles are cited according to their full article identifier (e.g. volume:article number) as follows:

Dudley AM, Janse DM, Tanay A, Shamir R, Church GM (2005) A global view of pleiotropy and phenotypically derived gene function in yeast. Mol Syst Biol 1: 1

Kahlem P, Birney E (2005) Dry work in a wet world: computation in systems biology. Mol Syst Biol 2: 40

Illustrations

We can only accept one file per figure. Composite figures containing multiple panels must be collected into one file before submission and must be scaled such that they can be reproduced on a single printed page.

Composite figures may be assembled in Adobe Photoshop or Illustrator and may be submitted in the default formats offered by these programs. If it is not possible to send artwork in the above formats, the Editorial Office can accept line drawings and composite figures in EPS format, and halftone figures in TIFF (please be sure to use LZW compression) or EPS formats. High-quality PDF files for figures may also be acceptable. We cannot proceed to publication with MS PowerPoint files.

All lettering should be done using standard fonts (Helvetica, Times, Symbol, Courier) and retained in a separate layer (if possible) so that the production team can adapt any labels to the Journal's style if necessary. All fonts used for labelling the figures should also be embedded in the final files if the software package offers this option.

Non–vector graphics should be preserved at high resolution: 300 dpi minimum at final size for greyscale or colour halftone images, and 1000 dpi minimum for bitmap (b/w) artwork.

Further information regarding the preparation of electronic figures (PDF, 32.5 KB) is available, in PDF format.

When submitting a revised manuscript, it is essential to include high–quality computer files for all figures, which will be used for the production process.

Figure legends

All symbols and abbreviations used in the figure must be defined, unless they are common abbreviations or have already been defined in the text. Experimental details should, where possible, be given in the Materials and Methods section, and not repeated in the figure legends.

Figures should be labeled in consecutive Arabic numerals (1, 2, 3 ...). The final size of figures will be between 82 mm and 172 mm wide on the printed page of the pdf file. Please bear this in mind when submitting your manuscript for review and allow for sufficient resolution at a suitable size.

Figures divided into parts should be labeled with an upper-case, bold letter (A, B, C ...). Figures with several parts should also be in proportion, with consistently sized lettering so that the whole figure can be reduced by the same amount to the smallest size at which the essential details are visible. Use Helvetica font for all the lettering, Courier font for sequence data and Symbol font for any symbols.

Scale bars, rather than magnification factors, should be used, with the length of the bar defined in the legend rather than on the bar itself. In general, visual cues on the figure itself are preferred rather than verbal explanations (for example, 'broken line' or 'filled black triangles') in the legend.

Boxes

Boxes usually include didactic or explanatory material. A Box can include exclusively text or it may combine a single illustration with a textual explanation. The illustration may include several panels (labelled as described above), in which case the text should cite them accordingly.

Tables

Tables should be typed on separate sheets and numbered consecutively with Roman numerals (I, II, III, IV ...). Tables should be self-explanatory and include a brief descriptive title. Footnotes to tables indicated by lower-case superscript letters are acceptable, but they should not include extensive experimental detail.

Tables can be submitted in HTML format and can include hyperlinks.

Conventions

In general, the journal follows conventions given in Scientific Style and Format: The CBE Manual for Authors, Editors and Publishers (1994) Cambridge University Press, Cambridge, UK, 6th edn. Please follow Chemical Abstracts and its indexes for chemical names. For guidance in the use of biochemical terminology follow the recommendations issued by the IUPAC-IUBMB Joint Commission on Biochemical Nomenclature. In general, genotypes should be indicated in italics; phenotypes should not be italicized.

Abbreviations

Try to restrict the use of abbreviations to SI symbols and those recommended by the IUPAC. Abbreviations should be defined in brackets after their first mention in the text, not in a list of abbreviations. Standard units of measurements (SI symbols) and symbols of chemical elements may be used without definition in the body of the paper. Abbreviations of standard biochemical compounds, e.g. ATP, DNA, nucleotides in nucleic acids, and amino acids in proteins, need not be defined.

Supplementary information

Supplementary information is peer–reviewed material directly relevant to the conclusions of an article that cannot be included in the published version owing to space or format constraints. It is posted on the journal's web site and linked to the article when the article is published and may consist of additional text, figures, tables, multimedia files or datasets. The published article must be complete and self-explanatory without the supplementary information. Supplementary information should enhance, but not be essential to, a reader's understanding of the paper.

We strongly recommend that Supplementary Information including text, figures and small tables (less than 50 rows) is combined into a single PDF starting with a Table Of Content listing ALL the items included in Supplementary Information (including audio, video and datasets). Each legend should be written clearly beneath its figure.

Supplementary information must be supplied to the Editorial Office in its final form for peer review. Supplementary information is not subedited, so authors should ensure that it is supplied ready for publication online.

Supplementary information must be supplied in one of the following file formats:

• Figures (including their respective figure legends) or additional text as a single PDF files (.pdf)
• Movies or animations as MPEG files (.mpg)
• Large tables (more than 50 rows) as MS Excel spreadsheet documents (.xls) or tab-delimited text (.txt)
• Data sets as plain text or XML files (.xml .sbml .owl etc)
• Compressed zipped archives (.zip) for complex data sets requiring a folder/sub-folder structure

Data supplied in other formats cannot be considered for online publication.

File sizes must be as small as possible, so that they can be downloaded quickly. The number of files should in principle be limited to 8, and the combined total file size may not exceed 25 MB. Individual files should not be larger than 1 MB (PDF or Excel files) or 15 MB (movie files, data sets).

The supplementary information may not be altered, nor new supplementary information added, after the paper has been accepted for publication.

Please refer to each supplementary item in the body of the text or the figure legends.

System models

The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, regulatory networks, and many others. Where relevant and possible, authors are encouraged to submit datasets in SBML format. Authors should select 'SBML' from the available list of data file formats when uploading the data set file.

Besides submitting the SBML–format files of the systems models associated with their paper for publication on the Journal web–site (see above), authors are also strongly encouraged to deposit such models in the Biomodels database. Contact information: E-mail: lenov@ebi.ac.uk , Tel: +44 (0)1223 494521, Fax: +44 (0)1223 494468.

Microarray data

Authors should refer to the MGED open letter specifying microarray standards. Supplementary data describing the results of microarray studies or similar large-scale expression experiments should be deposited with one of the public databases ArrayExpress or GEO prior to submission of the paper. To avoid delays in publication of the manuscript, we encourage authors to deposit relevant data in public databases prior to submission. The authors may request that the data be stored in a confidential section of the database, in which they can request passwords from the database administrators, and these should be passed on the Editorial Office to allow the editors and referees to anonymously access the information during the review process. Authors may submit the data in a MIAME format on CD-ROMs in a form accessible on different computer systems at the time of submission if they have not received passwords from the database administrators yet.

Molecular Systems Biology requires provision of accession numbers before acceptance of the paper for publication.

Structural data

Molecular Systems Biology accepts and follows the recommendations of the International Union of Crystallography (IUCr), with regard to the deposition and release of macromolecular structural data. These guidelines are set out in the article by the IUCr Commission on Biological Macromolecules in Acta Crystallographica (2000), D56, 2. In summary, they state that all publications must be accompanied by deposition of both the atomic coordinates and the structure–factor amplitudes in the appropriate database (PDB or NDB). In the case of low-resolution structures for which only a chain trace is reported, a set of C alpha positions and structure–factor amplitudes may be sufficient.

For NMR structures, data deposited should include resonance assignments, and all restraints used in structure determination (NOEs, spin-spin coupling constants, amide exchange rates, etc) and the derived atomic coordinates for both an individual structure and for a family of acceptable structures.

Structures of biological macromolecules solved by electron microscopy must be submitted to the EMDB database. For a brief description of the database, see Tagari et al. (2002) Trends Biochem Sci 27:589.

Molecular Systems Biology strongly encourages authors to submit their SBML models to the BioModels database hosted at the EMBL-EBI.

Sequence data

Nucleotide sequence data can be submitted in electronic form to any one of the three major collaborative databases:

DDBJ: DNA Data Bank of Japan, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411, Japan. Tel: +81 559 81 6853; Fax: +81 559 81 6849; E-mail: ddbjsub@ddbj.nig.ac.jp (for data submissions); www.ddbj.nig.ac.jp/

EMBL: EMBL Nucleotide Sequence Submissions, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Tel: +44 1223 494400; Fax: +44 1223 494472; E-mail: datasubs@ebi.ac.uk; www.ebi.ac.uk/

GenBank: National Center for Biotechnology Information, National Library of Medicine, Building 38A, Room 8N-803, Bethesda, MD 20894, USA. Tel: +1 301 496 2475; Fax: +1 301 480 9241; E-mail: gb-sub@ncbi.nlm.nih.gov; www.ncbi.nlm.nih.gov/

The suggested wording for referring to accession number information in journal articles is "These sequence data have been submitted to the DDBJ/EMBL/GenBank databases under accession No. U12345".

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Revision

When a manuscript is returned to authors for revision, the revised version should be submitted within 3 months of the authors' receipt of the referee reports. If a revised manuscript is returned thereafter, it will generally be considered as a new submission. Additional time for revision can be granted upon request, at the Editors' discretion. Only a single round of revision will be permitted.

The journal aims for rapid publication of papers. Please help the Editors and publisher avoid delays by providing e-mail address(es), telephone and fax numbers at which author(s) can be contacted.

The following items are required when submitting a revision:

• The manuscript text in LaTeX, RTF or MS Word format.
• A letter with a detailed description of the changes made in response to the referees.
• Three to four "bullet points" highlighting the main findings of your study.
• A "standfirst text" summarizing in two sentences the study.
• An extended synopsis (full-length Articles only, see Instructions for authors). Synopsis, bullet points and standfirst text should be submitted as a separate manuscript file in LaTeX, RTF or MS Word format.
• A "thumbnail image" (211x157 pixels, jpeg format) to highlight the paper on our homepage.
• The Licence to Publish should be completed and signed on behalf of all authors, with their consent, and faxed to the editorial office on +44 (0)1256 321670 on the same day the revision is submitted.

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Proofs

Authors will access PDF proofs by e-mail. These should be printed, annotated for necessary corrections (which should be detailed in a covering letter in case the FAX is unclear), and then returned by FAX to Nature Publishing Group (0044 (0)1256 321670). In the interests of speed, corrections should be returned within 24 hours. Essential changes of an extensive nature may be made only by insertion of a 'Note added in proof', and only with the approval of the Editors. A charge will be made to authors who insist on extensive amendment within the text at the page proof stage. Excessive alterations may delay publication of the article.

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Open Access and Charges

Molecular Systems Biology levies an article-processing charge of £1700 ($3000) per article accepted for publication. We can waive charges for authors that can justify their claim that they are unable to bear the costs of publication or those from low-income countries.

'Author pays' policy

The article is universally and freely accessible to all via the Internet, in an easily readable format and deposited immediately upon publication, without embargo, in an agreed format - current preference is XML with a declared DTD - in at least one widely and internationally recognized open access repository.

Molecular Systems Biology articles are published either under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 licence or a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 licence, at the free choice of the authors.

Under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 licence, users are free to share (copy, distribute and transmit) and remix (adapt) the contribution under the following conditions (read full legal code):

• Attribution. Users must attribute the contribution in the manner specified by the author or licensor (but not in any way that suggests that they or their use of the contribution is endorsed by the author or licensor).
• Noncommercial. Users may not use this work for commercial purposes.
• Share Alike. If users alter, transform, or build upon this work, they may distribute the resulting work only under the same or similar license to this one.

Under the Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 licence, users are free to share (copy, distribute and transmit) the contribution under the following conditions (read full legal code):

• Attribution. Users must attribute the contribution in the manner specified by the author or licensor (but not in any way that suggests that they or their use of the contribution is endorsed by the author or licensor).
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Digital object identifier

Nature Publishing Group assigns a unique digital object identifier (DOI) to every article it publishes. The DOI initiative is an international effort for electronic content identification and is guided by the International DOI Foundation, composed primarily of academic publishers and societies. The DOI appears on the title page of the article. It is assigned after the article has been accepted for publication and persists throughout the lifetime of the article. It is important to include the article's DOI in the reference, as volume and page information is not always available for articles published online.