期刊名称：MOLECULAR SYSTEMS BIOLOGY
 期刊简介(About the journal)
投稿须知(Instructions to Authors)
About the journal
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Submission of a paper implies that it reports unpublished work and that it is not under consideration for publication elsewhere.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.
Instructions to Authors
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. Papers will be assigned by the Editor based at EMBO in Heidelberg to a Senior Editor, who will select appropriate referees and a member of the Editorial Advisory Board to review the manuscript. 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.
Post-publication comments and review
Reports published in Molecular Systems Biology will be open to comments and reactions from readers and authors are strongly encouraged to respond to these. The discussion threads will be moderated by the Editor and will be linked to the online version of the report.
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.
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).
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 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.
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 not be used unless 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.
Citing articles published in Molecular System Biology
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.
As Molecular System 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
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.
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.
Data Sets
Data sets must be supplied to the Editorial Office in its final form for peer review. Data sets are not subedited, so authors should ensure that it is supplied ready for publication online.
Submission of SBML files
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.
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, movies or extensive tables.
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.
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. Please see below for acceptable file formats and sizes.
Supplementary data describing the results of microarray studies or similar large-scale expression experiments should be deposited with one of the public databases (ArrayExpress (www.ebi.ac.uk/arrayexpress/) or GEO (www.ncbi.nlm.nih.gov/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.
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.
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