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Author Guide

This guide is intended to give you the information you need to submit your paper to Systems Biology and to present it in accordance with our requirements. Further queries should be addressed to the managing editor.

Types of paper

Original Research Papers. Scientific papers describing new research developments in systems biology.

Special Issue Papers. Sets of papers on a specific subject, led by a guest editor and submitted in response to a call for papers.

Reviews. Technical surveys of recent work in a particular field of systems biology. Reviews are by invitation, although proposals are considered. Authors wishing to write a review for Systems Biology should send a draft abstract to the managing editor for consideration.

Essays. General, non-research articles offering perspectives on aspects of systems biology. Essays are usually commissioned but may also be submitted to the managing editor for consideration.

Technical Notes. Short descriptions about novel software or new algorithm implementations, tools and databases.

Submission

Papers should be submitted in electronic (PDF) form via our?Manuscript Central site. If you encounter problems submitting your paper, please use the online support tool by clicking the Get Help Now icon at the top of the submission screen. If this does not resolve the problem, please contact [email protected]

To accelerate the reviewing process when submitting their manuscript, authors of original research papers should provide the names of three suitable reviewers, which the editors may use at their discretion. A list of up to six keywords or short phrases should also?be provided to characterise the paper, the specific research area to which results apply.

Papers should be submitted as a single PDF file including all figures and tables. Supplementary material should be submitted as separate files.

Revised versions of papers accepted subject to revision should be submitted in both PDF and source-file format.

Acceptable source-file formats are Microsoft Word (.DOC or .RTF) (Windows), PostScript, ASCII (Windows) with a description of the version used, or LaTeX.

Illustrations are preferred in the following formats: EPS; JPEG; TIFF. The resolutions on these formats should be high, i.e. colour: minimum 400 dpi, line: 1000dpi minimum, halftone: 300dpi minimum and combination 500dpi minimum.

Copyright

Submitted papers should be accompanied by an IEE Statement of Originality and Assignment of Copyright form signed by all authors. If this is not practical, the corresponding author may sign on behalf of all authors by indicating this next to their signature. Authors unable to include the form with their submission will be sent a copy for signing as soon as their paper is received. We will not normally send your paper into referral until we receive the copyright form.

All papers submitted to the IEE for publication must record original work not previously published. The submission should not be under consideration for publication by any other journal or other publisher. If we find that an author has deliberately plagiarised another work or has submitted his work to us while it is at the same time under consideration by another publisher we will instantly withdraw the paper and will refuse to consider any future papers by that author.

Papers should provide significant results and the reporting of incremental work is discouraged. Follow-up papers, particularly those based on conference submissions by the same author, should contain significant additional new material (~30%) to that already reported. Where an article is based on a previous conference paper, the conference paper should accompany your submission and you should provide details of how your new submission is different.

Should your paper draw on previously published work, proper acknowledgment should be given by its citation.

The authors should obtain, from the owners of the copyright, written permission to reproduce any illustration for which the copyright is not their own. The source of the illustration must be given in full.

Referral

Submitted papers will undergo screening by the editors to ensure that only those papers must relevant to the readership are sent out for review.

Papers will be sent out to a minimum of two expert reviewers chosen by the editors. To accelerate the reviewing process, when submitting their manuscript authors of original research papers should provide the names of three suitable reviewers, which the editors may use at their discretion.

Presentation

Length

Original research papers and special issue papers submitted to Systems Biology should be between 3000 and 4000 words in length. Additional material, e.g. derivations, algorithms, computer programs, etc. may be published online as supplementary material containing detailed proofs, algorithms, tables with parameter values, experimental materials & methods, and any other additional information which as supplementary material makes the main text more concise and readable. The supplementary material should be submitted as separate files. The recommended maximum number of figures is 10 and the number of tables is 5. Additional figures and tables may also be published online as supplementary material.

Reviews should generally not exceed 10000 words but this can be discussed with the managing editor. Supplementary material may be published online.

It is recommended that essays do not exceed 3000 words although this too can be discussed with the managing editor.

Technical notes should not exceed 1000 words and a maximum of three figures.

Language, spelling and grammar

All papers must be written in UK English. If English is not your first language, you should ask an English-speaking colleague to proofread your paper. Papers containing English that is so unclear as to obscure the meaning will be rejected by the editors without being sent out for review. All manuscripts should be spellchecked using a UK English spellchecker before they are submitted.

Acronyms and abbreviations

Specialist or uncommon acronyms and abbreviations should be clearly defined on their first occurrence in the text by writing the term out in full and following it with the abbreviation in round brackets.

Title

This should be concise but informative and should not include a subtitle. Avoid starting your title with the words “a”, “novel”, “new” or “the”, since these make your article difficult to find in journal databases.

Author affiliations

These should immediately follow the title. For multiple-authored articles list the names of all the authors first, followed by the full postal and email addresses, using identifiers to link an author with an address, where necessary. If an author’s present address is different from the address at which the work was carried out, this should be given as a footnote.

Abstract

This should be informative and not only indicate the general scope of the article but also state the main results obtained, methods used, the value of the work and the conclusions drawn. No table numbers, figure numbers, references or displayed mathematical expressions should be included. It should be suitable for direct inclusion in abstracting services as a self-contained article and should not exceed 250 words.

Headings

Papers and should be divided into numbered sections, subsections and, if necessary, subsubsections (e.g. 3, 3.1, 3.1.1, etc.).

Fonts and text layout

Use a TrueType font and normal face, allow generous margins and set your manuscript in single-column format.

Figures and figure captions

All figures should be submitted electronically and are preferred in the following formats: EPS; JPEG; TIFF. The resolutions on these formats should be high, i.e. colour: minimum 400 dpi, line: 1000dpi minimum, halftone: 300dpi minimum and combination 500dpi minimum.

Line drawings and pathway diagrams will not be redrawn or relabelled. It is therefore important that these are of sufficient quality for publication, i.e. clear and sharp with lettering that is in proportion to the rest of the figure. The use of characters, subscripts and superscripts in figures should also be consistent with that in the rest of the text.

Photographs and screenshots will be used as submitted and should therefore be of the highest resolution possible.

You should insert figures and figure captions in the text in the position that you wish them to appear in the proof. Each figure should be explicitly referred to in the text. Figures should be referred to in numerical order.

Colour should be used sparingly and only where absolutely necessary for an understanding of the paper. Colour should not be used for distinguishing data in line diagrams; instead use lettering, numbering or different types of line (full, dashed, dotted) or data point (square, triangle, cross). Note that light colours do not reproduce well when printed in black and white and could therefore make your data indistinguishable.

Tables

Each table should be referred to explicitly in the text in numerical order.

Avoid the use of unusual mathematical characters or graphical material in tables, since the markup language may not be able to reproduce this. If your table contains such material, it will be set as a figure.

Algorithms

Algorithms should not be boxed and should be set as normal text and not as figures or tables.

Computer code

Computer code will be set in two columns. This means that a long line of computer code that fits onto one single-column page may have to be separated into two lines when typeset. Please take this into account when writing any code. Code may be printed as a figure to enable full-page-width code.

Software

If any software has been developed as part of the research associated with the manuscript, a description on the availability, license agreement and a weblink should be provided. If the results were dependent on the use of software and algorithms, the authors should ensure that it is possible to validate the results with the information provided in the manuscript or using a supplement if necessary. Software and/or data should be freely available for a period of at least two years after publication.

Mathematics and equations

When writing mathematics, be sure to avoid confusion between characters that could be mistaken for one another, e.g. the letter ‘l’ and the figure one.

If your paper contains superscripts or subscripts to superscripts or subscripts, take special care to ensure that the positioning of the characters is unambiguous.

Ensure that superscripts and subscripts are used consistently in the body text, figures and tables.

Exponential expressions should be written using superscript notation, i.e. 5×103 not 5E03. A multiplication sign should be used, not a dot.

Symbols representing vectors and matrices should be in bold font.

Refer to equations using round brackets, e.g. (1)

Acknowledgments

Acknowledgments, if any, should appear at the end of your article, immediately before the References section, and not as footnotes.

References

Systems Biology uses the Vancouver (numerical) system for references. You should number your references sequentially through the text and each reference should be individually numbered. The numbers should be given in square brackets. The reference list at the end of the paper should list the references in numerical order.

Please ensure that references in the reference list at the end of the paper are referred to in the text and vice versa. (This is important so that readers of your paper can click on the in-text reference and be taken to the full reference.) If you do not we will have to ask you do so at proof stage and this will delay production of your article.

Please also ensure that you provide as much information as possible to allow the reader to locate the article concerned. This is particularly important for articles appearing in conferences, workshops and books that may not appear in journal databases. Please provide all author name(s) and initials, date published, title of journal or book, volume number, editors (if any) and, for books and conferences, the publisher and town of publication (in parentheses), and finally the page range.

Sample reference styles

Follow the reference styles below. These styles can be done automatically by using EndNote or similar reference software):

Note in particular

  1. The general sequence of information
  2. The different punctuation used depending on the kind of publication cited. A comma precedes journals and periodicals while a period (full-stop) precedes conferences, theses, technical reports, etc.
  3. In paper titles, only the first word is capitalised (with the exception of proper names)
  4. The use of punctuation in the authors’ names and initials, the order (surname then initial) and the space between an author’s initials.

Use the following style for references in a journal. Carefully follow the use of punctuation and note the general sequence of information, the order of author names (surname and then initial), the use of bold for volume and italics for the publication name, and the conventional method of abbreviation:

GOVAN, S. and GOVAN, S.: ‘This is a test journal paper’, Syst. Biol., 2004, 1, pp. 1-7

Use the following style for references in a conference. Carefully follow the use of punctuation and note the general sequence of information, the order of author names (surname and then initial), the use of bold for volume and roman face for the publication/conference name, and the conventional method of abbreviation:

GOVAN, S. and GOVAN, S.: ‘This is a test conference paper’. Proc. Int. Conf. Syst. Biol., 2002, Stockholm, Sweden, 1, pp. 1-7

Use the following style for references in a book. Carefully follow the use of punctuation and note the general sequence of information, the order of author names (surname and then initial), how to mention editions, the use of brackets to give information on the publisher, location and date) bold for volume and italics for the publication name, and the conventional method of abbreviation:

“GOVAN, S. and GOVAN, S.: ‘This is a test book paper’, in GOVAN, S. (Ed.) ‘Handbook of Systems Biology, 1st edition’ (IEE Press, Stevenage, UK, 2004), pp. 1-7

Checklist

What we look for in your paper

Referees are more likely to provide insightful feedback on your paper if it is well-written, interesting and easy to understand. Please use this checklist to help you ensure that your paper meets the standards we expect from submitted papers. (We ask our referees to look at these aspects when they review your paper.)

  • Scientific merit: is the work scientifically rigorous, accurate and correct?
  • Motivation: does the problem considered have a sound motivation? All papers should clearly demonstrate the scientific interest of the results. Papers should not rely solely on previous literature or novelty to motivate publication
  • Originality and justification: is the work relevant and novel? Does the work contain significant additional material to that already published and has its value been demonstrated?
  • Referencing: has reference been made to the most recent and most appropriate work? Is the present work set in the context of the previous work? Is there a balance of references from archival material (journals and conferences) and informal but up to date sources (websites, manuals and reports)?
  • Balance: is the overall balance and structure of the paper good? Should the authors concentrate more on a specific area of the paper, or are there sections which are unnecessary and which could be reduced or eliminated?
  • Appropriateness: is the material appropriate to the scope of the journal?
  • Clarity: is the English clear and well-written? Poorly written English may obscure the scientific merit of your paper. Are the ideas expressed clearly and concisely? Are the concepts understandable? Is the discussion written in a way that is easy to read and understand?
  • Length: Manuscripts should generally be between 3000 and 4000 words in length (10000 words for reviews).
  • Title: is it adequate and appropriate for the content of the article?
  • Abstract: does it contain the essential information of the article? Is it complete? Is it suitable for inclusion by itself in an abstracting service?
  • Diagrams, figures, tables and captions: are they clear and essential? Are all figures and tables labelled and referred to in the text?
  • Screenshots: can these be clearly read? If the lettering is too small, ensure that each picture is enlarged so that everything can be read.
  • Graphs and tables: are these clear and necessary? Where several graphs are on one set of axes, are they clearly distinguishable? Are the numbers in the tables readily understandable?
  • Mathematics: is the mathematics necessary? Does it use commonly understood symbols? Are equations numbered if referred to in the text?
  • Related work: related work should be mentioned at the end of the paper (before the conclusion).
  • Conclusion: does the paper contain a carefully written conclusion, summarising what has been learned and why it is interesting and useful?

Proofs and reprints

Proof correction

After your paper is accepted, we will upload the page proof of your paper to our website and will send you an email notifying you that it is available for viewing. We ask you to return your corrections within three working days or sooner. Note that your paper will be published online in advance of printed publication and it is therefore in your interest to return your corrections to us as soon as possible.

Requests for last-minute corrections, i.e. amendments to the original manuscript, may be denied at the managing editor’s discretion, particularly if these are likely to delay publication. Major changes-of-mind, e.g. rewriting of whole sections, is not permitted at this stage.

We prefer that you return your corrections by email. Corrections should be indicated in list form by giving the precise location of each correction (page and line number).

Reprints, journal copies and permissions

After the paper is printed, we will send the corresponding author 50 digital reprints of the paper and a complimentary copy of the issue in which the paper appears.

Permissions to reproduce articles published in Systems Biology should be emailed to the managing editor.