Author Guidelines

Revisions to these Guidelines

PLEASE NOTE THAT MOLECULAR SYSTEMS BIOLOGY NOW REQUIRES A COMPLETE AUTHOR CHECKLIST (RIGHT CLICK AND 'DOWNLOAD') TO BE SUBMITTED WITH ALL REVISED MANUSCRIPTS.

For an illustrated technical guide to preparing figures, please download our figure preparation PDF.

About the Journal

Aims and Scope

Systems biology is an integrative discipline that seeks to explain the properties and behaviour of biological systems in terms of their components and their interactions.

Molecular Systems Biology is a peer-reviewed open access journal that publishes high-quality research in the fields of systems biology, synthetic biology and systems medicine. The Editors select manuscripts based on their novelty and wide biological significance with an emphasis on understanding the dynamic and complex nature of living systems. Reports of new methods and resources are also considered.

Topics falling within the scope of the journal include, but are not limited to: integrative and genome-scale biology, quantitative biology, computational biology, metabolic and regulatory networks, evolution of genomes and biological networks, systems medicine, synthetic biology and genome-scale biological engineering.

Molecular Systems Biology publishes research articles as full-length Articles or short Reports. The journal publishes also Reviews, Perspectives, News & Views, Correspondences and Editorials.

Bibliometrics

Impact Factor (2015): 10.5 (Thomson Reuters) 5-year Impact Factor (2015): 12.3 (Thomson Reuters) Immediacy Index (2015): 1.5 (Thomson Reuters) Eigenfactor (2015): 0.04 (eigenfactor.org) Article Influence (2015): 6.3 (eigenfactor.org) SJR (2014): 8.6 (JournalM3trics) SNIP (2014): 3.2 (JournalM3trics) h5 (2011-2015): 70 (Google Scholar)

Subject Categories

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

Systems & Synthetic Biology categories
Quantitative Biology & Dynamical Systems	Genome-Scale & Integrative Biology
Network Biology	Synthetic Biology & Biotechnology
Systems Medicine	Computational Biology
Methods & Resources

Molecular & Cell Biology categories
Ageing	Metabolism
Cancer	Microbiology, Virology & Host Pathogen Interaction
Cell Adhesion, Polarity & Cytoskeleton	Molecular Biology of Disease
Cell Cycle	Neuroscience
Cell Death & Autophagy	Pharmacology & Drug Discovery
Chemical Biology	Plant Biology
Chromatin, Epigenetics, Genomics & Functional Genomics	Post-translational Modifications, Proteolysis & Proteomics
Development & Differentiation	Protein Biosynthesis & Quality Control
DNA Replication, Repair & Recombination	RNA Biology
Evolution	Signal Transduction
Genetics, Gene Therapy & Genetic Disease	Stem Cells
Immunology	Structural Biology
Membrane & Intracellular Transport	Transcription

Editorial Policies

Submission of a manuscript implies that it reports unpublished work and that neither itself, nor parts of it, have been published or are under consideration for publication elsewhere. By submitting a manuscript, the authors guarantee that they have the appropriate authority from their employers and/or funding agencies to publish the work. Any related work under consideration, review, revision or accepted for publication elsewhere must accompany the submission if they are relevant to its scientific assessment.

Preprint Servers

All EMBO Press Journals encourage the posting of primary research manuscripts on non-peer-reviewed recognized community preprint servers such as arXiv, bioRxiv and PeerJ Preprint before - or in parallel with - formal submission to the journal. Versions of articles that have been revised to address referee comments, accepted for publication or indeed published in an EMBO Press journal should not be posted on a preprint server (note that doing so would also conflict with BioRxiv and Crossref's policies against duplicate DOI assignment). Manuscripts posted on bioRxiv will automatically forward-link to papers published in EMBO Press journals.

Manuscripts posted on recognized community preprint servers will not be considered in the evaluation of the conceptual advance of a manuscript submitted for publication in an EMBO Press journal.

BioRxiv posts can be directly transferred for formal submission to any EMBO Press journal using the B2J functionality. Please declare a preprint version of a manuscript in the cover letter accompanying submission to an EMBO Press journal.

We encourage formal citation of preprints in the reference list, where appropriate. The citation in the text is: (preprint: NAME1 et al, YEAR; in the reference list: Author NAME1, Author NAME2 (YEAR) article title. bioRxiv doi:

This policy applies to primary research papers, but not to reviews and commentary. The journal reserves the right not to publish material that has already been formally published, completely or substantially, in peer reviewed journals or in persistent digital media such as blogs that are not recognized as preprint servers. Conference presentations (including summaries, abstracts and posters) and doctoral (PhD) or master (MSc) theses are exempt (see Originality and Plagiarism).

Scooping Protection extended to include preprints

Other papers published in peer reviewed journals, or manuscripts posted on recognized preprint servers after submission of a manuscript to Molecular Systems Biology, are not considered relevant to the editorial assessment of the conceptual advance/novelty of the submitted manuscript.

A manuscript submitted to Molecular Systems Biology is subject to scooping protection from the day of submission to Molecular Systems Biology, and extends through the agreed revision period. For transferred manuscripts, scooping protection applies from the day of submission to the EMBO Press sister journal.

Scooping Protection has now been extended to also apply from the day of posting a manuscript on a recognized preprint server in the same form as the manuscript submitted to Molecular Systems Biology, provided the manuscript is submitted to the journal within 4 months of posting.

Note that related papers, and where appropriate preprints, have to be cited appropriately if they are published before the manuscript proofs stage.

Note that scooping protection does not apply for related papers with an overlapping set of authors (see originality and plagiarism)

Transparent Process

Since 2009, all EMBO Press journals have made the editorial process transparent for papers by publishing as an online supplementary document all correspondence between authors and the editorial office relevant to the decision process. This will by default include all referee reports, the editorial decision letters, the author checklist, as well as the authors' point-by-point responses. Internal communications and informal consultations between editors, editorial advisors, referees, and authors peripheral to the scientific assessment are not included. Referee anonymity will be strictly maintained, unless a referee chooses to sign his or her report. Authors who are, for specific reasons or as a matter of principle, not comfortable with these disclosures will have the possibility to opt out of the transparent process at any stage prior to publication. Authors may request that data specifically included in the response to referees and intended for publication elsewhere be redacted from the document. Currently, 95% of primary research papers at Molecular Systems Biology are linked to a Peer Review Process File. More information about the EMBO Press Transparent Process can be found below and on the EMBO Press website. Please note that the author checklist forms part of the review process file.

Authorship Guidelines

Submission of a manuscript requires that all authors have seen and approved the manuscript and its contents, and that they are aware of the responsibilities connected to authorship. Each of the listed authors has to concur with the text of the submitted manuscript, confirm the integrity of the data and its presentation, and agree with its interpretation as discussed in the manuscript. Signatures from all the authors are not required; it is the corresponding author’s responsibility to obtain agreement from all authors supporting the submission. All authors will be notified upon peer-review of a new manuscript and upon acceptance of a manuscript, but the editorial office generally corresponds only with the Corresponding Author, whose responsibility it is to communicate information sent from the editorial office with all other authors. Editors may send information such as referee reports to all the authors where they consider this to be essential

Submission of a manuscript requires that all authors agree to the authorship as listed in the manuscript. The nature of every author’s contribution must be specified both in the manuscript submission system and in the manuscript under the heading “Author Contributions”.

Our authorship policies conform to international standards (see, for example, ICMJE authorship guidelines).

We encourage all authors to register for ORCID iD digital identifiers (iDs) to ensure unambiguous name assignment. Corresponding authors are required to supply an ORDCID ID for their name upon submission of a revised manuscript (EMBO Press signed a joint statement to encourage ORCID adoption). Registration takes less than two minutes, and adoption of digital identifiers enables accurate attribution and improves discoverability of published work.

In order to link your ORCID iD to your account in our manuscript tracking system, please do the following:

Click the 'Modify Profile' link at the bottom of your homepage in our system.
On the next page you will see a box half-way down the page titled ORCID*. Below this box is red text reading 'To Register/Link to ORCID, click here'. Please follow that link: you will be taken to ORCID where you can log in to your account (or create an account if you don't have one).
You will then be asked to authorise Wiley to access your ORCID information. Once you have approved the linking, you will be brought back to our manuscript system.

We regret that we cannot do this linking on your behalf for security reasons. We also cannot add your ORCID iD number manually to our system because there is no way for us to authenticate this iD number with ORCID.

The journal encourages the submission of a completed author checklist (right click to download) at submission (which covers animal welfare, human subjects, data deposition and ethics), and will require it to be filled and returned to the editorial office at revision, either via the online submission system (upload as a supplementary file) or by email to the editorial office. All information covered in the checklist should be included in the manuscript. Please note that the author checklist will be included in the transparent process information.

Use of living organisms

For Research Articles submitted to EMBO Press journals reporting experiments on live vertebrates and/or higher invertebrates, the corresponding author must confirm that all experiments were performed in accordance with relevant guidelines and regulations. The manuscript must include a statement in the Materials and Methods identifying the institutional and/or licensing committee approving the experiments, including any relevant details. For experiments involving human subjects, authors must identify the committee approving the experiments, and include with their submission a statement confirming that informed consent was obtained from all subjects.

Right click to download and complete the author checklist here.

Animal welfare

For studies reporting experiments on live vertebrates and/or higher invertebrates, the corresponding author must confirm that all experiments were performed in accordance with relevant guidelines and regulations. The manuscript must include a statement in the Materials and Methods identifying the institutional and/or licensing committee approving the experiments. The editors reserve the right to consult with board members or external experts and reject manuscripts that contain animal experiments that do not conform to NIH or MRC guidelines for animal welfare. For further information see: Office of Laboratory Animal Welfare; The journal encourages authors to follow the ARRIVE guidelines (PLoS Biol. 8(6), e1000412, 2010) for reporting studies involving animals. Please see the following website for details: http://www.equator-network.org/reporting-guidelines/improving-bioscience-research-reporting-the-arrive-guidelines-for-reporting-animal-research/

Right click to download and complete the author checklist here.

Human Subjects

For experiments involving human subjects the corresponding author must identify the committee approving the experiments and include a statement that informed consent was obtained from all subjects and that the experiments conformed to the principles set out in the WMA Declaration of Helsinki and the Department of Health and Human Services Belmont Report. Editors or referees may request further documentation confirming that this is the case.

Any restrictions on the availability or on the use of human data or samples should be clearly specified in the manuscript. Any restrictions that may detract from the overall impact of a study or undermine its reproducibility will be taken into account in the editorial decision.

For clinical trials reporting, the authors should fill out a CONSORT flow diagram and submit it as supplementary information. The journal also encourages authors to follow the CONSORT reporting guidelines http://www.consort-statement.org. Please see the EQUATOR website for details. Clinical trials should also be registered as recommended by the International Committee of Medical Journal Editors, and the trial registration number should be provided.

Right click to download and complete the author checklist here.

Reporting Guidelines

Authors are encouraged to follow the EQUATOR Network reporting guidelines for the following:

Type of Study	Guidelines
Animal research	ARRIVE
Parallel group randomized trials	CONSORT
Conensus-based Clinical Case Reporting	CARE
Prognostic marker studies	REMARK
Diagnostic Accuracy	STARD
Meta-analysis of observational studies	MOOSE
Systematic reviews and meta-analysis	PRISMA
Observational studies	STROBE
Genetic association studies	STREGA
Statistical analyses and methods	STAMPL
Microarray/deep sequencing studies	MIAME
Studies using biospecimens	BRISQ

Biosecurity

Planned research and results from experiments should be evaluated at an early stage for possible dual use concerns. In such cases, authors should first consult with an appropriate local body concerning the implications for biosecurity and public health. For further information see the U.S. National Science Advisory Board for Biosecurity's recommendations and the US National Select Agent Registry.

Authors should explicitly describe any potential biosecurity implications and the local body's assessment in their cover letter at submission and in the author checklist. The threat posed by the potential abuse of certain experimental data or material for bioweapons, terrorist or other criminal activities may require that editors balance the risks and benefits of publication. The ultimate decision whether to publish the paper as submitted or with suggested changes is the prerogative of the editors after consultation with board members or external experts in biosafety, biosecurity, or public and environmental health.

Right click to download and complete the author checklist here. Please note that the author checklist will be included in the transparent process information.

Availability of published material, data and software

It is understood that by publishing a paper in this journal, the authors agree to make available to colleagues in academic research all new reagents, including organisms (or means to produce them), viruses, cells, nucleic acids and antibodies, that were used in the research reported and that are not available from public repositories or commercial suppliers. Human patient samples and data should be made available in accordance with the relevant ethical standards. Materials must be made available at a reasonable cost that reflects production and distribution. The distribution of published materials does not automatically confer a right of co-authorship. The guidelines below 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). Right click to download and complete the author checklist here.

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. Human patient samples and data should be made available in accordance with the relevant ethical standards.
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.
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.

The journal will only review and publish manuscripts if the authors agree to make all data that cannot be published in the journal itself (e.g. novel nucleotide sequences, structural data, or data from large-scale gene expression experiments) freely available, where possible in an appropriate public database (detailed guidelines can be found below).

Right click to download and complete the author checklist here.

Conflicts of interest

In the interests of transparency and to help editors and reviewers assess any potential bias, the journal requires authors of original research papers to declare any competing commercial interests in relation to the submitted work. It is difficult to specify a threshold at which a financial interest becomes significant, but as a practical guideline, we would suggest this to be any undeclared interest that could embarrass you were it to become publicly known. Referees and editors are also subject to Conflict of Interest regulations.

Scientific Integrity

The editorial staff are committed to maintaining high standards of integrity of the published scientific record. Journal staff undertake routine image analysis of data in manuscripts submitted for publication and will request source data and an author response to image aberrations.

The journal requests that authors take note of and adhere to national standards, as well as guidelines established by the U.S. Department of Health and Human Services Office of Research Integrity (http://ori.dhhs.gov). The journal will investigate suspected instances of scientific fraud, inappropriate image manipulation or processing, plagiarism, misrepresentation, duplicate publication and other cases that violate research ethics in submitted manuscripts or published papers. Depending on the outcome of these investigations, the journal may opt to publish errata or corrigenda (see below), or, in cases of serious scientific misconduct, either to ask authors to retract their paper, or to impose retraction on them. In such cases, the authors’ current employers and the research institution of the corresponding author at the time of publication of the paper will also be informed. The journal may also issue an editorial note attached to the paper to alert readers to an ongoing investigation. As a matter of policy, the journal will collaborate with independent institutional investigations into misconduct and, where appropriate, will accept the outcome of such investigations.

All EMBO Press journals are members of the Committee on Publication Ethics (COPE).

Corrigenda, errata, addenda and refutations

Correction and additions to a paper are published at the sole discretion of the editors.

An erratum is notification of a significant error made by the journal that would mislead the readership if left uncorrected.

A corrigendum is notification of a significant error made by the author(s). A corrigendum may include a communication by the authors and/or an editorial statement.

An editorial note may be used to alert readers to a specific issue related to a paper.

An addendum may be published in rare cases where additional data directly relevant to central aspects of a paper emerge and it is apparent that publication would strengthen the paper in question fundamentally. All additional data is subject to peer review.

Refutations of articles published in the journal can be considered for the Correspondence section of the journal. Such correspondence will almost always include data to support the arguments of the correspondent and will have to concern central aspects of a paper. The original authors of the article will be offered the opportunity to respond side-by-side with the correspondence. Both the refutation and the response will be peer reviewed at the discretion of the editor and acceptance depends on the strength of the arguments raised as well as the importance of the matter to a general readership. Publication of the correspondence does not automatically entail publication of a response of the authors of the challenged research paper. After one round of correspondence, the journal will consider the matter closed and will not publish further exchanges.

Data collection and presentation

Presented data must represent the findings in an unbiased, accurate and transparent manner. This includes appropriate statistical analysis and image processing. For further details, please refer to these guidelines.

The Editors reserve the right to request minimally processed versions of figures and the source data that were used to assemble the figure from the authors of a paper under consideration, or of a paper already published in the journal.

Data integrity of Images

The EMBO Press data integrity policy aims to ensure that EMBO Press journals publish research that is reliable, reproducible and conforms to international scientific research standards.

Journal staff conduct an analysis of all image based data presented in manuscripts before acceptance for publication. Editors may request source data for any figure as a requirement for publication. Editors reserve the right to forego publication of a manuscript if key data do not meet journal data integrity, ethical or reproducibility standards. When journal staff note potential aberrations in image-based data, the severity is classified according to a three-tiered system. The authors will be contacted, and depending on the severity of the issue (please see Classifying image aberrations), the authors’ research institution may be contacted.

Preserving data integrity

Authors are expected to follow basic guidelines for preserving data integrity, which have been outlined in the Figure/Data Presentation section. In summary, authors are requested to:

Prepare figures that accurately reflect the results of the experiments using appropriate controls, markers, and scale bars included in all panels.
Use minimally processed images to create figures
Retain their unprocessed data and metadata files
Use clearly demarcated borders when juxtaposing images
Exercise prudence during data acquisition
Avoid using touch-up tools, or any feature that deliberately obscures manipulations
Correctly represent the original data and conform to community standards if image processing must be used

Originality and Plagiarism

Plagiarism is the misappropriation of intellectual property and the substantial unattributed textual copying of another's work, including ideas, text, images or materials and methods.

Any information published in the journal should represent a substantial, novel contribution to the scientific record. The journal reserves the right not to publish material that has already been published, completely or substantially, in peer reviewed journals, persistent news media or online information platforms and blogs. Posts on recognized non-peer reviewed preprint servers (see Preprint Servers), as well as oral or written conference presentations (including summaries, abstracts and posters), meeting reports, as well as doctoral (PhD) or master (MSc, MA) theses are exempt (if your institution requires formal publication of your thesis, please contact the editorial office).

Manuscripts submitted for publication elsewhere that are conceptually related to a submission to this journal, and that feature one of more of the same authors must be declared in the cover letter and included in full with the submission.. It is at the discretion of the editors whether publication of such related material prevents publication in the journal.

Any text, data, material, images, ideas or quotes must be attributed to the original source, even if it is by the same authors. If necessary, authors should seek permission to use the material from the copyright holder in accordance to licensing stipulations. The journal’s policies on attribution follow the standards set by the Associated Press, including formal citation of the primary source and clearly demarked quotation. The journal has no limit on references and all relevant references must be included in the reference list.

Manuscripts with overlapping authors are not subject to the journal’s ‘scooping protection’ policy.

The journal uses CrossCheck to screen submitted content for plagiarism (including self-plagiarism) prior to publication. It is at the discretion of the editors whether related text is inadmissible for publication in the journal.

Embargo Policy

The content of papers and any associated press releases is strictly embargoed until the official date of publication of a manuscript. Accepted contributions can be discussed with the media from one week before the publication date provided the journalist respects the embargo date. We will press release selected papers with summaries. Authors may arrange their own publicity, but must adhere to the embargo conditions. Further details can be provided by the editorial office.

Citation Policy

Comprehensive and accurate citation of the relevant literature is essential. We require citation of the primary literature wherever appropriate. There are no limits on the total number of references in the bibliography, and the reference list is not subject to manuscript length format requirements (for details, see below). Similarly, page charges will apply only to the body of a published article, not to the reference list.

Editorial Process

All submissions are initially assessed by a dedicated scientific editor specialised in the scientific topics covered in the manuscript, and may also be evaluated by an appropriate Editorial Advisory Board member, Senior Editor, or another external expert advisor. All research manuscripts and reviews published in the journal are subject to peer-review. Non-research articles, editorial material and commentaries are usually not reviewed, although editors may elect to undertake review in the interest of authoritative and balanced reporting.

Double blind review: As a default, the referees are aware of the identities of the authors and referee names are withheld from authors (single-blind review). We will withhold author names from referees on request by the authors. The authors may chose this option during the submission process, but it is the authors’ responsibility to anonymize their manuscript. The editorial offices will not edit the manuscript files submitted for anonymity and will not alert authors who have chosen the anonymization option, but who have not anonymized the manuscript files. The journal may consult with the referees after conditional acceptance of a manuscript on a de-anonymized manuscript to assess the changes applied in revision.

Research manuscripts judged by the editors to be potentially suitable for publication in the journal with realistic experimental revision are sent out for formal peer review, so that manuscripts with a low probability of success can be returned to the authors without delay. Manuscripts are typically reviewed by three appropriate independent experts selected by the editors. Authors may exclude a small number of experts if they are concerned of a conflict of interest or bias.

Referee Cross-commenting: Referees are routinely invited to comment on each other’s reports and may discuss issues under moderation of the editors. Referees are not informed of each other’s identities.

Based on the arguments and recommendations of the referees, the editors decide whether to offer publication or revision, or whether to reject the manuscript. This decision might involve further consultation with the referees, the Editorial Advisory Board and/or the authors. Revisions are invited only for manuscripts that have a high probability of acceptance after one major round of experimental revision.

‘Scooping’: During the editorial and peer review process and the agreed author revision period, other studies that may appear in the literature are not taken into account in assessing the conceptual advance of a study. Please inform editors once you become aware of other studies directly relevant to your study.

Authors may appeal decisions if there is concrete evidence for a misunderstanding or mistake at the editorial or referee level. Appeals are evaluated in depth and without prejudice.

Transparent Process: The journal makes the editorial process transparent for all accepted manuscripts, by publishing as an online supplementary document (the Review Process File, RPF) all correspondence between authors and the editorial office relevant to the decision process. This will include all referee comments directed to the authors, as well as the authors’ point-by-point responses. Internal communications and informal consultations between editors, editorial advisors or referees will remain excluded from these documents. Importantly, referee anonymity will be strictly maintained. Authors have the possibility to opt out of the transparent process at any stage prior to publication. Please note that the author checklist will still be published even if authors opt-out of the transparent process.

To further facilitate transparency, the journal has removed the “Confidential Comments” field from our referee reporting forms. This is to ensure that the authors receive all information pertinent to the decision made on a manuscript. Referees should be aware that all comments will be transmitted to the authors and the other referees. Should there be any issues with the manuscript, in particular concerns about ethical standards, data integrity, biosecurity, or conflicts of an academic or commercial nature that need to be communicated directly and confidentially to the editor, this can be done by email.

Please see the EMBO Press website for more information on these policies.

Extended Scooping Protection

Other papers published in peer reviewed journals or manuscripts posted on recognized preprint servers after submission of a manuscript to Molecular Systems Biology are not considered relevant to the editorial assessment of the conceptual advance/novelty of the submitted manuscript.

A manuscript submitted to Molecular Systems Biology is subject to scooping protection from the day of submission to Molecular Systems Biology and extends through the agreed revision period. For transferred manuscript scooping protection applies from the day of submission to the EMBO Press sister journal.

Note that related papers, and where appropriate preprints, have to be cited appropriately if they are published before the manuscript proofs stage.

Please inform editors as soon as you become aware of other studies directly relevant to your study. Conceptually related studies formally published elsewhere must be cited (citations can be added at proofs stage where necessary).

Note that scooping protection does not apply for related papers with an overlapping set of authors.

Related manuscripts submitted, in press or published elsewhere must be declared at submission and cited where appropriate (see Originality and Plagiarism). It is at the discretion of the editors whether prior publication of such related material prevents subsequent publication in the journal.

Appeals

Authors may appeal decisions if there is concrete evidence for a misunderstanding or mistake at the editorial or referee level. Appeals are evaluated in depth and without prejudice.

Transfer policies

The EMBO Press journals are editorially independent from their publishers, one another and EMBO.

Authors can choose to transfer manuscripts rejected from any one of the EMBO Press journals to any other of the EMBO Press journals by following the instructions appended to the editorial decision letter. Authors may also request transfer by contacting the MSB office directly. Both peer-reviewed and non-peer-reviewed manuscripts can be transferred.

We also offer seamless transfer to the new open access journal Life Science Alliance, launched in partnership between EMBO Press, Rockefeller University Press, and Cold Spring Harbor Laboratory Press. Where appropriate, an editor at the original journal will confidentially pre-consult with the editors of Life Science Alliance to explicitly invite transfer. Authors who do not wish to be considered for transfers can opt out at submission stage.

Manuscripts transferred post-review will automatically include the referees’ reports and identities of referees (unless the referee has opted out), and authors are invited to include a point-by-point rebuttal and a revised manuscript as part of the transfer. The editors will aim to use the transferred referee reports in arriving at a rapid decision – where necessary, they may involve an arbitrating expert, who is asked to adjudicate based on the information provided by the authors and referees. Editors may choose to seek additional advice from referees or editorial advisory board members in cases where this would enhance informed decision-making.

Transfers of manuscripts with referee reports from Journals unrelated to EMBO Press to MSB are also possible at the editor’s discretion. If anonymous, authenticated referee reports are available, the editors will aim to work with this information to arrive at a timely decision without entering a de novo review process. This may involve expert advice in an adjudicating function. Please contact the editors to discuss options. EMBO Press is committed to a rapid, efficient and fair editorial process.

Manuscript Preparation

Molecular Systems Biology publishes the following article types:

Research Articles - full length articles
Reports - short format articles
News & Views
Reviews
Perspectives
Correspondence
Commentary

Research Article Submission

YOU DO NOT NEED TO REFORMAT YOUR MANUSCRIPT FOR A FIRST SUBMISSION

The following guidelines refer to Research Articles. While published manuscripts are expected to conform tightly to the following guidelines, this is not a requirement at first submission.

Manuscripts must be written in clear and concise English and be intelligible to a broad readership. Prior to submission, authors may benefit from having their manuscript reviewed for clarity by colleagues and/or by using one of the many English language-editing services that are available.

Text Format

The Editorial Office will only accept text files in RTF or MS Word format. The final character count must be clearly indicated on the title page of the manuscript. Revised manuscripts that do not comply with the formatting guidelines, or exceed the length restrictions, may be returned to the authors for amendment.

Please submit the full text (including figure legends, expanded view figure legends, (note: tables may also be provided as separate Word or Excel Files, they need to be editable), and references) as a single MS Word or RTF file.

Submitted manuscripts should be divided into the following sections:

Title page
Abstract
Introduction
Results
Discussion
Materials and Methods
Acknowledgements
Author contributions
Conflict of interest
References
Figure legends
Tables and their legends
Expanded View Figure legends

Title Page

The title should be short and informative, and should not contain any abbreviations (for example, Epithelial-Mesenchymal Transition should not be abbreviated to EMT). However, commonly used gene or protein acronyms are acceptable. The total length of the title should not exceed 100 characters (including spaces). Serial titles are not accepted.

The full name (middle names as initials) of each author should be given. Multiple first-authorships are acceptable and should be indicated. 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, although we will by default address all correspondence to the single author listed as Corresponding Author upon submission.

Please provide a running title of no more than 40 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 (/).

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 where possible (as for the title). Reference citations within the abstract are not permitted. The abstract should describe all key novel findings of the study.

Introduction

The Introduction should be succinct and without subheadings. It should provide only the necessary background information, rather than comprise a comprehensive review of the field. Citation of the primary literature is required where appropriate (see section on Citation Policy).

Results

The Results section, and associated figures, tables and Expanded View information, must accurately describe the findings of the study. Figure, Table, Expanded View figure, Expanded View table, Expanded View movie etc. order should follow the text. Detailed methodological descriptions should be restricted to the Materials and Methods section. ‘Data not shown’ is not permitted (see below): all significant data should be displayed in the main figures or Expanded View information.

Discussion

The Discussion should accurately interpret the results, but not be repetitive with the Results section. Authors are encouraged to discuss their work in the broader context. Related published data must be appropriately discussed and cited. Speculation is allowed but should be clearly labelled as such. For shorter articles, the Results and Discussion sections can be combined.

Materials and Methods

In this section, methods should be described in sufficient detail so that all procedures performed in the study can be repeated by others. Cited references can be included but should not be used as a substitute for providing methodological details. “As previously described in (reference)" can be used only when it directly applies to a specific method and only when the cited reference includes a detailed description of this method. If necessary, it is acceptable to re-use descriptions of methods from the authors’ previously published work. Reagents must be described in such a way as to allow readers to identify them unequivocally and/or reproduce them. For example, antibodies epitopes should be described and siRNA and other probe sequences must be provided. In cases where detailed methods cannot be described within the length limits of the article, additional Materials and Methods can be included as part of the Appendix. This additional information should, however, not be of immediate importance for the understanding of the manuscript, and it is not permissible to move the entire “Materials and Methods” section into the Appendix.

Structured Methods
Method papers should include a structured Material and Methods section that includes a Reagents and Tools Table followed by a Methods and Protocols section.

Please note that this format is not required at initial submission. It is only mandatory for Methods papers and is optional for Articles and Reports.

To adhere to this format please include the following two sections (see an example here and download our Excel template or Word template for the Table):

Reagents and Tools Table: Key reagents, experimental models, software and relevant equipment should be listed in this table, including their sources and relevant identifiers. Please fill one of these templates (.xls file or .doc file) and upload it to the manuscript tracking system as a ‘Reagent Table’ file. This example shows how the table will display in the published article and includes examples of the type of information that should be provided for the different categories of reagents and tools. Please list your reagents/tools using the categories provided in the template and do not add additional subheadings to the table. Reagents/tools that do no fit in any of the specific categories can be listed under “Other”.

Methods and Protocols: We encourage the authors to describe their methods using a step-by-step protocol format with bullet points and notes on “tricky steps” in the procedure (see example). We strongly recommend this ‘protocol’ format for novel methodologies and procedures that will be relevant for readers to use in their own studies. Using the protocol format is optional unless otherwise specified by the editor. The protocol format does not need to be applied throughout the Materials & Methods section.

Acknowledgements

These should be placed at the end of the text and not in footnotes. Personal acknowledgements should precede those of institutions or agencies. Grant numbers are permissible. Dedications are discouraged.

Author contributions

The journal requires a statement specifying the contributions of every author. Further details on authorship can be found here.

Conflict of interest

The journal requires a statement specifying whether or not the authors have a Conflict of interest (see above for details). In the case of a Conflict of interest, this must be specified.

References and Citations

As a matter of policy, the journal requires the citation of primary literature (over review articles) wherever appropriate. The reference list at the journal is not subject for length restriction: within reason, all relevant citations should be included. Authors are responsible for the accuracy of the references. Authors are responsible for ensuring that the related literature is accurately and comprehensively discussed and cited. Review articles should only be cited for general background information, the proposal of certain concepts or similar purposes, whereas primary research articles should preferentially be referenced to introduce the question being addressed or to support the conclusions and interpretations of the results.

Only articles that have been published or that are accepted for publication at a named publication should be cited in the reference list. Papers accepted for publication must be cited with the corresponding author’s permission and should include title and all author names (or initials if any of the authors are co-authors of the present contribution), as well as either the DOI, if available, or the term ‘in press’. 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 (i.e. Smith & Jones, 2003; Smith et al, 2000). In the reference list, citations should be listed in alphabetical order and then chronologically, with the authors’ surnames and initials inverted; where there are more than 20 authors on a paper, the first 20 will be listed, followed by ‘et al.’. 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 as follows:

Akhmedkhanov A, Toniolo P, Zeleniuch-Jacquotte A, Koenig KL, Shore RE (2002) Aspirin and lung cancer in women. Br J Cancer 87: 49-53

Book chapters and books can be cited in the following way:

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

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

Citations to manuscripts posted on recognized preprint servers can be cited the following way:

Author NAME1, Author NAME2, (YEAR) article title. bioRxiv doi:

Links to online resources and websites should be cited in the text only, and should be available long-term (e.g. permalinks or DOI wherever possible). URLs are not accepted in the reference list.

Tables

Tables should be provided in .doc or .xls format and need to be editable (no image files). They can be included at the bottom of the main manuscript file or be sent as separate files. Tables should be numbered consecutively with Arabic numerals (1, 2, 3, 4). 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.

Conventions and Abbreviations

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, genes and genotypes should be indicated in italics; proteins and phenotypes should not be italicized.

Authors should use approved gene and gene product nomenclature and apply the italicization and capitalization formatting as appropriate for each organism’s standard nomenclature. Please consult the appropriate nomenclature databases for correct gene names and symbols. Some useful general resources are: Entrez Gene (http://www.ncbi.nlm.nih.gov/gene); UniProt (http://www.uniprot.org/).

Try to restrict the use of abbreviations to SI symbols (standard units of measurements) and those recommended by the International Union of Pure and Applied Chemistry (IUPAC). Abbreviations should be defined in brackets after their first mention in the text, not in a list of abbreviations. 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.

Figures

Figure Legends

Figure legends should contain sufficient information to allow the reader to follow the data presented without referring back to the text, but should not be redundant with the Results section. Each figure must contain a heading, and each panel a subheading. 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. Figure legends should be formatted such that each panel, or group of panels, has its own entry with the panel letter (or range) on the left and the description on the right, the panels should be described in sequential order in the legend. Details on the statistical analysis and the number of replicates should be indicated for each panel where appropriate.

Figure 1 - Generation of hiPSCs from a patient with type-2 long-QT syndrome.

A Bright-field images of neurospheres obtained from SVZ neural stem cells of P15 control and hGFAP-SDHD mouse brains. Scale bars: 500 μm.

B, C Neurosphere (NS) forming efficiency (B) and core diameter (C) in cultures grown from SVZ of P15 control and hGFAP-SDHD mice (n = 6 cultures/mice for each genotype).

D Quantitative RT–PCR detection of SdhD expression levels in SVZ neurospheres of wild-type (flox/+) and mutant (flox/-, and flox/- cre) mice (n = 4 mice for each group).

Data information: In (B–D), data are presented as mean ± SEM. *P≤0.05 (Student's t-test).

Figure Formatting

Figures and Expanded View figures should be presented in the order they are mentioned in the text. Figures use the numbering system Fig 1, while Expanded View figures use the system Fig EV1. The figure count in each is separate, such that there will be both a Fig 1 and a Fig EV1 (and so on) in a manuscript.

The final size of figures will be between 87 mm and 180 mm wide on the printed page. Please bear this in mind when submitting your manuscript for review and allow for sufficient resolution at a suitable size. For help preparing figures, please download our figure guide PDF.

Figures divided into parts should be labelled with an upper-case, bold letter (Helvetica Font). 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 Courier font for sequence data and Symbol font for any symbols.

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.

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.

When preparing figures of microscopy images, please note that we strongly encourage the use of colours that are suitable for colour-blind readers: for example, the use of magenta/green is preferred over red/green for 2-channel images.

For publication, we require PowerPoint, TIFF or EPS files in PC or Macintosh format, preferably from PhotoShop or Illustrator software. We cannot accept Freehand, Canvas, CorelDRAW or MacDrawPro files. These files must be converted to postscript (eps) format. For any figures submitted in photoshop or tiff format we require layered files to be sent whereby all text, arrows or additional attributes are placed on individual layers within the file. For line art/charts/graphs we prefer to work with Adobe Illustrator AI or EPS files. We can also accept high-resolution PDF files.

All colour artwork must be submitted in CMYK or RGB colour mode. Non-vector graphics should be preserved at high resolution: 300 dpi minimum at final size for greyscale or colour halftone images, and 600 dpi minimum for bitmap (b/w) artwork. Combinations of monochrome and greyscale/photographs should be at 600 dpi.

Further detailed guidelines regarding the preparation of artwork is available to download in this document [pdf].

The journal does not have colour charges for figures, and the authors are therefore welcome to submit full colour figures.

Figure/Data Presentation

Figures must accurately reflect the results of the experiments. Appropriate controls, markers and scale bars should be included in all panels. Statistical tests must be clearly defined and appropriate to the data.

Source Data
The EMBO Press journals strongly encourage authors to upload the ‘source data’ – for example, tables of individual numerical values and measurements or uncropped gels – that were used to generate figures. These files are separate from the Expanded View information files and are submitted using the "figure source data" option in the manuscript submission system. Source data are directly linked to specific figures so that interested readers can directly download the associated ‘source data’ for the purpose of alternative visualization, re-analysis or integration with other data.

The data should at minimum allow users to redraw the figures using an alternative graphical representation, or to identify how a gel was cropped or otherwise edited for inclusion in the original figure. The data should be annotated to provide essential information to interpret the source data.

Image Processing
Images submitted with a manuscript for review should be minimally processed (for instance, to add arrows to a micrograph). Authors should retain their unprocessed data and metadata files, as editors may request them to aid in manuscript evaluation. If unprocessed data are unavailable, manuscript evaluation may be stalled until the issue is resolved.

A certain degree of image processing is acceptable for publication (and for some experiments, fields and techniques is unavoidable), but the final image must correctly represent the original data and conform to community standards. The guidelines below will aid in accurate data presentation at the image processing level; authors must also take care to exercise prudence during data acquisition, where misrepresentation must equally be avoided. Where appropriate, manuscripts should include further Methods as part of the Expanded View that describe for each figure the pertinent instrument settings, acquisition conditions and processing changes.

Authors should list all image acquisition tools and image processing software packages used. Authors should document key image-gathering settings and processing manipulations in the Methods.

Images gathered at different times or from different locations should not be combined into a single image, unless it is stated that the resultant image is a product of time-averaged data or a time-lapse sequence. If juxtaposing images is essential, the borders should be clearly demarcated in the figure and described in the legend.

The use of touch-up tools, such as cloning and healing tools in Photoshop, or any feature that deliberately obscures manipulations, is to be avoided.

Processing (such as changing brightness and contrast) is appropriate only when it is applied equally across the entire image and is applied equally to controls. Contrast should not be adjusted so that data disappear. Excessive manipulations, such as processing to emphasize one region in the image at the expense of others (for example, through the use of a biased choice of threshold settings), is inappropriate, as is emphasizing experimental data relative to the control.

When submitting revised final figures upon conditional acceptance, authors may be asked to submit original, minimally processed images.

Electrophoretic gels and blots
Positive and negative controls, as well as molecular size markers, should be included on each gel and blot. For previously characterized antibodies, a citation must be provided. For antibodies less well characterized in the system under study, a detailed characterization that demonstrates not only the specificity of the antibody, but also the range of reactivity of the reagent in the assay, should be published as part of the Expanded View. The display of cropped gels and blots in the main paper is permitted if it improves the clarity and conciseness of the presentation. Cropped gels in the paper must retain all important bands, and space (several band-widths) should be retained above and below the relevant band(s). Vertically sliced images that juxtapose lanes that were non-adjacent in the gel must have a clear separation or a black line delineating the boundary between the gels. Quantitative comparisons between samples on different gels/blots are discouraged; if this is unavoidable, the figure legend must state that the samples derive from the same experiment and that gels/blots were processed in parallel. Loading controls must be run on the same blot. High-contrast gels and blots are discouraged, as overexposure may mask additional bands. Authors should strive for exposures with gray backgrounds. Multiple exposures should be presented in the Expanded View information if high contrast is unavoidable. Immunoblots should be surrounded by a black line to indicate the borders of the blot, if the background is faint. For quantitative comparisons, appropriate reagents, controls and imaging methods with linear signal ranges should be used.

Microscopy
Authors should be prepared to supply the editors with original data on request, at the resolution collected, from which their images were generated. Cells from multiple fields should not be juxtaposed in a single field; instead multiple supporting fields of cells should be shown as part of the Expanded View. Specific guidelines: Adjustments should be applied to the entire image. Threshold manipulation, expansion or contraction of signal ranges and the altering of high signals should be avoided. If ‘Pseudo-colouring’ and nonlinear adjustment (for example ‘gamma changes’) are used, this must be disclosed. Adjustments of individual colour channels are sometimes necessary on ‘merged’ images, but this should be noted in the figure legend. We encourage inclusion of the following with the final revised version of the manuscript for publication: In the Methods, specify the type of equipment (microscopes/objective lenses, cameras, detectors, filter model and batch number) and acquisition software used. Although we appreciate that there is some variation between instruments, equipment settings for critical measurements should also be listed. A further Methods section as part of the Expanded View (or part of a larger Methods section) titled ‘equipment and settings’ should list for each image: acquisition information, including time and space resolution data (xyzt and pixel dimensions); image bit depth; experimental conditions such as temperature and imaging medium; and fluorochromes (excitation and emission wavelengths or ranges, filters, dichroic beamsplitters, if any). The display lookup table (LUT) and the quantitative map between the LUT and the bitmap should be provided, especially when rainbow pseudocolor is used. If the LUT is linear and covers the full range of the data, that should be stated. Processing software should be named and manipulations indicated (such as type of deconvolution, three-dimensional reconstructions, surface and volume rendering, ‘gamma changes’, filtering, thresholding and projection). Authors should state the measured resolution at which an image was acquired and any downstream processing or averaging that enhances the resolution of the image.

Statistical analysis
The description of all reported data that includes statistical testing must state the name of the statistical test used to generate error bars and P values, the number (n) of independent experiments underlying each data point (not replicate measures of one sample), and the actual P value for each test (not merely 'significant' or 'P < 0.05'). Discussion of statistical methodology can be reported in the materials and methods section, but figure legends should contain a basic description of n, P and the test applied.

Descriptive statistics should include a clearly labelled measure of centre (such as the mean or the median), and a clearly labelled measure of variability (such as standard deviation or range). Ranges are more appropriate than standard deviations or standard errors for small data sets. Standard error or confidence interval is appropriate to compare data to a control. Graphs must include clearly labelled error bars for cases where more than two independent experiments have been performed (error bars for replicate samples are less useful). Authors must state whether a number that follows the ± sign is a standard error (s.e.m.) or a standard deviation (s.d.) Authors must justify the use of a particular test and explain whether their data conform to the assumptions of the tests. In particular:

When using statistical methods based on the normal distribution authors should explain how they tested their data for normality. If the data do not meet the assumptions of the test, then a non-parametric alternative should be used.
When making multiple statistical comparisons on a single data set, authors should explain how they adjusted the alpha level to avoid an inflated Type I error rate, or they should select statistical tests appropriate for multiple groups.
For each experiment, the number of both technical and biological replicates should be clearly stated. Biological replicates are derived from independent experiments using separately obtained biological samples, while technical replicates are created by repeated measurements on the same biological sample. In general, technical replicates should be averaged before any statistical inference tests are performed.
In cases where n is small, appropriate statistical tests should be employed and justified in the text.

Since for complex biological experiments the number of independent repeats of a measurement often has to be limited for practical reasons, statistical measures with a very small n are commonplace. However, statistical measures applied to too small a sample size are not significant and they can suggest a false level of significance. We recommend that the actual individual data from each experiment should be plotted if n < 5, alongside an error bar. In cases where n is small, a justification for the use of the statistical test employed has to be provided. Presenting a single ‘typical result’ of n experiments is sometimes unavoidable, but should be accompanied by an indication of the variability of data between independent experiments. If n is not based on independent experiments (that is, n merely represents replicates of a measurement), statistics may still be useful, but a detailed description of the repeated measurement is required.

For more information on the appropriate use of standard deviation, standard error, and confidence intervals please refer to Sullivan et al (2016), American Statistical Association guidelines (2016), Motulsky (2014), and Cumming et al (2007).

Expanded View (replacing Supplementary Information)

YOU DO NOT NEED TO REFORMAT YOUR MANUSCRIPT FOR A FIRST SUBMISSION.

Please follow the guidelines below when submitting a revision.

EMBO Press journals encourage the inclusion of extra figures in the HTML version of the main manuscript. These figures are presented in an expandable format inline in the main text so that readers who are interested can access them directly as they read in the context of the article. They are also provided for download in a separate PDF to accompany the Article PDF.

Figures appropriate for the Expanded View format are those of particular value to specialist readers, but which are not essential to follow the main thread of the paper for the general reader. Previously, important data would have been difficult to find and access as Supplementary Information. EMBO Press strongly encourages authors to select a limited number (typically 5) of supplementary figures for inclusion in the article proper as Expanded View figures in order to improve their accessibility, visibility and utility. Any extra figures that are not promoted to the Expanded View should be included in a 'traditional' supplementary PDF (along with supplementary text and tables) now called the Appendix.

We intend that by promoting only the essential elements of the supplementary information to be fully integrated in the main manuscript, authors and journals can reduce the often excessive amounts of information that is largely hidden in supplementary information sections. Note that it is explicit policy at all four EMBO Press journals to only include data directly relevant to the scientific claims of the paper.

Our editors will be happy to help you to decide which figures to promote to the Expanded View, or to explain about the Expanded View in more detail. There is no extra typesetting cost for figures that you choose promote in this way. However, please keep in mind the limit of 5 extra figures, unless agreed otherwise with the editor.

Your paper will now include 4 levels of information designed to add more structure and more flexibility to read or browse:

LEVEL 1 (Main manuscript and figures)

Main manuscript text, main figures and simple tables (Figures nomenclature: Figure 1, Table 1 etc.)
UPLOAD using file types: Manuscript File (including main text and tables), Figure File (as separate image files).

LEVEL 2 (Expanded View)

Expanded View figures (Expanded View figure nomenclature: Figure EV1)
[These figures will be displayed in the main HTML of the paper in a collapsible format. They will also be collected by the publisher into a single PDF and made available for download]
UPLOAD as separate image files using the file type Figure File (as for Main Figures, but note the different nomenclature when naming your Expanded View figures in the system).

Expanded View large tables and files (nomenclature: Table EV1, Dataset EV1 etc.)
[These extra files will be collected at the end of the manuscript in the Expanded View section]
UPLOAD as separate files (.txt, .xls., .ZIP etc.) using the file type Expanded View File.

LEVEL 3 (Appendix PDF)

Appendix PDF: Extra figures not promoted to the Expanded View, simple Tables not provided as separate Excel files and extra text (e.g. extra methods) provided in a single PDF (nomenclature to name and refer to Appendix items in the main text: Appendix Figure S1, Appendix Table S1, Appendix Supplementary Methods)
Please use this format for figures/tables/text beyond the limitations set of the main manuscript (level 1) and Expanded View (level 2). The Appendix should begin with a short table of contents.
[The Appendix will be provided at the end of the manuscript as PDF]
UPLOAD as a single PDF using the file type Expanded View File

LEVEL 4 (Source Data)

Source Data for main figures: Source Data should be uploaded using the Source Data file type to link source data underlying regular figures (level 1) or Expanded View figures (level 2) to the relevant figures. Source Data can include minimally processed version of data presented in figures, numerical data underlying plots or charts, as well as replicates.
UPLOAD as single files using the file type Source Data

Source Data for Expanded View and Appendix figures: We cannot currently link Source Data to Expanded View Figures (level 2) and Appendix files (level 3) for technical reasons. It should therefore be uploaded using the Expanded View File filetype in a single ZIP file containing all the Source Data for Expanded View and Appendix content.
UPLOAD as a single ZIP file containing multiple folders/files relating to individual Expanded View items using the file type Expanded View File

To take advantage of the Expanded View

Authors will need to:

1. Select from their current Supplementary Information up to 5 figures for inclusion in the Expanded View.
2. Provide these figures as separate figure files (as for main figures in EPS, TIFF, PPT format etc.) using the file type Figure File in our manuscript submission system.
3. Include the legends for these figures in the main manuscript document file in a section called Expanded View Figure Legends after the main Figure Legends section.
4. Use the nomenclature Figure EV1 (and so on) for the figure legends and making reference to the figures in the text. The figures should be included in numerical sequential order (note that the EV sequence is separate from the sequence for regular figures).

For the figures that are not promoted to Expanded View format, and for supplementary text and tables, we ask authors to provide a single PDF file titled Appendix, containing:

1. A table of contents on the first page
2. Supplementary figures, text and simple tables and their legends (i.e. traditional Supplementary Information)
3. Use the nomenclature Appendix Figure S1, Appendix Table S1, Appendix Supplementary Methods etc. to ensure readers are not confused between Appendix figures and Expanded View figures
4. Reference these items in the manuscript text as: Appendix Figure S1, Appendix Table S1, Appendix Supplementary Methods
5. The Appendix PDF should be uploaded using the file type Expanded View File in our manuscript submission system.

For complex tables (more than 5 columns or 20 rows), datasets, computer code and so on, authors are asked to supply individual ZIP files using the nomenclature: Dataset EV1, Table EV1 and so on. Each ZIP file should contain the data file (movie, excel file, computer code) AND a separate plain text README file with item title and description. Submit these using the file type Expanded View File in our manuscript submission system.

Source data for Expanded View figures, Appendix content and individual files should be provided in a single ZIP file called Source Data for Expanded View and Appendix. Within the ZIP file, the Source Data should be included in individual folders pertaining to the figure/table that the Source Data is for. Submit this using the file type Expanded View File in our manuscript submission system.

File naming conventions

Files should be named based on manuscript number, file type and sequence position as in the following examples. Your Manuscript ID can be seen at the top of the page when you begin submission.

manuscriptID_Fig1.tiff
manuscriptID_SourceDataForFigure1A-F.PDF
manuscriptID_SourceDataForFigure2E.xls
manuscriptID_FigEV1.tiff
manuscriptID_MovieEV1.zip
manuscriptID_DatasetEV1.zip
manuscriptID_ComputerCodeEV1.zip
manuscriptID_Appendix.PDF
manuscriptID_SourceDataForExpandedView.zip

Unpublished Data

The journal does not permit citation of “Data not shown”. All data referred to in the paper should be displayed in the main or Expanded View figures. “Unpublished observations” may be referred to in exceptional cases, where these are data peripheral to the major message of the paper and are intended to form part of a future or separate study, the names of the persons that reported the observation should be listed in brackets. Personal communications (Author name(s), personal communications) must be authorised in writing by those involved, and the authorisation sent to the editorial office at time of submission. Care should be taken that embargo policies are not contravened. References to manuscripts in preparation or submitted, but not yet accepted, should be cited in the text as (Author names(s), in preparation), and should not be included in the list of references. Copies of such manuscripts should be enclosed at submission for reviewing purposes where relevant, as should manuscripts in press, which should be cited in the reference list (see above)

Data deposition

Large-scale datasets, sequences, atomic coordinates and computational models should be deposited in one of the relevant public databases prior to submission (provided private access is available at the database) to enable referees to consider this data as part of the peer review process. Accession codes should be included in a “Data Availability” section at the end of Materials & Methods (suggested wording: “The [protein interaction | microarray | mass spectrometry ] data from this publication have been deposited to the [name of the database] database [URL] and assigned the identifier [accession | permalink | hashtag ]).” Where applicable, please include in the cover letter at submission username and password for confidential access by peer-reviewers.

Data for which no suitable public database exists should be deposited in a database for unstructured data (for example: BioStudies, Dryad, Zenodo, Figshare) or included as dataset files in the Expanded View section of the manuscript, if the file size allows this. In cases where data can not be confidentially deposited in a public database, please contact the editorial office for advice on how to make these data available for refereeing purposes.

Summary table of data repositories recommended by EMBO press:

Data types	Repositories	Standards (via BioSharing*)
Functional genomics	ArrayExpress, GEO	MIAME, MINSEQE
Mass spectrometry proteomics	Pride, PeptideAtlas	MIAPE
Molecular interactions	IMEx	MIMIx
Metabolomics	Metabolight	MSI
Sequences	GenBank, ENA, DDBJ
Flow Cytometry	FlowRepository	MIFlowCyt
Structure data	PDB, NDB, EMDB
Genotypic and phenotypic data	dbGAP, EGA, dbSNP
Computational models, code	BioModels, JJWS, Zenodo	Combine
Unstructured data	BioStudies, Dryad, Zenodo, Figshare

*We provide links to standards via the BioSharing platform (https://biosharing.org), which provides access to additional related resources and further information on standards in biology.

Functional genomics data

Microarray and sequencing-based functional genomics data should be deposited in the ArrayExpress or GEO databases in compliance to the MIAME standards and the MINSEQE draft proposal.

Proteomics, metabolomics and molecular interactions

Mass spectrometry datasets should be deposited in a machine-readable format (e.g. mzML if possible) in one of the major public database, for example Pride or PeptideAtlas and authors should follow the MIAPE recommendations.

Molecular interaction data should be deposited with a member of the International Molecular Exchange Consortium (IMEx) prior to submission of the manuscript. Authors should follow the MIMIx recommendations.

Metabolomics data should be deposited following the recommendations of the Metabolomics Standards Initiative (MSI) in a recognised repository such as MetaboLights.

Flow cytometry data

Data from FACS analysis should be deposited in https://flowrepository.org/ and annotated, as far as possible, using the MIFlowCyt standard.

Sequence data

Nucleotide sequence data should be submitted to an International Nucleotide Sequence Database Collaboration member: GenBank, European Nucleotide Archive or DDBJ.

Computational models

Computational models should be provided in a machine-readable form at submission stage to allow reviewers to reproduce the analysis and simulations performed in the study. When possible, standardize format (SBML, CellML) should be used instead of scripts (e.g. MATLAB). Authors are strongly encouraged to follow the set of guidelines provided by Combine and deposit their model in a public database such as Biomodels or JWS Online. We recommend depositing computer code in Zenodo (see also how code shared on GitHub can be archived on Zenodo https://guides.github.com/activities/citable-code/).

Structural data

The journal 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 by the IUCr Commission on Biological Macromolecules (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 (see Lawson et al. (2011) Nucleic Acids Res. 39: D456-D464).

Human clinical and genomic datasets

The journal encourages authors to provide access to genotype and clinical data with as few restrictions as possible while respecting ethical obligations to the patients and relevant medical and legal issues. If compatible with the individual consent agreement used in the study, such data should be deposited in one of the major public access-controlled repositories such as dbGAP or EGA. Simple genetic polymorphisms should be submitted to dbSNP.

Submission

Presubmission Enquiries

Presubmission enquires allow authors to receive rapid feedback on whether a manuscript in preparation is likely to be of interest to the journal. Presubmission enquiries should be submitted via our online submission system (http://msb.msubmit.net) or by e-mail and should minimally include a list of all authors, a cover letter and an abstract.

If you have already prepared a manuscript, you should submit this via our online system as an article, rather than sending a presubmission enquiry. This allows the editors to make a more informed decision as to whether or not the manuscript is potentially appropriate for the journal. Initial editorial assessment of full submissions is usually rapid, with an average decision time of four days. Full manuscripts should not have been submitted elsewhere, even if they are sent as a presubmission enquiry.

How to Submit

YOU DO NOT NEED TO REFORMAT YOUR MANUSCRIPT AT FIRST SUBMISSION

We use an online manuscript submission and tracking system: http://msb.msubmit.net

In order to submit, you must have registered for an account (on any of the four EMBO Press journals). After this, please consult the following instrutions for submission via our secure server. Please be sure that your browser is set to accept cookies. Our tracking system requires cookies for proper operation.

Please refrain from submitting your manuscript by e-mail attachment.

For original submissions, you will need to upload a cover letter, a Word file of the text of the manuscript (including figure legends), and a PDF file containing all the figures. Alternatively, individual figure files can be uploaded separately, but please note that this can be more time-consuming than a PDF submission. You can also submit all of these files within a single ZIP file. The system will expand it for you. Additional Expanded View files can also be uploaded when applicable (please refer to the section ‘Expanded View’ above).

Once you have submitted your files and the conversion is in progress, it can take up to 30 minutes before the PDF, created in the conversion process, is ready for approval. Please contact the editorial office if the conversion engine takes longer than this. It is important to check the quality of the figures in the converted PDF before approving the submission. You can also upload your own PDF for each file if this is faster and/or provides the quality you require. Please remember that your manuscript will not be submitted until you have approved the converted or uploaded PDF files.

To avoid any unnecessary delays, please refer to the most current electronic formatting guidelines when preparing your manuscript for submission. Authors using computer systems with non-Western type encoding are strongly encouraged to eliminate all occurrences of non-standard fonts in both the manuscript and the figures. We suggest using only the fonts Times, Symbol, Courier and Helvetica.

We will acknowledge receipt of a submitted manuscript by e-mail to the Corresponding author as soon as the quality check (appropriate manuscript format and image quality) has been completed. All further correspondence will also be by e-mail. Please ensure that your servers are set up to allow e-mails from the journal, and contact us if you do not receive an acknowledgement e-mail within a few days of submission.

Overleaf Link

We offer a LaTex-based collaborative, cloud-based authoring tool via Overleaf Link. It features a dedicated article submission template, where you can write and edit your article in Overleaf, and then submit directly to the editorial office.

The article submission template is available at https://www.overleaf.com/read/kyxgttpbzhht

For more information, please visit the Overleaf Link webpage or contact them at support@overleaf.com for assistance.

Manuscript Status

You can check the status of your manuscript at any time in the review process by:

Accessing the system with your password or link sent to you in the acknowledgement e-mail.
Clicking on the link represented by your manuscript tracking number and abbreviated title.
Clicking on the “Check Status” link at the bottom of the displayed page.

This procedure will display tracking information about where your manuscript is in the submission/peer review process.

Please feel free to contact the editorial office with status queries.

Submission of Revisions

When a manuscript is returned to authors for revision, the revised version should be submitted within three months of the authors’ receipt of the referee reports, unless another date is specified in the decision letter. Please contact the editor by the deadline in cases where extra time is required for revision. Additional time may be granted upon request at the Editors’ discretion, assuming the conceptual advance of the study stands (with regard to the current literature). As a matter of policy, we do not consider any competing manuscripts published during the specified revision period as negatively impacting on the conceptual advance presented by your study. However, we request that you contact the editor as soon as possible upon publication of any related work, to discuss how to proceed. Only a single round of revision is generally permitted. The initial decision letter on the original version of the manuscript provides a URL that should be used for submission of revised manuscripts. Please do not upload revisions as new submissions.

Revisions should be accompanied by a point-by-point response to the referees’ comments and editorial decision letter, in PDF or Word format. To facilitate the re-evaluation, we encourage authors to intercalate their response with the referee comments.

Revisions must also be accompanied by a completed author checklist. Right click to download and complete the author checklist here. Please note that the author checklist will be included in the transparent process.

At this stage, you must also conform for our formatting guidelines, and the following items are mandatorily 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 short 'blurb' text summarizing in two sentences the study (max. 250 characters). Bullet points and standfirst text should be submitted as a separate manuscript file in LaTeX, RTF or MS Word format.
A "synopsis image" (Illustrator, PowerPoint, OmniGraffle or jpeg format), which can be used as "visual title" for the synopsis section of your paper. (This image can be provided in two sizes: 211 (w) x 157 (h) px, or 550 (w) x 200-400 (h) px.)
The latter three are for the paper's synopsis, which ensures the paper is more visible and browsable by a wide readership - this text is also used in condensed form on the electronic Table of Contents to complement the titles of papers.

For Acceptance and Publication

Before acceptance and transfer to our publishers, manuscripts will be checked for appropriate formatting and image processing, and for plagiarism. We cannot proceed to acceptance until data are available in public databases when required; see above for details.

Speed of publication

The journal aims for rapid publication of papers, usually within 15 to 20 working days. Please help the Editors and publisher avoid delays by providing current e-mail address(es), telephone and fax numbers at which author(s) can be contacted.

The journal offers a fast-track (10 working day) publication route for manuscripts under competition. Please notify the editor as soon as possible in such circumstances.

Proofs

Authors will be sent an e-mail with a link to access and annotate their proof. It is the authors’ responsibility to check that the final proof is accurate. In the interests of speed, corrections should be submitted within 24 hours. If you have any trouble submitting corrections through the system, please contact the production office immediately. 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.

Press Embargo

When discussing unpublished data (including data in accepted papers not yet published) with the press, authors should take care not to break the journal embargo policy (see above for details)

Open Access and Charges

The journal levies an Article Processing Charge (APC) of 3,300 EUROS (4,200 USD/GBP 2,750) for Research Articles or Reports accepted for publication. There are no additional costs (such as page charges or submission charges).

No charges apply for Reviews, News & Views, Perspectives, Commentaries and Correspondences.

At revision stage, authors are prompted by the system to fill in their funding and payment details.

We will automatically waive or discount charges for corresponding authors working in countries covered by the Research4Life Initiative (see the Wiley Open Access Waiver Country List). In exceptional circumstances charges may be reduced for authors who can provide evidence that they are unable to pay the fees.

Upon acceptance, the corresponding author will receive instructions by email for completing the relevant license forms.

Processing of an accepted manuscript for publication can only proceed once the funding and payment details have been provided via the system and the licence to publish has been returned.

Authors who receive funding from an agency or institution with a Wiley Open Access Account do not pay directly - the charge is paid by the institution or funder. Authors whose institutions have paid the Wiley Open Access partner fee are eligible for a discount on the publication charge - on acceptance a discounted fee is payable by the author. Please see additional details on the online payment page when you submit your revised manuscript.

The journal's articles are freely accessible to all via the Internet and are also deposited immediately upon publication, without embargo, to the Open Access repository PubMed Central.

The journal publishes articles under the Creative Commons Attribution CC BY 4.0 License. This license permits users to access, download, copy, display and redistribute the journal's articles, as well as adapt, translate, text- and data-mine the content subject to the following conditions:

The authors' moral rights are not compromised. These rights include the right of "paternity" (also known as "attribution" - the right for the author to be identified as such) and "integrity" (the right for the author not to have the work altered in such a way that the author's reputation or integrity may be impugned).
If article content is copied, downloaded or otherwise reused, a link to the appropriate bibliographic citation (authors, journal, article title, volume, issue, page numbers, DOI and the link to the definitive published version) should be maintained. Copyright notices and disclaimers must not be deleted.
Where content in the article is identified as belonging to a third party, it is the obligation of the user to ensure that any reuse complies with the copyright policies of the owner of that content.

Please note that any file labeled “Source Data”, “Dataset” or “Resource” is released under a Creative Commons CC0 1.0 Universal Licence. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

Cover Charges

We now feature journal covers based on the research presented in a paper selected by the journal editors. Please note that charges apply for this feature. Two options are available:

A. The authors provide a high-resolution 2575 pixels (w) x 3354 pixels (h) image, which will be optimized for use on the cover. The charge of €1,400 includes design and production of the cover for digital media (website, slide and high resolution PDF) and three poster printouts.
B. Our expert graphics designers, Uta Mackensen and Sandra Krahl, can create a custom designed cover (for an example, see http://embomolmed.embopress.org/content/7/8?variant=cover-expansion) in full consultation with you. The charge for a custom design is €2,600, which includes the production costs and three poster printouts as above.

Digital Object Identifier

EMBO Press and its publishers assign 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.

Citing this Article: eLocators

This journal now uses eLocators. eLocators are unique identifies for an article that service the same function page numbers have traditionally served in the print world. When citing this article, please insert the eLocator in place of the page number. For more information, please visit the Author Services eLocator page here.

Help and Contact

If you need additional help, you can click on the help signs (icon) spread throughout the system. A help dialogue will pop up with context sensitive help. For questions regarding our policies and guidelines, please contact Molecular Systems Biology editorial office (msb@embo.org).

Search

Journal

Authors & Referees

Info

About the journal

Editorial Policies

Editorial Process

Manuscript Preparation

Submission

For Acceptance and Publication

Help and Contact

About the Journal

Aims and Scope

Bibliometrics

Subject Categories

Editorial Policies

Preprint Servers

Scooping Protection extended to include preprints

Transparent Process

Authorship Guidelines

Use of living organisms

Animal welfare

Human Subjects

Biosecurity

Availability of published material, data and software

Conflicts of interest

Scientific Integrity

Corrigenda, errata, addenda and refutations

Data collection and presentation

Data integrity of Images

Preserving data integrity

Originality and Plagiarism

Embargo Policy

Citation Policy

Editorial Process

Extended Scooping Protection

Appeals

Transfer policies

Manuscript Preparation

Research Article Submission

Text Format

Title Page

Abstract

Introduction

Results

Discussion

Materials and Methods

Acknowledgements

Author contributions

Conflict of interest

References and Citations

Tables

Conventions and Abbreviations

Figures

Figure Legends

Figure Formatting

Figure/Data Presentation

Expanded View (replacing Supplementary Information)

To take advantage of the Expanded View

File naming conventions

Unpublished Data

Data deposition

Other Article Types

Reports

Methods

Reviews

Perspective

News & Views

Correspondence

Commentary

Submission

Presubmission Enquiries

How to Submit

Overleaf Link

Manuscript Status

Submission of Revisions

For Acceptance and Publication

Speed of publication

Proofs