This section explains the editorial processes at the npj Series, which can be outlined in the following steps:
- The author submits a manuscript and it receives a tracking number.
- An Editor is assigned to the manuscript.
- The editorial team decides whether to send the manuscript out to review. If the decision is not to send the manuscript for review, the Editor contacts the author with the decision.
- The Editor assigns potential Reviewers to the manuscript and the author is notified.
- Reviewers agree to review the manuscript.
- Reviewers submit their reports to the Editor.
- The editorial team discusses the reports and the Editor makes the final decision. This process may involve further consultation with the Reviewers and editor-mediated communications between the Reviewers.
- The Editor contacts the author with the decision.
- If the decision is negative, the author can choose to transfer their manuscript to another journal. If the manuscript was peer reviewed the referee comments are also transferrable on request by the author.
Please see our Manuscript Transfer FAQ for more information about this service.
npj Systems Biology and Applications is part of the npj Series: open access community journals from Nature Portfolio publishing high-quality research, reviews and commentary across the life, health, physical, applied and environmental sciences. Research papers published by the journals represent important advances bringing new insight to a specialized area of research.
The journals operate under a collaborative editorial model, with active researchers engaged as manuscript-handling Editors, supported by in-house, PhD-trained Nature Portfolio managing Editors. For more information about the npj Series and a list of journals, see https://www.nature.com/nature-portfolio/about/npj-series.
Manuscripts should be submitted via the online submission system: Submit manuscript. The corresponding author should indicate whether the work described in the manuscript has been discussed with a specific Editor at npj Systems Biology and Applications before submission. Copies of any papers containing related work that are under consideration or in-press at other journals should be included with the submission as additional supplementary information.
Manuscripts submitted to the npj Series journals do not need to adhere to our formatting requirements at the point of initial submission; formatting requirements only apply at the time of acceptance.
When a new submission is received, it is assigned to an Editor in Chief, who assesses the paper and assigns it to an Associate Editor if the paper meets key criteria for suitability for the journal. The Associate Editor evaluates the submission, potentially in collaboration with other Editors (including in-house Managing Editors), and decides whether it should be sent for peer review based on the editorial criteria of the journal of novelty and significance and overall technical quality. When the Editors have reached a first decision on the paper, they notify the corresponding author by email.
The novelty of a submitted paper is considered to be compromised if it has significant conceptual overlap with a published paper or one accepted for publication by npj Systems Biology and Applications. Preprint archives do not compromise novelty.
If a paper was previously reviewed at another Nature Portfolio journal, the authors can use an automated manuscript transfer service to transfer the referees' reports to npj Systems Biology and Applications via a link sent by the Editor who handled the manuscript. The Reviewer identities and their full reports will be transferred, and although the journal Editors will take the previous reviews into account when making their decision, the Editors will likely choose to take advice from additional or alternative referees. Alternatively, authors may choose to request a fresh review, in which case they should not use the automated transfer link, and the Editors will evaluate the paper without reference to the previous review process. However, this decision must be made at the time of initial submission and cannot be changed later.
If the authors ask the Editors to consider the previous reviews, they should include a note explaining the relationship between the submitted manuscript and the previous submission and (assuming it has been revised in light of the referees' criticisms) give a point-by-point response to the referees. In cases where the work was felt to be of high quality, papers can sometimes be accepted without further review, but if there were serious criticisms, the Editors will consider them in making the decision. In the event of publication, the received date is the date of submission to npj Systems Biology and Applications. More details are available on the manuscript transfer service.
If the Editors of npj Systems Biology and Applications decline publication of a manuscript, before or after peer review, the authors can easily resubmit it to a different journal within the Nature Portfolio, in most cases without the need to reformat or upload the files, by following the link provided in the Editor’s decision email. More information about the manuscript transfer service can be found here.
Follow this link for a list of all journals in the Nature portfolio and subject areas.
Peer review overview
All npj Series journals are guided by the Nature Portfolio editorial peer review policy.
The following types of contribution to npj Series journals are peer-reviewed: Articles, Brief Communications, Case Report, Comment, Matters Arising, Meeting Report, Perspective, Protocol, Resource, Reviews. Correspondence and all forms of published correction may also be peer-reviewed at the discretion of the Editors. Other contributed articles are not usually peer-reviewed. Nevertheless, articles published in these sections, particularly if they present technical information, may be peer-reviewed at the discretion of the Editors.
The corresponding author is notified by e-mail when the Editor decides to send a paper for review. Manuscripts judged to be of potential interest to our readership are sent for formal review, typically to two or three Reviewers. Reviewer selection is critical to the publication process, and we base our choice on many factors, including expertise, reputation, specific recommendations and our own previous experience of a Reviewer's characteristics. When selecting Reviewers, we seek to avoid conflicts of interest and close associates of the authors. Springer Nature is committed to diversity, equity and inclusion; Nature Portfolio journals strive for diverse demographic representation of Peer-Reviewers. At submission, authors may suggest referees; these suggestions are often helpful, although they are not always followed. Authors are strongly encouraged to consider geographical regions, gender identities, racial/ethnic groups, and other groups when providing such suggestions for Peer-Reviewers. Authors may also indicate a limited number of scientists who should not review the paper. Excluded scientists must be identified by name.
The npj Series operate a single-anonymized peer review process. In line with policy, referees are not identified to the authors, except at the request of the referee. npj Series referee reports, whether signed or not, are subsequently shared with the other Reviewers.
npj Series journals require potential referees to disclose any professional and commercial competing interests before undertaking to review a paper, and require referees not to copy papers or to circulate them to un-named colleagues. All referees agree to these conditions before the journal sends them a manuscript to assess. Although our Editors go to every effort to ensure manuscripts are assessed fairly, the journal is not responsible for the conduct of its referees.
The Editors then make a decision based on the Reviewers' advice, from among several possibilities: (a) Accept, with or without editorial revisions (b) Invite the authors to revise their manuscript to address specific concerns before a final decision is reached (c) Reject, but indicate to the authors that further work might justify a resubmission (d) Reject outright, typically on grounds of specialist interest, lack of novelty, insufficient conceptual advance or major technical and/or interpretational problems.
Collections and special issues follow the standard peer review policy. The peer review process of any submission associated with a collection or special issue is handled by an Editor who is responsible for assigning at least two referees to each article and evaluating the reviews. The Editors-in-Chief then makes a final decision of accept or reject on any special issue article. The peer review of any submissions for which the Editor has a competing interest is handled by another Editor who has no competing interests, to ensure that the evaluation of these submissions is completely objective.
Decision after review and revision
In cases where the referees have requested well-defined changes to the manuscript that do not appear to require extensive further experiments, Editors may request a revised manuscript that addresses the referees' concerns. The revised version is normally sent back to some or all of the original referees for re-review. The decision letter will specify a deadline, and revisions that are returned within this period will retain their original submission date.
In cases where the referees' concerns are more wide-ranging, Editors will normally reject the manuscript. If the Editors feel the work is of potential interest to the journal, however, they may express interest in seeing a future resubmission. The resubmitted manuscript may be sent back to the original referees or to new referees, at the Editors' discretion.
In either case, the revised manuscript should be accompanied by a cover letter explaining how the manuscript has been changed, and a separate point-by-point response to referees' comments. Ideally no more than two resubmissions will be considered for each manuscript, following which we will try to reach a final decision on publication.
An invited revision should be submitted via the revision link to the online submission system provided in the decision letter, not as a new manuscript.
In the event the manuscript is rejected after review, authors have the option to transfer to another Nature Portfolio journal via our transfer portal. Authors may also choose to submit their manuscript to a journal outside of the Nature Portfolio.
Final submission and acceptance
If the authors have successfully addressed all the comments of the Reviewers and the Editors, the Editors will deem the paper acceptable for publication in npj Systems Biology and Applications. They will send a request for final submission accompanied by detailed instructions for final changes that need to be made.
For the final revision, authors should use the revision link to the online submission system provided in the decision letter to upload a final version of the text with all the requested format changes. Electronic files of the final figures, at high resolution, should be submitted at this time. When all remaining editorial issues are resolved, the paper is formally accepted.
Once a manuscript is accepted, the corresponding author will be asked to sign a Licence to Publish and arrange payment of any applicable article processing charge on behalf of all authors. Failure to promptly complete these steps will result in delay of publication.
Publishing Open Access will mean the paper is freely accessible online immediately upon publication. Authors are permitted to post the final, published PDF of their article on a website, institutional repository or other free public server, immediately on publication.
Open access articles are published under a CC BY licence (Creative Commons Attribution 4.0 International Licence). The CC BY licence is preferred by many research funding bodies. It allows for maximum dissemination and re-use of open access materials: users are free to share (copy, distribute and transmit) and remix (adapt) the contribution including for commercial purposes, providing they attribute the contribution in the manner specified by the author or licensor.
Under Creative Commons licences, authors retain copyright in their work. Authors should note that some funders require papers to be published under a specific licence and so should check the funder mandate to ensure compliance.