Molecular Systems Biology Submission Process

Molecular Systems Biology explicitly supports presubmission enquiries through eJP. The official guidance says these enquiries are intended for informal feedback on whether a manuscript's scope is appropriate. They should include an abstract, cover letter, and contact details. The same guidance says presubmission enquiries are not a route for submitting a full manuscript and email enquiries will not be considered.

Use this route when the manuscript is scientifically close but the journal owner is uncertain. Typical MSB uncertainty looks like this:

• the paper has a serious computational model, but the biological validation is still borderline for MSB
• the experiment is strong, but the systems-level insight may be better owned by EMBO Journal, Cell Systems, PLOS Computational Biology, Genome Biology, or a specialist biology journal
• the manuscript could be a Research Article, Report, Method, or Resource, and the process implications differ
• a Review Commons transfer or prior editorial discussion changes how the cover letter should frame the record

Do not use a presubmission enquiry to avoid making the hard internal decision. If the abstract cannot name the systems-level behavior, and the cover letter cannot explain how computation and experiment depend on each other, the enquiry will only expose the same weakness earlier.

Initial Quality Check starts with whether the eJP record is administratively usable. The official guidance says submissions use eJournal Press, authors can save work and finalize later, and submitted manuscripts are acknowledged to all authors by email. It also says correspondence after acknowledgement goes to the corresponding author only.

Before upload, confirm the process basics:

• the eJP account is ready and linked to the correct ORCID profile
• the title, abstract, authors, affiliations, and corresponding author are final enough for the submitted record
• the manuscript can be uploaded as a single PDF or LaTeX file, or as separate manuscript and primary figure/table/dataset files
• supplementary information is clearly labeled and includes material needed to understand or replicate the study
• the cover letter explains significance, related or competing papers, any editor pre-discussion, reviewer requests, and whether peer-review comments from another journal should be considered
• authorship, competing interests, dual publication, and funding-source declarations are complete

The MSB-specific risk is that the first check passes while the paper is not process-ready. A format-neutral initial submission can still be scientifically incoherent. Do not mistake "any format" for "any package." The file package should still make the model, experiment, data, source materials, and systems claim easy to inspect.

Editorial Assignment starts when the submission is complete enough to route. The editor or editorial team has to decide whether the manuscript belongs in Molecular Systems Biology and whether reviewers can evaluate it.

At MSB, editorial assignment is often a model-experiment routing problem. A conventional molecular mechanism paper may be good science but not MSB-owned. A computational paper may have a strong model but insufficient experimental testing. A multiomics study may be data-rich but not explanatory at the systems level. The eJP package should help the editor identify the correct reviewer community without reconstructing the authors' intention from disconnected sections.

The first screen should make these signals agree:

Molecular Systems Biology sits inside the EMBO Press process, where accepted research papers carry transparent process-file expectations. The submission guidelines say a reporting checklist is included in the transparent process file accompanying published articles, and revised research papers require a point-by-point response, reporting checklist, reagents and tools table, and source data.

That does not mean every submitted paper receives a published process file. It means authors should prepare as if the review history, response logic, source-data support, and reproducibility posture may become part of the publication record if the paper succeeds.

For MSB, transparent peer review changes the author-side process in three ways:

1. Reviewer concerns should be answerable with traceable manuscript changes, not only persuasion.
2. Source-data, code, reagent, and protocol details should be organized before review pressure exposes them.
3. The response strategy should treat model assumptions, validation experiments, and limitations as publishable reasoning, not private negotiation.

EMBO Press guidance says source data used to generate figures are required when submitting a revised manuscript. The same guidance says source-data files are linked to figures for inspection, re-analysis, or integration, and deposited in BioStudies for archiving. It also describes Expanded View data, Appendix files, complex datasets, software code, README files, and source data for Expanded View and Appendix material.

That makes source data a process issue, not just a publication polish issue. If the manuscript relies on omics analysis, model simulations, perturbation screens, imaging, time-course inference, or interaction networks, the authors should know before submission which files will support each claim.

The Final Decision is the editor's synthesis of fit, reviewer reports, source-data sufficiency, revision feasibility, and whether the transparent process record would support the paper. Outcomes can include reject, revise, transfer, or accept after successful revision and production checks.

If revision is invited, the official process matters. Revised research papers must include a point-by-point response, the reporting checklist, the reagents and tools table, and source data. The guidelines state that revised versions should generally be submitted within three months unless the decision letter specifies another date, and that more time may be granted at editorial discretion.

For authors, the main question is whether the revision can preserve the conceptual advance. If reviewers ask for deeper perturbation validation, source-data clarity, model sensitivity analysis, or a narrower claim, the response should not only answer comments. It should rebuild the manuscript record so the systems claim, data, model, and experiment now agree.

If the paper enters external review, reviewers usually test the full MSB argument:

• Is the manuscript genuinely systems biology rather than molecular biology with a computational layer?
• Does the model or quantitative framework carry the central claim?
• Are predictions, mechanisms, or system behaviors experimentally tested?
• Are source data, code, datasets, reagents, and protocols sufficient for review?
• Does the cover letter position the paper honestly against nearby journals?
• Is the contribution broad enough for MSB rather than a specialist journal?

The strongest submissions make those questions easy to answer before reviewers are invited. The weakest submissions leave reviewers to infer whether the computational and experimental halves belong to one paper.

MSB submissions can slow down for ordinary reasons: editor availability, reviewer invitation declines, delayed reports, or a complex decision letter. The journal also has field-specific bottlenecks:

In Manusights pre-submission work on Molecular Systems Biology manuscripts, the process failures are usually visible before eJP upload. They are not only scientific weaknesses. They are mismatches between the manuscript's process record and the decision MSB has to make.

MSB format-neutral trap. Authors read "initial submissions in any format" and under-prepare the submission package. The file uploads are accepted, but the abstract, figure order, supplementary information, data statements, code files, and cover letter do not make a coherent systems-biology case.

Model-experiment split. The quantitative framework and the wet-lab validation are both present, but they answer different questions. The editor can see computation and biology, yet cannot see why they are co-primary. That creates reviewer-routing friction before the first invitation.

Source-data afterthought. The central claim depends on figure panels, model outputs, or processed omics results that are not mapped to source files. This becomes more expensive at revision because EMBO Press source-data expectations are no longer optional polish.

Presubmission enquiry misuse. Some authors use the enquiry route as a substitute for deciding the paper's owner. The enquiry should clarify a near-fit case; it should not carry a manuscript whose abstract and cover letter still cannot explain why MSB owns it.

Across these reviews, the same pattern repeats: the eJP record is complete, but the editorial story is not. Manusights submission analysis treats this as a specific failure pattern, not a style preference. We observe the abstract, first figure, model diagram, perturbation experiment, source-data plan, code availability, supplement labels, competing-interest statements, and cover letter as one process object. When those pieces disagree, the submission can look administratively clean and still feel difficult to send to reviewers.

The strongest packages do not ask the editor to assemble the systems-biology argument from scattered clues. They make the model-experiment dependency visible in the title, abstract, figure sequence, files, and letter before the editor opens the reviewer-invitation screen. In practice, this is an editorial triage pattern: editors specifically screen whether the system claim can be reviewed by a coherent reviewer pool, not merely whether the upload checklist is complete.

Check whether your MSB eJP record tells one story →

Check whether your MSB source-data package is review-ready →

Check whether your MSB model and experiments are co-primary →

This guide tells you what the MSB process tests before and after eJP submission; the review tells you whether your paper passes that process check before the upload becomes the editor's first impression. Manusights reviews are read by multiple expert reviewers, include a 60-day money-back guarantee, and we never train on submitted manuscripts.

While the paper is active in eJP, prepare materials that will matter if the decision is revise, reject with useful comments, or transfer:

Do not rewrite the manuscript while it is active unless the editor asks. Use the waiting period to make the response path clean.

Is the MSB first submission really format-neutral?

Yes, the official guidance says EMBO Press welcomes submissions in any format and authors do not need to follow journal formatting guidelines for initial submission. That flexibility should not be confused with a low bar. The paper still needs clear English, an intelligible structure for a broad readership, a usable manuscript file, title and abstract, author details, supplementary information, and policy declarations.

Does MSB require source data at initial submission?

The official page says source data are required when submitting a revised manuscript, not as a universal initial-submission file. Practically, authors should prepare the source-data map before initial submission because reviewer and editor concerns often reveal source-data gaps during review.

Should I submit a presubmission enquiry or the full paper?

Use a presubmission enquiry when the manuscript is not yet being submitted and the scope question is real. If the full manuscript is already written and the authors are ready to submit, the official guidance says to proceed with a full formal submission.

What is the biggest process mistake for MSB?

The biggest process mistake is a complete upload package that does not tell one systems-biology story. MSB can be forgiving about first-submission formatting, but the editor still has to decide whether the computation, experiment, source data, and manuscript claim belong together.

1. Molecular Systems Biology submission guide, Manusights sibling page.
2. Is my paper ready for Molecular Systems Biology?, Manusights sibling page.
3. Molecular Systems Biology under review, Manusights sibling page.