For authors

If you write your papers in markdown — or are willing to — PABC is built for you. Here is the case for choosing PABC, how to prepare a submission, and how review works once you submit.

Aims and scope

PABC publishes original research at the interface of biology and computation, broadly construed. In scope:

• Computational methods and algorithms for biological problems — sequence analysis, structure, imaging, single-cell, epigenomics, phylogenetics, simulation, and machine learning applied to biological data.
• Software tools and infrastructure — implementations, libraries, workflows, and platforms that other researchers can use.
• Data resources and standards — reference data, ontologies, metadata specifications, and interoperability work.
• Biological findings driven by computation — results whose primary evidence is computational analysis of biological data, including reanalyses of existing datasets.
• Benchmarks and evaluations — systematic comparisons of methods, and negative or null results the field needs but rarely sees published.

Out of scope: purely experimental biology with no computational component, and purely theoretical computer science with no biological application. We are deliberately more interested in whether work is sound and useful than in whether it is fashionable.

Article types

Every type uses the same markdown-first preparation, the same review process, and the same fee: Research article, Methods, Software, Data resource, Benchmark and evaluation, Brief report, and Perspective. Methods and Software are deliberately separate — a novel algorithm is reviewed on whether the idea is sound; a well-engineered tool on whether it works, installs, and is maintainable. We do not currently publish commissioned reviews or editorials.

How publishing works here

PABC costs almost nothing to publish in because we removed the most expensive parts of traditional publishing, not because we cut corners on the parts that matter.

• We accept one format, not every format. PABC takes markdown and generates the typeset web article and the printable version from that single source. Production stops being a per-paper labor cost.
• Reviewers agree in advance. Our reviewers are Academy members who committed to reviewing as a condition of membership. Review starts in days.
• Reviewers choose their own papers. Instead of an editor guessing who might fit, reviewers self-select from papers matching their expertise.
• AI does the groundwork before a human reads. AI reviewers search prior art, check reproducibility, and flag clarity problems — never assigning a tier or recommending a verdict.
• Reviewers read the finished article, not a manuscript, and comment directly on the passage they concern, the way you would in a Google Doc.
• We fix trivia instead of mailing it back. Small mechanical corrections are made for you and shown to you — no round trip.
• Checks run in minutes and go to the author. References resolved, claims checked against sources, figures measured, overlap screened — automatically, on submission.
• Open access with no asterisk. Every article is free at publication under an open license, and authors keep copyright.

Three structural choices produce nearly all of this: one computable source format, reviewing tied to membership, and automating everything that is not judgment. The journal runs on HydraPub, an open-source journal platform built for exactly this model.

Submission tracks

Like PNAS, PABC accepts submissions through two tracks. Both are peer reviewed.

• Community submissions — open to any author; reviewed and tiered on their merits.
• Member submissions — from Academy members, who have agreed to carry the reviewing load. What distinguishes this track is not yet decided: candidates include a communicated route (a member sponsors a submission), a reduced fee, or simply a separate queue. Whatever is chosen must be a concrete difference rather than a status perk.

Preparing your manuscript

PABC accepts manuscripts in markdown. There are no formatting requirements at submission beyond a well-formed source.

What you provide

• Your manuscript body in markdown, with pandoc-style citation keys ([@smith2020])
• Figures as image files, referenced from the markdown
• A bibliography as BibTeX or CSL-JSON — whatever your reference manager already exports
• Author and affiliation metadata, entered once in the byline editor

You can hand us a link-shared Google Drive folder containing all of the above and we will sort out which file is which, or upload the files directly.

What you do not do

• No journal template to fill in
• No re-typesetting figures or tables
• No wrestling with a submission-system formatter
• No house-style data entry. Small mechanical corrections are made for you and shown to you.

What we check automatically

The moment you submit, an automated battery runs and reports back within minutes: figure resolution and legibility, figure citation order, reference resolution against Crossref and OpenAlex, whether cited sources actually support the claims made about them, and text-overlap screening. You see the results before a reviewer does. From your single markdown source, PABC then generates the typeset web article and a printable page-based version automatically; you'll see and approve a proof before publication.

The submission process

The pipeline runs on HydraPub. From the author's side it is deliberately short.

1. Submit. Upload your markdown manuscript and metadata. Choose your track.
2. Review. Reviewers read the typeset paper and provide feedback in place.
3. Revise. Respond to reviewer comments and submit a revision.
4. Decision and tiering. Editors record a decision and the paper is placed into its tier.
5. Proof. You review and approve the final typeset proof.
6. Publish. The article goes live with a DOI, open license, and is queued for indexing.

We have no real timing data yet — nothing has been published — but the design targets are worth stating: automated checks within minutes of submission, reviewers self-selected in days rather than weeks, reviews back in weeks rather than months, a decision in days once reviews are in, and proof-to-publication in days because production is automatic. The savings come from the queues, not from rushing the reading.

How review works

Peer review is the hardest cost to cut without destroying quality, so PABC redesigns it rather than skips it. Review is really two problems, and journals usually only try to solve the first:

Finding reviewers

Academy members carry an annual reviewing assignment — reviewing is a condition of membership — so the months traditionally spent cold-emailing strangers simply do not happen. Submissions are posted to an internal queue where reviewers self-select the papers matching their interests, closer to how Stack Overflow contributors pick questions than to an editor guessing who might fit. Editors can still invite a specific person when a submission needs expertise the pool does not cover. Review service earns points and a visible, citable record.

The review process itself

Reviewers receive the paper as it would be published: properly typeset, figures in place, references resolved — not a double-spaced document with the figures in an appendix. Feedback is left directly on the passage it concerns, the way you would comment in a Google Doc, rather than compiled into a numbered list and emailed back. Before a human opens the paper, the automated checks have run and the AI reviewers have filed their reports. Better tooling produces better reviews, which are less miserable to write — so reviewers are more willing to review again, which keeps the pool healthy and review fast.

AI reviews, and what they are for

AI does write substantive reviews at PABC. What it does not do is render judgment: it never assigns a tier, never recommends accept or reject, and never counts toward a decision or a quorum. The distinction is enforced in the software — an AI review is structurally incapable of carrying a verdict, and the code that computes quorum and tier placement reads only human reviews.

The AI reviewers, each with a distinct remit:

• Novelty — works out what the paper claims, then searches the literature for the nearest prior art. Held to what it actually retrieved: a citation outside the retrieved set is rejected mechanically, so it cannot invent prior art.
• Rigor — reproducibility and internal consistency. Are methods described well enough to repeat? Are data and code available? Do the numbers agree?
• Clarity — structure, undefined terms, figure legibility, and claims that outrun the evidence.
• Generalist — an overall read of the manuscript.

This frees the human reviewer to spend their attention on what only they can supply: whether the question matters, whether the approach is sound, whether the conclusions follow, and where the paper belongs. That judgment is the part AI is kept away from. Under the proposed tier model, reviewers decide where a paper belongs rather than merely whether to accept it.

Fees and open access

PABC's target publishing fee is under $1000 per article, well below typical open-access charges. Publishers rarely say where an article processing charge actually goes; F1000Research is a welcome exception and publishes a breakdown. Three categories dominate it — pre-publication checks (35%), peer review management (20%), and platform development (15%), together about 70% of the cost. We believe we can cut those by roughly 90%:

• Peer review management — a pre-agreed reviewer pool (reviewing is a condition of membership), AI-assisted matching and self-assignment, and volunteer associate editors for the small residue. Much of this is already built into HydraPub.
• Pre-publication checks — restricted input format (markdown, never Word or LaTeX) and a full battery of automated checks run on every submission in minutes: figure quality and citation order, similarity screening, reference resolution, citation–claim support, AI summaries, and editorial pre-flight QC. Trivial fixes are applied automatically and shown to the author.
• Platform development — HydraPub is open-source software shared across journals, not a bespoke system maintained for one publisher.

After the big three, the next cost is marketing (14%); we rely on word of mouth and organic growth. The goal is not to grow huge — it is to be useful to the subset of people who find this approach useful. The fee buys nothing editorial: never a favorable decision, faster review, or any outcome. See Ethics and integrity.