About PABC

The Academy of Biology and Computation (ABC) is a scholarly society for researchers working at the interface of biology and computation. Its flagship activity is publishing the Proceedings of the Academy of Biology and Computation (PABC) — an open-access, ultra-low-cost, rigorously reviewed journal.

Why a new society and journal

Academic publishing has drifted into a false dichotomy: journals are either selective but expensive, or cheap but with weak review and low impact. No existing outlet combines all of:

1. Open access — science freely available to everyone
2. Affordable — under $1000 per article
3. Professional — proper typesetting, a beautiful web version and a printable page-based version
4. Efficient — modern submission, no formatting hoops
5. Rigorous — selective peer review that actually improves papers
6. Impactful — indexed, read, and respected

The Academy exists to prove this combination is possible. The mechanism is efficiency: a highly opinionated, single-source publishing model and a peer review system designed to run itself. PABC is explicitly not trying to be everything to everyone — we publish for the community of researchers willing to write in markdown and work within a streamlined, computable pipeline. That constraint is where the cost savings come from.

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.

Tiers: one submission, one review

One of the deepest inefficiencies in academic publishing is re-review: a paper rejected from one journal is sent to the next, where fresh reviewers repeat the same work. PABC proposes to remove this by reviewing once. When you submit, you submit to PABC, and reviewers bin your paper into the tier its impact and rigor warrant. At the bottom is a no-impact-required tier: any scientifically sound paper is guaranteed to publish there. The goal of review is to populate the higher-impact tiers above it — the question shifts from "should this be published?" to "where does this belong?"

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.

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.

Origins

The Academy began as a straightforward frustration: the cost of publishing a paper bears almost no relation to the cost of the work actually required to publish it. Three things changed recently that make solving this possible now — AI assistants can do the careful, repetitive work that used to require staff; a system built today on a computable source format carries none of publishing's inherited technical debt; and AI-assisted development has collapsed the cost of building serious software.

The Academy is being founded out of the Sheffield Computational Biology Lab at the University of Virginia, which also builds HydraPub, the open-source platform PABC runs on. The lab's role is to get the society started and maintain the software; the Academy is intended to be independent of it, governed by its members and its editorial board. The Academy is in formation — its leadership is not yet seated, and most specific policies are still open.

Frequently asked questions

Can I submit a Word document?

No. PABC is markdown-first by design — that's where the cost savings come from. If you can't or won't write in markdown, PABC isn't the right venue.

Is it really open access?

Yes, fully. No paywall, no embargo, no hybrid option. See Open access and licensing.

How can the fee be so low?

By removing the two biggest costs in publishing — manual review management and one-off production work — through a self-managing review system and a single-source pipeline.

Will my paper be rejected?

Under the tier model currently proposed, scientifically sound papers would be guaranteed publication in the base tier, with review deciding placement rather than acceptance. That model is still under consideration.

Will you send my paper back over formatting trivia?

No. Small mechanical corrections are made automatically and shown to you. Your paper comes back only when something needs your judgment. See For authors.

Does AI review my paper?

Several AI reviewers read every submission, covering prior art, rigor, and clarity, and file advisory reports labeled as AI. What they cannot do is judge: no AI review assigns a tier, recommends accept or reject, or counts toward a decision. A human reviewer decides.

Is PABC indexed in PubMed?

Not yet — PABC has not published anything, so it is not indexed anywhere. PubMed requires roughly two years of sustained volume. See Archiving and indexing.

Is any of this actually decided?

The commitments — open access, markdown-first, an ultra-low fee, reviewing as a condition of membership, real peer review — are fixed. Most specifics are open until the Academy's leadership is seated. See Policies under review.