Biochemoinfo Journal accepts Commercial Software Articles — papers describing software that is sold, licensed, or otherwise commercially distributed — provided that end users can independently verify the software's claims without prohibitive cost. Almost no journal in computational biology, bioinformatics, or cheminformatics offers a clear, fair pathway for commercial software publication. We aim to provide one — with strict conditions that protect scientific integrity.
TL;DR — The Short Version
- Your software must be verifiable by the end reader — either through a public free SaaS interface or through a free trial of at least 15 days.
- You must explain the method openly, even if the source code is closed.
- You must provide reviewers with full unrestricted access during review.
- You must commit to maintaining the verification mechanism for at least 5 years.
- You must accept the "Commercial Software Description" label on your paper.
- You bear sole responsibility for preventing trial abuse.
APC: Free. All published articles are open access under CC BY-NC 4.0.
1. The Verifiability Principle
Commercial software is welcome here, but the journal's editorial line draws a firm boundary: no paper can claim a result that the reader has no way to test. This is non-negotiable. A reader does not need to own your software, but they must be able to confirm that it does what your paper says it does.
You can satisfy this requirement in one of two ways — SaaS Form or Download Form. You may also satisfy both, in which case both badges apply.
🔵 Tier 3-S — SaaS Form (Web-accessible)
The software must be reachable through a publicly accessible web interface. Registration is permitted; payment is not.
- Free quotas must allow at least 3× the volume of the paper's largest reported experiment, within a 30-day window.
- Authentication may use email, ORCID, or institutional sign-on.
- Anti-abuse measures (rate limiting, captcha, account verification) are your responsibility, not the journal's.
🟣 Tier 3-D — Download Form (Trial-based)
The software must be downloadable as a binary, with a free trial sufficient to reproduce the paper's main results.
- Trial duration: at least 15 days, or long enough to reproduce the paper's main results — whichever is longer.
- The trial must be fully featured. Feature-locked demos that prevent reproducing the paper's experiments are not accepted.
- You are the sole party responsible for preventing trial abuse (multi-account exploitation, trial reset, hardware fingerprint bypass, etc.). The journal does not police your licensing.
2. Reviewer Access — Mandatory Full License
During peer review, you must provide reviewers with fully unrestricted access — not the public free tier. This typically means a temporary license key, premium account, or equivalent that removes all quota and feature limits for the duration of the review.
- Reviewer identity is kept confidential by the journal under our double-blind policy. The journal acts as the intermediary; you provide a license to "the journal", not to a named individual.
- The license is revoked at the end of the review.
- Refusing to provide reviewer access results in immediate rejection.
3. Method Openness — Closed Code, Open Method
⚠ This is the most important rule on this page.
Your source code may be closed. That is acceptable. However, the method — the algorithm, model architecture, training procedure, parameter choices, pre- and post-processing steps, evaluation methodology — must be open and described in scientific detail.
Reviewers cannot audit a black box. They evaluate your method based on what you describe in the paper. This means:
- "Trade secret" or "patent-protected" is not a valid reason to omit methodological detail.
- If your method cannot be openly described — for any reason — this journal is not the right venue for your paper.
- If a reader later finds that your software produces incorrect results, and your method was clearly described and the verification mechanism (SaaS or trial) was working, then you cannot blame the journal or the reviewers. Reviewers verify the method as you described it, not the closed-source implementation.
4. Mandatory Archival — Three Independent Archives
Commercial software has a higher disappearance risk: companies close, products are deprecated, websites vanish. We require three archival layers:
- Software Heritage — if any source code, scripts, or installer payload is shareable. Even partial deposits help future verification.
- Zenodo — the installer binary or distributable archive, with its own DOI.
- Wayback Machine + archive.today — snapshots of the software's public documentation pages, pricing pages, and feature descriptions, captured at submission time.
If your firm closes or your domain expires five years from now, the archived documentation will preserve the academic record of what your software did at the time of publication.
5. Cryptographic Verification — Binary Hash Chain
Bit-level verifiability is required. The reader must be able to confirm that the binary they downloaded today is the same binary that was reviewed at submission time.
Required Hashes
- Installer / Binary SHA-256 — the exact file users will download. SHA-512 acceptable for very large installers.
- Documentation snapshot URL — archive.org / archive.today links captured at submission.
- Optional but recommended: SHA-256 of any sample input/output files used to demonstrate the software's behavior in the paper.
For Tier 3, reproducible builds are not required. The hash refers to the published binary — the exact file your customers download — not to a build reproduced from source. If you later release an updated version, the new binary will have a different hash, and the article will be tagged "Software Updated Post-Publication". The original published version remains the citation reference.
Verification Block — Mandatory in the Paper
For step-by-step hash computation instructions, see our Software Hash & Verification Guidelines.
6. The "Commercial Software Description" Label
Every Tier 3 paper carries a clearly visible "Commercial Software Description" label in the PDF header, the article list, and the citation metadata. This is not a stigma — it is transparency. It tells readers that the paper describes a commercial product, that the source code is closed, and that reproducibility is verified through SaaS or trial mechanisms rather than open code.
A conflict-of-interest statement is mandatory. You must disclose any financial, employment, or ownership relationship with the software's vendor.
7. Trial-Maintenance Commitment — The 5-Year Rule
⚠ "Bait and switch" is treated as a serious breach.
By submitting, you commit to maintaining the verification mechanism (SaaS access or trial download) for at least 5 years from publication. Removing the trial, paywalling the SaaS endpoint, or otherwise breaking verifiability before this period results in:
- The article being flagged with 🚫 Verification Withdrawn.
- An editorial note attached to all future submissions from the same author or vendor.
- Possible referral to COPE for review of editorial misconduct.
8. Annual Verification Check
The journal will check, every year:
- Tier 3-S: Is the SaaS endpoint reachable? Are the free quotas still meaningful?
- Tier 3-D: Does the download link still work? Does the binary hash still match? Is the trial still as long as committed?
- Documentation archive snapshots are still readable.
If verification fails, the article is flagged accordingly. The article is not retracted — readers are simply informed.
9. Badge System
- 🔵 Tier 3-S — SaaS Verifiable
- 🟣 Tier 3-D — Trial Verifiable
- ⚠ Verification Expired — failed annual check
- 🚫 Verification Withdrawn — trial commitment broken before the 5-year mark
10. What This Journal Will Not Do
- We will not validate, endorse, certify, or recommend any commercial product. Publication is a description and a verification, not an endorsement.
- We will not assist users with licensing disputes, refunds, customer support, or contract issues with commercial vendors.
- We will not police trial abuse or pursue copyright violators on the vendor's behalf.
- We will not publish papers whose method is concealed under "trade secret" arguments, regardless of how strong the verification mechanism is.
11. Pre-Submission Checklist
- ☐ My software has a public verification mechanism (SaaS endpoint or downloadable trial).
- ☐ Tier 3-S: Free quotas allow at least 3× the paper's largest experiment within 30 days.
- ☐ Tier 3-D: Trial is at least 15 days (or long enough to reproduce results), fully featured.
- ☐ The method is openly described in the paper (algorithm, model, parameters).
- ☐ I am prepared to provide reviewers with full unrestricted license access.
- ☐ The installer/binary SHA-256 has been computed.
- ☐ The installer/binary has been deposited in Zenodo.
- ☐ Documentation pages have been archived in the Wayback Machine and archive.today.
- ☐ I have committed to maintaining trial/SaaS access for at least 5 years.
- ☐ I have included a conflict-of-interest statement.
- ☐ I accept the "Commercial Software Description" label on my paper.
- ☐ I understand that anti-abuse mechanisms are entirely my responsibility.
- ☐ I understand that I cannot blame the journal or reviewers for end-user issues, provided method openness and verification were maintained.
Questions about commercial software submissions? Write to info@biochemoinfojournal.com.