Biochemoinfo Journal accepts dedicated Software Articles in computational biology, bioinformatics, cheminformatics, molecular dynamics, and related fields. Outside of SoftwareX, very few journals in our domain systematically publish software-focused papers. We aim to fill that gap with rigorous, archive-backed, cryptographically verifiable software publishing.
TL;DR — The Short Version
If your software is open-source, here is the minimum we ask:
- Public GitHub (or equivalent) repository with an OSI-approved license (MIT, Apache 2.0, GPL, BSD, etc.).
- Deposit the release in Zenodo (DOI) and Software Heritage (SWHID).
- Include a Verification Block in the paper with the commit hash and the SHA-256 of the archive.
- Write the paper following our general formatting rules.
APC: Free. All published articles are open access under CC BY-NC 4.0.
1. Two Tiers of Open-Source Software
Our open-source track is split into two tiers, depending on how the software is licensed. Both tiers go through the same double-blind peer-review process.
🟢 Tier 1 — Fully Reproducible
Source code is fully open and publicly accessible under an OSI-approved license. Reviewers and readers can clone, build, modify, and redistribute the software.
- Dependencies must be clearly documented (
requirements.txt,environment.yml,package.json, etc.). - Installation and usage instructions must be in the repository's
README. - A minimal working example or test suite is strongly recommended.
🟡 Tier 2 — Academically Reproducible
Source code is visible but the license is restricted (e.g., source-available, free for academic use, paid for commercial use). Academic researchers can use it without payment; commercial licensing is the author's business and not the journal's concern.
- Authors must guarantee that academic access is preserved for at least 5 years from publication.
- If the academic-free policy is later revoked, the paper will be flagged with the ⚠ Verification Withdrawn badge.
2. Reviewer Access
- Tier 1: Reviewers clone the public repository directly — no extra access needed.
- Tier 2: Authors must ensure reviewers can obtain the academic license without delay. If the academic license is automatic upon registration, this is sufficient.
3. Mandatory Archival — Two Independent Archives
GitHub is not a permanent archive. Repositories can be deleted, accounts can be closed, licenses can change, and software can become unusable two months later due to a single dependency update. For this reason, two independent archives are mandatory for every accepted software paper.
Primary Archive: Software Heritage
- Non-profit code archive backed by INRIA and UNESCO.
- Archives the entire commit tree, not just snapshots.
- Provides a permanent SWHID identifier.
- Submit at: softwareheritage.org
Secondary Archive: Zenodo
- Open-access repository operated by CERN and OpenAIRE.
- Each release receives a unique DOI.
- GitHub–Zenodo integration can automate this for every release tag.
- Submit at: zenodo.org
The paper must reference the archive identifier (SWHID, Zenodo DOI) — not only the live URL. Live URLs are convenience; archives are permanence.
4. Cryptographic Verification — Hash Chain
The journal requires bit-level verifiability of the published software. This means that any reader, years from now, can confirm that the file they downloaded is byte-for-byte identical to what the authors submitted.
Required Hashes
- Git Commit Hash — SHA-1 minimum, SHA-256 preferred for new repositories. Get it with
git rev-parse HEAD. - Archive Hash — SHA-256 (or SHA-512 for very large archives) of the
.tar.gzor.zipfile deposited in Zenodo. - Cross-archive consistency — if the same archive file is uploaded to multiple locations, the SHA-256 must be identical across all of them.
Verification Block — Mandatory in the Paper
The paper must include a fenced block in this format (typically near the end of the methods section):
For step-by-step instructions on computing these hashes on Linux, macOS, and Windows, see our detailed Software Hash & Verification Guidelines.
5. Annual Verification Check
Each year, the journal automatically verifies that published software remains accessible and unchanged:
- Tier 1: Repository accessibility, build success, hash integrity.
- Tier 2: Academic license still free, download links still working.
If verification fails, the article is flagged with a ⚠ Verification Expired badge. The article is not retracted — readers are simply informed of the change in availability.
6. Badge System
Each published software article carries one of the following badges in the article list, PDF header, and citation metadata:
- 🟢 Tier 1 — Fully Reproducible
- 🟡 Tier 2 — Academically Reproducible
- ⚠ Verification Expired — failed annual check
7. Pre-Submission Checklist
- ☐ I know which tier my software falls under (Tier 1 or Tier 2).
- ☐ My repository has a clear OSI-approved license (Tier 1) or a documented academic-free license (Tier 2).
- ☐ A release has been deposited in Software Heritage — SWHID obtained.
- ☐ A release has been deposited in Zenodo — DOI obtained.
- ☐ The SHA-256 of the archive file has been computed and matches across all archives.
- ☐ The paper contains a complete Verification Block.
- ☐ The paper follows the general formatting rules (APA 7 references, etc.).
- ☐ Tier 2 only: I commit to keeping academic access free for at least 5 years.
8. About Software Articles by the Journal Team
In the interest of transparency: the editorial team also develops software, and these tools are published under the same standards as third-party submissions. Our editorial software is listed under the BioChemoLabs section of the journal site. When editorial-team software is submitted as a paper, it is reviewed by independent external reviewers, and a conflict-of-interest statement is mandatory.
Questions about software submissions? Write to info@biochemoinfojournal.com.