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Atlas of Computational Cell Reprogramming

Release history

Changelog

What changed, when, and why. Method additions, class re-placements, and audit refreshes are all tracked here.

Maintenance policy

The Atlas is a maintained index, not a one-time snapshot of the review corpus.

Release log

  1. 2026-10-22 v0.2.2

    Benchmark comparisons

    The Benchmark page lists the 14 method papers that compare themselves with another indexed method, the 11 methods those papers name, and the later comparisons by Plaugher and Murrugarra (2023) and Lauber and List (2026).

  2. 2026-10-19 v0.2.1

    Reprogramming settings

    The four boxes (I, D, T, P) are labeled reprogramming settings, matching Submission 3. Modality is reserved for data types and intervention types. The companion-paper title on the site is Computational Cell Reprogramming: A Systematic Review of Cellular Intervention Design.

  3. 2026-10-19 v0.2.0

    Sixty-method review corpus

    Index aligned with the Submission 3 SI_2 table. Added Reprogram-Seq, Iterative TF screening, TF Atlas, and Briggs combinatorial TF landscape. Removed TRAPT and DeepNEU. scREMOTE is Class C3. OCSANA+ is assigned to C1 and C3 and kept outside the single-class counts (7, 10, 10, 32). Audit headlines are 46 of 60 with code, 27 of 60 with all four resource items, and 15 of 46 at the FAIR4RS threshold. Dataset reuse is 125 of 135 catalogued identifiers linked to one method.

  4. 2026-05-29 v0.1.2

    Two-corpus model and index status banner

    Distinguishes the 57-method review corpus (frozen in Supporting Information S1) from the maintained Atlas index. Home and /methods show a status banner with live counts; header shows compact index stats. Added added_after_review flag for post-publication entries. Release metadata centralized in src/lib/corpus.ts.

  5. 2026-05-29 v0.1.1

    Sync with 2026 submission materials

    Corpus updated to 57 reviewed methods (DeepNEU excluded from scope). Terminology aligned with manuscript explicitness classes (C0-C3). Audit headline numbers, SI descriptions, taxonomy prose, and import/sync script paths refreshed against 2026_Submission2Materials.

  6. 2026-05-24 v0.1

    Initial private preview

    Site scaffold, taxonomy and modality pages, sample method entries spanning C0-C3, field-level audit landing, contact-only submission page.