A reference companion to the review
Computational cell reprogramming: a classification of published methods.
The Atlas reads 58 published computational methods through a single lens: a four-level taxonomy of inverse-design fidelity that ranks methods by how completely they answer the field's shared intervention-design question — applied across all four reprogramming modalities.
The classification
Four levels of inverse-design fidelity
The levels rank methods by how completely they instantiate the shared inverse-design objective — from feature ranking with no intervention model, to explicit forward simulation of each candidate.
Four typed problems
The reprogramming modalities
The four modalities are not four unrelated algorithmic problems; they are four typed versions of the same intervention-design question. Each constrains source state, target geometry, admissible interventions, timescale, and feasibility penalty differently.
Field-level audit
Code, reproducibility, and dataset reuse
Of the 58 reviewed methods, less than half can be independently rerun and only a fraction cross the FAIR4RS threshold. Validation data are almost entirely siloed: 121 of 129 datasets are used by exactly one method.
58
Reviewed methods
43
With public code
27
Independently rerunnable (4/4)
14
FAIR4RS ≥ 3/5
Curated, not crowdsourced
Authors of new methods are invited to contact the maintainer
The Atlas is curated by Paola Vera-Licona. Each method is placed in the taxonomy with a written rationale; authors of new methods are invited to propose additions and corrections directly.
Propose a method →In progress
Site status
Preview build, version v0.1. 58 of 58 methods currently populated. Companion review is under submission; full content will track publication.