Rahuman S. Malik‐Sheriff

Verification and reproducible curation of the BioModels repository

The paper updates and corrects SED-ML files for 1055 models in BioModels to improve reproducibility and verification across simulation engines.

Talk2Biomodels: AI agent-based open-source LLM initiative for kinetic biological models

Talk2Biomodels provides an AI platform for interacting with biological models using natural language, enhancing accessibility and FAIR principles.

FAIRification of computational models in biology

The paper proposes adapting FAIR indicators to assess and improve the quality and transparency of computational models in biology.

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

Poincare and SimBio: a versatile and extensible Python ecosystem for modeling systems.

Poincare and SimBio are Python packages for CRN modeling and simulation, offering extensibility and performance through Numba compilation and SBML support.

BioModelsML: Building a FAIR and reproducible collection of machine learning models in life sciences and medicine for easy reuse

This paper introduces a protocol to create a FAIR collection of machine learning models in life sciences and medicine, aiming to improve reproducibility and reuse through community curation.

Reproducibility in systems biology modelling

The paper investigates reproducibility of systems biology models, finding that 49% of 455 models could not be reproduced due to missing data or inconsistencies.

A FGF2-mediated incoherent feedforward loop inducesErk inhibition and promotes naive pluripotency

This study identifies an FGF2-mediated incoherent feedforward loop that inhibits Erk and promotes naive pluripotency in ES cells and embryos.

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Memote, open-source Python software, runs a community-maintained, partly scored test suite (consistency, biomass, annotations, optional experimental data) on SBML-encoded genome-scale metabolic models, once or through continuous integration.