Marvin van Aalst

From Field Photosynthesis to Genetic Architecture: Insights from the First Dedicated Photosynthesis Hackathon

The paper reports findings from a photosynthesis hackathon that identified key insights into genetic architecture using field photosynthesis data across four crop species.

Chilling Nights Do Not Cause Starch Over-Accumulation and Trigger a Shift in Carbon Partitioning via SPS Toward Sucrose in Arabidopsis - Differing from Acclimation to Permanent Cold

This study shows chilling nights in Arabidopsis increase sucrose, glucose, and fructose without starch over-accumulation, suggesting a different carbon partitioning strategy than permanent cold.

GreenSloth: a curated database and executable platform for mechanistic photosynthesis models

GreenSloth provides a curated database and platform for mechanistic photosynthesis models, enabling model discovery, comparison, and reuse through an open-source framework.

MxlPy - Python Package for Mechanistic Learning in Life Science

MxlPy is a Python package that combines mechanistic modelling with machine learning to provide explainable, data-informed solutions for biological research.

Alternatives to photorespiration: A systems-level analysis reveals mechanisms of enhanced plant productivity

Modelling 12 alternative photorespiratory pathways predicts the largest carbon-export gains for carbon-fixing designs (TaCo); complete decarboxylation bypasses help mainly by releasing CO2 in chloroplasts, raising carboxylation and recapturing lost CO2.

Hackathons as essential tools in an interdisciplinary biological training - report from trainings for Sub-Saharan students

This paper describes two computational biology summer schools in Kenya that used hackathons to train early-career researchers in interdisciplinary biological skills.

Rule-Based Deconstruction and Reconstruction of Diterpene Libraries: Categorizing Patterns & Unravelling the Structural Landscape

The paper deconstructs and reconstructs diterpene structures to categorize patterns and model synthesis mechanisms, revealing core skeletons and predicting compound diversity.

dismo: building and analysing discrete spatial ODE models

dismo is a Python package for creating and analyzing discrete spatial ODE models on various grid types.

What controls carbon sequestration in plants under which conditions?

The paper uses a mathematical model to study how external conditions affect control over carbon fixation in photosynthesis.

Network reconstruction and modelling made reproducible with moped

The paper introduces moped, a Python package for reproducible metabolic model construction, curation, and analysis, supporting both genome-based reconstruction and SBML import.

COBREXA.jl: constraint-based reconstruction and exascale analysis

COBREXA.jl is a Julia package for scalable constraint-based metabolic modeling, designed for high-performance computing environments and multi-organism community models.

Constructing and analysing dynamic models withn modelbasev1.0 - a software update

The paper updates modelbase, an open-source Python package for constructing and analysing dynamic models, enhancing its capabilities for model reuse, isotope labelling, and SBML compatibility.

Building mathematical models of biological systems with modelbase, a Python package for semi-automatic ODE assembly and construction of isotope-specific models

The paper introduces modelbase, a Python package for building and analyzing dynamic mathematical models of biological systems, with features for ODE assembly and isotope-specific modeling.