SBML Level 3: an extensible format for the exchange and reuse of biological models

SM Keating, D Waltemath, M König, F Zhang… - Molecular systems …, 2020 - embopress.org
Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …

Computational models for clinical applications in personalized medicine—guidelines and recommendations for data integration and model validation

CB Collin, T Gebhardt, M Golebiewski… - Journal of personalized …, 2022 - mdpi.com
The future development of personalized medicine depends on a vast exchange of data from
different sources, as well as harmonized integrative analysis of large-scale clinical health …

A pathway model of glucose-stimulated insulin secretion in the pancreatic β-cell

M Deepa Maheshvare, S Raha, M König… - Frontiers in …, 2023 - frontiersin.org
The pancreas plays a critical role in maintaining glucose homeostasis through the secretion
of hormones from the islets of Langerhans. Glucose-stimulated insulin secretion (GSIS) by …

Data integration in biological research: an overview

V Lapatas, M Stefanidakis, RC Jimenez, A Via… - Journal of Biological …, 2015 - Springer
Data sharing, integration and annotation are essential to ensure the reproducibility of the
analysis and interpretation of the experimental findings. Often these activities are perceived …

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

A Niarakis, D Waltemath, J Glazier… - Briefings in …, 2022 - academic.oup.com
Computational models are often employed in systems biology to study the dynamic
behaviours of complex systems. With the rise in the number of computational models, finding …

SBOL visual: a graphical language for genetic designs

JY Quinn, RS Cox III, A Adler, J Beal, S Bhatia… - PLoS …, 2015 - journals.plos.org
Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic
engineering. It consists of symbols representing DNA subsequences, including regulatory …

Harmonizing semantic annotations for computational models in biology

ML Neal, M König, D Nickerson, G Mısırlı… - Briefings in …, 2019 - academic.oup.com
Life science researchers use computational models to articulate and test hypotheses about
the behavior of biological systems. Semantic annotation is a critical component for …

Microbiome modeling: a beginner's guide

E Lange, L Kranert, J Krüger, D Benndorf… - Frontiers in …, 2024 - frontiersin.org
Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in
human health, environmental processes, and biotechnological applications and interact with …

A guide for develo** comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance

A Mazein, ML Acencio, I Balaur, A Rougny… - Frontiers in …, 2023 - frontiersin.org
As a conceptual model of disease mechanisms, a disease map integrates available
knowledge and is applied for data interpretation, predictions and hypothesis generation. It is …

Reproducibility in computational neuroscience models and simulations

RA McDougal, AS Bulanova… - IEEE Transactions on …, 2016 - ieeexplore.ieee.org
Objective: Like all scientific research, computational neuroscience research must be
reproducible. Big data science, including simulation research, cannot depend exclusively on …