185 citations · 261 across the 5 of their papers we have counts for
6 papers
Reproducibility and FAIR Principles: The Case of a Segment Polarity Network Model
Pedro Mendes
The issue of reproducibility of computational models and the related FAIR principles (findable, accessible, interoperable, and reusable) are examined in a specific test case. I ana…
ShinyCOPASI: a web-based exploratory interface for COPASI models
Abhishekh Gupta, Pedro Mendes
COPASI is a popular application for simulation and analysis of biochemical networks and their dynamics. While this software is widely used, it works as a standalone application and…
Reproducible research using biomodels
Pedro Mendes
Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent…
BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology
Alejandro F Villaverde, David Henriques, Kieran Smallbone +10
Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic model…
A Computational Model of Liver Iron Metabolism
Simon Mitchell, Pedro Mendes
Iron is essential for all known life due to its redox properties, however these same properties can also lead to its toxicity in overload through the production of reactive oxygen…
Large-scale generation of computational models from biochemical pathway maps
Finja Büchel, Nicolas Rodriguez, Neil Swainston +23
Background: Systems biology projects and omics technologies have led to a growing number of biochemical pathway reconstructions. However, mathematical models are still most often c…