The EcoCyc Database (2023)

PD Karp, S Paley, R Caspi, A Kothari… - EcoSal …, 2023 - journals.asm.org
EcoCyc is a bioinformatics database available online at EcoCyc. org that describes the
genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term …

The ecocyc database

PD Karp, WK Ong, S Paley, R Billington, R Caspi… - EcoSal …, 2018 - journals.asm.org
EcoCyc is a bioinformatics database available at EcoCyc. org that describes the genome
and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the …

The global trust inventory as a “proxy measure” for social capital: Measurement and impact in 11 democratic societies

JH Liu, P Milojev, H Gil de Zúñiga… - Journal of Cross …, 2018 - journals.sagepub.com
The Global Trust Inventory (GTI), conceptually assessing trust in others ranging from close
interpersonal relationships to relationships with government and financial institutions as a …

A systematic review of mathematical models of the Ebola virus disease

SJM Abdalla, F Chirove… - International Journal of …, 2022 - Taylor & Francis
Several studies have surveyed the literature of mathematical modelling of the Ebola virus
disease (EVD). However, most of these reviews did not report any work published after …

Accessing the role of trust profiles for the economic growth of societies: a stochastic rule-based simulation using the prisoner's dilemma game

P Monares, JH Liu, R Santibañez… - IEEE Transactions …, 2020 - ieeexplore.ieee.org
According to Robert Putnam, trust can be a proxy for social capital. Thus, a higher societal
trust could be related to economic growth. To test this hypothesis, we simulated the …

The explicit approximation approach to solve stiff chemical Langevin equations

K Nouri, H Ranjbar, L Torkzadeh - The European Physical Journal Plus, 2020 - Springer
The chemical Langevin equations are reputable simulation schemes to explore the
dynamics of chemical systems. We propose a new approach to simulate stochastic …

Atlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages

R Santibáñez, D Garrido, AJM Martin - Bioinformatics, 2020 - academic.oup.com
Motivation Cells are complex systems composed of hundreds of genes whose products
interact to produce elaborated behaviors. To control such behaviors, cells rely on …

Rule-based models and applications in biology

Á Bustos, I Fuenzalida, R Santibáñez… - … Cell Biology: Methods …, 2018 - Springer
Complex systems are governed by dynamic processes whose underlying causal rules are
difficult to unravel. However, chemical reactions, molecular interactions, and many other …

Pleione: A tool for statistical and multi-objective calibration of Rule-based models

R Santibáñez, D Garrido, AJM Martin - Scientific Reports, 2019 - nature.com
Mathematical models based on Ordinary Differential Equations (ODEs) are frequently used
to describe and simulate biological systems. Nevertheless, such models are often difficult to …

Multiscale modeling on biological systems

M Sulpizi, R Faller, S Pantano - Biochemical and Biophysical …, 2018 - escholarship.org
One of the many challenging and fascinating facets of biological systems is the
simultaneous and concerted occurrence of a variety of biochemical and biophysical …