An Introduction to Uncertainty in the Development of Computational Models of Biological Processes -- Reverse Engineering under Uncertainty -- Probabilistic Computational Causal Discovery for Systems Biology -- Macroscopic Simulation of Individual-Based Stochastic Models for Biological Processes -- The Experimental Side of Parameter Estimation -- Statistical Data Analysis and Modeling -- Optimization in Biology: Parameter Estimation and the Associated Optimization Problem -- Interval Methods -- Model Extension and Model Selection -- Bayesian Model Selection Methods and their Application to Biological ODE Systems -- Sloppiness and the Geometry of Parameter Space -- Modeling and Model Simplification to Facilitate Biological Insights and Predictions -- Sensitivity Analysis by Design of Experiments -- Waves in Spatially-Disordered Neural Fields: a Case Study in Uncertainty Quantification -- X In-silico Models of Trabecular Bone: a Sensitivity Analysis Perspective -- Neuroswarm: a Methodology to Explore the Constraints that Function Imposes on Simulation Parameters in Large-Scale Networks of Biological Neurons -- Prediction Uncertainty Estimation Despite Unidentifiability: an Overview of Recent Developments -- Computational Modeling Under Uncertainty: Challenges and Opportunities.