Modeling Biomolecular Site Dynamics : Methods and Protocols /
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| Format: | eBook |
| Language: | English |
| Published: |
New York, NY :
Springer New York : Imprint: Humana,
2019.
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| Edition: | 1st ed. 2019. |
| Series: | Methods in Molecular Biology,
1945 |
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Table of Contents:
- A Pycellerator Tutorial
- Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules
- Strategy-Driven Exploration for Rule-Based Models of Biochemical Systems with PORGY
- Using rxncon to Develop Rule-Based Models
- Efficiently Encoding Complex Biochemical Models with the Multistate Model Builder (MSMB)
- Multi-Level Modeling and Simulation of Cellular Systems: An Introduction to ML-Rules
- Using Python for Spatially Resolved Modeling with Simmune
- Rule-Based Modeling using Wildcards in the Smoldyn Simulator
- MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework
- Spatial Rule-Based Simulations: the SRSim Software
- CellOrganizer: Learning and Using Cell Geometries for Spatial Cell Simulations
- Using Mechanistic Models for Analysis of Proteomic Data
- Annotations for Rule-Based Models
- Markov Chain Aggregation and Its Application to Rule-Based Modelling
- In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response Dynamics
- Recipes for Analysis of Molecular Networks Using the Data2Dynamics Modeling Environment
- RKappa: Software for Analyzing Rule-Based Models
- A Step-by-Step Guide to Using BioNetFit. .