DSGRN

Dynamic Signatures Generated by Regulatory Networks

Software documentation for the [DSGRN] project.

[DSGRN]

Cummins, T. Gedeon, S. Harker, K. Mischaikow, and K. Mok. Combinatorial Representation of Parameter Space for Switching Systems. SIAM 15(4):2176–2212, 2016.

Installation

• Installation
  • Dependencies
  • Installation on macOS
  • Installation on Linux
  • Uninstalling
  • Troubleshooting

Basic Usage

• Networks
  • Network Spec Files
  • Network Builder
• Parameters
  • Network Nodes
  • Logics and Partitions
  • Description Files
  • Parameter Representation
• DSGRN Tutorial

Database Querying

• Signatures Tutorial
  • A crash course in SQL
  • Tables
  • Selecting things
  • Indexing
  • Selecting Individual Columns
  • Group concatenation
  • Joining tables
  • Counting things
  • Aggregate functions
  • Grouping things
  • More grouping
  • Even more grouping
  • Combinations of Labels
  • A Lesson in Query Planning

Reference

• API
  • Network Interface

• Search Page