STEPS

Inspired by The Long-Term Evolution Experiment, Serially Transferred Evolving Population Simulator (aka STEPS) models the dynamics of asexual populations as they grow and evolve throughout a serial transfer experiment. Information regarding how to install, compile, and run STEPS can all be found in the User Manual file along with other helpful information such as: example runs and how to interpret them, core assumptions made by model, and a walk through of web-based version. Basic installation, run, and compilation instructions can also be found below.

Instructions to build and run:

1. Install Rust and Cargo using rustup
2. Navigate to the root directory of the project
3. Compile as described below
4. Run ./target/release/steps help or ./target/debug/steps help for usage instructions

Compilation Options

• Basic compilation command is cargo build for debug or cargo build --release for release (optimized) mode
• To target the native CPU and allow better optimization, use RUSTFLAGS="-C target-cpu=native" cargo build [...]
  • A specific architecture like skylake can be specified instead of native
  • Make sure the target CPU selected will not cause issues for any computers you use to run the code
• Release mode and target specification are highly recommended
• On the MSU HPCC, use RUSTFLAGS="-C target-cpu=skylake" cargo build --release
• On a single personal computer, use RUSTFLAGS="-C target-cpu=native" cargo build --release
• For more portable libraries when compiling for Linux, the crt-static feature can be used
  • RUSTFLAGS="[...] -C target-feature=+crt-static" cargo build [...] --target=x86_64-unknown-linux-gnu

Building JOSS Paper

To build the paper submitted to JOSS regarding this project, run ./JOSS/generate_paper.sh from the project root. This file is generated locally and not tracked. The latest generated version of this paper can be accessed as an artifact from the "Draft PDF" GitHub workflow in this repository.