stepwise 0.5.0

Wetlab protocols that follow the Unix philosophy.

Stepwise is a program for managing scientific protocols. Its central idea is that it should be easy to create large, complex, single-use protocols by piecing together any number of smaller, simpler, multi-use protocols. This modular approach has several benefits:

1. It’s intuitive. Although it’s good for protocols to contain a fine-grained level of detail (e.g. add 5 µL of solution A, then incubate at 37°C for 15 min), it’s more natural to think about protocols at a higher level (e.g. do PCR, then run a gel).

2. It’s concise. Having to repeatedly write down similar details for similar experiments is tedious and prone to ambiguities or inconsistencies. Being able to easily reuse protocols eliminates this redundancy without sacrificing any detail.

3. It’s reproducible. By lowering the barrier to record every relevant detail for every protocol, it’s more likely that others (your future self included) will be able to reproduce your experiments.

More concretely, stepwise is a command-line tool. Protocols are either text files or scripts that produce text output. Most protocols start off as text files, and grow into scripts when they’re used enough to benefit from the extra complexity (e.g. by having optional steps, pre-calculated reagent volumes, etc). Protocols can be combined using Unix pipes, which turns out to be a very powerful and flexible approach. For example, a pipeline can be saved as a shell script and subsequently used as a standalone protocol, even in other pipelines. For more information on writing and using protocols, refer to the documentation.

Since protocols are just text files, they can be easily shared using standard tools like git. Below are links to some curated collections of commonly-used protocols. If you are new to stepwise, these collections make it easy to get started quickly and productively:

• Stepwise—Molecular Biology

• PhosphateDB