Here’s a quick update from REBELSCIENCE on where we’re taking our series.

DNA Toolkit

If you’ve been following us for a while, you’ll know DNA Toolkit, our beginner series. We started with simple Python functions to check and count DNA letters. By the last article, we’d put those pieces together into a tool that finds possible protein sequences in real DNA.

Genome Toolkit

Next we started Genome Toolkit as a bigger project. It began with a small Python script that could count a DNA pattern and find which patterns of a given length appear most often.

Starting in Part 4.1 and working through Part 4.7, we turned that script into a Python package for scientific work. These lessons go deeper into how we organize and test the code. That work lets us use the same functions on real genome files and gives us a place to add tools for other data, such as protein sequences, as the package grows.

Say a search finds four matches. We want to know which DNA we searched, which algorithm and settings we used, and which version of Genome Toolkit ran it. We keep those details with the answer. That record of where the result came from is its provenance. Using the same data and steps to get the same answer again is reproducibility. If you missed these lessons, start with Part 4.1 for why we made the change, or see Part 4.6 for how we keep that record.

Ori Finder

We’re excited to start Ori Finder. Like DNA Toolkit, it’s a place to start with a few simple functions and build something useful. We’ll make a small Python tool to look for clues to where a cell starts copying its DNA. We’ll start with two pattern searches on a small stretch of real DNA and compare what we find with published research. Then we’ll add what the tool needs to search a whole genome. You can start with Part 1, even if you’re new to Python.

We’ll take the same approach in future series. Each one will focus on one question and build a small tool in steps, so you can pick a project that interests you and follow it from the start.

Genome Toolkit is where we’ll bring those tools together. We’ll test and add the useful algorithms from Ori Finder and our future series, so we can use them together in real experiments. If you’re interested in how we build that software, follow Genome Toolkit alongside the smaller projects. We’ll go deeper into writing and testing the code and keeping a record of how we got each result.

We hope you’ll enjoy building Ori Finder with us. See you in Part 1!

Until next time, rebelCoder, signing out.

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