CV Publications
Engqvist Lab

Ambiguous Nucleotide Tool (ANT)
Degenerate codons are used to represent DNA positions that have multiple possible nucleotide alternatives. This is useful for protein engineering and directed evolution, where primers specified with degenerate codons are used as a basis for generating libraries of protein sequences. ANT provides Python code for generating and evaluating degenerate codons for natural and expanded genetic codes.

Manually editing a large number of plasmid files, to annotate them with mutations discovered in the lab or other features, is tedious and error-prone. DNApy provides Python code for DNA and plasmid editing. It allows for batch in silico cloning of an unlimited number of sequences from FASTA files as well as the batch introduction and annotation of mutations.

Making accurate color scales for communicating data in visualizations is critical. In many presentations and publications unbalanced scales are used. A common error is to use color scales which does not have smooth and constant change in lightness, leading to difficulty in interpreting the visualized data. colcol provides Python code to deal with color conversions as well as with generating publication-quality color scales.

Many good plotting libraries exist for Python, but sometimes it is necessary to generate custom vector art visualizations of data. wsvg is a light Python wrapper around the svg (scalable vector graphics) format, enabling scripting of svg files.

Reproducible research
Computational analysis of data in a research setting is often difficult to reproduce due to poor documentation of steps taken and software used. Determining which version of what script was used to process a raw data file to generate publishable results can be challenging. As ever-increasing amounts of data is being generated in biological research it is critical that this problem is addressed and that computational analysis becomes as reproducible as laboratory experiments. The reproducible research repository provides a folder structure and conventions aimed at achieving such reproducibility.

Note: This repository was originally created by others and made public here. The Engqvist Lab version has been modified from this source to fit our own research needs.

Reproducible reports
Scientific writing should not be bound to any given proprietary software or file format, especially one which is ill-suited for handling complex texts and large figures. Unfortunately many scientific publishers have built their publication pipelines around such software. An alternative in many journals is to submit LaTeX documents, by this is intimidating to most users. Pandoc offers a great alternative. By writing your documents using markdown Pandoc can convert that text into a whole range of common file formats, including LaTeX, pdf, doc, and others. The reproducible reports repository sets up a folder structure and utilities for using Pandoc to write reports.

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