Toolbox/Bio-Audacity

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We're intending to make Audacity compatible with biological sequence data, in fact sequence data of many kinds.

We'd expect scientists to be using their existing favourite specialised biological sequence browsers in the labs. Our reason for handling biological sequence data at all is as an ideas incubator. We believe that the approaches we have - often motivated by the needs of audio sequence analysis - will inspire ideas and improvements in the user interfaces of the lab tools. Our code is open source, so researchers are welcome to build on and adapt our code if that looks useful to them.

Here's a sequence browser for biological sequence data at jbrowse.org

JBrowse.png


It has affordances for zooming, panning, selecting and multiple tracks of different types. It should be clear that Audacity already is an audio sequence browser (and editor). We can add new track types, and handle more general sequences.

What can we offer?

Labels

Audacity has labels where one kind of label can label:

1) Individual positions. 2) A range of positions. 3) Boundaries - several consecutive ranges which share an edge.

Editing in these different cases should be easier than with three different kinds of labels. Our display of labels is also designed to keep the descriptive text of the label on screen, even as you zoom and pan. Without that, especially when zoomed in, it's very easy to lose track of what the label is for. We think these features are useful in a biological sequence browser.

We plan to improve on our labels, especially to get better at handling large numbers of labels, labels for different kinds of features, and connections between labels. The needs of biological sequence analysis will probably help us do labels for audio better.

Zooming

We have a prototype for continuous zooming of the timeline that we think is visually pleasing, clear, and uses little space. It makes it easy to precisely select a range. This is worth trying with non-audio sequence too.

Sequence Comparisons

This is an area currently almost entirely missing in Audacity. We have plans here for user interface for showing alignments of audio of tracks, including mixed alignment where we align different types of track, e.g. MIDI to audio.

Our current plan is design and implement both for audio and biological sequence alignment at the same time. As we work on MIDI to audio alignment we'll also be working on DNA to protein alignment (algorithms similar to tFASTY). We think that some of the pressures of aligning audio tracks will suggest user interface ideas for biological sequence tracks that are valuable and would not have been thought of if only working with DNA and protein.

Summary

None of this work is 'fundamental research' that directly in itself makes discoveries in molecular biology. It is work that tends to be somewhat neglected. It can be done by people who are programmers rather than molecular biologists. Done well, these changes make working with the data easier.