biological-crystallography-voice-in

Introduction

This repo contains voice commands about biological crystallography for the automated speech recognition software Voice In Plus. Voice In Plus is a Google Chrome extension. It only works in Google Chrome at this time. The utilization of these custom commands requires a subscription to Voice In Plus. These commands can be used in the text area of most websites opened in Google Chrome. They can be used when dictating protein and nucleic acid crystal structure manuscripts. The commands include the symbols for all space groups that can accommodate chiral molecules, such as biological molecules. The symbols are represented as LaTeX math (e.g., P2_{1}2_{1}2_{1}P2_{1}2_{1}2_{1} ). These short snippets of LaTeX are recognized and rendered correctly by most markdown typesetting languages including org-mode and markdown cells in Jupyter notebooks.

Usage

You can utilize the commands immediately after they have been uploaded. I toggle Voice In on and off by using a keyboard shortcut. I then dictate the command. See the Voice In plug-in documentation to learn how to configure keyboard shortcuts.

Examples of voice triggers and their results

We call these voice commands voice triggers in analogy to tap triggers in text editors with snippet libraries. You may have to reload this page to get the equations rendered by Mathjax.

Voice trigger	Result
expand jac	Journal of Applied Crystallography
expand iucr	International Union of Crystallography
expression for sigmaA 2fo minus fc	$$2mF_{o} - DF_{c}$$
expression for Wilson ratio	$$\left\langle I^2\right\rangle /\langle I\rangle^2$$
insert equation for the structure factor	$$\mathbf{F}(\mathbf{S})=\sum_{j=1}^n f_j \exp \left[2 \pi i \mathbf{r}_j \cdot \mathbf{S}\right]$$
P212121	$$P2_{1}2_{1}2_{1}$$
insert space group number for P212121	19

Installation

Each command is paired with the inserted text on a single line in a comma-separated value file (biocryst.csv). Equations, code snippets, and so on that span multiple lines are placed inside double quotes. You can upload these commands into your collection of custom commands using the Bulk Add button in Voice In Plus.

Contents of the library biocryst.csv

• Names of space groups that can accommodate chiral molecules (i.e., proteins and nucleic acids)
• Space group numbers for the space groups that can accommodate chiral molecules
• Software acronyms and their expansions
• Light source acronyms and their expansions
• Scientific society acronyms and their expansions
• Journal acronyms and their expansions
• Key equations
• URLs for software

Related repositories

See Voice Computing section of landing page. You will want to include the library of contractions at a minimum so that you can eliminate them from your formal prose.

Rules for developing voice commands

Pick word combinations rarely used in ordinary prose

The basic rule for developing a voice command is to pick a word combination that is very unlikely to be used in one's prose. This choice can avoid the accidental insertion of an unintended set of words.

Pick word combinations that do not contain other commands

If you pick a word combination with a subset of words already assigned to another command, the commands will collide, and you will not get the intended effect. It is better to pick a synonym for the new command than include the old one.

Use verbs are prefixes

I use the verb "insert" before the name of the computer code or equation I want to insert. I use the verb "expand" to expand acronyms. I use the verb "list" to list sets of items.

Test the commands

Like other forms of computer code, test the Voice In commands to ensure you get the intended effect. The speed with which you vocalize a command has a significant impact. You may have to verbalize the command at high speed to avoid inserting just the first word rather than the entire command.

Contributions are welcome

This project can benefit all biological crystallographers. It should be a community project. Make a pull request, post an issue, or send me an e-mail with additions in CSV format.

Sources of funding

• NIH: R01 CA242845
• NIH: R01 AI088011
• NIH: P30 CA225520 (PI: R. Mannel)
• NIH: P20 GM103640 and P30 GM145423 (PI: A. West)