This repository contains 2153 voice commands about biological crystallography for the automated speech recognition software Voice In Plus. Voice In Plus is a plugin for Google Chrome and Microsoft Edge. The commands include navigating the browser by voice to vital websites.
The snippets of math equations in LaTeX are recognized and rendered correctly by most Markdown typesetting languages, including GitHub Markdown. These math equations are also rendered in org-mode in Emacs, Markdown cells in Jupyter, and R Markdown notebooks. Of course, they work in documents on Overleaf, the online LaTeX editor for academics, and in other TeX and LaTeX editors.
The site command prefix is for inserting cite keys for commonly cited references.
(The word cite is interpreted as site, so we use site in the command.)
The corresponding BibTeX file is biocryst.bib.
If you are not using LaTeX, you will have to edit the biocryst.csv file to change the \cite{} to whatever format is required by your bibliography management system.
I write one sentence per line, so long cite keys at the end of a sentence are no problem.
This writing style greatly eases the shuffling of sentence order during rewriting, and it facilitates version control during collaborative writing.
intro212.mov
| Voice trigger | Result |
|---|---|
| expand jac | Journal of Applied Crystallography |
| open Journal of Applied Crystallography | opens journal's homepage |
| expand hepes | 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid |
| expand iucr | International Union of Crystallography |
| display sigmaA 2fo minus fc | |
| display Wilson ratio | |
| cite Wilson 1942 | \cite{Wilson1942DeterminationAbsoluteFromRelativeXRayIntensityData} |
| reference for MolRep | "Vagin, A. and Teplyakov, A. (2010) Molecular replacement with MOLREP. Acta Crystallographica Section D: Biological Crystallographica, 66, 22–25." |
| display equation for the structure factor | |
| P212121 | |
| insert space group number for P212121 | 19 |
You may have to reload this page to get the equations rendered by Mathjax. Likewise, when opening the biocryst.csv file in GitHub, you may have to reload the view to get the rendering by Mathjax.
The utilization of these custom commands requires a subscription to Voice In Plus. 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.
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.
- Names of all 230 space groups
- Commands to retrieve the corresponding space group number of a given space group name
- Commands to insert symmetry operation and point group symbols
- Software acronyms and their expansions
- Expansions of acronyms for buffer and other chemicals in crystallization screens
- Light source acronyms and their expansions
- Commands to open homepages of beamlines
- Commands to open webpages with crystallization forms and experimental designs
- Commands to open webpages of crystallization facilities
- Scientific society acronyms and their expansions
- Commands to open homepages of Scientific Societies
- Journal acronyms and their expansions
- Commands to open homepages of journals
- Select equations formatted in LaTeX for in-line and display mode
- Select cctbx code snippets in Python
- URLs for software
- Commands to open homepages of software
- URLs for vendors
- Commands to open the homepages of vendors
See Voice Computing section of landing page. You will want to include the library of contractions at a minimum to eliminate them from your formal prose.
You will likely want the Jupyter markdown library for writing prose in Markdown cells by voice command and the Jupyter commands library for running commands in code cells including line and cell magics.
See ACA 2024 talk
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.
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.
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.
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 quickly to avoid inserting just the first word rather than the intended text replacement.
| Voice trigger category | Count |
|---|---|
| URL | 22 |
| acronymExpansion | 192 |
| cctbx | 35 |
| citekey | 200 |
| conda | 2 |
| displayEquation | 15 |
| expansion | 4 |
| inlineEquation | 8 |
| intensityStatistics | 17 |
| jupyter | 1 |
| jupyterKernel | 1 |
| list | 3 |
| openJournal | 207 |
| openSoftwareDocumentation | 3 |
| openSoftwareHomepage | 35 |
| openWebService | 9 |
| openWebpage | 148 |
| openWikipediaPage | 4 |
| reference | 11 |
| software | 6 |
| spaceGroup | 741 |
| symbol | 8 |
| symmetryElement | 7 |
| textReplacement | 473 |
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.
- NIH: R01 CA242845
- NIH: R01 AI088011
- NIH: P30 CA225520 (PI: R. Mannel)
- NIH: P20 GM103640 and P30 GM145423 (PI: A. West)
| Version | Changes | Date |
|---|---|---|
| Version 0.3 | Added update table, video, link to slides, and some commands. | 2024 July 9 |
| Version 0.4 | Added voice commands for centrosymmetric space groups. | 2024 July 17 |
| Version 0.4.1 | Added 333 text replacements and expansions. | 2024 July 18 |
| Version 0.4.2 | Reached 1645 commands. Added biocryst.bib file with BibTeX entries for citekey items. | 2024 July 24 |
| Version 0.4.3 | Reached 1700 commands. | 2024 July 25 |
| Version 0.4.4 | Added table of counts by category to README.md file | 2024 August 1 |
| Version 0.4.5 | Added table of counts by category to README.md file | 2024 August 3 |
| Version 0.4.6 | Added Space Group voice commands witn the word "sub" included | 2024 August 7 |