“It was pretty inspirational,” Pimentel says. In front of the crowd at the conference, he used his method to dictate code instructing his laptop to read aloud a snippet of Monty Python’s Dead Parrot sketch. He developed a solution through months of painstaking work, and he calls it a “three-headed beast” because it runs three operating systems from one laptop.
In that video, Rudd describes his struggle with RSI - the result of constant coding in the emacs text editor, a condition he calls ‘emacs pinkie’ - and his strategy for overcoming it. Similarly to many other scientists, Pimentel and Saphra realized that voice coding was possible thanks to a video of Tavis Rudd, now director of technology at web-development firm Unbounce, demonstrating the process live at the P圜on 2013 conference for users of the Python programming language. And Pimentel studies how retention of the non-coding sections of RNA determines tissue specificity and disease susceptibility. She uses her code to explore the training process of neural language models.
It is a permanent condition of the nerves that connect the brain to the hands and feet, and causes the nerves to transmit pain in response to sensations that are not usually painful. Naomi Saphra, a PhD student in language cognition and computing at the University of Edinburgh, UK, has small-fibre neuropathy, the cause of which is unknown.
“These applications share data from some of the largest sequencing studies in the world,” he says. Matthew Solomonson, a software engineer at the Broad Institute of MIT and Harvard in Cambridge, Massachusetts, uses it to build web applications such as the Genome Aggregation Database (gnomAD), which is used to explore genomic data. Voice coding underlies a wide variety of science - any researcher who writes code could use it. And they say that there are unexpected advantages. It takes at least a month of difficult, sometimes frustrating, training to get set up, but coding by voice helps these programmers to keep doing their jobs or continue their studies. Now, a small but growing community has developed a workaround: coding by voice command. RSI can derail the careers of computational biologists and other scientists who code. The syndrome occurs when the ulnar nerve, which travels down the outer edge of the arm, becomes pinched at the elbow, causing numbness, pain and loss of fine motor control in the hands and fingers. Pimentel had cubital tunnel syndrome caused by repetitive strain injury (RSI). Three years later, as a computational-genomics postdoc at Stanford University in California, he does just that. “My adviser jokingly said, ‘Can’t you do this by voice?’” he recalls. As a computational-biology PhD student, his work involved constant typing - and he was born with only one arm. Debilitating hand pain is always bad news, but Harold Pimentel’s was especially unwelcome.
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