I remember seeing the earliest digital visualizations of DNA, long, long, long strings of letters, and more useful, long strings of symbols representing chunks of code. As digital tools evolved, I have been expecting the digital tools to inevitably move to “editing” features, giving humans a direct and simple interface that ties to powerful robotic labs.
I’m not sure why this has come so slowly but things are certainly moving now, in chemistry and biology. For obvious reasons, this is a mountain we have to climb, and is recognized as a “grand challenge” problem.
This month Sarah Richardson and colleagues published a study that demonstrates the use of their “BioStudio” software . This system adds the basic features of a text editor, including version control and “undo”, to genome visualization, to make a visual editor for genes.
(As a software guy, I’ll point out that these “innovations” in editing date back to the 1980s or earlier. The clever part is the integration with biological data.)
Richardson says that this seemingly obvious idea has been mind-blowing for some scientists inured to the bad-old ways.
“[E]xisting software focused on displaying long genome sequences and allowing researchers to annotate them as they laboriously figured out the purpose of various strings of DNA. When [Richardson] asked around about adding an editing function to let researchers change those intricate sequences, she got shocked responses. “You would have thought I’d suggested abandoning a toddler at the mall,” she says. “
Of course, things aren’t that simple. DNA strings are millions of letters long, so you don’t really want to be fiddling one letter at a time. Effective “editing” by humans requires considerable information chunking and development of “operations” to execute. The researchers have designed in logical constraints on the DNA, and assembly patterns to manipulate them. (This sounds like the beginnings of a grammar and syntax for editing DNA.)
One cool thing is that the software can “watermark” the synthetic DNA, so that it can be identified. Technically, this is done by introducing specific sequences that are functionally synonymous but easily distinguished from wild DNA. Cool!
The resulting tool is said to let you do a lot of things. But some kinds of edits will still need programing, just as complicated formatting needs macros. The software has a plug-in architecture, so people can add their own functions.
This software is supposed to be open source, though I’m not completely sure where the current source resides, or what exactly is included.
Nice job, all.
- Sarah Richardson. BioStudio-dev. 2015, https://bitbucket.org/notadoctor/biostudio-dev.
- Sarah M. Richardson, Leslie A. Mitchell, Giovanni Stracquadanio, Kun Yang, Jessica S. Dymond, James E. DiCarlo, Dongwon Lee, Cheng Lai Victor Huang, Srinivasan Chandrasegaran, Yizhi Cai, Jef D. Boeke, and Joel S. Bader, Design of a synthetic yeast genome. Science, 355 (6329):1040-1044, 2017. http://science.sciencemag.org/content/355/6329/1040.abstract
- Eliza Strickland, With Synthetic Biology Software, Geneticists Design Living Organisms From Scratch, in IEEE Spectrum – The Human OS. 2017. http://spectrum.ieee.org/the-human-os/biomedical/devices/with-synthetic-biology-software-geneticists-design-living-organisms-from-scratch
- The Center of Excellence for Engineering Biology. GP-write Meeting: May 9-10, 2017 | New York, NY. 2017, http://engineeringbiologycenter.org/may-2017-meeting.