Team:CLSB-UK/Software/SynBioBot
Synthetic Biology Bot
“Alexa, how do we win best software?”
Synthetic Biology Bot
Synthetic Biology Bot is our most exciting software tool. It’s an app for Amazon Alexa and Google Assistant that helps scientists in the lab by looking up parts, step-by-step protocol instructions and iGEM teams.
Contents
Features
Our app works on both Google Assistant and Amazon Alexa. We recommend trying it out - the usage instructions below detail how to set it up if you're unfamiliar with the platforms or just want more help. Our app can currently lookup parts and iGEM teams or lead you step-by-step through protocols.
One of the most important features is that it makes you feel like you’re in Star Trek.
Hands free
Being hands free eliminates the need to touch surfaces such as phone screens or keyboards. This reduces the contamination risk, especially while handling biologically hazardous materials. This in turn improves biosafety, but also means you’re less likely to contaminate your own experiment.
Not requiring books or laptops frees up space on the lab bench. This means you are less likely to knock over tubes when leaning over to look something up (trust us, we’ve done it)!
Integration with existing services
It sources parts data from iGEM’s Registry of Standard Biological Parts API, uses Protocat (Michigan Software 2014-2017 iGEM) for protocols and iGEM’s teams API.
It’s very easy to use the software in existing workflows; if your protocols aren’t already on Protocat they simply need to be uploaded and they’d instantaneously be available on our app.
We looked into protocols.io’s API, another protocol database, and contacted the team there to try and get access to the public protocols without the user’s login details. Their cofounder, Alexei Stoliartchouk, informed us that they are working on adding that ability but at the time of writing it had not yet been implemented.
We also looked into sourcing protocols from OpenWetWare. Despite having an immensely useful database the protocols are not in any standard format and thus very difficult to parse automatically. We talked with Michigan Software, who are looking into standardising a protocol format as part of their human practices work.
Testing and feedback
Several teams tested it at the UK meetup, including Judd-UK. Judd suggested the team lookup feature and the ability to repeat a step in the protocol (as opposed to just next and back), both of which we implemented soon after.
Judd also suggested having a command to skip to a particular step. We tried to implement this but found it wasn’t feasible as it caused conflicts with the part lookup feature. This was because the natural language processing algorithms tended to match the numbers to part IDs.
Future work
As it’s open-source (GPLv3 license) and available on Github, other teams are free to build other functions or improve the current ones. In the future all kinds of biological queries could be supported such as looking up particular reagents or safety instructions. It also has the potential to control future IoT lab equipment, such as WiFi-enabled centrifuges or electrophoresis power supplies.
Instructions
For Amazon Alexa devices, enable the skill on the skills store.
General setup instructions to get Google Assistant on your phone are avilable from Google. Please note Google Assistant is not supported on all phones and in all countries yet.
Start the app
Open Synthetic Biology
Hi! I'm Synthetic Biology Bot - should I search the iGEM Registry or find protcols?
Once open, you can ask for part information or for protocols.
Part lookup
What's part B0034?
Part B0034 is a RBS that works, designed by Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003.
Due to limitations of iGEM registry data dumps many of the latest parts are unavilable.
Team lookup
Who are team CLSB?
Team CLSB UK is an iGEM team from the United Kingdom on the High School track. They have 20 team members. Would you like to search for another team, search for a part or exit?
Protocols
And you can get a protocol by first asking the app to find some. Due to certain restrictions you can't "one-shot" the protocols command on Google Assistant (i.e. "find ligation protocols"). However, this does work on Amazon Alexa.
Find protocols
Sure. What protocol are you looking for?
The app will then prompt you to tell it what protocol you want. For example, if you want a ligation protocol you'd just say
Ligation
Ok, I've found Ligation protocol. Ligation lets you take a strand of DNA that has compatible sticky ends and insert it into a vector. Would you like a step-by-step guide or to exit?
The app will then search the Protocat database and find you relevant protocols. It will then read out the summary for that protocol. You can begin the step-by-step guide for that protcol by saying
A step-by-step guide
Step 1: Label a microcentrifuge tube to perform the reaction in
The app will then proceed to read out the first step. Once you're ready, you can ask the app to move on to the next step. If you missed a step you can ask the app to repeat it, and if you've gone too far you can ask the app to go back.
Next
Step 2: Add 2μL of T4 DNA Ligase Buffer to the tube
Repeat
Step 2: Add 2μL of T4 DNA Ligase Buffer to the tube
Back
Step 1: Label a microcentrifuge tube to perform the reaction in
Where possible, the app will try to remember where you are in the protocol in case you accidentally quit the app.
If you want to add your own protocols simply add them to ProtoCat, a protocols database created by Michigan Software's iGEM team. Once you’ve added protocols there, you'll be able to use them in the app within a couple of minutes.
Privacy
You can find out how we use data provided to the app in our privacy policy. We think it’s truly a gripping read.
