Biochemistry from a coffee shop in Vienna
02 Jun 2015Just a flat white and some E. coli please
Drinking a flat white in a coffeeshop in Vienna, I eagerly anticipate the arrival of a cell culture plate with bacteria on it.
The E. coli were in California and not on the table in font of me. The bacterial samples I had just sent to Transcriptic had arrived a couple of days ago. Whilst I was in Vienna I was keen to begin running experiments on the strains and start generating results.
Pioneers Festival
I was in beautiful Vienna because I was at Pioneers Festival 2015. It was a fantastic celebration of entrepreneurs and dreamers. The atmosphere was electric, everyone left with the desire to think bigger and go forth and execute.
Working on the Transcriptic platform
I was keen to get started on experimenting with my samples at Transcriptic so I was squeezing in the work around Pioneers. My main aim for the week was to ensure that the correct quantity of bacteria was being plated onto LB-Agar to ensure that single colonies could be grown and picked. This process forms the first stage of an assay I have planned.
What was really exciting is that I was working with a few of the new actions for the platform, spread,autopick and image_plate. I think the team knew I was super keen to get started using them, so these actions are currently still in flux and are not fully documented yet. These three commands work really nicely together to enable starting from stock strains and getting down to individual clonal colonies to conduct downstream work with. Below you can see the product of all two of the actions.
Every time I do work on the Transcriptic platform my mind is slightly blown. I just think it’s absolutely amazing that I can sit on a laptop and do experiments, even when I’m just doing a simple dilution.
I would say that the previous work I’ve done on Transcriptic was just playing but now I’m trying to do some actual work-work. And with that work-work I did run into a couple of challenges in using the platform.
Challenges
I had a couple of challenges, working from Vienna. Primarily the internet in the hotel was terrible so I was struggling to download large image captures from the workcell from the image_plate function. I also ran into a frontend bug, however Taylor at Transcriptic reached out to me to let me know they were aware I was having a problem. The team fixed the bug straight away, even before I’d got in touch with them! Preemptive customer support, I coined it ;).
1. Queuing (and I’m English!)
So I’ve been spoiled by PaaS and IaaS. One thing which I really didn’t think about is workcell capacity. Using AWS, Heroku or digital ocean one just doesn’t think about capacity. If you need more capacity on Heroku just create a new dyno, it’s done instantly. With cloud science, not so much…
The issue is that Transcriptic is so popular that there’s a lot of people trying to simultaneously conduct runs on the hardware. Runs are made up of multiple actions that may or may not need to be executed in sequence. It is possible to conduct multiple runs at once on a single workcell however that’s a tough scheduling task. To achieve this you basically need to solve some really hard traveling salesman like optimisation problems which, from speaking to the Transcriptic team at SynBioBetaUK, is one of their biggest areas of focus.
To be fair I don’t really have an issue with queuing but I would really like to know how long the queue is so I can manage my expectations. Queuing makes sense though right? If you’re a start up, you’d be fucking crazy to drop all that CapEx on building 50(?) work cells with unknown customer demand. If I was doing it, I’d probably push queue times to the point where a customer threatens to churn, then think about building another one! My impatience is really just a symptom of my excitement for the platform.
2. ‘Pacific Standard Time’ you cruel mistress
So this whole time difference thing is a little awkward. I might schedule a run at 9AM GMT, Transcriptic sees it 7 hours later at 8AM PST, then it possibly gets scheduled for 7PM PST (3AM GMT) if the workcells are super busy. That’s probably an exaggerated example, but I think it illustrates what feels like not such a great experimental cycle for me. That’s going to be the case though, until european work cells exist so I’ll just keep quiet and be thankful they work with europeans!
3. Run Chaining
Right now, you can’t chain successive runs together. This would be useful, because runs usually occur or finish during the US work hours when I’m asleep. So it would save a bit of wasted time re the whole time difference thing.
fin
So there are challenges with doing experiments over the internet, across the globe, on robots.. who’da thunk it?. The important thing however, is that it’s working really well and I am getting results. To be clear, these are my experiences and not complaints. I see these as challenges that Transcriptic are aware of and working to improve all the time. So Transcriptic, keep up the good work and I’ll keep updating y’all on my experiences using the platform.
PS
Oh by the way I found out that Kristian Nairn who plays Hodor in Game of Thrones is a house DJ which is pretty awesome. He actually played the Pioneers after party! Check out his sets on soundcloud.