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Hey, I'm the founder of Transcriptic. We're pretty excited about this. Happy to answer any questions!

by frisco 12y ago

kayhi 12y ago
Hey Max, any interest in moving into analytical chemistry? I think there could some great potential in quality control work, which almost by definition should be systematized. Have a slide bar for pH testing, conductivity, contaminates (this is where it gets complicated, but also awesome)
cryoshon 12y ago
Hi, I'm a researcher currently and your stuff looks really cool. I have a number of questions: 1. I saw that flow cytometry is listed on your features. Can you explain how you guys manage this? 2. How do you pay for reagents, etc? Or do people send their own? 3. Any chance for more tissue culture friendly technologies? Centrtifugation etc? 4. I noticed you offer use of a Tecan plate reader; how does the user configure the parameters that the plate reader uses? I have a few templates which I use when I read plates, but I'd hate to have to redefine all of them.
- frisco 12y ago
  1. Right now we're only doing analysis (no sorting). Eventually we'll develop an interactive UI where you'll be able to eg draw gates and get feedback in real time but right now it's just setting up analyzer runs fed by an autosampler that takes a microplate just like every other device. 2. You can send them in or buy commercially available reagents through us (sadly mostly not covered by the platform credits). 3. Yes! Lots more on tissue culture capabilities coming soon. 4. The only parameters you can set are the ones exposed in the low level API docs. So, we don't let you configure for example custom spatial reading patterns right now. If that's a deal breaker send me an email and we can discuss.
raldi 12y ago
Since the blog is down: Who are you? And what are you doing?
dnautics 12y ago
The biggest pain point I see in this market is that experimental parallelization is an intervention-heavy process. Ignoring the equipment costs, it's also capital-intensive (unlike say deploying to AWS). And finally, obtaining usable data still requires experiential knowledge. There's something about knowing and feeling the data (yeah, that's awfully fuzzy) that is still an important part about obtaining good results [0]. So for any biologic process that is parallelizing the operators are going to want to own the machines anyways. In order to capture a real market, you're going to have to figure out a way to offer parallelization services - be given a non-parallel experiment with certain parameters and scale it up on behalf of the users. So, the user has an experimental plan and just 'hands it over' to transcriptic. I still worry about the experiential knowledge part, putting the experimenter one step away from the experiment is potentially counterproductive. [0]http://onlinelibrary.wiley.com/doi/10.1002/pro.2339/full http://onlinelibrary.wiley.com/doi/10.1002/pro.2339/full In this paper, the grad student (and lead author) who had spent four years of her graduate work on a previous paper had a nagging feeling that the data were strange. By actually looking at the wells, she figured out post-publication (with nothing to gain) that the protein was sticking to sides of the 96-well plate and causing the observational data to be artefactual. Then there was the question of how to do more experiments to prove that was going on. And then the political problem of convincing her grad advisor to publish a retraction (well at least it was a retraction worth a 10 page paper and a new citation. The story has a happy ending; she got a position at a pharma company largely on the back of her due diligence).
- dnautics 12y ago
  that said, I don't want to be a total negative nancy! There are some services (like flow cytometry) that I think I might use for transcriptics. I think you could also capture an interesting market if you offered "evolution as a service" using your kit.
- frisco 12y ago
  I think the opposite is actually true: you get better data when you don't feel the samples. This is a highly unpopular view right now but I have to wonder what's going on when things like Amgen getting 11% reproducibility of foundational papers (http://www.nature.com/nature/journal/v483/n7391/full/483531a.html http://www.nature.com/nature/journal/v483/n7391/full/483531a...) are happening. There are things that are hard to automate because of their mechanical nature, but I think that for the reproducibility of science somewhat distancing the human from the process is a good thing. Of course, this adds short-term costs (which may sometimes be unacceptable) and requires a lot of behavior change for how people are used to working. I will say that we put a lot of thought into giving you the fidelity of interaction such that you can still make "breakthroughs from your errors" on Transcriptic, and improving those reporting capabilities are an ever-ongoing process. I'll also say that this challenge is bigger than just one company. Some things may make more sense to do via Science Exchange, for example if the method requires some very customized hardware or there are only a few experts in the world who are sufficiently familiar with an unusual method's sensitivities. I'm also excited to see what Riffyn comes out with to help labs understand where reproducibility comes from. We're just getting started, but I can't see a path forward that puts more humans at benches rather than less. The humans should be free to do real science.
teekert 12y ago
This sounds very interesting. Just curious, could I, for example culture large amounts of well plates with specific cell lines, add certain substances to said well plates and run RNA arrays or RNA-seq for each well? Any plans on adding ways to culture cells in 3D? Or culture Organoids? Could I visually inspect the growth of all those things growing in my plates (using fluorescence)? Can you quantify the growth for me in an objective manner? You know, we biologists like to see our cells, we generate hypothesis from the weird growth patterns or strange behaviors. You are addressing a very specific subset of biologists, not the classic ones. I guess it highlights the importance of interdisciplinary education :) Some high level publications using your service would help, but you know that. Anything planned?

Hey, I'm the founder of Transcriptic. We're pretty excited about this. Happy to answer any questions!

by frisco 12y ago

Hey, I'm the founder of Transcriptic. We're pretty excited about this. Happy to answer any questions!

kayhi 12y ago

Hey Max, any interest in moving into analytical chemistry? I think there could some great potential in quality control work, which almost by definition should be systematized. Have a slide bar for pH testing, conductivity, contaminates (this is where it gets complicated, but also awesome)

cryoshon 12y ago

Hi, I'm a researcher currently and your stuff looks really cool. I have a number of questions: 1. I saw that flow cytometry is listed on your features. Can you explain how you guys manage this? 2. How do you pay for reagents, etc? Or do people send their own? 3. Any chance for more tissue culture friendly technologies? Centrtifugation etc? 4. I noticed you offer use of a Tecan plate reader; how does the user configure the parameters that the plate reader uses? I have a few templates which I use when I read plates, but I'd hate to have to redefine all of them.

frisco 12y ago
1. Right now we're only doing analysis (no sorting). Eventually we'll develop an interactive UI where you'll be able to eg draw gates and get feedback in real time but right now it's just setting up analyzer runs fed by an autosampler that takes a microplate just like every other device. 2. You can send them in or buy commercially available reagents through us (sadly mostly not covered by the platform credits). 3. Yes! Lots more on tissue culture capabilities coming soon. 4. The only parameters you can set are the ones exposed in the low level API docs. So, we don't let you configure for example custom spatial reading patterns right now. If that's a deal breaker send me an email and we can discuss.

raldi 12y ago

Since the blog is down: Who are you? And what are you doing?

dnautics 12y ago

The biggest pain point I see in this market is that experimental parallelization is an intervention-heavy process. Ignoring the equipment costs, it's also capital-intensive (unlike say deploying to AWS). And finally, obtaining usable data still requires experiential knowledge. There's something about knowing and feeling the data (yeah, that's awfully fuzzy) that is still an important part about obtaining good results [0]. So for any biologic process that is parallelizing the operators are going to want to own the machines anyways. In order to capture a real market, you're going to have to figure out a way to offer parallelization services - be given a non-parallel experiment with certain parameters and scale it up on behalf of the users. So, the user has an experimental plan and just 'hands it over' to transcriptic. I still worry about the experiential knowledge part, putting the experimenter one step away from the experiment is potentially counterproductive. [0]http://onlinelibrary.wiley.com/doi/10.1002/pro.2339/full http://onlinelibrary.wiley.com/doi/10.1002/pro.2339/full In this paper, the grad student (and lead author) who had spent four years of her graduate work on a previous paper had a nagging feeling that the data were strange. By actually looking at the wells, she figured out post-publication (with nothing to gain) that the protein was sticking to sides of the 96-well plate and causing the observational data to be artefactual. Then there was the question of how to do more experiments to prove that was going on. And then the political problem of convincing her grad advisor to publish a retraction (well at least it was a retraction worth a 10 page paper and a new citation. The story has a happy ending; she got a position at a pharma company largely on the back of her due diligence).

dnautics 12y ago
that said, I don't want to be a total negative nancy! There are some services (like flow cytometry) that I think I might use for transcriptics. I think you could also capture an interesting market if you offered "evolution as a service" using your kit.
frisco 12y ago
I think the opposite is actually true: you get better data when you don't feel the samples. This is a highly unpopular view right now but I have to wonder what's going on when things like Amgen getting 11% reproducibility of foundational papers (http://www.nature.com/nature/journal/v483/n7391/full/483531a.html http://www.nature.com/nature/journal/v483/n7391/full/483531a...) are happening. There are things that are hard to automate because of their mechanical nature, but I think that for the reproducibility of science somewhat distancing the human from the process is a good thing. Of course, this adds short-term costs (which may sometimes be unacceptable) and requires a lot of behavior change for how people are used to working. I will say that we put a lot of thought into giving you the fidelity of interaction such that you can still make "breakthroughs from your errors" on Transcriptic, and improving those reporting capabilities are an ever-ongoing process. I'll also say that this challenge is bigger than just one company. Some things may make more sense to do via Science Exchange, for example if the method requires some very customized hardware or there are only a few experts in the world who are sufficiently familiar with an unusual method's sensitivities. I'm also excited to see what Riffyn comes out with to help labs understand where reproducibility comes from. We're just getting started, but I can't see a path forward that puts more humans at benches rather than less. The humans should be free to do real science.

teekert 12y ago

This sounds very interesting. Just curious, could I, for example culture large amounts of well plates with specific cell lines, add certain substances to said well plates and run RNA arrays or RNA-seq for each well? Any plans on adding ways to culture cells in 3D? Or culture Organoids? Could I visually inspect the growth of all those things growing in my plates (using fluorescence)? Can you quantify the growth for me in an objective manner? You know, we biologists like to see our cells, we generate hypothesis from the weird growth patterns or strange behaviors. You are addressing a very specific subset of biologists, not the classic ones. I guess it highlights the importance of interdisciplinary education :) Some high level publications using your service would help, but you know that. Anything planned?