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Heroku for Science

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Re: Heroku for Science

#11

Post by frisco »

irollboozers wrote: post #4
alejoriveralara wrote: post #3

I believe this startup is as close as it gets (for now!) to what you're describing, https://www.transcriptic.com/ . (I don't work there or anything)

There's been quite a few efforts in this. See Transcriptic and Emerald Therapeutics ( http://www.emeraldcloudlab.com/ ), while there's the more traditional suppliers for things like short oligos or expression vectors ( https://www.dna20.com/ and http://www.idt.com/ ). I think there's also been a lot of independent academic attempts at this (see: http://klavinslab.org/ which is CS/BioE at UWash), but all kind of waded…

Emerald doesn't really exist yet, and I believe they misrepresent their automation. They've posted a very pretty site with a bunch of mockups. They have a set of workflows that work for their internal antiviral research, but "Heroku for Science" is a completely different game.

Transcriptic, on the other hand, started taking orders six months ago and has customers at Stanford, Caltech, Harvard, and more.

Re: Heroku for Science

#12

Post by bignaj »

L_Rahman wrote: post #2

I studied biomedical engineering at Hopkins. Before I started there, research was the promised land. I dreamt of spending my time thinking about how to solve critical problems and testing solutions. What I saw instead were people spending the vast majority of their time pipetting. All the way up the ladder, upto and including postdocs. I sometimes thought our PI had it worse for having to spend most of her time apply…

I also thought research was the promised land. Went to Cornell for undergrad studying biological sciences and was amazed at the research opportunities... but then worked in a lab studying type II diabetes. I pipetted, cleaned beakers, measured out chemicals to prepare solutions, sucked up cell cultures and extracted DNA all day making $8/hour in extreme boredom. There were postdocs with Ph.Ds and loads of experience from prestigious schools doing the same grunt work alongside me, often confessing they were completely miserable and wishing they could start their life over again. They worked 7 days a week and long, long hours each day. I got the hell out of research and am enjoying my life much better now in tech. I also feel like the work I do is a lot more impactful. All of my peers did the same and went to consulting, finance or tech. In my view the basic research field is in total crisis...

Re: Heroku for Science

#13

Post by irollboozers »

skosuri wrote: post #9

In our lab today we are consistently dealing with the opposite problem. The experiments themselves are easy in comparison with the design and analysis.

The startup equivalent would be "it's easy to build the app, it's hard to get users". Not all apps can yield users, but lowering the bar to launch will certainly yield more opportunities for successful apps.

Re: Heroku for Science

#15

Post by irollboozers »

frisco wrote: post #11
irollboozers wrote: post #4

Earlier quoted context omitted.

There's been quite a few efforts in this. See Transcriptic and Emerald Therapeutics ( http://www.emeraldcloudlab.com/ ), while there's the more traditional suppliers for things like short oligos or expression vectors ( https://www.dna20.com/ and http://www.idt.com/ ). I think there's also been a lot of independent academic attempts at this (see: http://klavinslab.org/ which is CS/BioE at UWash), but all kind of waded…

Emerald doesn't really exist yet, and I believe they misrepresent their automation. They've posted a very pretty site with a bunch of mockups. They have a set of workflows that work for their internal antiviral research, but "Heroku for Science" is a completely different game. Transcriptic, on the other hand, started taking orders six months ago and has customers at Stanford, Caltech, Harvard, and more.

There are probably others much more familiar with cloud infrastructure who can chime in, but the AWS of science and the Heroku of science are two very different challenges, and I feel the analogies probably cross over pretty well.

Definitely having the infrastructure 'warehouse' layer that Transcriptic is building (with a real API! wow!) will be valuable. And like you hint at, power users won't need hand-holding, but 99% of the market of users will. That's where packaging, ease of use, and limited configuration seem to be the difference maker (Heroku starting exclusively with Rails).

Re: Heroku for Science

#16

Post by pdenya »

CHY872 wrote: post #6

A big problem is that scientists are traditionally very secretive. This would increase the possibility of leaks, and there'd need to be some way of assuring that the experiment was conducted correctly. Good idea, though.

If this was available convenience would trump security for many people.

Re: Heroku for Science

#17

Post by hikari8 »

Experimenting with a simulation is a great time saver as far as it goes, however, all models are just models, subject to the assumptions that went into them.

There is a great deal we do not know about cellular biology. Any simulation would be a fairly gross approximation. The point of many experiments is to further our understanding of the model of cellular mechanics.

Re: Heroku for Science

#18

Post by aheilbut »

The problem with this fantasy is that easily automated and distributed tasks are not the rate-limiting steps in most biomedical research. The hard parts (in addition to designing the right experiments and analyzing data..) are in constructing and validating relevant model systems and doing the specific experiments to address questions of interest.

These are extremely dependent on the question being studied and often are not amenable to automation, and may require very rare, expensive, and difficult-to-handle samples. For example, my collaborators work with transgenic mice that are a model for a particular disease, and these mice have to be bred then aged to 12 weeks until they exhibit the phenotype before we can even start doing an experiment. In another model, they have to do brain surgery on each mouse and then wait several weeks for the phenotype.

The 'easy' parts, such as DNA synthesis and sequencing, are already highly standardized and automated, and there is fierce competition to improve the technology and bring costs down.

Re: Heroku for Science

#19

Post by maciejgryka »

I've taken a very tiny first step towards something like this for computer graphics and vision: trying to make user studies as easy as possible: http://www.imcompadre.com It's not a ready product by any means, but two paper submissions have been made with it so far.

It's a difficult problem to solve, because these pesky researchers are always trying out new things that you didn't anticipate - who would've thought! But still, for the mundane things that can be automated, something like this is definitely the way to go. Of course, as other people here point out, figuring out what to actually test is always the hardest part.

Re: Heroku for Science

#20

Post by tkschmidt »

pdenya wrote: post #16
CHY872 wrote: post #6

A big problem is that scientists are traditionally very secretive. This would increase the possibility of leaks, and there'd need to be some way of assuring that the experiment was conducted correctly. Good idea, though.

If this was available convenience would trump security for many people.

I just have experience working in 3 different labs in Germany and I can tell you: secrecy is the holy grail and just using privat repos (for code not data) on github/sourcefore is forbidden. But this is perhaps just small sample size and a german habit ;)
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