Web-ready Refrideubator

[Avery louie]

Hey all,

I am working on a web-enabled incubator/refrigerator.  Right now, checking on growing cells is tedious and sometimes you have to travel to the lab at inconvenient times.  Sometimes you show up and nothing has happened, or even worse, the cells are overgrown.

With this system, a picture of the plate (and potentially other data, like absorption spectra of liquid cultures, temperature, etc) is served to you on a webpage, along with a form to set the temperature of the incubator.  This incubator is special because it can heat up or cool down.  Many cells basically stop growing at low temperatures- so all you have to do is set the temperature to 4C and come back to harvest your cells when it is convenient.

So far the software works and the hardware works, and integration is coming soon (tomorrow/this weekend).

If you are interested in this, check out the more detailed posts here.  I will hopefully make detailed documentation someday, but it is time consuming to do and finding time might take a while. If you really, really, want one, let me know*.

--Avery

*the one big technical snafu of this is that you cant host a website from home without port forwarding, which is complicated for folks who dont have admin access to their router.  one solution is to put a server in the middle (say, on heroku), but that is definitely not done yet.  However, the incubator is still accessible via the LAN.

[Cathal Garvey]

Hey Avery!
Really excellent idea; clearly the sort of thing that never gets
invented by a full-time scientist but which is highly practical for a
part-timer or hobbyist. :)
Could really use one of these myself!

Anyways, on the port forwarding front, check out pagekite as a (paid)
way to quickly get a public IP address for any device that can reach the
internet, without worrying about NAT and Forwarding (not always possible
with dynamic or shared IPs, corporate routers, etc.).

Pagekite's code is open source, too, so you can run your own Pagekite
server if you can't afford their service.

On 28/03/14 08:57, Avery louie wrote:
> Hey all,
>
> I am working on a web-enabled incubator/refrigerator. Right now, checking
> on growing cells is tedious and sometimes you have to travel to the lab at
> inconvenient times. Sometimes you show up and nothing has happened, or
> even worse, the cells are overgrown.
>
> With this system, a picture of the plate (and potentially other data, like
> absorption spectra of liquid cultures, temperature, etc) is served to you
> on a webpage, along with a form to set the temperature of the incubator.
> This incubator is special because it can heat up or cool down. Many cells
> basically stop growing at low temperatures- so all you have to do is set
> the temperature to 4C and come back to harvest your cells when it is
> convenient.
>
> So far the software works and the hardware works, and integration is coming
> soon (tomorrow/this weekend).
>
> If you are interested in this, check out the more detailed posts

> here<http://tequals0.wordpress.com/2014/03/28/refrigeubator/>.

> I will hopefully make detailed documentation someday, but it is time
> consuming to do and finding time might take a while. If you really, really,
> want one, let me know*.
>
> --Avery
>
> *the one big technical snafu of this is that you cant host a website from
> home without port forwarding, which is complicated for folks who dont have
> admin access to their router. one solution is to put a server in the
> middle (say, on heroku), but that is definitely not done yet. However, the
> incubator is still accessible via the LAN.
>

--
T: @onetruecathal, @IndieBBDNA
P: +353876363185
W: http://indiebiotech.com

[Tom Hodder]

On 28 March 2014 08:57, Avery louie <inact...@gmail.com> wrote:

Hey all,

I am working on a web-enabled incubator/refrigerator.  Right now, checking on growing cells is tedious and sometimes you have to travel to the lab at inconvenient times.  Sometimes you show up and nothing has happened, or even worse, the cells are overgrown.

I have a project to do something similar, I ended up using a solid state relay to control the heater and fan because the clicking of the relay was getting annoying... Also,  port forwarding sucks donkey balls on cheap routers, so I decided to run a python IRC bot on a pi and query it from an IRC channel like so;

15:06:02 <@tolland> .incubator

15:06:02 < biobot> The temp of the incubator at 20:05:45 is 16.562 degrees C

Though now I want to put the time series data from the temperature probe on the web, so I have to come up with a way to push the data out to a web service....

https://www.flickr.com/photos/37617570@N06/sets/72157643057992484/

[Cathal Garvey]

If you like Python, try pythonanywhere.com. Their free service should be
enough; you pay for your app to be allowed access non-whitelisted
websites, but there's no restriction on *incoming* data so you can
easily hack up a web-based logger, potentially also a web-based control
relay; hackubator polls the webapp periodically for new intructions and
to upload logging information, controllers can place commands in a queue
on the webapp for the hackubator to fetch next time it polls.

Consider security when putting the command-and-control channel for a
potentially hazardous item of equipment on the internet. There are
libraries in PyPI for authenticated JSON-RPC and so on, consider those.
Make sure they authenticate that it's a command from you or another
authorised person, and that they take measures to prevent replay attacks
(in case someone ever observed you instructing the oven to hit 220C and
copy/pasted it into the control input).

Don't roll your own. But if you do, make sure it uses hmac to
authenticate, using the hmac.compare_digest function to verify
authentication, and use once-only tokens for each command that are never
accepted by the application a second time, to prevent replays.

This is a cool effort; I'm tempted to knock one together, too, if
someone has a decent lead on a high-wattage solid-state relay? Could get
a cheap "cupcake" oven, set it to something not-insane, and then switch
on and off at the wall using the solid state relay; that looks like your
rig, Tom?

On 28/03/14 14:09, Tom Hodder wrote:
> On 28 March 2014 08:57, Avery louie <inact...@gmail.com> wrote:
>
>> Hey all,
>>
>> I am working on a web-enabled incubator/refrigerator. Right now, checking
>> on growing cells is tedious and sometimes you have to travel to the lab at
>> inconvenient times. Sometimes you show up and nothing has happened, or
>> even worse, the cells are overgrown.
>>
>
> I have a project to do something similar, I ended up using a solid state

> relay<http://www.amazon.co.uk/gp/product/B0087ZTHZE/ref=oh_details_o05_s00_i00?ie=UTF8&psc=1&tag=s6010000201-21>

> to
> control the heater and fan because the clicking of the relay was getting
> annoying... Also, port forwarding sucks donkey balls on cheap routers, so
> I decided to run a python IRC bot on a pi and query it from an IRC channel
> like so;
>
> 15:06:02 <@tolland> .incubator
> 15:06:02 < biobot> The temp of the incubator at 20:05:45 is 16.562 degrees C
>
> Though now I want to put the time series data from the temperature probe on
> the web, so I have to come up with a way to push the data out to a web
> service....
>
> https://www.flickr.com/photos/37617570@N06/sets/72157643057992484/
>
>
> [image: Inline images 2]
>

[Cathal Garvey]

Wow, took a look at the picture set; CO2 and shaking? Awesome! :)

On 28/03/14 14:09, Tom Hodder wrote:

> On 28 March 2014 08:57, Avery louie <inact...@gmail.com> wrote:
>
>> Hey all,
>>
>> I am working on a web-enabled incubator/refrigerator. Right now, checking
>> on growing cells is tedious and sometimes you have to travel to the lab at
>> inconvenient times. Sometimes you show up and nothing has happened, or
>> even worse, the cells are overgrown.
>>
>
> I have a project to do something similar, I ended up using a solid state

> relay<http://www.amazon.co.uk/gp/product/B0087ZTHZE/ref=oh_details_o05_s00_i00?ie=UTF8&psc=1&tag=s6010000201-21>

> to
> control the heater and fan because the clicking of the relay was getting
> annoying... Also, port forwarding sucks donkey balls on cheap routers, so
> I decided to run a python IRC bot on a pi and query it from an IRC channel
> like so;
>
> 15:06:02 <@tolland> .incubator
> 15:06:02 < biobot> The temp of the incubator at 20:05:45 is 16.562 degrees C
>
> Though now I want to put the time series data from the temperature probe on
> the web, so I have to come up with a way to push the data out to a web
> service....
>
> https://www.flickr.com/photos/37617570@N06/sets/72157643057992484/
>
>
> [image: Inline images 2]
>

[Tom Hodder]

On 28 March 2014 14:40, Cathal Garvey <cathal...@cathalgarvey.me> wrote:

Wow, took a look at the picture set; CO2 and shaking? Awesome! :)

If you press the CO2 button, it reads off this sensor;

http://www.ebay.co.uk/itm/MG811-CO2-Dioxide-Sensor-Module-/230856678272

The agitator stage is still a work in progress (gentle swirling is probably more accurate ;-), I initially started working on a XY stage like this;

https://www.youtube.com/watch?v=2xpoM_o_mnk

but I am planning to switch over to a roller system, that rotates individual bottles. (more research is needed)

 

 

[Tom Hodder]

On 28 March 2014 08:57, Avery louie <inact...@gmail.com> wrote:

*the one big technical snafu of this is that you cant host a website from home without port forwarding, which is complicated for folks who dont have admin access to their router.  one solution is to put a server in the middle (say, on heroku), but that is definitely not done yet.  However, the incubator is still accessible via the LAN.

I was thinking of maybe writing a collectd plugin as a client, and then sending the data to a central data logger, and graph it using pretty javascript library du jour , or maybe graphite or cacti

 

[Avery louie]

@Tom nice incubator!  I do want to make some nice graphs, but I promised myself I would not do that until the incubator was totally working :p

@Cathal good idea about pagekite, although I will probably still write my own webapp thing to go in the middle (I am a mechE, so sometimes I am vague on names).  There are obvious security concerns so I am thinking that maybe the external page would be read-only and you could VPN back in to change the settings.  At the same time, the input to the browser is always sanitized before updating the temperature value, so not even I can set it to some BS number.  There is also an over-heat shutdown condition, and if the Pi fails, the relays should open.

My hope however, is to have my very own router someday, which I will have no problem port forwarding :)

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[Avery louie]

@Tom, what are you using to control it?

[Tom Hodder]

On 28 March 2014 14:38, Cathal Garvey <cathal...@cathalgarvey.me> wrote:

This is a cool effort; I'm tempted to knock one together, too, if
someone has a decent lead on a high-wattage solid-state relay? Could get
a cheap "cupcake" oven, set it to something not-insane, and then switch
on and off at the wall using the solid state relay; that looks like your
rig, Tom?

Yeah. I got a cheapo 200W cartridge heater element off ebay, and am controlling it with PWM off the solid state relay from ebay here.

Version 2 is going to have a peltier device like Averys, because despite them being inefficient, I don't think it's that important at this type of power use... and they seem safer than 240v elements.

Though saying all that, these cooler-warmers range from about 10-50C and use a peltier device, and are cheapo second hand, and only about 65GBP new;

http://www.ebay.co.uk/itm/BCR-25-mini-fridge-25l-/281235138594

They just need some brain surgery to add the PI to do the ON/OFF stuff....

 

[Avery louie]

Really the important thing is not having to get out of bed to check your cells :)

That said, peltier are extremely good heaters (I would dare to say more efficient), since they have resistive (R2I) and peltier heating going for them.  Peltier coolers ate less efficient than regular liquid/gas refrigeration but have 0 moving parts, are tiny, are portable etc.

--A

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[Nathan McCorkle]

What about dynDNS for getting past the IP issue?

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[Tom Hodder]

On 31 March 2014 16:58, Nathan McCorkle <nmz...@gmail.com> wrote:

What about dynDNS for getting past the IP issue?

I think that solutions that put the pi on the internet as a web server are just kicking down the road, the can containing the issue of scaling.

Which is basically that for these nice graphs, to get real time updates,  your going to be running a bunch of XMLHTTPRequest() to pull data into a AJAX/jQuery or other nice visualization running in the browser. And these are all going to be served by the pi. If you have 10 users watching some experiment in progress, and then they would all be polling the pi continuously. Eventually this is going to compromise the pi's ability as a controller/sensor.

For scaling, it would be better just to have the pi batch a bunch of data, say every 10 seconds, and post it to a dedicated server, with decent resources, which can scale to dishing out lots of updates to web browsers. Load might bring down the web server, say an AWS virtual, or https://www.pythonanywhere.com/, but the Pi would go on oblivious.

(and  you would definitely not lose ssh access to the pi, during a critical experiment etc, the important thing that would result in you having to get out of bed ;-)

Cheers,

Tom

 

[Nathan McCorkle]

those requests would be quite small though, so as long as the pi
doesn't throw them out, rather queues them, it might take a second or
three long but it should be fine... the returned data is just a few
bytes of text, and the packet overhead should be 20 bytes (according
to a quick google for ipv4). Someone else should probably comment on
the best server for the pi, but basically it should have a decent
timeout set and the ability to queue requests. I'd give flask a quick
try:
http://mattrichardson.com/Raspberry-Pi-Flask/

If the pi was trying to do the temp control PID loop, well you're
already in bad paradigm unless you have a RTOS/realtime kernel
running, but if you do just make sure the priority (nice, renice) of
the control process is lower (higher priority) than the server... and
no harm should be done. Worst case if the server does crap out for a
user, it just keeps trying until it gets the good response. I doubt
any small-time lab has to worry about this, and maybe even a medium
sized one would be fine too without another server (but likely those
companies/organization would have another better server, so it would
be easy to scale then).

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[Avery louie]

Not too worried about super-real time data right now.  Currently, the photo only updates every 10 seconds- nothing grows THAT fast, to my knowledge.  The plan is to take the logs and make it into a jpeg and throw it up next to the image.

Control loop does not need to run super fast either, since the time response of the system is sluggish, .5C/second for heating at the heatsink, and much slower for the circulated air.

@nathan, I will have to try dyndns.

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[Cathal Garvey (Phone)]

Easier I feel to use XMLHttp.Server to host an XML-HTTP API server and use the corresponding Client module to pull and process data on another machine? Consider installing a secure XML monkeypatch though.

Sent from my Android device with K-9 Mail. Please excuse my brevity.

[John Griessen]

On 03/31/2014 11:32 AM, Tom Hodder wrote:
> it would be better just to have the pi batch a bunch of data, say every 10 seconds, and post it to a dedicated server, with decent
> resources, which can scale to dishing out lots of updates to web browsers. Load might bring down the web server, say an AWS
> virtual, or https://www.pythonanywhere.com/,

Does this amount to just ordinary web programming to get data forwarded? Can it be by something like RSS?
Or does it need to be some custom app, like a django python app that updates with some kind of handshake as
the every ten second updates arrive?

I do see having some of your lab, or process automation being public for view as a good thing.
Like bragging. So, you could get lots of onlookers occasionally.

Most of the time this kind of thing is considered private info, so would not need the proxy server
since an R-Pi is such a strong, big memory microcontroller.

Nathan's idea of http://mattrichardson.com/Raspberry-Pi-Flask/ might be good for integrating several instruments
into a "lab control panel" for particular experiments. Then with an R-Pi, with a full OS, you
could have a deployment system like Salt load up different experiments to do, and all you have to
do is change some instruments, plug some more cables, and have a new experiment control panel to run them.
All open, no LabView costs, easy hiring of web HTML5 consultants to help with creating new ones...

[Avery louie]

I could do it on another machine, or on a PaaS, but right now the important thing for me is to try it out- what is it like to just let your cells chill in the lab?

The other question is in integration of other devices.  There is really no reason to have something like this for regular pcr (maybe for qpcr) since PCR machines already tell you when they will be done, and store products at 4c (normally) once they are done.  Electrophoresis on the other hand would be perfect for something like this.  Set it up, go get coffee, watch tv...check you gel.  So now the question is how I want to set up the rest of the tools so I can re-use code to make more machines.

Basically I need to map computers/device architecture to how they should be available.  I also need to decide if I am building the system to be portable (in the code sense of transferring the build info) to other peoples labs.

--A

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[John Griessen]

On 03/31/2014 12:22 PM, Avery louie wrote:
> Electrophoresis on the other hand would be perfect for something like this. Set it up, go get coffee, watch tv...check you gel.
> So now the question is how I want to set up the rest of the tools so I can re-use code to make more machines.

Just like I was thinking. Salt is a python-coded deploy/version-control for server setups. Needs a linux so far
to run, can't be done on a bare ARM cortex M3 machine with no OS. Could work with R-Pi though.

> Basically I need to map computers/device architecture to how they should be available. I also need to decide if I am building the
> system to be portable (in the code sense of transferring the build info) to other peoples labs.

For portability purposes, I'm learning about Docker -- a container system for running code in
exact duplicate environments, so it can be replicated elsewhere. Besides isolating processes for
security, it also cures dependency hell in setting up linux based systems, which also help with replicating it elsewhere.

[Josiah Zayner]

I have been working on a bunch of code that allows one to plug in a couple Arduinos to a Linux computer running a webserver using Perl.  One can communicate with the arduino through a webpage and see the output of the Arudino. So I can say change the temperature on an incubator or control a PCR machine. I saw this thread so I just made a blog post about it: http://doitourselfscience.blogspot.com/2014/03/sending-and-receiving-data-from-arduino.html

The code is a little complicated but it all works great. I have the incubator code up on the blog as that is all I have accomplished so far. It controls a fan and some heating element through MOSFETs, which I find are easiest.

Anyways, if you have questions or want to hack it to do something else let me know and I can probably help.


Thanks,
     Josiah Zayner
     http://DoItOurselfScience.blogspot.com

[Nathan McCorkle]

Why perl?

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[Josiah Zayner]

Well, C is overkill and python doesn't use brackets.

And I have been programming in Perl for dare I say > 10 years? Considering that, I should be much better at Perl than I am.

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[Avery louie]

I do c and python.  I'm tabbing and bracketing and semicoloning and always in the wrong spot :p

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[Tom Hodder]

 

Nathan's idea of http://mattrichardson.com/Raspberry-Pi-Flask/  might be good for integrating several instruments
into a "lab control panel" for particular experiments.  Then with an R-Pi, with a full OS, you
could have a deployment system like Salt load up different experiments to do, and all you have to

Coming from a sysadmin background, and the tool of choice at my previous employer being opscode Chef, I was going to use chef to deploy collectd clients and a server, and then use some nice gui;

http://graphite.wikidot.com/screen-shots

[Tom Hodder]

On 31 March 2014 18:22, Avery louie <inact...@gmail.com> wrote:

 

The other question is in integration of other devices. 

If you are going to have multiple Pis running different things, then it would be cool to have a munin or nagios or webmin style centralized command/control web server, which naturally would have to sit on another machine.

 

[Cathal Garvey]

Anyway, that's all nonsense. Python *does* support brackets and
semicolons if you want to use them:

def something(arg1, arg2): #{
arg1 += arg2 #;
return arg1 #;
# }

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--

[Nathan McCorkle]

LOL

--
-Nathan

[John Griessen]

On 03/31/2014 02:17 PM, Tom Hodder wrote:
> If you are going to have multiple Pis running different things, then it would be cool to have a munin or nagios or webmin style
> centralized command/control web server, which naturally would have to sit on another machine.

ROS (Robot OS) is good for that.

[John Griessen]

On 03/31/2014 02:21 PM, Cathal Garvey wrote:
> def something(arg1, arg2): #{
> arg1 += arg2 #;
> return arg1 #;
> # }

Hmmm.... what emoticons do those translate to? #{ # } #;

;-|

[Tom Hodder]

I've not heard of that before, I think it shall be my next weekend project to install that somewhere ... :-) 

[John Griessen]

On 03/31/2014 05:17 PM, Tom Hodder wrote:
I think it shall be my next weekend project to install that somewhere ... :-)

My recommendation was researched, i.e. 2nd hand... I may be able to collaborate on that. I'd like to know more about ROS myself.

[Avery louie]

Question for all of you @josiah @tom, why haven't you posted your projects to the list yet?  Just curious, they seem cool and very useful.

--A

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[Tom Hodder]

On 1 April 2014 02:24, Avery louie <inact...@gmail.com> wrote:

Question for all of you @josiah @tom, why haven't you posted your projects to the list yet?  Just curious, they seem cool and very useful.

These posts are just procrastination... ;-)

I've got some coursework to be handed in tomorrow, that I should be working on, once that's in I'll take another crack at the shaker mechanism.

 

[Avery louie]

Mmm.  I know that feeling.

--A

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[Mü]

Hey guys, cool thread. For those of you in the Bay Area I'll be talking about tools I've been working with and developing for 'biobots" at a Counter Culture Labs meetup in a few weeks. You may find it of interest for what you're working on. http://www.meetup.com/Counter-Culture-Labs/events/173475402/

-Greg

[Josiah Zayner]

Hey Greg I am in the bay area. Do you have more info on what you have developed?

Thanks,
     Josiah Zayner

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[Mü]

Hey man, I do some work with a software company named Plot.ly and am going to show how you can easily visualize data from sensors into real-time graphs. I also have been working on control system software with friends that enables actuation control of the bot through a web interface. I've been working on an incubator prototype used for cell culture with a series of sensors and actuators to showcase the functionality of the software tools. Seems we have a good community around the globe brewing up on this work, pretty exciting

[Scott D Nelson]

Hi All- I used to work for Applied Biosystems/Life Technologies and we had something like this for PCR machines. Here's a cute (commercial) video about it- this sounds a lot like what you want to do. 

http://www.youtube.com/watch?v=Rrd1hJydZrM

I also worked on the Smart Monitoring project there. Connected instruments periodically sent packets of operational data (like your car's dashboard) to a server where it could be viewed real-time from anywhere web-connected. A few details here:

chrome-extension://oemmndcbldboiebfnladdacbdfmadadm/http://www3.appliedbiosystems.com/cms/groups/services/documents/generaldocuments/cms_040187.pdf

and here

chrome-extension://oemmndcbldboiebfnladdacbdfmadadm/http://tools.lifetechnologies.com/content/sfs/brochures/Remote_Diagnostics_FAQ.pdf

I'm not a software engineer but have trained our field personnel how to access and use the interface. I would love to learn more about what you're doing with similar technology. 

Thanks!

Scott Nelson

On Thursday, April 10, 2014 9:10:54 AM UTC-7, Josiah Zayner wrote: