[DIYbio] mycovirus therapy

Citizen Scientists,

I have a question: From what I can tell, no one has used bacteriophage
filtration protocol on fungi. However fungi have there own viruses,
mycoviruses.

Is there a reason why there are so little/no publications on soil
collection to syringe filtration on mycoviruses to infect fungi?

Curious Regards,
Louis

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Re: [DIYbio] Web-ready Refrideubator

Mmm.  I know that feeling.

--A


On Mon, Mar 31, 2014 at 10:19 PM, Tom Hodder <tom@limepepper.co.uk> wrote:
On 1 April 2014 02:24, Avery louie <inactive.e@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.



 

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Re: [DIYbio] Web-ready Refrideubator

On 1 April 2014 02:24, Avery louie <inactive.e@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.



 

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Re: [DIYbio] Web-ready Refrideubator

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


On Mon, Mar 31, 2014 at 7:32 PM, John Griessen <john@industromatic.com> wrote:
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.


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Re: [DIYbio] Re: Ultra low cost SPR?

Hi Ryan.
How much does your system cost? I have a little bit of money left from a small project at the moment.
Regards

--Mathieu

On 26 Mar 2014 10:56, "Ryan Denomme" <rdenomme@nicoyalife.com> wrote:
Those sound like some good ideas - would you evaporate gold on top of the etched plastic? 

We have already started building an SPR-like system that is quite affordable and has shown good performance so far. We are trying to see what level of interest there is in a product like that from a commercial point of view. So we are looking at academic researchers, DIY bio hackers, small biotech firms, etc. If you have a couple of minutes, filing out our research survey would be really helpfulhttps://www.surveymonkey.com/s/openSPR


On Monday, March 24, 2014 2:02:36 AM UTC-4, Mathieu H wrote:
Hi Ryan.
I am interested in that.
I believe we could try and use microstructured, thin plastics on top of a low-cost prism. We etch plastics with low-cost lasers. Then recycle a printer stepper motor and program it. Finally I need to check but the sensor shouldn't be expensive either and interface it with a computer is cheap and easy.
We are going to try sometime this semester I think. I can let you know how it goes.

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[DIYbio] Re: Yeast as biosensor?

You are looking essentially for an alternative to ELISA? I am not sure if the features provided by ELISA can matched using a much more complex system involving a eukaryote.
Yeast two hybridization assays have a high false positive rate. 
Something using yeast phage display of antibodies may work.
Still... there are already highly sensitive analytical methods available.

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Re: [DIYbio] Web-ready Refrideubator

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.

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Re: [DIYbio] Web-ready Refrideubator

On 31 March 2014 22:27, John Griessen <john@industromatic.com> wrote:
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.

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

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Re: [DIYbio] "Nano-paper filter removes viruses" full article?

It lives here:
http://onlinelibrary.wiley.com/doi/10.1002/adhm.201300641/abstract

I may be able to get it when I get home.

On Mon, Mar 31, 2014 at 2:23 PM, John Griessen <john@industromatic.com> wrote:
> Know where to find full article on this nano cellulose?
>
> "Nano-paper filter removes viruses" published in the Advanced Healthcare
> Materials journal on March 31, 2014.
>
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Re: [DIYbio] Web-ready Refrideubator

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? #{ # } #;

;-|

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Re: [DIYbio] Web-ready Refrideubator

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.

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[DIYbio] "Nano-paper filter removes viruses" full article?

Know where to find full article on this nano cellulose?

"Nano-paper filter removes viruses" published in the Advanced Healthcare Materials journal on March 31, 2014.

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[DIYbio] Re: Spare pOpen Taq plasmids anyone?

Hi there, I have also tried to buy some of the pOpenTaq plasmid but no answer from the guys from Openbiotech. If someone can send some in Bulgaria/Europe that would be great ! Thanks



18 април 2013, четвъртък, 17:29:32 UTC+3, Open BioLab Graz написа:

Hi!

Since the openbiotech guys arent answering to our emails since weeks, we thought we try it here:

Does anyone here have some spare pOpenTaq plasmids and would be so kind to send them to our biohacking space in Austria/Europe? We would really like to test our nice equipment :)


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Re: [DIYbio] Web-ready Refrideubator

LOL

On Mon, Mar 31, 2014 at 12:21 PM, Cathal Garvey
<cathalgarvey@cathalgarvey.me> wrote:
> 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 #;
> # }
>
> On 31/03/14 19:57, Avery louie wrote:
>> I do c and python. I'm tabbing and bracketing and semicoloning and always
>> in the wrong spot :p
>>
>> --A
>> On Mar 31, 2014 2:41 PM, "Josiah Zayner" <josiah.zayner@gmail.com> wrote:
>>
>>> 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.
>>>
>>>
>>>
>>>
>>> On Mon, Mar 31, 2014 at 11:28 AM, Nathan McCorkle <nmz787@gmail.com>wrote:
>>>
>>>> Why perl?
>>>> On Mar 31, 2014 11:19 AM, "Josiah Zayner" <josiah.zayner@gmail.com>
>>>> wrote:
>>>>
>>>>> 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
>>>>>
>>>>>
>>>>> On Monday, March 31, 2014 10:22:18 AM UTC-7, Avery wrote:
>>>>>>
>>>>>> 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
>>>>>>
>>>>>>
>>>>>> On Mon, Mar 31, 2014 at 1:13 PM, Cathal Garvey (Phone) <
>>>>>> cathal...@cathalgarvey.me> wrote:
>>>>>>
>>>>>>> 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.
>>>>>>>
>>>>>>>
>>>>>>> On 31 March 2014 17:51:01 GMT+01:00, Nathan McCorkle <nmz...@gmail.com>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> 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).
>>>>>>>>
>>>>>>>> On Mon, Mar 31, 2014 at 9:32 AM, Tom Hodder <t...@limepepper.co.uk> wrote:
>>>>>>>>
>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> -- You received this message because you are subscribed to the Google Groups
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> DIYbio group. To post to this group, send email to diy...@googlegroups.com.
>>>>>>>>> To unsubscribe from this group, send email to
>>>>>>>>> diybio+un...@googlegroups.com. For more options, visit this group at
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> https://groups.google.com/d/forum/diybio?hl=en
>>>>>>>>> Learn more at www.diybio.org
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ---
>>>>>>>>>
>>>>>>>>> You received this message because you are subscribed to the Google Groups
>>>>>>>>> "DIYbio" group.
>>>>>>>>> To unsubscribe from this group and stop receiving emails from it, send an
>>>>>>>>> email to diybio+un...@googlegroups.com.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> To post to this group, send email todiy...@googlegroups.com.
>>>>>>>>> Visit this group at http://groups.google.com/group/diybio.
>>>>>>>>>
>>>>>>>>> To view this discussion on the web visit
>>>>>>>>> https://groups.google.com/d/msgid/diybio/CAB%2BzPJAvpkXqVae9zMdq%2BsYDvgaRqXZou-3y4dOLa-dQ2Byr_Q%40mail.gmail.com.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>> Sent from my Android device with K-9 Mail. Please excuse my brevity.
>>>>>>>
>>>>>>> --
>>>>>>> -- You received this message because you are subscribed to the Google
>>>>>>> Groups DIYbio group. To post to this group, send email to
>>>>>>> diy...@googlegroups.com. To unsubscribe from this group, send email
>>>>>>> to diybio+un...@googlegroups.com. For more options, visit this group
>>>>>>> at https://groups.google.com/d/forum/diybio?hl=en
>>>>>>> Learn more at www.diybio.org
>>>>>>> ---
>>>>>>> You received this message because you are subscribed to the Google
>>>>>>> Groups "DIYbio" group.
>>>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>>>> an email to diybio+un...@googlegroups.com.
>>>>>>> To post to this group, send email to diy...@googlegroups.com.
>>>>>>> Visit this group at http://groups.google.com/group/diybio.
>>>>>>> To view this discussion on the web visit https://groups.google.com/d/
>>>>>>> msgid/diybio/1159c3ea-7e68-4cbf-b355-8f26c0fc3305%40email.android.com<https://groups.google.com/d/msgid/diybio/1159c3ea-7e68-4cbf-b355-8f26c0fc3305%40email.android.com?utm_medium=email&utm_source=footer>
>>>>>>> .
>>>>>>>
>>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>>
>>>>>>
>>>>>> --
>>>>> -- You received this message because you are subscribed to the Google
>>>>> Groups DIYbio group. To post to this group, send email to
>>>>> diybio@googlegroups.com. To unsubscribe from this group, send email to
>>>>> diybio+unsubscribe@googlegroups.com. For more options, visit this group
>>>>> at https://groups.google.com/d/forum/diybio?hl=en
>>>>> Learn more at www.diybio.org
>>>>> ---
>>>>> You received this message because you are subscribed to the Google
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>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>> an email to diybio+unsubscribe@googlegroups.com.
>>>>>
>>>>> To post to this group, send email to diybio@googlegroups.com.
>>>>> Visit this group at http://groups.google.com/group/diybio.
>>>>> To view this discussion on the web visit
>>>>> https://groups.google.com/d/msgid/diybio/75b1f685-4e00-4482-a842-283f451e5617%40googlegroups.com<https://groups.google.com/d/msgid/diybio/75b1f685-4e00-4482-a842-283f451e5617%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>>> .
>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>
>>>> --
>>>> -- You received this message because you are subscribed to the Google
>>>> Groups DIYbio group. To post to this group, send email to
>>>> diybio@googlegroups.com. To unsubscribe from this group, send email to
>>>> diybio+unsubscribe@googlegroups.com. For more options, visit this group
>>>> at https://groups.google.com/d/forum/diybio?hl=en
>>>> Learn more at www.diybio.org
>>>> ---
>>>> You received this message because you are subscribed to a topic in the
>>>> Google Groups "DIYbio" group.
>>>> To unsubscribe from this topic, visit
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>>>> To unsubscribe from this group and all its topics, send an email to
>>>> diybio+unsubscribe@googlegroups.com.
>>>> To post to this group, send email to diybio@googlegroups.com.
>>>> Visit this group at http://groups.google.com/group/diybio.
>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/diybio/CA%2B82U9L0r9seOkNiRQtyNm0xD2p2zid-eR77_rbiEQdE%3DOJ%3D6Q%40mail.gmail.com<https://groups.google.com/d/msgid/diybio/CA%2B82U9L0r9seOkNiRQtyNm0xD2p2zid-eR77_rbiEQdE%3DOJ%3D6Q%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>> .
>>>>
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>
>>> --
>>> -- You received this message because you are subscribed to the Google
>>> Groups DIYbio group. To post to this group, send email to
>>> diybio@googlegroups.com. To unsubscribe from this group, send email to
>>> diybio+unsubscribe@googlegroups.com. For more options, visit this group
>>> at https://groups.google.com/d/forum/diybio?hl=en
>>> Learn more at www.diybio.org
>>> ---
>>> You received this message because you are subscribed to the Google Groups
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>>> To unsubscribe from this group and stop receiving emails from it, send an
>>> email to diybio+unsubscribe@googlegroups.com.
>>> To post to this group, send email to diybio@googlegroups.com.
>>> Visit this group at http://groups.google.com/group/diybio.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/diybio/CAEUkM4uiSWhnBxBjWtSA7DwXdD6b_o2sgqJErQoouuuiN_JOcQ%40mail.gmail.com<https://groups.google.com/d/msgid/diybio/CAEUkM4uiSWhnBxBjWtSA7DwXdD6b_o2sgqJErQoouuuiN_JOcQ%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>> .
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>
> --
> T: @onetruecathal, @IndieBBDNA
> P: +353876363185
> W: http://indiebiotech.com



--
-Nathan

--
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Re: [DIYbio] Web-ready Refrideubator

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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 #;
# }

On 31/03/14 19:57, Avery louie wrote:
> I do c and python. I'm tabbing and bracketing and semicoloning and always
> in the wrong spot :p
>
> --A
> On Mar 31, 2014 2:41 PM, "Josiah Zayner" <josiah.zayner@gmail.com> wrote:
>
>> 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.
>>
>>
>>
>>
>> On Mon, Mar 31, 2014 at 11:28 AM, Nathan McCorkle <nmz787@gmail.com>wrote:
>>
>>> Why perl?
>>> On Mar 31, 2014 11:19 AM, "Josiah Zayner" <josiah.zayner@gmail.com>
>>> wrote:
>>>
>>>> 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
>>>>
>>>>
>>>> On Monday, March 31, 2014 10:22:18 AM UTC-7, Avery wrote:
>>>>>
>>>>> 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
>>>>>
>>>>>
>>>>> On Mon, Mar 31, 2014 at 1:13 PM, Cathal Garvey (Phone) <
>>>>> cathal...@cathalgarvey.me> wrote:
>>>>>
>>>>>> 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.
>>>>>>
>>>>>>
>>>>>> On 31 March 2014 17:51:01 GMT+01:00, Nathan McCorkle <nmz...@gmail.com>
>>>>>> wrote:
>>>>>>>
>>>>>>> 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).
>>>>>>>
>>>>>>> On Mon, Mar 31, 2014 at 9:32 AM, Tom Hodder <t...@limepepper.co.uk> wrote:
>>>>>>>
>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> -- You received this message because you are subscribed to the Google Groups
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> DIYbio group. To post to this group, send email to diy...@googlegroups.com.
>>>>>>>> To unsubscribe from this group, send email to
>>>>>>>> diybio+un...@googlegroups.com. For more options, visit this group at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> https://groups.google.com/d/forum/diybio?hl=en
>>>>>>>> Learn more at www.diybio.org
>>>>>>>>
>>>>>>>>
>>>>>>>> ---
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>>>>>>>> You received this message because you are subscribed to the Google Groups
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>>>>>>>> To unsubscribe from this group and stop receiving emails from it, send an
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>>>>>>>>
>>>>>>>>
>>>>>>>> To post to this group, send email todiy...@googlegroups.com.
>>>>>>>> Visit this group at http://groups.google.com/group/diybio.
>>>>>>>>
>>>>>>>> To view this discussion on the web visit
>>>>>>>> https://groups.google.com/d/msgid/diybio/CAB%2BzPJAvpkXqVae9zMdq%2BsYDvgaRqXZou-3y4dOLa-dQ2Byr_Q%40mail.gmail.com.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> --
>>>>>> Sent from my Android device with K-9 Mail. Please excuse my brevity.
>>>>>>
>>>>>> --
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>>>>>> at https://groups.google.com/d/forum/diybio?hl=en
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>>>>>> To view this discussion on the web visit https://groups.google.com/d/
>>>>>> msgid/diybio/1159c3ea-7e68-4cbf-b355-8f26c0fc3305%40email.android.com<https://groups.google.com/d/msgid/diybio/1159c3ea-7e68-4cbf-b355-8f26c0fc3305%40email.android.com?utm_medium=email&utm_source=footer>
>>>>>> .
>>>>>>
>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>
>>>>>
>>>>> --
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>>>> .
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>>>>
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>

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P: +353876363185
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Re: [DIYbio] Web-ready Refrideubator

On 31 March 2014 18:22, Avery louie <inactive.e@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.

 

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Re: [DIYbio] Web-ready Refrideubator

 
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;



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Re: [DIYbio] Web-ready Refrideubator

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

--A

On Mar 31, 2014 2:41 PM, "Josiah Zayner" <josiah.zayner@gmail.com> wrote:
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.




On Mon, Mar 31, 2014 at 11:28 AM, Nathan McCorkle <nmz787@gmail.com> wrote:

Why perl?

On Mar 31, 2014 11:19 AM, "Josiah Zayner" <josiah.zayner@gmail.com> wrote:
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


On Monday, March 31, 2014 10:22:18 AM UTC-7, Avery wrote:
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


On Mon, Mar 31, 2014 at 1:13 PM, Cathal Garvey (Phone) <cathal...@cathalgarvey.me> wrote:
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.


On 31 March 2014 17:51:01 GMT+01:00, Nathan McCorkle <nmz...@gmail.com> wrote:
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).

On Mon, Mar 31, 2014 at 9:32 AM, Tom Hodder <t...@limepepper.co.uk> wrote:
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











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