Re: [DIYbio] Potentiostat controlled by Arduino



On Mon, Sep 24, 2018, 1:02 AM Brian Degger <brian.degger@gmail.com> wrote:
Qualifying note: Why would I want a potentioatat as a DIYbio person?

pH for example

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Re: [DIYbio] #35C3 call for participation

I likely won't have time to put anything new together, but I'll almost certainly be there.


Cheers,
—mlp

On 25 Sep 2018, at 19:34, Brian Degger <brian.degger@gmail.com> wrote:

I'm definitely intending to go... And up for putting together a diybio or biohack talk and /or workshop. 

On Tue, 25 Sep 2018, 15:53 Lucy Patterson, <lucypattersn@gmail.com> wrote:
Hi!

+++ apologies for cross-posting +++

For folks who may have missed it, the call-for-participation for this year's Chaos Communication Congress, 27-30th December 2018 in Leipzig Germany, is out! And already for a little while. In case you hadn't noticed, there is a SCIENCE TRACK \o/, just like every year. Here's the specifics...

DEADLINE: 15th October

Here's the science track text (unfortunately the one on the blog is still the old one from last year...):

SCIENCE TRACK
We see science as a method of "reverse engineering" the world and are interested in the latest results. How can we free our orbital front yard from all its accumulated space junk? How can we develop algorithms and feed them with data that won't perpetuate existing discrimination? How can DNA editing cure diseases without causing a zombie apocalypse?
To benefit from new knowledge and the technologies that come from it we need to understand how it all relates to and influences our environment and society. No matter if you work at a research center, university or in a garage: If you explore and evaluate interesting and important developments from a scientific point of view, this is your track!

A nice thing this year is that they're specifically asking for what they call "Foundation Talks" - this should be entry level backgrounders for people who are new to a topic - great both to apply for and to listen to. You can also check out the other tracks of course - hardware, art and culture... many of them could be (and have been) a good home for the kind of open sciencing we do on this list. You can apply for a 30min (plus 10mins Q&A) or 45min (plus 15min Q&A) talk. Also, it's helpful to know that the CCC doesn't really go for talks that focus exclusively on a specific project. They'd much rather hear about ongoing research, issues, movements, opinions… 

About the CCC
The CCC (Chaos Computer Club) is Europe's largest association of hackers, and the CCC (Chaos Communication Congress) is it's annual meeting. Topics range from Resilience, Security, Privacy and digital rights to broader digital culture, art, politics, society, hardware and Science! It's a completely independent, self-organised, self-financed event, for 13000+ people, around 3000 of which contribute voluntarily to running the event. This means that everyone pays their ticket (which can be quite tricky to get btw), with speakers being the only exception. The talks are only a small part of everything that goes on there. It's like a huge hacker family party to round off the year. Hope to see some folks there!

--
Lucy Patterson

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Re: [DIYbio] #35C3 call for participation

I'm definitely intending to go... And up for putting together a diybio or biohack talk and /or workshop. 

On Tue, 25 Sep 2018, 15:53 Lucy Patterson, <lucypattersn@gmail.com> wrote:
Hi!

+++ apologies for cross-posting +++

For folks who may have missed it, the call-for-participation for this year's Chaos Communication Congress, 27-30th December 2018 in Leipzig Germany, is out! And already for a little while. In case you hadn't noticed, there is a SCIENCE TRACK \o/, just like every year. Here's the specifics...

DEADLINE: 15th October

Here's the science track text (unfortunately the one on the blog is still the old one from last year...):

SCIENCE TRACK
We see science as a method of "reverse engineering" the world and are interested in the latest results. How can we free our orbital front yard from all its accumulated space junk? How can we develop algorithms and feed them with data that won't perpetuate existing discrimination? How can DNA editing cure diseases without causing a zombie apocalypse?
To benefit from new knowledge and the technologies that come from it we need to understand how it all relates to and influences our environment and society. No matter if you work at a research center, university or in a garage: If you explore and evaluate interesting and important developments from a scientific point of view, this is your track!

A nice thing this year is that they're specifically asking for what they call "Foundation Talks" - this should be entry level backgrounders for people who are new to a topic - great both to apply for and to listen to. You can also check out the other tracks of course - hardware, art and culture... many of them could be (and have been) a good home for the kind of open sciencing we do on this list. You can apply for a 30min (plus 10mins Q&A) or 45min (plus 15min Q&A) talk. Also, it's helpful to know that the CCC doesn't really go for talks that focus exclusively on a specific project. They'd much rather hear about ongoing research, issues, movements, opinions… 

About the CCC
The CCC (Chaos Computer Club) is Europe's largest association of hackers, and the CCC (Chaos Communication Congress) is it's annual meeting. Topics range from Resilience, Security, Privacy and digital rights to broader digital culture, art, politics, society, hardware and Science! It's a completely independent, self-organised, self-financed event, for 13000+ people, around 3000 of which contribute voluntarily to running the event. This means that everyone pays their ticket (which can be quite tricky to get btw), with speakers being the only exception. The talks are only a small part of everything that goes on there. It's like a huge hacker family party to round off the year. Hope to see some folks there!

--
Lucy Patterson

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[DIYbio] #35C3 call for participation

Hi!

+++ apologies for cross-posting +++

For folks who may have missed it, the call-for-participation for this year's Chaos Communication Congress, 27-30th December 2018 in Leipzig Germany, is out! And already for a little while. In case you hadn't noticed, there is a SCIENCE TRACK \o/, just like every year. Here's the specifics...

DEADLINE: 15th October
CFP: https://events.ccc.de/2018/09/11/35c3-call-for-participation-and-submission-guidelines 

Here's the science track text (unfortunately the one on the blog is still the old one from last year...):

SCIENCE TRACK
We see science as a method of "reverse engineering" the world and are interested in the latest results. How can we free our orbital front yard from all its accumulated space junk? How can we develop algorithms and feed them with data that won't perpetuate existing discrimination? How can DNA editing cure diseases without causing a zombie apocalypse?
To benefit from new knowledge and the technologies that come from it we need to understand how it all relates to and influences our environment and society. No matter if you work at a research center, university or in a garage: If you explore and evaluate interesting and important developments from a scientific point of view, this is your track!

A nice thing this year is that they're specifically asking for what they call "Foundation Talks" - this should be entry level backgrounders for people who are new to a topic - great both to apply for and to listen to. You can also check out the other tracks of course - hardware, art and culture... many of them could be (and have been) a good home for the kind of open sciencing we do on this list. You can apply for a 30min (plus 10mins Q&A) or 45min (plus 15min Q&A) talk. Also, it's helpful to know that the CCC doesn't really go for talks that focus exclusively on a specific project. They'd much rather hear about ongoing research, issues, movements, opinions… 

About the CCC
The CCC (Chaos Computer Club) is Europe's largest association of hackers, and the CCC (Chaos Communication Congress) is it's annual meeting. Topics range from Resilience, Security, Privacy and digital rights to broader digital culture, art, politics, society, hardware and Science! It's a completely independent, self-organised, self-financed event, for 13000+ people, around 3000 of which contribute voluntarily to running the event. This means that everyone pays their ticket (which can be quite tricky to get btw), with speakers being the only exception. The talks are only a small part of everything that goes on there. It's like a huge hacker family party to round off the year. Hope to see some folks there!

--
Lucy Patterson

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Re: [DIYbio] Potentiostat controlled by Arduino

Qualifying note: Why would I want a potentioatat as a DIYbio person?

Simply put... This device has the potential to be useful in monitoring chemical reactions in solution. And biology is all about solutions of solutes.

Havent read the paper yet but i guess its a more friendly cheapstat. 

On Sun, 23 Sep 2018, 16:01 Markos, <markos@c2o.pro.br> wrote:

Hi Simon,

And the link to paper:

Building a Microcontroller Based Potentiostat: A Inexpensive and Versatile Platform for Teaching Electrochemistry and Instrumentation

https://pubs.acs.org/doi/pdf/10.1021/acs.jchemed.5b00961

Many thanks,
Markos

Em 23-09-2018 09:45, Simon Quellen Field escreveu:

On Sun, Sep 23, 2018 at 5:27 AM Markos <markos@c2o.pro.br> wrote:
An "open access" paper at Journal of Chemical Education:

An Easily Fabricated Low-Cost Potentiostat Coupled with User-Friendly
Software for Introducing Students to Electrochemical Reactions and
Electroanalytical Techniques

https://pubs.acs.org/doi/ipdf/10.1021/acs.jchemed.8b00340

Suplementar Info:

https://pubs.acs.org/doi/suppl/10.1021/acs.jchemed.8b00340/suppl_file/ed8b00340_si_002.pdf

Markos

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[DIYbio] Re: Mad scientist 72 attempts to replicate Miller Urey experiment

https://www.youtube.com/watch?v=P4pXK1ogclw

And Now we have this experiment. 

On Sunday, June 17, 2018 at 8:38:42 PM UTC-7, Ryan Vitug-Gavieres wrote:
https://m.youtube.com/watch?v=Mp9l3LhPLgE

This is nice though given that its been mentioned in biochemistry lectures as the experiment that attempted to explain how life started on earth.

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Re: [DIYbio] Mushroom Cloning Project

No Im just watching how cloning Mushrooms work. I never knew you can do that. I've cloned Saccharomyces cerevisiae and E. coli before in a college biotech lab before. I was just watching out of curiosity how that worked. 

On Sunday, September 23, 2018 at 10:44:13 AM UTC-7, InstantLife wrote:
What is the project you want to do with mushrooms. I have used this technique before with various kinds of mushrooms

On Sun, Sep 23, 2018, 10:42 AM Cabalen sciences <ryangav...@gmail.com> wrote:
https://www.youtube.com/watch?v=TDhQcRPPd9c

Freshcap Mushrooms produced a video has produced a video on cloning Mushrooms. 

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Re: [DIYbio] Mushroom Cloning Project

Here's a step-by-step HOWTO I wrote in 2014 of what looks like the
same overall procedure:
"First DIYbio project" -
https://groups.google.com/d/msg/diybio/zoBvHPXiPNM/xuD-pChXzcIJ
On Sun, Sep 23, 2018 at 10:44 AM IsInstantLife
<xthechallengerx@gmail.com> wrote:
>
> What is the project you want to do with mushrooms. I have used this technique before with various kinds of mushrooms
>
> On Sun, Sep 23, 2018, 10:42 AM Cabalen sciences <ryangavieres123@gmail.com> wrote:
>>
>> https://www.youtube.com/watch?v=TDhQcRPPd9c
>>
>> Freshcap Mushrooms produced a video has produced a video on cloning Mushrooms.
>>
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>> Learn more at www.diybio.org
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-Nathan

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Re: [DIYbio] Mushroom Cloning Project

What is the project you want to do with mushrooms. I have used this technique before with various kinds of mushrooms

On Sun, Sep 23, 2018, 10:42 AM Cabalen sciences <ryangavieres123@gmail.com> wrote:
https://www.youtube.com/watch?v=TDhQcRPPd9c

Freshcap Mushrooms produced a video has produced a video on cloning Mushrooms. 

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[DIYbio] Mushroom Cloning Project

https://www.youtube.com/watch?v=TDhQcRPPd9c

Freshcap Mushrooms produced a video has produced a video on cloning Mushrooms. 

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Re: [DIYbio] Potentiostat controlled by Arduino

Hi Simon,

And the link to paper:

Building a Microcontroller Based Potentiostat: A Inexpensive and Versatile Platform for Teaching Electrochemistry and Instrumentation

https://pubs.acs.org/doi/pdf/10.1021/acs.jchemed.5b00961

Many thanks,
Markos

Em 23-09-2018 09:45, Simon Quellen Field escreveu:

On Sun, Sep 23, 2018 at 5:27 AM Markos <markos@c2o.pro.br> wrote:
An "open access" paper at Journal of Chemical Education:

An Easily Fabricated Low-Cost Potentiostat Coupled with User-Friendly
Software for Introducing Students to Electrochemical Reactions and
Electroanalytical Techniques

https://pubs.acs.org/doi/ipdf/10.1021/acs.jchemed.8b00340

Suplementar Info:

https://pubs.acs.org/doi/suppl/10.1021/acs.jchemed.8b00340/suppl_file/ed8b00340_si_002.pdf

Markos

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Re: [DIYbio] Potentiostat controlled by Arduino


On Sun, Sep 23, 2018 at 5:27 AM Markos <markos@c2o.pro.br> wrote:
An "open access" paper at Journal of Chemical Education:

An Easily Fabricated Low-Cost Potentiostat Coupled with User-Friendly
Software for Introducing Students to Electrochemical Reactions and
Electroanalytical Techniques

https://pubs.acs.org/doi/ipdf/10.1021/acs.jchemed.8b00340

Suplementar Info:

https://pubs.acs.org/doi/suppl/10.1021/acs.jchemed.8b00340/suppl_file/ed8b00340_si_002.pdf

Markos

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[DIYbio] Potentiostat controlled by Arduino

An "open access" paper at Journal of Chemical Education:

An Easily Fabricated Low-Cost Potentiostat Coupled with User-Friendly
Software for Introducing Students to Electrochemical Reactions and
Electroanalytical Techniques

https://pubs.acs.org/doi/ipdf/10.1021/acs.jchemed.8b00340

Suplementar Info:

https://pubs.acs.org/doi/suppl/10.1021/acs.jchemed.8b00340/suppl_file/ed8b00340_si_002.pdf

Markos

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[DIYbio] RNA stained fatty acid vesicles (stained with SYBR 1)

https://www.youtube.com/watch?v=TdPhlIvPlc0

Cool Experiment by Mad Scientist 72 

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[DIYbio] Re: Climate change solutions?

The biggest problem with carbon capture and sequestration (CCS) is that the efficiencies go down dramatically the more diluted the carbon is. So capturing CO2 at a smokestack is way more efficient than sucking it straight from the air. 

By extrapolation, by far the most efficient form of carbon capture and sequestration would be to capture the carbon in its purest form. That is, take coal and other fossil fuels, and bury them underground!

Patrik

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Re: [DIYbio] Climate change solutions?

Here in NCL, scientists are experimenting with carbon capture meadows, where stony rubbish + plants   provides a substrate/calcium + energy/biome for carbon-> calcium carbonate fixation on Brownfield i.e. Post-Industrial landsites. (the science is in infancy)
NCL is aslo the centre of Coal -> Biochar revolution

https://www.ncl.ac.uk/press/articles/archive/2016/12/carboncapture/
"Carbonation involves the combination of calcium – which is abundant in brownfield soils that contain demolition wastes such as concrete dust and lime – with atmospheric CO2 to form calcium carbonate (calcite).
But whereas the large amounts of organic carbon locked away in peatlands have accumulated very slowly, inorganic carbon in calcite can form very rapidly in brownfield soils, making them more useful in cutting atmospheric CO2."

Cheers
B

On Fri, Sep 21, 2018 at 8:21 PM Nathan McCorkle <nmz787@gmail.com> wrote:
On Fri, Sep 21, 2018 at 11:49 AM Tito <titojankowski@gmail.com> wrote:
>
> Hi everybody,
> Anyone here interested in direct air capture for carbon removal? https://www.fastcompany.com/40510680/can-we-suck-enough-co2-from-the-air-to-save-the-climate
>
> The current generation of tech is chemical engineering. I'm curious what solutions biology might offer. Figured some people on this list might be thinking about it already.
>
> Thoughts?

Seems like to meet the desired CO2 target levels in reasonable time
period, biology is going to be too slow.

Something I don't know is how long the past (pre-human) era of
high-CO2 lasted in time... was it sufficient to enable evolutionary
selection/optimization of fast CO2 consumers?

It seems fast CO2 capture has already been on scientists' and
engineers' minds for some time, for example in the forestry and
agriculture fields. I remember an internship I almost accepted years
ago at ORNL, where they were looking at the microbiome (among other
things) of Poplar because it grows quite fast, and that would be a
boon to people wanting wood for product manufacturing.

It seems to me the best solution would be hooking up a clean/green
nuclear plant to an industrial-scale CO2 chemical capture system. If
we could figure out a way to produce something more-dense than water,
then we could just start dumping diamonoids into a pile at the bottom
of the ocean, etc.

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Re: [DIYbio] Climate change solutions?

On Fri, Sep 21, 2018 at 11:49 AM Tito <titojankowski@gmail.com> wrote:
>
> Hi everybody,
> Anyone here interested in direct air capture for carbon removal? https://www.fastcompany.com/40510680/can-we-suck-enough-co2-from-the-air-to-save-the-climate
>
> The current generation of tech is chemical engineering. I'm curious what solutions biology might offer. Figured some people on this list might be thinking about it already.
>
> Thoughts?

Seems like to meet the desired CO2 target levels in reasonable time
period, biology is going to be too slow.

Something I don't know is how long the past (pre-human) era of
high-CO2 lasted in time... was it sufficient to enable evolutionary
selection/optimization of fast CO2 consumers?

It seems fast CO2 capture has already been on scientists' and
engineers' minds for some time, for example in the forestry and
agriculture fields. I remember an internship I almost accepted years
ago at ORNL, where they were looking at the microbiome (among other
things) of Poplar because it grows quite fast, and that would be a
boon to people wanting wood for product manufacturing.

It seems to me the best solution would be hooking up a clean/green
nuclear plant to an industrial-scale CO2 chemical capture system. If
we could figure out a way to produce something more-dense than water,
then we could just start dumping diamonoids into a pile at the bottom
of the ocean, etc.

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Re: [DIYbio] Climate change solutions?

For a few billion dollars you could put a giant inflatable sunshade into orbit. It seems that most people want to complain about climate change instead of doing anything about it.

On Fri, Sep 21, 2018 at 1:48 PM, Tito <titojankowski@gmail.com> wrote:
Hi everybody,
Anyone here interested in direct air capture for carbon removal? https://www.fastcompany.com/40510680/can-we-suck-enough-co2-from-the-air-to-save-the-climate

The current generation of tech is chemical engineering. I'm curious what solutions biology might offer. Figured some people on this list might be thinking about it already.

Thoughts?

Cheers,
Tito


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[DIYbio] Climate change solutions?

Hi everybody,
Anyone here interested in direct air capture for carbon removal? https://www.fastcompany.com/40510680/can-we-suck-enough-co2-from-the-air-to-save-the-climate

The current generation of tech is chemical engineering. I'm curious what solutions biology might offer. Figured some people on this list might be thinking about it already.

Thoughts?

Cheers,
Tito


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[DIYbio] Re: Travel fellowships for open source biology/bioinformatics

I missed the deadline because i was traveling for open science ;)

Maybe there will be another chance

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Re: [DIYbio] Re: BioCoder : a high-level programming language for expressing biology protocols


On Thu, Sep 13, 2018 at 8:40 PM Nathan McCorkle <nmz787@gmail.com> wrote:
Hi Thomas,
I'm not on the BioCoder team... and only took the ZIP file download of
BioCoder 1.0 and uploaded it to github, then made the changes to get
it to compile on Ubuntu.

You can find the link you referenced here on The Internet Archive:
https://web.archive.org/web/20161110125136/http://research.microsoft.com/en-us/um/india/projects/biocoder/

But I see there it says this same documentation is included in the code repo.

Also, I was the one who created the readme.md file... and only
copy-pasted the journal article title-page text there (along with some
minor formatting).

Please feel free to send me any updates and I can integrate them, or
if you'd like you can simply fork my repo and then I can pull your
changes once you've made any.

Best,
-Nathan

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Re: [DIYbio] Re: BioCoder : a high-level programming language for expressing biology protocols

Hi Thomas,
I'm not on the BioCoder team... and only took the ZIP file download of
BioCoder 1.0 and uploaded it to github, then made the changes to get
it to compile on Ubuntu.

You can find the link you referenced here on The Internet Archive:
https://web.archive.org/web/20161110125136/http://research.microsoft.com/en-us/um/india/projects/biocoder/

But I see there it says this same documentation is included in the code repo.

Also, I was the one who created the readme.md file... and only
copy-pasted the journal article title-page text there (along with some
minor formatting).

Please feel free to send me any updates and I can integrate them, or
if you'd like you can simply fork my repo and then I can pull your
changes once you've made any.

Best,
-Nathan

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[DIYbio] Re: BioCoder : a high-level programming language for expressing biology protocols

Hey BioCoder Team, 

Great to see more people working on software for biology. Just wondering if you have any additional documentation? "http://research.microsoft.com/en-us/um/india/projects/biocoder/" does not seem to point anywhere and I would be keen to check out examples and use cases. 

Also it might help to expand your outline/goals in your readme.md. Perhaps discuss other languages and their shortfalls, e.g., autoprotocol is python based, anthalang uses go.. Why did you choose C? Where there specific applications that you targeted? What would you like to achieve through open sourcing? What aspects do you feel are still missing in your language?

Please keep the DIYBio group updated! 

Best, 
Tom

On Tuesday, 8 December 2009 12:26:51 UTC, Vaishnavi. A wrote:
Hi all,
I am one of the developers of the BioCoder language. BioCoder is
essentially a C library with various functionalities included,
pertaining primarily to the field of Molecular Biology. We envision
the replacement of natural language description of protocols in
published papers with code written in BioCoder, thus making the
protocol standardized and amenable to automation and re-usability.We
are in the process of working out the release of BioCoder.

It is a widely accepted fact that most descriptions of protocols in
published papers are ambiguous and incomplete and we are unsure why
that is the case. We have come up with a survey to try and understand
the problem. It would be great if you could take this short 10-
question survey which tries to zero in on the problem. Results will be
made available on DIYbio when enough data points have been collected.

Please click on the link below to take the survey:
http://www.surveymonkey.com/s/SYJM23Q

For more information about the language:
http://research.microsoft.com/en-us/um/people/thies/thies-iwbda09.pdf

To know what BioCoder code looks like, you can check out the following
examples from OpenWetWare:
http://www.google.co.in/search?q=BioCoder+site%3Aopenwetware.org&ie=utf-8&oe=utf-8&aq=t&client=firefox-a&rlz=1R1WZPB_en-GB___IN356

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