Re: [DIYbio] Re: Climate change solutions?

I'm excited about these new foods. It's hard to make a case to raise cattle on Mars for example, so many better things to do with the space and energy. Algae food all the way! Good luck at your show in Dubai.

Cheers,
Tito


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Re: [DIYbio] Re: Climate change solutions?

Hi,

I agree with Tito, CO2 production so far exceeds the capacity of capture technologies that we are nowhere near to breaking even. In addition, the carbon economy is based on a cycle, its not a linear process. In our example, algae produced using flue gas will be used as animal feed or a food additive, so after consumption the captured carbon will be released again as CO2. Therefore its not carbon negative, but a zero carbon solution. If we want carbon negative, then we need to make sure the organics created are not broken down again and released into the air. As an example, dried algae can be used as a soil additive or a plastic feedstock, both cases trapping most of the carbon and making the process a carbon negative one. So should we in the distant future end up capturing more CO2 than we produce, we can release it back into the cycle to keep a desired concentration if we wish to.

CO2 concentrations are actually increasing because we are bringing dormant stocks into the cycle, like carbon trapped underground via the oil industry, or carbon stored in the soil and the sea, which is brought into the cycle by farming and fishing.

And also, Tito, you may be interested to know that we received some funding to develop a proof-of-concept alga bioreactor for Mars. Algae are the top choice as fresh food source for future Mars missions so technologies to that end are being developed by Algacraft, and others. Next month we will be showcasing our work at the Space Research for Food & Water Security on Earth  Conference in Dubai, if anyone is around, you are welcome to come by. The event will be held alongside the Humans in Space Flight Symposium: https://www.his2019.com/ .

Cheers,
Mate

On Monday, 28 October 2019 16:17:15 UTC, Tito wrote:
Ice age 2.0!

There's a million million tons of excess carbon dioxide in our atmosphere. 10^12. Current capacities for removing carbon are in the tens or hundreds of tons per year. So we're not there yet. My sense is the technologies become attractive for use on Mars, their atmosphere is 95% carbon dioxide.

Cheers,
Tito


Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Monday, October 28, 2019 8:14 AM, S James Parsons Jr <sjamesp...@gmail.com> wrote:

Not to seem negative, with the great work being done by harvesting carbon from the air. But what happens when we have a CO2/green-house-gas deficit? Our lifestyles created cars, green-house producing food chain, pollution from consumable goods where the negative externality. But what happens when our lifestyle makes zero-emission cars, green-house free foods, and carbon offsetting consumer goods. What happens to the O2 harvesting companies? Do they go out of business, or do they become the enemy? 






On Oct 28, 2019, at 11:01 AM, Tito Jankowski <ti...@titojankowski.com> wrote:

Wow Algacraft looks cool! Submit it to the AirMiners index, http://airminers.org

Also, click "Join Community" to join AirMiners Slack, the world's largest community of scientists, engineers, and entrepreneurs mining carbon from the air.

Cheers,
Tito


Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Monday, October 28, 2019 2:36 AM, Ravasz <ravasz...@gmail.com> wrote:

This thread is from last year...

Since then we also formed an alga biotech startup: www.algacraft.com

We are currently being funded by the Edinburgh Centre for Carbon Innovation and hope to build bioreactors that that can mitigate the carbon output of other industries.
Our idea is too hook our systems up to the flue gas of power plants, cement factories and similar, and use the CO2 rich gas to grow algae even more rapidly than they would with plain old air.
If anyone is more interested in this, do not hesitate to write.

Cheers,
Mate


On Sunday, 27 October 2019 21:33:24 UTC, Jonathan Cline wrote:


On Friday, September 21, 2018 at 11:48:57 AM UTC-7, Tito 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



Quote

Hypergiant Industries wants to use algae boxes to solve the problem.

...

The prototype bioreactor is 3' x 3' x 3', and holds 55 gallons of water and algae. "Algae wants CO2 and light," the company explains on its website. "The light can be from the sun, or in this case, artificial light. The algae and water are pumped through a series of tubes to maximize their exposure to light sources lining the inside of the Reactor."

Inside the reactor, the algae absorbs the carbon dioxide and in the process creates a biomass, essentially dried algae. In the oceans, dried algae has a crucial role: It sinks to the bottom of the ocean and creates food for microorganisms. The company says the algae biomass can then be "harvested and processed to create fuel, oils, nutrient-rich high-protein food sources, fertilizers, plastics, cosmetics, and more."

The Hypergiant team claims the device is 400 times more effective than trees at carbon sequestration. 

"With the first generation Eos, we have precise control of every aspect of the algae's environment and life cycle," Ben Lamm, CEO and founder, tells Fast Company. "It's a photobioreactor, but it's also an experimentation platform. We'll be using this platform to better understand the environment that best suits biomass production under controlled circumstances, so that we can better understand how to design reactors for the variety of environmental conditions we're going to encounter in the wild."

The company has a local vision for the biogenerators. Rather than (at least at first) a field of the algae boxes in an energy grid, Hypergiant envisions HVAC units, close to exhaust and industrial pipes, breathing in the carbon dioxide from a office building.

According to the International Energy Agency, buildings and building construction account for 36 percent of global final energy consumption and nearly 40 percent of the world's total direct and indirect CO2 emissions.

But a prototype is still just a prototype, and Libby says the company has no plans to start selling quite yet. The next step, in spring 2020, will be to make the design for the algae boxes open-source and see what the world will make of them.

End Quote


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Re: [DIYbio] Re: Climate change solutions?

Ice age 2.0!

There's a million million tons of excess carbon dioxide in our atmosphere. 10^12. Current capacities for removing carbon are in the tens or hundreds of tons per year. So we're not there yet. My sense is the technologies become attractive for use on Mars, their atmosphere is 95% carbon dioxide.

Cheers,
Tito


Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Monday, October 28, 2019 8:14 AM, S James Parsons Jr <sjamesparsonsjr@gmail.com> wrote:

Not to seem negative, with the great work being done by harvesting carbon from the air. But what happens when we have a CO2/green-house-gas deficit? Our lifestyles created cars, green-house producing food chain, pollution from consumable goods where the negative externality. But what happens when our lifestyle makes zero-emission cars, green-house free foods, and carbon offsetting consumer goods. What happens to the O2 harvesting companies? Do they go out of business, or do they become the enemy? 






On Oct 28, 2019, at 11:01 AM, Tito Jankowski <tito@titojankowski.com> wrote:

Wow Algacraft looks cool! Submit it to the AirMiners index, http://airminers.org

Also, click "Join Community" to join AirMiners Slack, the world's largest community of scientists, engineers, and entrepreneurs mining carbon from the air.

Cheers,
Tito


Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Monday, October 28, 2019 2:36 AM, Ravasz <ravaszmeister@gmail.com> wrote:

This thread is from last year...

Since then we also formed an alga biotech startup: www.algacraft.com

We are currently being funded by the Edinburgh Centre for Carbon Innovation and hope to build bioreactors that that can mitigate the carbon output of other industries.
Our idea is too hook our systems up to the flue gas of power plants, cement factories and similar, and use the CO2 rich gas to grow algae even more rapidly than they would with plain old air.
If anyone is more interested in this, do not hesitate to write.

Cheers,
Mate


On Sunday, 27 October 2019 21:33:24 UTC, Jonathan Cline wrote:


On Friday, September 21, 2018 at 11:48:57 AM UTC-7, Tito 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



Quote

Hypergiant Industries wants to use algae boxes to solve the problem.

...

The prototype bioreactor is 3' x 3' x 3', and holds 55 gallons of water and algae. "Algae wants CO2 and light," the company explains on its website. "The light can be from the sun, or in this case, artificial light. The algae and water are pumped through a series of tubes to maximize their exposure to light sources lining the inside of the Reactor."

Inside the reactor, the algae absorbs the carbon dioxide and in the process creates a biomass, essentially dried algae. In the oceans, dried algae has a crucial role: It sinks to the bottom of the ocean and creates food for microorganisms. The company says the algae biomass can then be "harvested and processed to create fuel, oils, nutrient-rich high-protein food sources, fertilizers, plastics, cosmetics, and more."

The Hypergiant team claims the device is 400 times more effective than trees at carbon sequestration. 

"With the first generation Eos, we have precise control of every aspect of the algae's environment and life cycle," Ben Lamm, CEO and founder, tells Fast Company. "It's a photobioreactor, but it's also an experimentation platform. We'll be using this platform to better understand the environment that best suits biomass production under controlled circumstances, so that we can better understand how to design reactors for the variety of environmental conditions we're going to encounter in the wild."

The company has a local vision for the biogenerators. Rather than (at least at first) a field of the algae boxes in an energy grid, Hypergiant envisions HVAC units, close to exhaust and industrial pipes, breathing in the carbon dioxide from a office building.

According to the International Energy Agency, buildings and building construction account for 36 percent of global final energy consumption and nearly 40 percent of the world's total direct and indirect CO2 emissions.

But a prototype is still just a prototype, and Libby says the company has no plans to start selling quite yet. The next step, in spring 2020, will be to make the design for the algae boxes open-source and see what the world will make of them.

End Quote


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Re: [DIYbio] Re: Climate change solutions?

Not to seem negative, with the great work being done by harvesting carbon from the air. But what happens when we have a CO2/green-house-gas deficit? Our lifestyles created cars, green-house producing food chain, pollution from consumable goods where the negative externality. But what happens when our lifestyle makes zero-emission cars, green-house free foods, and carbon offsetting consumer goods. What happens to the O2 harvesting companies? Do they go out of business, or do they become the enemy? 







On Oct 28, 2019, at 11:01 AM, Tito Jankowski <tito@titojankowski.com> wrote:

Wow Algacraft looks cool! Submit it to the AirMiners index, http://airminers.org

Also, click "Join Community" to join AirMiners Slack, the world's largest community of scientists, engineers, and entrepreneurs mining carbon from the air.

Cheers,
Tito


Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Monday, October 28, 2019 2:36 AM, Ravasz <ravaszmeister@gmail.com> wrote:

This thread is from last year...

Since then we also formed an alga biotech startup: www.algacraft.com

We are currently being funded by the Edinburgh Centre for Carbon Innovation and hope to build bioreactors that that can mitigate the carbon output of other industries.
Our idea is too hook our systems up to the flue gas of power plants, cement factories and similar, and use the CO2 rich gas to grow algae even more rapidly than they would with plain old air.
If anyone is more interested in this, do not hesitate to write.

Cheers,
Mate


On Sunday, 27 October 2019 21:33:24 UTC, Jonathan Cline wrote:


On Friday, September 21, 2018 at 11:48:57 AM UTC-7, Tito 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



Quote

Hypergiant Industries wants to use algae boxes to solve the problem.

...

The prototype bioreactor is 3' x 3' x 3', and holds 55 gallons of water and algae. "Algae wants CO2 and light," the company explains on its website. "The light can be from the sun, or in this case, artificial light. The algae and water are pumped through a series of tubes to maximize their exposure to light sources lining the inside of the Reactor."

Inside the reactor, the algae absorbs the carbon dioxide and in the process creates a biomass, essentially dried algae. In the oceans, dried algae has a crucial role: It sinks to the bottom of the ocean and creates food for microorganisms. The company says the algae biomass can then be "harvested and processed to create fuel, oils, nutrient-rich high-protein food sources, fertilizers, plastics, cosmetics, and more."

The Hypergiant team claims the device is 400 times more effective than trees at carbon sequestration. 

"With the first generation Eos, we have precise control of every aspect of the algae's environment and life cycle," Ben Lamm, CEO and founder, tells Fast Company. "It's a photobioreactor, but it's also an experimentation platform. We'll be using this platform to better understand the environment that best suits biomass production under controlled circumstances, so that we can better understand how to design reactors for the variety of environmental conditions we're going to encounter in the wild."

The company has a local vision for the biogenerators. Rather than (at least at first) a field of the algae boxes in an energy grid, Hypergiant envisions HVAC units, close to exhaust and industrial pipes, breathing in the carbon dioxide from a office building.

According to the International Energy Agency, buildings and building construction account for 36 percent of global final energy consumption and nearly 40 percent of the world's total direct and indirect CO2 emissions.

But a prototype is still just a prototype, and Libby says the company has no plans to start selling quite yet. The next step, in spring 2020, will be to make the design for the algae boxes open-source and see what the world will make of them.

End Quote


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Re: [DIYbio] Re: Climate change solutions?

Wow Algacraft looks cool! Submit it to the AirMiners index, http://airminers.org

Also, click "Join Community" to join AirMiners Slack, the world's largest community of scientists, engineers, and entrepreneurs mining carbon from the air.

Cheers,
Tito


Sent with ProtonMail Secure Email.

‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Monday, October 28, 2019 2:36 AM, Ravasz <ravaszmeister@gmail.com> wrote:

This thread is from last year...

Since then we also formed an alga biotech startup: www.algacraft.com

We are currently being funded by the Edinburgh Centre for Carbon Innovation and hope to build bioreactors that that can mitigate the carbon output of other industries.
Our idea is too hook our systems up to the flue gas of power plants, cement factories and similar, and use the CO2 rich gas to grow algae even more rapidly than they would with plain old air.
If anyone is more interested in this, do not hesitate to write.

Cheers,
Mate


On Sunday, 27 October 2019 21:33:24 UTC, Jonathan Cline wrote:


On Friday, September 21, 2018 at 11:48:57 AM UTC-7, Tito 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



Quote

Hypergiant Industries wants to use algae boxes to solve the problem.

...

The prototype bioreactor is 3' x 3' x 3', and holds 55 gallons of water and algae. "Algae wants CO2 and light," the company explains on its website. "The light can be from the sun, or in this case, artificial light. The algae and water are pumped through a series of tubes to maximize their exposure to light sources lining the inside of the Reactor."

Inside the reactor, the algae absorbs the carbon dioxide and in the process creates a biomass, essentially dried algae. In the oceans, dried algae has a crucial role: It sinks to the bottom of the ocean and creates food for microorganisms. The company says the algae biomass can then be "harvested and processed to create fuel, oils, nutrient-rich high-protein food sources, fertilizers, plastics, cosmetics, and more."

The Hypergiant team claims the device is 400 times more effective than trees at carbon sequestration. 

"With the first generation Eos, we have precise control of every aspect of the algae's environment and life cycle," Ben Lamm, CEO and founder, tells Fast Company. "It's a photobioreactor, but it's also an experimentation platform. We'll be using this platform to better understand the environment that best suits biomass production under controlled circumstances, so that we can better understand how to design reactors for the variety of environmental conditions we're going to encounter in the wild."

The company has a local vision for the biogenerators. Rather than (at least at first) a field of the algae boxes in an energy grid, Hypergiant envisions HVAC units, close to exhaust and industrial pipes, breathing in the carbon dioxide from a office building.

According to the International Energy Agency, buildings and building construction account for 36 percent of global final energy consumption and nearly 40 percent of the world's total direct and indirect CO2 emissions.

But a prototype is still just a prototype, and Libby says the company has no plans to start selling quite yet. The next step, in spring 2020, will be to make the design for the algae boxes open-source and see what the world will make of them.

End Quote


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[DIYbio] Re: Climate change solutions?

This thread is from last year...

Since then we also formed an alga biotech startup: www.algacraft.com

We are currently being funded by the Edinburgh Centre for Carbon Innovation and hope to build bioreactors that that can mitigate the carbon output of other industries.
Our idea is too hook our systems up to the flue gas of power plants, cement factories and similar, and use the CO2 rich gas to grow algae even more rapidly than they would with plain old air.
If anyone is more interested in this, do not hesitate to write.

Cheers,
Mate


On Sunday, 27 October 2019 21:33:24 UTC, Jonathan Cline wrote:


On Friday, September 21, 2018 at 11:48:57 AM UTC-7, Tito 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



Quote

Hypergiant Industries wants to use algae boxes to solve the problem.

...

The prototype bioreactor is 3' x 3' x 3', and holds 55 gallons of water and algae. "Algae wants CO2 and light," the company explains on its website. "The light can be from the sun, or in this case, artificial light. The algae and water are pumped through a series of tubes to maximize their exposure to light sources lining the inside of the Reactor."

Inside the reactor, the algae absorbs the carbon dioxide and in the process creates a biomass, essentially dried algae. In the oceans, dried algae has a crucial role: It sinks to the bottom of the ocean and creates food for microorganisms. The company says the algae biomass can then be "harvested and processed to create fuel, oils, nutrient-rich high-protein food sources, fertilizers, plastics, cosmetics, and more."

The Hypergiant team claims the device is 400 times more effective than trees at carbon sequestration. 

"With the first generation Eos, we have precise control of every aspect of the algae's environment and life cycle," Ben Lamm, CEO and founder, tells Fast Company. "It's a photobioreactor, but it's also an experimentation platform. We'll be using this platform to better understand the environment that best suits biomass production under controlled circumstances, so that we can better understand how to design reactors for the variety of environmental conditions we're going to encounter in the wild."

The company has a local vision for the biogenerators. Rather than (at least at first) a field of the algae boxes in an energy grid, Hypergiant envisions HVAC units, close to exhaust and industrial pipes, breathing in the carbon dioxide from a office building.

According to the International Energy Agency, buildings and building construction account for 36 percent of global final energy consumption and nearly 40 percent of the world's total direct and indirect CO2 emissions.

But a prototype is still just a prototype, and Libby says the company has no plans to start selling quite yet. The next step, in spring 2020, will be to make the design for the algae boxes open-source and see what the world will make of them.

End Quote

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[DIYbio] Re: Climate change solutions?



On Friday, September 21, 2018 at 11:48:57 AM UTC-7, Tito 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



Quote

Hypergiant Industries wants to use algae boxes to solve the problem.

...

The prototype bioreactor is 3' x 3' x 3', and holds 55 gallons of water and algae. "Algae wants CO2 and light," the company explains on its website. "The light can be from the sun, or in this case, artificial light. The algae and water are pumped through a series of tubes to maximize their exposure to light sources lining the inside of the Reactor."

Inside the reactor, the algae absorbs the carbon dioxide and in the process creates a biomass, essentially dried algae. In the oceans, dried algae has a crucial role: It sinks to the bottom of the ocean and creates food for microorganisms. The company says the algae biomass can then be "harvested and processed to create fuel, oils, nutrient-rich high-protein food sources, fertilizers, plastics, cosmetics, and more."

The Hypergiant team claims the device is 400 times more effective than trees at carbon sequestration. 

"With the first generation Eos, we have precise control of every aspect of the algae's environment and life cycle," Ben Lamm, CEO and founder, tells Fast Company. "It's a photobioreactor, but it's also an experimentation platform. We'll be using this platform to better understand the environment that best suits biomass production under controlled circumstances, so that we can better understand how to design reactors for the variety of environmental conditions we're going to encounter in the wild."

The company has a local vision for the biogenerators. Rather than (at least at first) a field of the algae boxes in an energy grid, Hypergiant envisions HVAC units, close to exhaust and industrial pipes, breathing in the carbon dioxide from a office building.

According to the International Energy Agency, buildings and building construction account for 36 percent of global final energy consumption and nearly 40 percent of the world's total direct and indirect CO2 emissions.

But a prototype is still just a prototype, and Libby says the company has no plans to start selling quite yet. The next step, in spring 2020, will be to make the design for the algae boxes open-source and see what the world will make of them.

End Quote

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[DIYbio] Centrifuge safety PSA

OK, I know a lot of you trained and skilled in lab work might be thinking "what an idiot" but I thought I'd share a safety PSA on centrifuges since not everyone in this space has formal training in lab equipment.

I have a cheap $100 centrifuge at 10k rpm to do ethanol extraction on and it worked great. Yes, I read the manual and I also used a balance tube and haven't had a problem using basically the exact same protocol for a while. Like most accidents this happened since I got too comfortable in my routine.

Today I decided to switch up the ethanol content in the first spin to possibly improve precipitation. So this obviously changed the density and weight of the sample but I used the same standardized balance tube I have been using. I think the sample vial may have been too full as well. When the oscillation sounds started from the centrifuge I knew something was up and while I was making sure I wasn't  just hearing things the plastic rotor spun off into the centrifuge cover. Luckily it was plastic and only had two tubes and the cover (mostly) held taking away the momentum so only the rotor and shredded vials fell out. But anyway I was lucky I only lost a cheap centrifuge and wasn't injured.

So boys and girls remember to weigh your samples and balance tubes to make sure the opposite vials are always about 0.1g or less different in weight. I would hate to hear about some 16 year old killing themselves with the same mistake.

Some good links:
http://media.clemson.edu/research/safety/centrifuges.pdf
https://ehs.umass.edu/sites/default/files/Fact%20Sheet%20Centrifuge%20Safety.pdf

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Re: [DIYbio] Announcing DIYbiosphere -- connecting DIYbio activities worldwide

Hi Jason,
Can we list services available there? I'd like to advertise my Focused Ion Beam system for nano milling and imaging. I need to figure out pricing that would be DIY friendly, but I'm hoping to attract people wanting micro/nanofluidic masters for molding replica chips. Imaging is easy, and produces images with resolution akin to scanning electron microscopy (SEM)(albeit the sample is eroded/destroyed in the process). 

On Sat, Mar 17, 2018, 7:05 AM Jason Bobe <jasonbobe@gmail.com> wrote:

With significant growth in activities globally, our /local page has strained to keep up and simply is not a great representation of the the larger community. So we're happy to unveil this alpha system at sphere.diybio.org. You can get involved in shaping it.


Our aim with DIYbiosphere is to make it easier for the community to share structured information about projects and organizations. It's a venue for community members to help raise awareness about opportunities to get involved in various activities and to provide those activities with context across the larger movement.


By adopting Github as the backend platform and using simple markdown-based entries, we hope this approach is a convenient way for members of the community to collaborate on the development of this shared information resource.


We hope you'll check out the site.  There you'll find information about:

  • community labs
  • projects
  • incubators
  • start-ups
  • networks
  • events
  • local groups
  • other (for the misfits)

Is your project or organization represented? If you feel something is missing or incorrect, we invite you to contribute! Social commentator Jenny Reardon has noted that we live in an era in which: "Nothing endures; all is 'in-formation.'"


As such, we'll need many hands to help shape the formation of this community over time!


And while it's a bit recursive, this project does have it's own project page on DIYbiosphere. 🙂


Jason

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



On Tue, Oct 15, 2019, 8:14 AM AdrianMolecule <buzzwordy@gmail.com> wrote:

Hi James,



Basically I wanted something that can be as granular that can be used for a simulator or an automated lab directly or could be used for a high level paper.

Isn't that already supported in BioCoder?

It's using the Ontology idea (describes the structure in an XML) 

Eww, I much orefer writing C++ than XML.

where the operations (steps) can be added to a global repository

Isn't that just including an existing C file using BioCoder?

I am considering uploading it

I'll take a look if you post the full URL, hopefully you're using GIT for development version control.

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Re: [DIYbio] Re: Free of cost plasmid vector



On Mon, Oct 14, 2019, 10:12 AM AdrianMolecule <buzzwordy@gmail.com> wrote:
Hi Tom,

Odin is quite cheap once you order a larger quantity but they charge you an extra 30$ for delivery which becomes hefty.

I ordered about $200 worth of products the first time, paid $25 shipping for a huge box full of stuff. Ordered a gel box later, paid $15 shipping. Ordered plasmids later, shipping was free (probably just a promotion).

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Re: [DIYbio] Free of cost plasmid vector



On Mon, Oct 14, 2019, 10:12 AM AdrianMolecule <buzzwordy@gmail.com> wrote:
They are pretty slow to reply or give you credit so don't count on that.

My experience has been far from slow. I get my orders in a few days to a week max. Shipping has always been within reason for a given order's weight.

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

Hi Adrian,  this looks like a good start.   I'm creating a laboratory robot that executes instructions.  I've been playing around with a few idea's on how to control my robot.  I don't know If I want to use XML, JSON, or my own protocol. Right now I'm using my own protocol attached to the comment section of gCode to hold other commands that is processed by the gCode sender. 


My current protocol works as follows:

DEVICE - ACTION - VERIFY - RECORD 




On Oct 15, 2019, at 11:14 AM, AdrianMolecule <buzzwordy@gmail.com> wrote:

Hi James,



Basically I wanted something that can be as granular that can be used for a simulator or an automated lab directly or could be used for a high level paper.

It's using the Ontology idea (describes the structure in an XML)  where the operations (steps) can be added to a global repository edited with an open source editor called 

so they can be extended yet standardized. By using a tree one can collapse lower level nodes into more high level protocol.
I am considering uploading it on my bio club. URL is specyal.com 
Here is a test screenshot.

Cheers,
Adrian



<wetprotocol.png>



On Monday, October 14, 2019 at 1:56:01 PM UTC-4, S James Parsons Jr wrote:
Adrian,

Do you have a link for your bio code language? 


On Oct 14, 2019, at 1:25 PM, AdrianMolecule <buzz...@gmail.com> wrote:

I looked at BioCoder and based on my needs I found it insufficient. I started to develop a new standard and interface and I worked on it for several good months until I got a working beta.
I put it on hold as I was more involved with other research but I'm looking forward to complete it. If you are still interested, I would e happy to engage some form of collaboration.


Cheers,
Adrian


On Tuesday, December 8, 2009 at 7:26:51 AM UTC-5, 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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<wetprotocol.png>

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

Hi James,



Basically I wanted something that can be as granular that can be used for a simulator or an automated lab directly or could be used for a high level paper.

It's using the Ontology idea (describes the structure in an XML)  where the operations (steps) can be added to a global repository edited with an open source editor called 

https://protege.stanford.edu 
so they can be extended yet standardized. By using a tree one can collapse lower level nodes into more high level protocol.
I am considering uploading it on my bio club. URL is specyal.com 
Here is a test screenshot.

Cheers,
Adrian



wetprotocol.png



On Monday, October 14, 2019 at 1:56:01 PM UTC-4, S James Parsons Jr wrote:
Adrian,

Do you have a link for your bio code language? 


On Oct 14, 2019, at 1:25 PM, AdrianMolecule <buzz...@gmail.com> wrote:

I looked at BioCoder and based on my needs I found it insufficient. I started to develop a new standard and interface and I worked on it for several good months until I got a working beta.
I put it on hold as I was more involved with other research but I'm looking forward to complete it. If you are still interested, I would e happy to engage some form of collaboration.


Cheers,
Adrian


On Tuesday, December 8, 2009 at 7:26:51 AM UTC-5, 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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