Science

Eh basically given up. They have no plans on lowering their fees to entry, so it's not like many labs can afford to go, when they could be spending resources on actual projects. There isn't really the goal of innovating in bioengineering anymore on the institutional level: that stopped years ago when the original MIT folks went to do their own things (like Ginkgo). It's now much more about putting on a very nice show, which gets funders, so they can do a better show. 

I'm working on the FreeGenes project (have for a while) on building another parts repository that is actually open source (iGEM simply doesn't use terms or conditions with their plasmid stocks, we're using the OpenMTA). It turns out it's actually really hard to build large quantities of parts: for about a year we messed around with in house cloning, and got pretty far, but now we're just ordering clonal DNA directly from Twist. I'm beginning to hit on toolkits that are generally useful by spreading out the number of suppliers we have rather than cleverness to clone hard things in house, so it's just taking a while. It's also just hard to scale the DNA design process.

The FreeGenes parts collections aren't out yet, but will be sooner or later. For now, if you want parts and are unaffiliated with an institution, you either know people, get them from the odin, or get affiliated. 

koeng
On Wednesday, April 10, 2019 at 8:08:00 AM UTC-7, Christopher Monaco wrote:

Hi all,

I'm getting ready to gear up our synbio efforts at my DIYbio space and was looking iGEM and their biological parts registry as routes to go. It seems really difficult to have acess to the tools they offer and I'm honestly not sure if there's even a community iGEM track anymore. Based on posts on this mailing list (the most recent of which are several years old), it looks like the DIYbio community has more or less given up hope of having a working relationship with these folks. Which is a real shame because closing off access to parts from the public does not seem like any way to further the mission of innovating bioengineering.

Anyway, that long intro is to ask what are people in this community doing when wanting to perform synthetic biology? Is there another parts respository out there other than the one controlled by iGEM? Do you just have the requisite parts synthesized? I guess the big question is how can someone unaffiliated with an institution do work in this field?

Will Greenleaf at Stanford had hacked Illumina sequencers as imaging platforms. Might be worth contacting him.

On Sat, Apr 27, 2019 at 9:07 AM Dakota Hamill <dko...@gmail.com> wrote:

This guy is cool.  A lot of people I know in sequencing mention his blog.  (I know next to nothing about NGS).  Maybe he'd give you a shoutout, maybe not. 

http://omicsomics.blogspot.com/

On Sat, Apr 27, 2019 at 11:57 AM Kaspar Emanuel <kaspar...@gmail.com> wrote:

Hi folks,

John is right, the campaign is only for writing software to allow people to drive the machines. You will be able to use the Micromanager interface and scripting capabilities to do whatever you want, including patented procedures, if you can get your hands on the consumables and if you aren't exploiting them commercially, but IANAL, just a software developer.

Looks like this will be a close call as to whether we will reach our funding goal, any suggestions on where else to post are very much appreciated.

Cheers,

Kaspar

On Thursday, April 25, 2019 at 3:05:18 PM UTC, John Griessen wrote:

On 4/24/19 10:23 PM, Abizar Lakdawalla wrote:
> any plan on getting the consumables for the HiSeq? They cost US$10ks per run if they are bought from Illumina.

My take on reading the https://wemakeit.com/projects/reseq-reuse-dna-sequencers pages is that
components will be developed for uses first and maybe some day allow open uses, but not really in conflict with Illumina's
patents, and so not using their consumables.  They did not say they were going to make the machines run as they did
when new.

Driving them as an automated microscope was first on the to do list.

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In an office park on a leafy side street in Mountain View, California, a few miles from the headquarters of Google and Facebook, NovoNutrients CEO David Tze is showing off a technology so powerful, it just might avert human civilization from its 200-year collision course with disaster.

Striding past humming electrolyzers separating water molecules into their component elements and liquid chromatographers analyzing the molecular components of samples, he stops before a fluorescent-lighted cylindrical water tank with tiny specks floating in it. "These are the only macroscopic organisms we have here," he says. "These are Artemia."

Artemia salina, that is, a crustacean found in brackish waters and better known by its common name, brine shrimp. If you've heard of brine shrimp, it's likely because, in 1964, a man named Harold von Braunhut began marketing them as a pet-cum-novelty toy under the brand name Sea-Monkeys.

The cutting-edge science I'm looking at is a 55-year-old children's amusement from the back of a comic book?

"Yes," Tze confirms. But, he adds, "we don't give them the official Sea-Monkey feed. They just get our product."

That product is Novomeal, a protein developed for use in aquaculture, and the Sea-Monkeys are proof of concept. Fish food for fish farms, basically. The key ingredient in the commercial feed formulations used in the farming of salmon, tuna, and other carnivorous species prized by consumers is something called fishmeal, a powder made from the ground-up bodies of tiny fish such as anchovies. ("Fishmeal is strangely named: It's meal made from a fish, but it also happens to be an important part of a meal for a fish," Tze says.) Novomeal, a nutritionally complete substitute for fishmeal, is made from the proteins of bacteria and other single-celled organisms, incubated in giant steel vessels akin to beer vats, called bioreactors. Feed is the biggest cost of fish farming, a $232 billion global industry, and, given that the output of the world's overexploited oceans continues to decline, it's only getting more expensive. The supply of bacteria, on the other hand, is effectively infinite, as long as you have the nutrients to feed them.

That part--the nutrients--is why this particular fish food could play such a meaningful role in determining the fate of the planet. What the bacteria that make up Novomeal eat is CO2. You know: carbon dioxide, the stuff that's been building up in the atmosphere since the start of the Industrial Revolution, trapping solar energy and turning the seas acidic. If you believe the U.N.'s Intergovernmental Panel on Climate Change--­or the U.S. Department of Defense, or the big petroleum companies--manmade global warming is a danger on par with no other, threatening to redraw coastlines, spark wars, imperil food and water supplies, alter weather patterns and marine currents, and displace hundreds of millions of people, all within our lifetimes. In the U.S., increasingly severe hurricane and wildfire seasons have already offered a preview of climate change's long-term effects; according to the IPCC, the world's economies must cut their carbon output in half by 2030 to avoid passing a critical threshold beyond which the consequences grow rapidly worse.

"The path to getting out of here," says synbio investor Vijay Pande, "is not as bleak as it may seem."

But if the need to curb carbon emissions is clear, how to do it without torpedoing the world's economy is anything but. Global energy demand is rising fast, and oil, coal, and gas continue to satisfy most of that need. As hundreds of millions of people in China, India, and other developing nations enter the middle class, they're demanding all the perquisites of the Western lifestyle, from hamburgers to new cars. Even if the electricity required to make all that stuff can be obtained from clean renewables, like wind and solar--and we're a long way from that--the production remains a dirty, carbon-intensive business. The plastic that's in everything from yogurt containers to carpet fibers is derived from fossil fuels, typically using energy also derived from fossil fuels. Cows raised for milk and meat have a carbon footprint comparable to that of automobiles. Even something as simple as growing rice can't be done without contributing to warming: Rice farming produces 13 percent of the world's methane, a potent greenhouse gas, because flooding the ground to make paddies brings dormant anaerobic bacteria roaring back to life. As long as more humans are eating more food and buying more stuff, getting a handle on climate change will be fiendishly difficult.

Or not, if David Tze has his say. What his company is constructing--along with others working similar angles in San Francisco and Berkeley and Skokie, Illinois--is nothing less than the infrastructure for an entirely new economy, one premised on producing food, energy, and material goods by sequestering harmful chemicals rather than by emitting them. It's an economy where we'll turn landfill into jet fuel, weave clothing out of spider silk, and make furniture out of mushrooms, all using primarily renewable power. "What we're doing has the potential to change not only the food system," Tze says, "but also the way other goods are manufactured."

On 4/24/19 10:23 PM, Abizar Lakdawalla wrote:
> any plan on getting the consumables for the HiSeq? They cost US$10ks per run if they are bought from Illumina.

My take on reading the https://wemakeit.com/projects/reseq-reuse-dna-sequencers pages is that
components will be developed for uses first and maybe some day allow open uses, but not really in conflict with Illumina's
patents, and so not using their consumables.  They did not say they were going to make the machines run as they did
when new.

Driving them as an automated microscope was first on the to do list.