Backyard Biosynth

Berex, thanks for the breakdown. In actuality, we have a pretty low price with IDT because of how much we buy from them.

Most importantly, we also have a nice courier delivery system that guarantees a less-than-24 hour turnaround between typing the sequences into their website and having it appear on our benches; this is again free because of the large amount of DNA that our lab and Stanford buys from them!

We could go cheaper (to plate rates, $0.09-0.10/base) but we’d incur a delay of about a week from typing in your designs and the DNA getting to us. Your e-mail does make me think whether we should somehow set up an ‘eterna’-specific quote – if you or other garage bioscientists end up purchasing stuff from IDT, let me know!

Thanks for the quick response! :slight_smile:

Ahh so you’d go for the same Day oligo’s. Which retails for 60c per nt, but obviously you are getting it less than that.

Thank you for the clarification. Was a bit scary when I thought I found better pricing than your current pricing structure.

It would be awesome to have an ‘eterna’ specific quote. You’d just have to be aware that you’d have to get at least 3 quotes. A US one, a AUS one and a NZ one.
But in general, if someone did setup a garage lab in the States, that would be the best and cheapest option at 18c per nt. Would require an amount of their time though. I’m not aware of how long it takes for each design to be processed.

Maybe there could be an additional eterna page. Where people could pay for their designs to be synthesized, and an additonal fee for it to be processed? At the moment, it’d be like $20 per design, but with the falling sequencing costs, could easily fall. When it finally hits the $5 price point, then a lot more synthesis would be able to be subsidised possibly. :slight_smile:

List of some DNA Sequencing facilities
http://www.nucleics.com/DNA_sequencin…

According to openwetware, this is what is available at Stanford.
I’m assuming this is also what the Das lab are using.
DNA Sequencer ABI 3100, Sequence Detector ABI 7900HT, Spectrophotometer ND-1000
http://openwetware.org/wiki/Stanford_…

Das Lab uses 5’ T7 Promoter (20nts), 3’ tail Primer (20nts), and a 5’ buffer (15nts). Total 55nts are needed to be added to the sequence.

Revision for Branches is 210nts.
@18c is $37.80 USD
@12c is $25.20 USD

@rhiju quick question, what books would you recommend? In general books and some extensive lab prep books.

Hello rhiju,

Regarding your comment:“We could go cheaper (to plate rates, $0.09-0.10/base) but we’d incur a delay of about a week from typing in your designs and the DNA getting to us”.

Would going to the cheaper plate rate reduce the cost enough to allow for more player’s designs to be synthesized per round? And, if so, how many?

I understand that it would mean waiting two weeks (instead of one) for the results.

Regards,
merryskies

Yes, if we’d wait 2 weeks instead of one we could certainly have 16 made per round, and perhaps 24 … if there’s a consensus among active players that they prefer this route, then we can take it. That cycle could also allow for more time to consider and debate new results before diving into the next cycle!

@Berex, not sure what lab prep books are good – I learned through hands-on teaching from a great mentor (Rick Russell, now a professor at U.T. Austin) and by checking his notebooks.

Also, @Berex, the devs have debated opening up the EteRNA pipeline to allow ‘pay-for-play’. The main thing we worry about is that EteRNA might start being considered a ‘service’ rather than what it is: a cutting-edge scientific and social project that is tackling (and, by all the current evidence, *solving*) some fundamental problems in biology and bioengineering.

At the same time, we are working overtime to apply for grants to help us keep EteRNA going. It has sometimes been a tough sell because government agencies are facing tighter budgets and are getting even more conservative about what they will fund.

Obviously if you or others have leads for agencies, private foundations, donors or other funding sources, we’d love to hear about them. We’re setting up gift accounts to collect donations for the EteRNA project, but we don’t want to ask players to contribute money, since they are already contributing an enormous amount just by playing and posting.

Hi rhiju,

Regarding your response: “Yes, if we’d wait 2 weeks instead of one we could certainly have 16 made per round, and perhaps 24 … if there’s a consensus among active players that they prefer this route, then we can take it. That cycle could also allow for more time to consider and debate new results before diving into the next cycle!”

It’s ok with me if my designs are not synthesized. I can still play and learn from the synthesis results. But the option of having a larger number of player’s designs synthesized per round is very appealing for several reasons.

I am aware that major changes to the voting system are planned to be implemented soon. Perhaps sometime after the new system has been introduced and tested, then this topic could be put forth to the players for further discussion.

Thanks for your response,
merryskies

Hi rhiju,

Hmm, well if we could do 24 every 2 weeks, might be better overall. Although a mix of same day and normal plates might be better. That way you have some samples to work on while waiting for the rest, although of course that will most probably require a bit more administration. But that would allow the results to trickle out as they get processed, so the in-between period will seem less obvious.
You could get the players to vote… or the eterna team could just make an executive decision as to what way they want to go.

Hehe we all arent that lucky to have access to a practical mentor and his notebooks. But if you ever come across any good books, please let me know. :wink:

I was thinking along the lines of ‘pay-for-service.’ Like you’d keep everything as it is right now, but for those willing to pay, then their designs would also join the synthesis queue as additional secondary priority. Main priority is to process the main eterna designs.
Thats why I added the caveat, who knows who will take it up. It would be somewhat simpler if a player started up their own independent lab for the service, but there isn’t enough documentation to see how viable that is yet.
Who knows the ‘pay-for-service’ might even be able to subsidise the main eterna synthesis program. Now that would be cool :slight_smile:

I second Merry’s point, I do feel strongly that the limitation of 8 slots/week is pretty much constraining the number of super-active designers to around a dozen or so, and that’s not something that even a perfect voting system would “fix”. It usually takes several iterative designs for people to test out their ideas fully enough that they gain some intuition rather than an isolated one shot in the dark, something that is just difficult with so few slots.

Perhaps the two-week turnaround could be compensated by staggering two, independent design challenges separated by one week? Just a thought. I think that the self-sustaining “critical mass” in terms of the number of super-active lab participants has not been reached yet. More discussion of designs and feedback certainly would not be a bad thing - if too many people are “throwing together” a design at the last minute to meet an arbitrary deadline it dilutes the cool stuff learned. . .

http://cshlpress.com/default.tpl?cart…

I haven’t actually read this book but the TOC and reviews look good. Nothing can substitute for having access to an actual molecular biologist to show you the ropes, of course. But even then, most will not be super-familiar with RNA specific concerns (like the need for special RNAse free chemicals, water, lab supplies etc), hence the need for a book like this.

Cheers,
Alan

@rhiju

How are we going with the procedures and the list of consumables?
Also as a far off idea, would your lab be able to sell consumables?

@berex – I don’t think we’re allowed to sell consumables, unfortunately. I like the idea of having those interested start looking for good prices for consumables and compile answers in a central location.

We made a list of stuff here: Google Spreadsheet with Consumables

Perhaps you could make a copy and start filling in additional notes/questions? I and others can also check in with our current serial numbers (this might take a few weeks since we’re getting eterna experiments completely back on track after a few weeks of experimental delays).

Also,
http://www.amazon.com/Handbook-RNA-Bi…

You don’t need to ask, some of us are already passionate about the project’s premise. Please let me know when the gift accounts become available to donate into.

Thank you.

I second Berex’s comment - please let us know where we can donate to help with the project :slight_smile:

Thanks again for the support … we just set up an EteRNA Research Fund that allows donations to the project that we will use for syntheses. We put a little blurb in ‘about eterna’. The link to the actual ‘giving’ website is on there as well [Direct link here.]

Again, I want to emphasize that is not our expectation that players donate money to keep EteRNA going --you are already contributing greatly by playing and posting!