ros86

Cradle (https://cradle.bio) | Scientific Software Engineer | Amsterdam | Onsite | Full-time

We're an AI platform for protein engineering (customers include Novo Nordisk, J&J, Grifols). We run our own wet lab in Amsterdam to generate training data for our ML models and to build the automation playbook we share openly with the field. We're hiring a software engineer to work embedded with our bioengineering team. You'd build things like: computer vision pipelines for colony picking, interfaces for lab automation workcells, integrations between lab instruments and Benchling. Python, APIs, databases, some frontend.

No PhD or biotech background needed. You'll pick up the biology. We care about solid engineering skills and curiosity about working at the intersection of software and hardware.

Apply: https://jobs.ashbyhq.com/cradlebio/7a4f7d2d-714e-4c01-84bb-9...

Nice idea! (and very soon you have 1000s of startup ideas ;-))

My point is not about having the cheapest solution. I just don't trust anyone else with my genomic information, even if they say it's anonymous. (I'm a biotech engineer, from Europe; maybe that explains my reservation ;-))

At some point, I would love to setup something like this but then completely local and open-source. This could e.g. include a sequencing kit (Nanopore MinION sequencer (<$ 1,000) plus necessary consumables), protocols, and in silico workflows for basecalling, SNP calling, and interpretation.

I can recommend checking out https://openepaperlink.de/. It's a project to repurpose e-ink electronic shelf labels (in various sizes, ranging from 1.54" to 7.4"). I have been playing around with it the last few weeks and it's a lot of fun! The community around this is very active on Discord.

Yeah, good point - don't know. When I tried I actually did get a (personal?) email saying that it didn't match closely enough. After uploading another sample (based on a different text) it went through.

I like your idea of just training on the consent text! That wasn't the case when I tried it as you needed around 3h (optimally) of training data.

When I tried this service previously, you had to read (out loud) something saying that you were giving consent.

Some wonderful music from Bach, his Weihnachtsoratorium (2.5 hours): https://open.spotify.com/album/48eINR6FEINQEvDTrbig9X

There are indeed a few practical applications. Next to Berkely lights, there is e.g. the LabChip from PerkinElmer that separates DNA and proteins. I had hoped that there would be many more examples by now. Most presentations that I see about microfluids still go in a lot of detail on how difficult it is to make. This hasn't really changed over the last decade, which signals to me we still need quite some innovation to make this mainstream.

If you want to play around with digital microfluids at home, check out the OpenDrop from gaudi.ch (http://www.gaudi.ch/OpenDrop/). I haven't played around with it yet, as I haven't found a practical use of this.

In the biotech field is indeed quite common to refer to microbes as bugs. Thanks for reminding that this is ambiguous outside the field!

Just a random thought (lived both in the US and in the EU): could it be that US ovens are more often gas ovens while in the EU it's mostly electric? (might be easier to get higher temperatures with gas).

Couldn't find statistics on this with a quick search...

Another useful resource is hadolint (https://github.com/hadolint/hadolint), which not only gives additional recommendations, but also a way to enforce this.

Are you interested in salary ranges in the US and/or NL?

What about some MOOCS? There are plenty that will introduce you to this area.

I think this depends a bit on the area. I work in the field of metabolic engineering (i.e. engineering microbes to make new products). When I worked at a biotech company in the Bay Area, I had a pretty decent salary, while still a bit lower than software engineers. Right now, I live in the Netherlands and my guess is that the discrepancy is a big larger here.

I don't think so, as alcohol is not degraded via P450 enzymes..

This isn't a scientific study of course, but still I do miss the negative reference (i.e. without any detergent). Additionally, it would be nice to quantify the 'cleanness' of a run (perhaps weighing the dishes before and after?). Hmm, perhaps we should take this study to the next level ;-).

I'm wondering whether that's indeed the case. It seems that at least some genotype has been identified to cause such a phenotype (https://science.sciencemag.org/content/346/6213/1084). If you know what to look for it would just be a couple of bucks to Sanger sequence it. (Then you don't even have to sequence it by e.g. Illumina, which would still be just a couple of hundred bucks per batch). I don't know what margins they get for these kind of products, but I guess a recall will be quite expensive as well.

Does anyone know why sequencing is not used to QC such seeds before releasing them?

I see a ton of founders and funders with zero biology background thinking that they have the vision and can just hire biology expertise.

Genuinely curious about your data here. The two first companies mentioned in the article (Zymergen and Gingko) have founders with biology background. Many other companies I know as well.

You would never use CRISPR if you had the option of using Cre. I’ve made several stable transgenic animal lines using Tol2 transgenisis, which is much higher efficiency, too.

That probably depends on the organism you're working with. E.g. with baker's yeast, my preference would definitely be CRISPR/Cas9 instead of cre recombinase (see e.g. https://academic.oup.com/femsyr/article/15/2/fou004/534426 ).

You're right that you don't need CRISPR for genome engineering of S. cerevisiae (baker's yeast) or E. coli.

However, having worked with both prokaryotes and eukaryotes it definitely makes life easier. During my PhD (about metabolic engineering of S. cerevisiae) CRISPR started to get traction. Before I could incorporate one change at a time. Using CRISPR/Cas9 I could do up to 6 (at different places). That's a big deal!

I also PoC'ed CRISPR in a bacterium (C. glutamicum). Also there it opened up new avenues.

Wow. That's pretty cool! Bummer that nothing comes up when you search for logosear.?ch ;-).

* substrate level phosphorylation (SLP) and

* electron transport phosphorylation (ETP)