Consider working on genomics

Agreed that competition is good to have. There is also Sentieon and similar solutions which run on common hardware but are optimized.

Speaking of costs (both upfront and licensing), dragen imo is not expensive relative to sequencing costs (e.g. sequencers and flowcells). Surely it would be expensive to buy for occasional use.

By making parabricks free to use Nvidia tries to gain a market share I guess. In professional settings you still end up buying support and likely dedicated hardware (which is comparable in pricing). Good fit for the cloud and research environments that already have access to GPUs and/or are decoupled from actual sequencing.

https://github.com/TimothyStiles/poly

A large part of my project's community are devs that want to get into the field but can't tolerate the ridiculously low pay, laughably bad management, disrespect, and what amounts to 40+ years of technical debt that's endemic to biotech software.

I've had companies here in the Bay Area offer me 100K a year with a straight face. I've had companies during interview tell me they're looking for someone to help, "set up GitHub". I've seen job listings for low paid web dev positions require applicants to have PhDs.

The reality is that except for a growing handful of places management straight up won't know the difference between IT and software engineers. It's what I call the naive buyers problem.

The demand for software engineers in biotech is generated by naive buyers that don't know what they need, why they need it, or how to get it.

Benchling and Recursion Pharmaceuticals have reputations in the industry of paying, "standard software salaries". So do the research divisions at places like deepmind/microsoft/google but in my experience there's even new multi-billion dollar institutes where senior management has never even heard the term devops.

Most places advertise for "data scientist", positions or some analog, instead of software engineers. This is mostly because upper management has never met an actual practicing software engineer in a professional setting. Many come from academia where the culture and work requirements heavily disincentivize standard software engineering practices.

It's also not uncommon for a biotech company to either have a very under qualified CTO whose main programming experience is what they learned doing ML research like stuff during their PhD or not even have one at all which has huge downstream consequences.

This week a software engineer trying to make the switch to biotech actually DM'd me to ask why they were seeing a ton of data science / ML job positions but no software engineering / devops positions.

They were worried that these companies were trying to save on costs by forcing their data scientists to create infrastructure but it's actually worse than that. Most of these companies aren't even aware that there's supposed to be infrastructure.

Despite all of this the future is looking better and I'm starting to find new companies and positions that are well... reasonable. I learned about this thread from a friend at a party last night that works at one of these companies. There's a small, strong new wave of companies and developers out there pushing biotech software forward. Hopefully some (including myself) make it big while pushing the idea that better tech equals better biotech.

I disagree strongly however with the management's tech approach, the Broad cannot compete with the other companies in the Boston area in terms of comp. What worked in the past is smart people came to the Broad for the fun, autonomy and intellectual challenge over pay.

If you reduce people to just worker-bee's finishing CRUD tickets on an Agile board - you'll get efficiency for the 1st 2 years but you'll lose so much institutional/domain knowledge and collaboration; the PMs will get promoted in 1 year while projects on a 5 year timeframe get uber-delayed; the smart people will get bored and leave and even the good efficient engineers in the system will also leave for the better well paid tech jobs that Broad cannot compete with. I've seen it in every company who has run this playbook.

On that note :) I'm starting a forward-looking research lab at UofT to advance massive-scale (think petabytes) genetic analyses and am looking to find the right few individuals who have a similar vision. It's difficult to find passionate engineers with a solid CS and HPC background who are willing to meet halfway and work _together_ with biologists in getting the analysis right. Robert does this _very_ well, and that's why we recently co-wrote a landmark Nature paper: https://www.nature.com/articles/s41586-021-04332-2.

Job post: https://jobrxiv.org/job/university-of-toronto-27778-full-sta...