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Consider working on genomics

claymcleod.dev

231–240 of 299 posts

Re: Consider working on genomics

#231

Earlier quoted context omitted.

Hmm as an ex-Broad employee (and now in another genomics center), what did you find really toxic about the Broad? FWIW, I really loved Broad the people, my direct line manager and co-workers. The management was horrible and the management at DSP (not the line folks/managers) were the worst.

Since my post was upvoted a tad... I'll give more feedback about the Broad. When I joined, it was running really like an academic center. Like literally in my lab, if I wanted to go into the lab and pipet and do library prep, the wet lab scientist would teach me and vice versa. It was lit. a place where anybody could pivot their career to anything. We worked on NIAID/NIH grants and went to conferences even as SWE's a…

This is a great read. Thanks for the information. What you originally described is basically my dream job: software engineers working alongside scientists and engineers, where the software engineers become domain knowledgeable if not experts in certain areas.

I had a job similar to that at a similar places (actually places), but I ended up leaving because I was a one man team and got burnt out. Writing software for scientific purposes and true R&D is very fun and interesting, and I think there is a lot of untapped potential for doing some interesting things there. But there is a balance between the wild west, then what your first described, and then what you later described. Keeping things organized enough to not be chaos but loose enough to not get siloed.

Re: Consider working on genomics

#232

Warning sign. You can't even select the text on the site.

Don't know why HN still have down votes. Down voters are among the most stupid people on the planet. The site changed you stupid f*ckers.

https://web.archive.org/web/20221119162905/https://claymcleo...

Re: Consider working on genomics

#233
People seem to be responding to the pitch in a different way to how it is intended. It's entirely a pitch that there is a need for this. So if you aren't highly motivated by doing something valuable and useful, this isn't for you.

For me, working in the field is worth doing because I have come to a place in my life where I value doing something useful more than I value other things. You really can't put a value on being able to get up every single day and know that you are actually doing something good for the world that day. And getting paid, while less than your absolute highest potential, still a really good salary by comparison to most of society.

Plus you do get a lot of freedom and autonomy, and exposure to absolutely fascinating research and biology, and if you want to dabble in academia, it's surprisingly easy if you have a supportive group.

Re: Consider working on genomics

#234
post #114

Usually, scientific oriented companies or organizations have little regard for software as a domain, craft, etc. It’s just a thing that gets in the way, despite being vital. It’s almost just a utility to them rather than a differentiator and active component of the advanced work going on. For example, the Broad Institute is super interesting, but having applied there several times, they are esoteric, to say the least…

I live next to Broad's offices and see people leaving/entering the office at odd hours on Saturday and Sunday. That (and the fact that they pay about 75% what I made as a new grad) prevented me from ever applying there.

Re: Consider working on genomics

#235
post #114

Usually, scientific oriented companies or organizations have little regard for software as a domain, craft, etc. It’s just a thing that gets in the way, despite being vital. It’s almost just a utility to them rather than a differentiator and active component of the advanced work going on. For example, the Broad Institute is super interesting, but having applied there several times, they are esoteric, to say the least…

Current Broad SWE with 5 years’ tenure. Feel free to ask any questions.

I’m in the “bunch of software people together” department so it’s not as insular or PI driven as working in a lab.

I still mostly like the role but it has become more generic over the years as the department acquiesced to the working ways & programming languages of outside private funders.

Re: Consider working on genomics

#236

Earlier quoted context omitted.

Hmm as an ex-Broad employee (and now in another genomics center), what did you find really toxic about the Broad? FWIW, I really loved Broad the people, my direct line manager and co-workers. The management was horrible and the management at DSP (not the line folks/managers) were the worst.

Since my post was upvoted a tad... I'll give more feedback about the Broad. When I joined, it was running really like an academic center. Like literally in my lab, if I wanted to go into the lab and pipet and do library prep, the wet lab scientist would teach me and vice versa. It was lit. a place where anybody could pivot their career to anything. We worked on NIAID/NIH grants and went to conferences even as SWE's a…

Current DSPer since 2017 and broadly agree with OP.

Re: Consider working on genomics

#237
I am a founder of a startup (Octant - a16z backed) that has a small & growing software engineering and data science team (see the Nov who's hiring post). Some thoughts on some of the discussion here:

1. Compensation – In academia, you will likely take a big salary hit (much of this is discussed). There are a few exceptions like newer institutes like Chan Zuckerberg, Arc Institute, etc that are paying much more competitive salaries though. In well-backed startups and larger biotech/pharma, cash is likely equal (or often more) to software comps elsewhere – the bigger hit you take is usually in equity – no one has been able to match FAANG on total comp with RSUs in the mix. Startups can provide options, but it's not very fungible. For example, we benchmark salary on comparable A16Z pre-public non-bio companies use as well as stats from the broader SV SWE salary datasets. There are startups in bio that pay even higher to lure talent.

2. Research vs Product – Over the last decade, there are a bunch of highly profitable tech companies and large funded new startups (e.g., Calico, Altos, Deepmind, etc) trying to take on bio as the next frontier. These places (like those named in the blog post) pay very competitively. Thus far, these places often turn into a big mess because it becomes hard to deliver products (like drugs) in a mostly academic-y atmosphere. I don't think anyone has really cracked this nut yet (or if it's even possible).

2. Culture of SW importance – In a lot of startups these days, this has changed quite a bit over the last 5 years. Lots of software & data science first startups. I think in the larger pharma/biotech though, the centrality of drug discovery takes a lot more oxygen than software, which are often thought of as innovation bets and different places have different levels of long term commitment.

3. I think one important difference is the type of company. There are many software companies in healthcare/bio that are software products supporting R&D, healthcare, drug development etc. Many of them have done quite well (e.g., Benchling, Komodo Health etc in A16Z portfolio alone) and are basically just software companies that just happen to be in bio. There are many others like most drug discovery companies (like us) where software and data science is enabling, but the product is often ultimately drugs. For a lot of SWEs, this becomes problematic because people often want the satisfaction of having externally deployed software products to push into the world. The heroes and heroines of this world are often drug hunters over tool developers, and this has cultural consequences as well. Some people are really good with this (getting a lot of satisfaction out of enabling new drugs to treat serious disease), but a lot of folks aren't.

4. The current biotech crash has been bigger and more sustained than the tech crash thus far. High interest rates impact this industry much more than others, because revenue on new drugs, which drive a large part of the industry usually take a decade or more to develop before revenues are flowing. This is less of an issue in healthtech companies that can often deploy much more quickly (90% of healthcare costs are not drugs).

5. Finally, there are many happy SWEs and DS in bio at companies that value software and can build good careers in it building products that ultimately help human health in new ways. It's a pretty amazing time in biology, with a suite of new technologies to read, interpret, write, edit, deploy molecules/DNA/cells that are really unlocking many of the mysteries of human diseases. I feel lucky every day we get to continue building in this space.

Re: Consider working on genomics

#238
post #114

Usually, scientific oriented companies or organizations have little regard for software as a domain, craft, etc. It’s just a thing that gets in the way, despite being vital. It’s almost just a utility to them rather than a differentiator and active component of the advanced work going on. For example, the Broad Institute is super interesting, but having applied there several times, they are esoteric, to say the least…

> Good luck trying to use a functional-first language

Good luck trying to use a functional-first language at any company (be in bioinformatics or otherwise).

Re: Consider working on genomics

#239

Earlier quoted context omitted.

This please. I would love to start working on (or create from scratch) some software that helps people in that field.

Creating pipelines is still a problem. Typically one needs to call a bunch of other tools in order to get to the final result. There could be map/reduce behavior in the middle where chunks of data are processed in parallel in order to gain speed. And you need some kind of data management/tracking as well (putting samples in groups, ingesting raw data, exporting results). And sane monitoring especially if something br…

I also found the quality & proliferation of data pipeline tools to be baffling. Somehow always more painful to put these together than it seemed like it ought to be.

At one point we wrote an internal tool (I think lots of organizations do this, since all the 100s of existing tools somehow don't fit, so you invent #101) and while it was tremendously satisfying getting batch jobs with 1000's of cpu's churning away, that kind of data infrastructure needs to be standardized. I think some companies are doing this, e.g. saw a presentation about Arvados/Curii that seemed interesting (but haven't used it so not sure). Maybe CWL will turn out to be the way forward here?

Re: Consider working on genomics

#240

Earlier quoted context omitted.

> As with most other kinds of software, the biologists should be treated as customers (or trained up to be skilled-enough engineers), as it is done in other disciplines. To create good accounting software you also wouldn't propose to have the accountant write the initial version of the software, would you? Accounting is a bit different, because it has already been invented. There are standards and best practices for…

Accounting is not a static thing, and is also constantly changing with new legislation and financial instruments popping up. Most bioinformatics tasks nowadays are not any more "creative" in their research. Specifically in the last few years a good chunk of the research is just okayish application of ML research to their field of research. For many specific problem sets in the natural science informatics disciplines,…

There is a good chunk of research like that, but there is also a good chunk of research where the "biologist as a customer" model does not work. In research like that, it's the job of the person writing the software to figure out which biological problems they are trying to solve and how.
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