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Consider working on genomics

372 pointsby clmcleodover 2 years ago

91 comments

lebovicover 2 years ago
I&#x27;m a software engineer who works on genomics. I see a lot of negativity in this thread, which mirrors my experience: in most places, you&#x27;ll be paid like a researcher with the respect of a lab assistant – unless you have a PhD and a postdoc.<p>That said, it&#x27;s possible find work that&#x27;s respected and pays well. Most of that kind of work is happening in the context of startups or freelancing. My favorite example of this is Robert Edgar: he&#x27;s a freelance computational biologist with over 100k citations who has made a living for the past 20 years by selling licenses to his bioinformatics software (<a href="https:&#x2F;&#x2F;scholar.google.com&#x2F;citations?user=RzVMRc0AAAAJ" rel="nofollow">https:&#x2F;&#x2F;scholar.google.com&#x2F;citations?user=RzVMRc0AAAAJ</a>).<p>To find those kinds of jobs, I&#x27;d try YC&#x27;s Work at a Startup, Flagship Pioneering&#x27;s portfolio companies, and emailing founders of companies that have a bioinformatics component (my email is in my profile!).<p>I think the issues with the field are because it&#x27;s a new and growing space. We do need better tooling, respect for engineering, and established best practices, but that seems to have been the case in the past for other domains that moved from research to industry – including software engineering itself.
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bmitcover 2 years ago
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.<p>For example, the Broad Institute is super interesting, but having applied there several times, they are esoteric, to say the least, in their hiring. They pay well below market, and their process is opaque and slow and sometimes downright non-communicative. They are also not really open to remote work, so you gotta move there and commute to the heart of Cambridge. Budgets are set by folks maybe a couple years out of a PhD program, who will also make technical decisions in terms of the software design (the latter an assumption given my experience in similar places).<p>These organizations are also pretty traditional in their selection of stacks. Good luck trying to use a functional-first language, aside from <i>maybe</i> Scala (usually lots of Java stacks), and be prepared to write lots of Python, the only language that exists to many scientists. I once saw a Python signature (function name and arguments) spill over 10-20 lines, in a file over 10,000 lines long. They had given up on another software stack because “it wasn’t working for them”.<p>This is all painting with broad strokes, of course. But I think scientific organizations that would embrace software as a major component of their technological and scientific development would do well. There’s a lot of opportunity.
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DonsDiscountGasover 2 years ago
I&#x27;ve worked on genomics, at the Broad. Can confirm there is a ton of toxicity. There&#x27;s also a lot of smart and great people, if you can find a team specifically dedicated to software I would recommend it. Also the pay is good...for a non-profit.<p>More broadly...shortages like this aren&#x27;t because SWEs just love ad-tracking and hate health improvements. People need to be willing to pay for these services (case in point; the jobs link for AWS has 3 links which appear unrelated to genomics, for Microsoft there are 2 for interns, and for Google its empty).<p>There are a lot of opportunities in biotech for SWEs, and many firms (though not all) really do respect the power of software. Worth looking around if you&#x27;re interested in the area.
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aWidebrantover 2 years ago
&quot;From my experience, what works incredibly well is a partnership between biologists and software engineers: the biologists first come up with the first concept of the tool, which is purely focused on ensuring good results. After this first iteration is completed, engineers then come in and rewrite the tool using modern engineering practices with things like speed and reliability in mind.&quot;<p>Like others have pointed out, this really makes the engineer&#x27;s end of the bargain sound like janitorial work. There&#x27;s no lack of fields where researchers and engineers both sit at the table from the beginning to pick which projects to pursue and how to implement them.
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whimsicalismover 2 years ago
Call me when non-tech fields learn to treat engineers as equal partners rather than disposable labor.<p>Academia? Yeah they&#x27;re going to be one of the last to realize, PIs don&#x27;t want to cede any power in their little fiefdom. Very familiar with the dynamics there.
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hobofanover 2 years ago
&gt; the biologists first come up with the first concept of the tool, which is purely focused on ensuring good results. After this first iteration is completed, engineers then come in and rewrite the tool using modern engineering practices with things like speed and reliability in mind.<p>I think that is already accepted as good practice, and the way most people in the field work, which is part of the reason why the field is in this shoddy state right now. Because in reality, most of the time those engineers don&#x27;t exist and it will never advance to the second stage, but will still be used regardless. And even if you manage to find an engineer for your team, the same problem exists in many layers down your stack.<p>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&#x27;t propose to have the accountant write the initial version of the software, would you?<p>&gt; Many of the projects that are critical to the foundation of genomics are reaching or have eclipsed the ten-year mark. How much longer can we expect these individuals to single-handedly maintain these code bases?<p>What you propose sounds more like &quot;hey, be the next idiot that commits to maintaining critical software for nothing&quot;, rather than any systemic change. The ugly secret of bioinformatics is the same one as in broader tech: Most of it runs on the backs of unpaid OSS maintainers (in this case a handful of motivated PIs that carve out some of their time for that).<p>If you want to have good software in the sciences, you first have to solve the OSS funding problem.<p>PS: the `user-select: none;` on your page is really annoying
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uvestenover 2 years ago
Anecdata, but I did a master’s in bioinformatics a few years ago, and as part of that I spent about a year in a human genomics lab.<p>I fully agree that the software used is really bad in general, but what is worse is the level of IT literacy among the PhD’s and post-docs from the biology side. (Also statistics, I guess a lot of p-hacking is the result of authors simply being clueless…)<p>After finishing my thesis, I was offered to stay and work at the lab. After thinking about it, and accepting, I was told that funding wasn’t secured yet, but that it should come ”any day now”…<p>Thanks, but no thanks.<p>Anyway, I fully see the need for professional software engineers in this field, but job security and even job availability (aside from the low salaries) in academia is abysmal, so I don’t think the current situation will change any time soon.
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neilvover 2 years ago
When considering software roles in science organizations, forget assumptions you might make about a typical tech job, joining a bunch of other software and hardware people -- or you&#x27;ll risk accidentally ending up on the other side of a distorted status system (not the side that normally pampers techbros).<p>You need to feel out the particular person you&#x27;ll be reporting to on how well they personally <i>respect</i> and understand the role, and also whether they&#x27;ll have clout&#x2F;funding and have your back if the org turns out to be rough (think AMZN). And also try to feel out respect within the organization, and some of the people&#x2F;teams with whom you&#x27;ll be collaborating.<p>You also need to check <i>compensation</i>, so you don&#x27;t wind up a low-paid person who later discovers they&#x27;re competing for local house offers with others in the org who are getting big-bucks TC (plus consulting on the side).<p>You also probably have to be OK with <i>never being the star</i> (like you hypothetically could someday be in a software company). Supporting actors should still get respect and get paid.<p>Find the right science situation, and you might have much more positive impact on the world than you could have in a software company, <i>while also being happy and comfortable</i>.<p>Some more quick of-the-cuff comments about this (sorry for run-ons, but I need to get back to my weekend)...<p>* RESPECT -- Whether or not the organization is university-affiliated, a lot of the researchers and administrators might have only worked in academia-like environments before. Academia is very hierarchical, software engineering might be considered commodity technician or support staff, and the high-status people almost certainly don&#x27;t understand your discipline, though they might think they do. (They often think software is relatively easy grunt work, and that software people just have oversized egos, which has some truth to it, but not that much.)<p>(Some real-life instances of this I&#x27;ve heard of include: someone with no understanding overriding software engineering technical decisions, because a colleague from their academic caste made an offhand comment, and they assume an academic who hasn&#x27;t even looked at the system knows more than an experienced practitioner developing it; not wanting to include people who made key software contributions as coauthor on a paper for a software system, but making sure professors who had near-zero involvement were included; scientists openly speaking of the software people as having commodity interchangeable skillsets, in way they&#x27;d never speak about peers in their domain; getting an unsalvageable monstrosity of pasted-together incompatible frameworks and Stack Overflow posts done by a summer intern, dumped on software engineer to &quot;clean up&quot; or &quot;extend&quot;, and being unable to convince that this is orders of magnitude harder to fix than to just make a viable system in the same time the intern took; in an academic environment, a grad student being higher status than key software people, and bossing them around with bad decisions, while treating their own obligations like homework they were trying to sneak past a grader rather than as a system that has to actually work.)<p>* COMPENSATION -- Related to the above. If you&#x27;re very experienced and marketable in tech, and would be making key enabling contributions, are you getting paid like it?<p>(The most recent life sciences software engineering opportunity I talked with, with a high-profile organization, they needed FAANG-like Staff&#x2F;Principal experience in multiple areas, all-in-one person, for key bespoke computational infrastructure on which a lot was riding. When we got to salary, it was capped at less than a new grads were getting offered elsewhere, and despite being in a top HCOLA city. The recruiter half-heartedly argued about it being for the science, etc. I said, if they&#x27;re thinking of this as an academic non-profit, that would be OK, so long as everyone there is making this level of money. But that wasn&#x27;t the case: the science domain people were considered the valuable assets, making good money, and software was seen as more a commodity support skill by whomever set the pay grade. Maybe within a decade that will agree with the market, everyone will decide that someone who can learn organic chemistry should get paid more than someone who doesn&#x27;t seem to do much more than fingerpaint in a Web framework builder and type nonsense in Jira, :) and maybe then most software people will be thankful for any job at all, but not yet.)<p>(I did actually look at a science company with a strong software tech company influence. But, though they claimed to be rethinking how the tech company did things, they seemed to carbon-copy the single most obvious bad side of that company. Talking with colleagues after I withdrew my application, the gossip was that they were getting lots of software people who&#x27;d burnt out on the tech company. So I guess maybe the rethinking was on what had been bothering those people, who were already at the tech company, and so who weren&#x27;t entirely representative of the talent pool that included people for whom the tech company had showstoppers.)
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clusterhacksover 2 years ago
I work in this field at a large medical research institution. There is a significant amount of genomics analysis that occurs here on a day-to-day basis. The genomic processing pipeline work all falls directly into my group.<p>There is next to zero demand for tool development internally. I do it <i>on the side of &quot;normal&quot; IT data management</i> because I love high performance computing, algorithms, and multithreaded hackery. But even at my large, well-funded institution, there isn&#x27;t a specific role where that is all that you do by design.<p>I do <i>suck at marketing</i> - meaning, despite having some success with big improvements in research tools that folks have definitely appreciated, no one comes to me asking for help with better engineering of genomic applications. Partly that is due to many researchers maybe only know R, so they will default to whatever packages are already available in Bioconductor, install those, and throw the resulting mash-up for their current research effort onto the compute cluster and simply wait for hours or days for the jobs to finish.<p>PIs are often insulated from software engineering problems too - if work is completed before the next bi-weekly meeting and update session, well, it must be ok.
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anonymous_bioover 2 years ago
The author completely neglects the downsides:<p>- The compensation <i>absolutely</i> do not match the workload and education required. - The sheer number of disreputable PIs and their unrealistic goals for software. - The data is likely questionable and often underpowered. - Institutional politics. everywhere. - Marketing (&quot;Curing Cancer&quot;). The role is actually just juggling various bioinformatics file formats.
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photochemsynover 2 years ago
Related HN discussion (May 2022) on similar article:<p><a href="https:&#x2F;&#x2F;news.ycombinator.com&#x2F;item?id=31577376" rel="nofollow">https:&#x2F;&#x2F;news.ycombinator.com&#x2F;item?id=31577376</a><p><a href="https:&#x2F;&#x2F;www.nature.com&#x2F;articles&#x2F;d41586-022-01516-2" rel="nofollow">https:&#x2F;&#x2F;www.nature.com&#x2F;articles&#x2F;d41586-022-01516-2</a><p>&gt; &quot;Fundamentally, RSEs build software to support scientific research. They generally don’t have research questions of their own — they develop the computer tools to help other people to do cool things.&quot;
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AlbertCoryover 2 years ago
20 years ago I got interested in &quot;bioinformatics.&quot; I loved learning something about molecular biology, after all those years of hearing about DNA and not understanding it. And &quot;Molecular Biology of the Cell&quot; is, hands down, the greatest textbook ever written.<p>That said: a lot of the comments are spot on. You&#x27;re working in a field where the hard scientists and business people rule and you&#x27;re a helper. Maybe they&#x27;re grateful for your help OR maybe they regard you as an overpaid lab assistant. After all, they have PhD&#x27;s and postdocs, and you don&#x27;t.<p>I&#x27;ve never actually worked in that field. I&#x27;d guess that it might be very satisfying, despite the low pay. Or not.
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samthoover 2 years ago
I’ve had a growing interest in the power of DNA and what the data can be used for since discovering no less than 3 family secrets (one of which pertaining to me) after taking an Ancestry DNA test. Did I know I was going to find 18 half siblings the moment my results came in? Nope, but yet there they are, listed in order of most shared DNA.<p>Despite my interest, I’ve found that landing a job in this field at my desired compensation level is very difficult especially if you not have the ”correct” academic background. Who does a double degree for computer science and forensic genealogy? I’m sure some people but for $75k&#x2F;yr you’d think the companies need to at least adjust their expectations.
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cuttothechaseover 2 years ago
I&#x27;ve been a software engineer in this space. I just want to say that there is exactly 1 job (non-intern) job between Microsoft, Google and Amazon listed according to the search links provided in the article.
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the_jeremyover 2 years ago
&gt; Often, it&#x27;s not required to know the domain before you join a group, and they will teach you on the job.<p>I looked. There are zero full-time, remote roles that don&#x27;t require previous genomics experience at any of the companies listed.
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debacleover 2 years ago
Science programming jobs suck. You get all the bad parts of academia, including less money, plus you&#x27;re seen as a janitor rather than an engineer, and you get to deal with scientists all day.<p>Tooling roles in SWE in every other field are highly regarded. Why not here?
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metalforeverover 2 years ago
Look, I did this at multiple places for a number of years. The issue is that you often form an adversarial relationship with the scientists. They don&#x27;t really want you there. They are perfectly happy just organizing everything by hand with post its and excel spreadsheets. They do not want you to mess with their flow with your software, even if it would help them to be more efficient.
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lowbloodsugarover 2 years ago
Even large corporations in this space pay relatively little for software engineers, and treat them with little importance.<p>I also experienced &quot;software engineers&quot; who had no idea what they were doing being given more credence because they had a PhD in some bio-related field. Oh, you got a PhD in some molecular aspect of some tiny piece of biology, and that makes you qualified to build big data systems? It did not. Apparently what that gives you is an adherence to reading decades old textbooks about database design. It was like working with a first year software engineering undergrad from twenty years ago.<p>To be fair, it looks like the same can be said for machine learning. Many software engineers I know are in the &quot;machine learning space&quot;, but report that they are just operations support for data scientists, and don&#x27;t actually get to learn about, let alone be involved with creating, the models they support.<p>If you are a software engineer, work in a software company, where engineering is the value proposition.
fxtentacleover 2 years ago
Google already axed all job offers, Microsoft and AWS are searching student interns...<p>I used to work in genomics and computational biology. It was incredibly interesting. But it&#x27;s university research and gets paid as such. 2-year time-limited contracts, lots of interns and students, extremely low salaries.
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jesse__over 2 years ago
Shameless self-promotion incoming.<p>I&#x27;m interested in contributing to this field. I have significant experience in 3D graphics, game engines, compilers and language runtimes. I&#x27;m a competent low-level engineer.<p>There&#x27;s a lot of red-flags in this thread about adverse working conditions, but I&#x27;m running under the assumption there are a handful of companies out there that work with a software-minded approach.. ie. respect SWEs for who they are and what they do. If you represent one such company, and are looking for engineers who have a keen eye for performance and architecture, I&#x27;d love to hear from you.<p>jesse@scallywag.software<p><a href="https:&#x2F;&#x2F;scallywag.software&#x2F;resume.html" rel="nofollow">https:&#x2F;&#x2F;scallywag.software&#x2F;resume.html</a><p>EDIT: Largely interested in remote roles, but could relocate for the right offer.
spacemadnessover 2 years ago
Sorry, no. This was my dream area to work in and I obsessed over degree programs in bioinformatics many years ago. Then I realized it’s incredibly low paying for the work, finding work in the area was a chore, and a masters might not even get your foot in the door. Nothing communicated that you would be valued. The harsh reality of the world won out in the end.
arnaudsmover 2 years ago
I hope this FAANG downturn will push software engineers to new industries, and bring some cross-pollination.<p>What happens when the world&#x27;s most brillant minds do something else than making us click on more ads ?
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pengwingover 2 years ago
Can you provide a list of the top problems in that space? Much rather try to understand them deeply myself and build a company solving them than just getting a job.
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YouWhyover 2 years ago
I am a career SW engineer that has worked on genomics in a startup. The field is genuinely exciting.<p>The endemic disease of the field is the leadership. A leadership made out of Principal Investigators forged in academia, appear simply incapable of producing any item which is not articles (or equivalents thereof).
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foobiekrover 2 years ago
My first job offer out of college for compsci was for a genomics research company that desperately needed software engineers. At the time they were storing sequences as ATGC strings in an oracle database using perl scripts. It was really below even undergraduate-level basic stuff.<p>The offer was $38k a year. About two days later, I got my second offer, $50k from a game company, and then a real offer, $60k, which I took. This was in the late 1990s.<p>That was 20+ years ago, of course, but I sort of wonder if things have changed. I frankly think a lot of SWE work for fundamentally evil, socially destructive companies, and I honestly don&#x27;t think you have to to earn a good living, but you also don&#x27;t have to work for companies that deliriously underpay you.
j7akeover 2 years ago
Genomics is still predominantly a research field. In research, software development and hence software engineers are not valued much, because technologies change rapidly, new ideas come every day, so it is about being able to hack together a workable solution enough to write a paper or get funding.<p>Software development becomes important when certain data processing methods have been standardised, eg mapping sequencing data to mouse or human genome, differential expression analysis, pca visualisations.
faizshahover 2 years ago
This is very true and I loved working with bioinformaticians but the pay is so much lower than a normal SWE role which is why SWEs will pick tech over genomics companies.
asciimovover 2 years ago
Not quite a decade ago, I took some work for a lab to replace some aging software (circa 1990) used to do peptide synthesis.<p>It was an enlightening experience. While I was the programming expert with a CS degree, I wasn&#x27;t trusted for anything, because I wasn&#x27;t a PhD or had a background in bioinformatics. However, I did get to work with lots of smart people, fixed and improved the code and processes that the Phd level statisticians and bioinformaticians used.<p>It is a real joy to work in hard science, with brilliant people who love their work. I learned a ton and gained a healthy respect for the people that do this kind of work.<p>However, the downsides are pretty bad. Pay and compensation is awful. Most people, myself included, could have made as good if not better pay waiting tables. There end up being different levels of people Administrators, Private investigators, and lab workers (peons). Unless you are an admin or a high level PI you&#x27;re not gonna be getting much money.<p>Everybody lives and dies by the grant. If funding dries up, you will be out of a job.<p>Ethics. Us CS people are woefully under educated on ethics. You will find yourself asking why we can simply do something, often the answer will be ethics.<p>Regulations, like ethics, you will have to bend to regulations. It&#x27;s not a bad thing, just a different thing.<p>Unless you find yourself in a admin role, you will just be another lab peon. Its not a a bad place to be, but you will never be at the top of the totempole.<p>Loads and loads of ego. You will work with very smart and sometimes unreasonable people. Learning to navigate this with tact is important.
danking00over 2 years ago
I don&#x27;t have any funding to hire right now, but I&#x27;m always happy to chat about the industry and my experience building Hail (<a href="https:&#x2F;&#x2F;hail.is" rel="nofollow">https:&#x2F;&#x2F;hail.is</a>, <a href="https:&#x2F;&#x2F;github.com&#x2F;hail-is&#x2F;hail" rel="nofollow">https:&#x2F;&#x2F;github.com&#x2F;hail-is&#x2F;hail</a>), a tool widely used by folks with large collections of human sequences.<p>The other posters are not wrong about compensation. Total compensation is off by a factor of two to three.<p>However, it is absolutely possible to work with a group of top-notch engineers on serious distributed systems &amp; compilers in service of an excellent scientific-user experience. I know because I do. We are lucky to have a PI who respects and hires a diversity of expertise within his lab.<p>I enjoy being deeply embedded with our users. I do not have to guess what they need or want because I help them do it every day.<p>I also enjoy enmeshing engineering with statistics, mathematics, and biology. Work is more interesting when so many disciplines conspire towards the end of improved human health.
UncleOxidantover 2 years ago
Yes, Genomics may be important, but are there really that many jobs for software developers? (same could be said for many other important fields - I recently saw an article about how software engineers should move to green energy - but who is going to pay them?)
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jugg1esover 2 years ago
I have a BS in neurobiology but have been working in software for 20 years. I&#x27;d always wanted to get into a more biology-focused software after interning at NIDA (NIH) and saw how bad the software support was. I spent most of internship developing software to make it easier to digitize the dozens of giant drawers full of index cards where they recorded all their raw data.<p>The problem is that the organizations involved in this sort of work often still consider software development as a cost center and therefore do not offer competitive salaries.
dottedmagover 2 years ago
This field does not _need_ software engineers.<p>This field needs marketing, product and project managers (for-profit or non-profit variety) that could figure out:<p>1. what product to build to have the biggest impact<p>2. how to build it.<p>Once 1. and 2. is clear it will be equally clear that if you have a bunch of scientists you won&#x27;t get a great product, as nobody will build the product, everyone will build a prototype.<p>So then it will follow that the project needs to hire (=attract) software engineers to be in charge of software, and attracting software engineers means giving them competitive compensation.
amrx101over 2 years ago
Would love to but I don’t think academia will want masters at least and years of industry experience will be discarded completely. I have 6 years experience in data intensive IoT applications and yet that would not be considered useful by academia
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wesleywtover 2 years ago
The code is bad because transient Phds and Post-docs are writing it. If there was money in it then the best software developer would already be working on it. Sadly there is none.
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mherdegover 2 years ago
What is the opportunity here -- writing new algorithms, implementing them accurately, optimizing them for special execution architectures, or just building more usable tools?<p>I remember Manolis Kellis sprinkled some pretty interesting genomic questions into his Algorithm class&#x27;s problem sets. There were a number of cool problems about optimally aligning strings, searching within text, etc.<p>This was like 15 years ago and I haven&#x27;t kept up with the discipline at all. But is there still algorithmic low hanging fruit?<p>I do keep reading about an ongoing series of problems with Microsoft Excel distorting analysis in the scientific literature (<a href="https:&#x2F;&#x2F;www.nature.com&#x2F;articles&#x2F;d41586-021-02211-4" rel="nofollow">https:&#x2F;&#x2F;www.nature.com&#x2F;articles&#x2F;d41586-021-02211-4</a>) and wondering if the tooling is having trouble..?
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mshockwaveover 2 years ago
Is there any open source projects on genomics that I can start looking into as a hobby rather than jumping right into a full time position in this field?
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dankleover 2 years ago
&gt; There is a significant gap between how software is currently developed in this space versus how it should be developed. The vast majority of genomics-related software is not written with speed or reliability in mind.<p>True, but working in academia is very VERY different working in a tech&#x2F;product company.
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d4nyllover 2 years ago
I have a degree in biochemistry. Would love to combine my passion in software and biology, but academic research is often funded by governments which means the salary is (super) low.<p>It&#x27;s the same reason why there&#x27;s a lack of qualified computer science teachers in schools.
raphaeljltover 2 years ago
Quick plug here for Atomic AI ( <a href="https:&#x2F;&#x2F;atomic.ai&#x2F;" rel="nofollow">https:&#x2F;&#x2F;atomic.ai&#x2F;</a> , <a href="https:&#x2F;&#x2F;boards.greenhouse.io&#x2F;atomai" rel="nofollow">https:&#x2F;&#x2F;boards.greenhouse.io&#x2F;atomai</a> ), which could be added to the list. We value and respect (and pay) our engineers—I myself trained as a SWE and worked at FAANG.<p>Shoot me a message at raphael@atomic.ai if you want to learn more.
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elricover 2 years ago
Would love to, both out of interest and out of a belief that it might one day improve the world. But it&#x27;s not happening. I have 20+ years of experience as a software engineer, but I don&#x27;t have a degree, so anything that has even a whiff of academia rejects me outright. Not to mention that it would involve a big paycut over fintech.
roughlyover 2 years ago
I work at at a SynBio company and heartily second this. If you&#x27;re looking for interesting work where you can make an impact, it&#x27;s an incredible field to be in.<p>I&#x27;m a nerd about everything - I love learning, and this field is incredible for it. The complexity and depth of biological systems dwarfs what we&#x27;re doing in the software industry. I work with brilliant people doing absolutely fascinating work, and I get to learn more every day. At the same time, I get to build things that make a genuine contribution to the people I&#x27;m working with - I can see the value and impact of my skillset in a way that was a lot harder when I was working at a software company. The leverage that good software folks can provide to folks outside the industry is almost impossible to overstate - our ability to scale up what the practitioners in the field are doing can offer an almost category change in what they can attempt.<p>At the same time, there&#x27;s still really, really knotty software problems to be had - computer science has benefited quite a lot from our ability to segment and structure our problems, but biology doesn&#x27;t allow for that - everything that we&#x27;re working with is operating at every scale, from molecular interactions up through genomics into protein design and folding and into metabolic modelling. Add to that that the data structures you&#x27;re dealing with can vary from a few characters up to a couple megabytes (within the same represented &quot;object&quot;), distant elements within the same object can interact meaningfully, the objects themselves tend to be embedded in larger structures with which they meaningfully interact, and you&#x27;ve got some fiendishly complex problems.<p>And at the end of all that, you&#x27;ve got a field which offers a legitimate possibility of helping us move past petrochemicals; an enormous expansion in the kinds, potency, and specificity of healthcare; and a new and novel set of tools for shaping our world. It&#x27;s an incredibly exciting place to be, and I&#x27;ve found people are genuinely thrilled to have good software folks along.
mdlmover 2 years ago
Those who are interested in the Broad Institute can reach out directly to me at mdelamaz@broadinstitute.org
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joefreemanover 2 years ago
Thanks for posting this, and your learngenomics.dev resource looks great - I&#x27;m looking forward to reading this though. I recently started working as an engineering manager&#x2F;lead in a genomics startup (<a href="https:&#x2F;&#x2F;www.genpax.co" rel="nofollow">https:&#x2F;&#x2F;www.genpax.co</a>), and I&#x27;ve been picking this up as I go. I&#x27;ve also started working my way through the &#x27;Micro binfie&#x27; podcast, which is great.<p>Our company values software quality and we&#x27;re very product focussed. We&#x27;re actively hiring in London: <a href="https:&#x2F;&#x2F;news.ycombinator.com&#x2F;item?id=33423547" rel="nofollow">https:&#x2F;&#x2F;news.ycombinator.com&#x2F;item?id=33423547</a>
mehphpover 2 years ago
I did do this, there were a lot of great people on my team but it paid (a lot) less and is more stressful than just building another CRUD app.
iainctduncanover 2 years ago
I worked for a while at a consultancy supporting genomics through LIMS (lab info management software) customization, so not really genomics, but in the genomics biz (big genomics companies were our clients). For me, it was the least interesting software work I have done in my 20 year coding career. On the other hand, for people who just wanted a steady pay cheque and to go home at 5pm, it was a good gig. But man, software that moves samples and test tubes and their data around, it could be cars in a parking lot for all that the science makes it interesting.<p>We had bad attrition to both more interesting and higher paying work. (I left for both after a year at the consultancy)
brofallonover 2 years ago
Most of the discussion here seems to assume bioinformatics &#x2F; genomics jobs are academic, but I work for a clinical testing lab where production-quality code is a must. We&#x27;re probably a 10&#x2F;12 on the Joel test.<p>If you&#x27;re into bioinformatics or genomics, but aren&#x27;t excited about an academic setting, take a peek: <a href="https:&#x2F;&#x2F;recruiting2.ultipro.com&#x2F;ARU1000ARUP&#x2F;JobBoard&#x2F;62cc791d-612e-42e6-909f-0de27efe2038&#x2F;OpportunityDetail?opportunityId=231c94de-5b8e-479e-8ec9-738818db6529" rel="nofollow">https:&#x2F;&#x2F;recruiting2.ultipro.com&#x2F;ARU1000ARUP&#x2F;JobBoard&#x2F;62cc791...</a><p>We hire fully remote positions and starting salaries are about US$100k.
jdeatonover 2 years ago
As someone who puts tremendous value in technical mentorship when considering a role this is about the worst possible advertisement for being a swe in genomics as it amounts to &quot;all our code is awful- come fix it!&quot;
fastaguy88over 2 years ago
It may be worth pointing out that several of the leaders in the Genomics field started off in commercial software development. I agree that it does not make monetary career sense to move into genomics -- academic labs cannot pay you more than the lab head makes, which is probably much less than many software developers are worth in other markets.<p>But I&#x27;ve known several financially successful developers who have gone back for a PhD in bioinformatics and genomics, and, after getting over their distaste for existing tools, have made important and well-recognized contributions. But they did not make more money.
pabs3over 2 years ago
I wonder how popular open source is in genomics, there does seem to be a lot of open source genomics&#x2F;med&#x2F;science related software.<p><a href="https:&#x2F;&#x2F;wiki.debian.org&#x2F;DebianGenomics" rel="nofollow">https:&#x2F;&#x2F;wiki.debian.org&#x2F;DebianGenomics</a> <a href="https:&#x2F;&#x2F;blends.debian.org&#x2F;med&#x2F;tasks&#x2F;" rel="nofollow">https:&#x2F;&#x2F;blends.debian.org&#x2F;med&#x2F;tasks&#x2F;</a> <a href="https:&#x2F;&#x2F;blends.debian.org&#x2F;science&#x2F;tasks&#x2F;" rel="nofollow">https:&#x2F;&#x2F;blends.debian.org&#x2F;science&#x2F;tasks&#x2F;</a>
wdwvt1over 2 years ago
Somewhat self-interested plug here: consider working in metabolomics as well. Metabolomics is where sequencing was in ~2008. The physics and chemistry are pretty well worked out (though many improvements are surely coming in the same way that 454 gave way to Illumina, PacBio, Nanopore, etc.). The software and computational workflows are truly awful, like hard to describe bad. The company that figures out metaboloimcs well is going to command a much larger market than genomics - genomics tells you what&#x27;s possible, metabolomics tells you actually what&#x27;s happening.
bambaxover 2 years ago
&gt; <i>Google Genomics. Careers link.</i> &gt; <i>Microsoft Genomics. Careers link.</i><p>Google and Microsoft probably know how to make software?<p>Side note: why does this page have user-select: none on body? It&#x27;s annoying; what does it accomplish?
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theGnuMeover 2 years ago
Couple of things I know.<p>Bioinformaticians come in two flavors. Those that studied biology and then took up coding and then the even rarer computer scientists who learned biology. The latter are so rare that they are almost all professors or founders or work at Deep Mind etc... Then, there are the biomedical engineers, etc...<p>The computer scientists will go off a solve protein folding when the bioinformaticians and chemists worked on it for years.. I am exaggerating a little here, I imagine there were plenty of bioinformaticians on the Alpha Fold team, but the fundamental breakthrough was DNNs.
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throwawaysleepover 2 years ago
I’ve worked at a lot of places and for researchers was my worst job ever by far. I’ll never work for someone with a PhD again, as Sheldon Cooper’s attitude towards engineers is no joke.
denvaarover 2 years ago
I&#x27;m most definitely not an expert in this area, but I have recently taken interest in learning about &quot;succinct data structures&quot;, which from what I understand have their place in bioinformatics.<p>It&#x27;s been a challenging topic to learn about, because most of the information comes from Computer Science papers and articles where the information is presented in a very formal, mathematical way, which I am just not used to.<p>Normally when thinking about data structures and algorithms, we&#x27;re mostly concerned with optimizing for speed. Space complexity is not usually as big of a consideration. Succinct data structures are all about creating ways to achieve good runtime performance while representing the data in a &quot;compressed&quot; format. I think this comes in handy when doing things like DNA sequencing since data sets are so large.<p>I&#x27;m excited to check out some of links in the post, and in case any one else is interested in learning more about succinct data structures, here&#x27;s a few resources I&#x27;d recommend:<p>Prof. Ben Langmead&#x27;s YouTube channel: <a href="https:&#x2F;&#x2F;www.youtube.com&#x2F;user&#x2F;BenLangmead&#x2F;featured" rel="nofollow">https:&#x2F;&#x2F;www.youtube.com&#x2F;user&#x2F;BenLangmead&#x2F;featured</a><p>Alex Bowe&#x27;s blog has some good content: <a href="https:&#x2F;&#x2F;www.alexbowe.com&#x2F;articles&#x2F;" rel="nofollow">https:&#x2F;&#x2F;www.alexbowe.com&#x2F;articles&#x2F;</a><p>Prof. Erik Demaine&#x27;s &quot;succinct&quot; lectures from his adv. data structures course at MIT on YouTube: <a href="https:&#x2F;&#x2F;www.youtube.com&#x2F;watch?v=3Y2weLDiUWw" rel="nofollow">https:&#x2F;&#x2F;www.youtube.com&#x2F;watch?v=3Y2weLDiUWw</a><p>Edward Kmett&#x27;s Haskell live coding session going into some details about succinct: <a href="https:&#x2F;&#x2F;www.youtube.com&#x2F;watch?v=9MKEmNNJgFc" rel="nofollow">https:&#x2F;&#x2F;www.youtube.com&#x2F;watch?v=9MKEmNNJgFc</a><p>There&#x27;s also a lot of research papers, which you should be able to find by searching for &quot;succinct data structures&quot; (Jacobson, Munro, Brodnik, Raman, Rao, Navaro, Sadakane just to name a few). I at least have a basic CS undergraduate degree, but many of these papers are over my head, but I have still been able to slowly understand more and more. Some I had to purchase.
moron4hireover 2 years ago
This is tangentially related to what I&#x27;m currently doing.<p>I basically work in EdTech. The company is not an EdTech company, it&#x27;s a education services company. I was hired on to develop software that we couldn&#x27;t find in the market[0].<p>I&#x27;m the process of building this <i>thing</i>, we&#x27;ve been attending and speaking at conferences in our industry. And I&#x27;m seeing a lot of the same stories: academia is trying to do research, the research fundamentally requires software to make the research happen, the quality of the software can have a huge impact on results, but because software development is tangential to the research goals, there&#x27;s little to no allocation to software developers. This leaves the researches to cobble together a solution that maybe kinda fulfills their need, not corky, and certainly not perpetually (a lot of reliance on trial software and services).<p>We would love to offer our software to researchers in our field. We&#x27;ve gotten feedback from several that what we are building is exactly the sort of thing they need. But they have <i>no</i> money, and even if we were in a position to give it away for free, we can&#x27;t even make those connections come to fruition.<p>So I don&#x27;t know what to do. I really am thinking of starting to give it away for free, because at least we&#x27;d benefit from more research results in our field pricing the efficacy of our approach. But that&#x27;s a really slow burn.<p>[0] Specifics don&#x27;t matter, but if you&#x27;re curious, I make a VR environment for foreign language training emphasizing culture.
jefftkover 2 years ago
I recently switched from software engineering on ads and web performance at a FAANG to (meta)genomics at a nonprofit startup; happy to answer questions
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whatever1over 2 years ago
These should be separate in academia.<p>SWEs cannot write code that maps equations that may change daily completely due to modeling &#x2F; assumptions change.<p>Too much focus on modularizing, premature optimization, useless unit testing etc. Who cares about all these if the underlying model is wrong?<p>If things are stable enough to go into production then the code should leave academia and be re-written properly by SWEs, not by clueless bio phds.
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thrway2342over 2 years ago
&gt; ADVANCED DEGREE HOLDING SOFTWARE ENGINEERS: consider working on genomics<p>fixed the title.
didipover 2 years ago
heh, you think scientists automatically understand computing nature?<p>You’ll be the janitor cleaning up their 20k LoC, one file Python with zero abstraction.<p>If this is already a thing at a FAANG, it will be worse at a pure science shop.
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sargstuffover 2 years ago
From past work experience &amp; funding source priorities, computational genomics usually considered a supporting role as information analyst when needs to be a research software engineer. (unless building software for ct, mri, x-ray scanning process).<p>aka need to be able to develop the dna &#x2F; dna number system equivalent of things (aka something other than binary &#x2F; punch card block based number system) such as:<p><pre><code> treesitter nyquest : https:&#x2F;&#x2F;en.wikipedia.org&#x2F;wiki&#x2F;Nyquist_(programming_language) slippery chicken : https:&#x2F;&#x2F;ccrma.stanford.edu&#x2F;workshops&#x2F;algorithmic-composition-with-slippery-chicken </code></pre> but wind up doing the equivalent of automated statistical analysis, because focus is NOT to develop software package&#x2F;system.<p>short broader subject take, what programming groups dont get about applicative programming vs. algol&#x2F;block programming
gedyover 2 years ago
If you enjoy programming, don&#x27;t work for fields or companies that view you as a cost center, it&#x27;s a drag.
babuloseoover 2 years ago
I want to study Bioinformatics at McGill for a Masters or Grad school. I was doing some cheminformatics related work and basically was working along Bio students and grad students literally before the pandemic hit. Heck, even Boston University would be a good fit for me because I was helping students at hackathons build their solutions or mentoring them right before the pandemic hit for AstraZenacs challenge, and the team I was helping out created a hardware prototype that would give you your daily meds (great for seniors that forget to take pills or what). But honestly I feel like there is a lot of gatekeeping in this community, I would have to spend approximately 7 years before I could get taken seriously in this domain. In that 7 years you can do a lot of other meaningful work than being stuck in grad school. I dunno.
robertlagrantover 2 years ago
&gt; Of course, this would not be the fault of the individuals who maintain the software, who are often brilliant: it&#x27;s just simply not fair to expect individuals to ensure this consistency using their own, ad-hoc processses<p>I think this is a little generous. Engineers of all stripes should take responsibility for their work. If they say, &quot;Yes I can add methylation analysis in three weeks,&quot; then they should make sure that means it&#x27;s made well, with tests and all. I&#x27;ve definitely encountered people who don&#x27;t communicate the scale of the task, and for most of them it&#x27;s because they don&#x27;t do software engineering; they do informatics scripting.
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jjthebluntover 2 years ago
I quit several years of a dream job in Apple engineering to work on genomics in mid 2016; the small company i joined tanked in 6 months. I think the problems impacting this space include vague customer needs. Caveat emptor, so to speak.
possiblydrunkover 2 years ago
Genomics was a pretty good place for software engineers that have an interest in molecular biology; however, the pay is not generally comparable with that earned in a tech industry job. Interesting (to me) is that the software engineers that I&#x27;ve worked with in genomics-oriented labs treat biologists and biological data as the gold standard, while the biologists in those labs are fairly reverential towards the software engineers and computational results! Of course, both are overly optimistic ... Unfortunately, the best software engineers I worked with eventually jumped to software startups or tech industry jobs.
shadowgovtover 2 years ago
Average salary of $58k.<p>Genomics companies: consider paying more.
teekertover 2 years ago
I work in genomics, this is very true. I know of some modernization efforts, ie by companies working with new file formats, like GenomSys [0] with mpeg-genomics [1].<p>It feels like it’s going very slowly though. The field just really depends on their Unix philosophy tools, there is a lot of gzipped text files that are piped through bash scripts and tool like awk and grep. It works, mostly, but there is a lot of weirdness.<p>[0] <a href="https:&#x2F;&#x2F;genomsys.com&#x2F;" rel="nofollow">https:&#x2F;&#x2F;genomsys.com&#x2F;</a><p>[1] <a href="https:&#x2F;&#x2F;mpeg-g.org&#x2F;" rel="nofollow">https:&#x2F;&#x2F;mpeg-g.org&#x2F;</a>
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Nikskoover 2 years ago
Sounds like the only way you could ensure a healthy environment in this field would be to follow the Matlab or the Wolfram model. In other words, create a software company whose customers are bioinformaticians. Maybe find a bioinformatics academic to help guide product development enough to get some contracts with research institutions, and take it from there.<p>It sounds like academia is simply too toxic, entitled, full of itself and hierarchical to provide an environment with good software practices can thrive.
jokethrowawayover 2 years ago
Simply put, I can get a better paid gig just developing for the web, without understanding any complicated domain (what the developers do is the complexity).<p>Working in research in general doesn&#x27;t seem to pay that well or the well paid jobs are few and far.<p>Maybe it&#x27;s a sector ready to be disrupted by a startup with quality developers; but I still have to see disruption based on improving code quality. It&#x27;s a tangential aspect as well and doesn&#x27;t impact much the actual business.
dekhnover 2 years ago
In addition to genomics, the other area that could greatly benefit from professional SWE experience is imaging. Many of the most effective techniques today combine microscopic images with genomics- for example variable transcriptomics approaches. Imaging is a more natural fit for people who like to work with dense, visualizable matrices, although genomics data is now trending more towards matrices (all genes x some observable metric).
tdullienover 2 years ago
So if one was financially independent and wished to write something open-source in that field, where would the highest impact be?
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rafiki6over 2 years ago
It seems to me like we&#x27;d probably be better off partnering with domain experts in Genomics who want to build software that can be used across the board. Sounds like an interesting opportunity for a business. I&#x27;m open to the idea if anyone wants to chat, let me know. I&#x27;m SWE but would want to partner with a Genomics Expert.
ericbover 2 years ago
What would I need to get started on an open source genomics program?<p>Where do they live? What do they do?<p>Like, do you need a genome interpreter? Does one exist? Are there any open source products used by the field currently? I know the names of the programs and items I&#x27;d look at to get started in AI, for example. But for genomics, it&#x27;s a total mystery.
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JaDoggover 2 years ago
From what is said in the article and comments, this may be a good place to be if you are bootstrapping your own company.
captainoatsover 2 years ago
If you’re interested in genomics I’d recommend working for a commercial entity in clinical&#x2F;translational genomics side rather than in academia. I have worked for a few of the big names in the space and although they had their problems the work was very rewarding as you’re closer to the patient impact.
astatineover 2 years ago
I keep thinking of this space but don&#x27;t know where to start. Any pointers for good resources? - books that are accessible to software engineers with no background in genomics, open source projects which are widely used, etc.... in short a good place to start in exploratory&#x2F;hobby&#x2F;learning mode.
pryelluwover 2 years ago
It might seem like an exaggeration but this morning I was thinking of doing more work in scientific software. I lost my mother to cancer. This seems like a way to channel that energy and motivation. Thanks for posting, OP.<p>PS. Feel free to reach out. Email in profile. I’ll be happy to email around the subject.
zmmmmmover 2 years ago
People seem to be responding to the pitch in a different way to how it is intended. It&#x27;s entirely a pitch that there is a <i>need</i> for this. So if you aren&#x27;t highly motivated by doing something valuable and useful, this isn&#x27;t for you.<p>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&#x27;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.<p>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&#x27;s surprisingly easy if you have a supportive group.
aaauaucuggaaover 2 years ago
I will add Mammoth Biosciences to the list. We are looking for Software Engineers, Data Engineers, Data Scientists and more.<p><a href="https:&#x2F;&#x2F;mammoth.bio&#x2F;careers&#x2F;" rel="nofollow">https:&#x2F;&#x2F;mammoth.bio&#x2F;careers&#x2F;</a>
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JZL003over 2 years ago
I work at the broad institute and it&#x27;s a pretty cool place, can be long hours but they&#x27;re investing heavily in software and the like. Can be a nice intermediate between research and applications
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awill88over 2 years ago
&gt; There is a significant gap between how software is currently developed in this space versus how it should be developed<p>I appreciate the authors honesty. Been there, take it easy bud.
noname123over 2 years ago
I just want to add my $0.02 to respond to the low pay and low respect as a Software Developer&#x2F;Engineer in the genomics. This is 100% true and also not true [bear with me]... you get it back in the back end.<p>First the comp, most people think about the income they get as in levels.fyi TC. IMHO, The no. 1 value add is working for an academic center is the freedom in both time and spirit you get in pursuing your interest and the side ventures &amp; hustles which eventually compounds. The hours are very reasonable in academia and in most places, you can take classes internally on campus or get reimbursed for it and get supportive managers who let you take time off from work to study. Or just great WLB to pursue something you really enjoy. And this compounds both spiritually and financially.<p>Just a data point of one, I took an online data science degree whilst working like 15hrs&#x2F;week and 25hrs on classes. From the classes, I got the bug to apply data science I learned on my degree and on the genomics analysis job to apply to the financial markets&#x2F;automated trading. Now over the past 4 years, I&#x27;ve achieved CAGR of 35%, and sharpe of 2.5 where my options trading portfolio capital gains outsizes consistently my W-2 pay and keep me par on L5 of FAANG engineer. To give you an idea, my other co-workers have gone into side-hustles real estate (not sure about now) or running day-care to great success. Yes because you have that much free time.<p>Now autonomy&#x2F;academic stimulation, I would not give it up for the world even if I was doing it for free. Previously I was working for a &quot;hot tech&quot; company where I was bored out of my minds cranking CRUD widgets and re-learning JS frameworks every year and attending BS lunch n&#x27; learn work sessions of new crappy libraries with hipster names. In genomics, you get to apply traditional stat techniques (bioconductor), deep learning techniques (tensorflow, AlphaFold, GANs) and learn latest sequencing protocols (scRNASeq, ChIPSeq, CRISPR screenings) and learn the biology domain too (immunology, viral responses, cell regulatory networks, synthetic biology. It&#x27;s like being on the front-seat to a movie cinema or basketball court where the scientific evolution is happening. You&#x27;re learning something new everyday and you are at the center of it all as PIs, wet lab bench scientists all depend on you to perform the analysis and build the pipelines... and 8 years in, and I&#x27;m still excited with the only disappointment that I will never learn it all.<p>Obv. a subjective data point of one, but I just want to add my data point just in case somebody out there on the fence. Yes sometimes you can truly have it all.
baran1over 2 years ago
I started working at a genomics company about a couple of years ago and my experience is very different from the post. Although there might be a handful of bioinformatics tools that are quite old, the ones at the heart of of operations are worked on by teams and reasonably maintained, and although I agree with the headline that there&#x27;s a lot of work to be done in the area - my perspective is a little different. Although this doesn&#x27;t apply to all genomics companies, I&#x27;m at a company that has a lab, and the software we write makes the lab about 8x more efficient and the next generation of sequencing technology will bring sequencing costs down by about 5x. Meanwhile the science and literature keep pushing further and newer generations of physicians are putting a stronger emphasis on genomic counseling. Thanks in part to the power of viral sequencing data the government is starting to trust laboratories that bring valuable and actionable insights. I think all of those combined with the fact that CRISPR technologies are getting further along puts genomics in a unique position. TLDR; yes genomics is exciting and on the brink of something big, but no it&#x27;s not a dumpster fire that needs saving. Oh and as a bonus - I get to work with really smart scientists and they are very friendly :)
allyourbasepairover 2 years ago
I write synthetic biology software for a living and maintain this open source, Go package for engineering DNA that has high test coverage and a nice little dev community around it.<p><a href="https:&#x2F;&#x2F;github.com&#x2F;TimothyStiles&#x2F;poly" rel="nofollow">https:&#x2F;&#x2F;github.com&#x2F;TimothyStiles&#x2F;poly</a><p>A large part of my project&#x27;s community are devs that want to get into the field but can&#x27;t tolerate the ridiculously low pay, laughably bad management, disrespect, and what amounts to 40+ years of technical debt that&#x27;s endemic to biotech software.<p>I&#x27;ve had companies here in the Bay Area offer me 100K a year with a straight face. I&#x27;ve had companies during interview tell me they&#x27;re looking for someone to help, &quot;set up GitHub&quot;. I&#x27;ve seen job listings for low paid web dev positions require applicants to have PhDs.<p>The reality is that except for a growing handful of places management straight up won&#x27;t know the difference between IT and software engineers. It&#x27;s what I call the naive buyers problem.<p>The demand for software engineers in biotech is generated by naive buyers that don&#x27;t know what they need, why they need it, or how to get it.<p>Benchling and Recursion Pharmaceuticals have reputations in the industry of paying, &quot;standard software salaries&quot;. So do the research divisions at places like deepmind&#x2F;microsoft&#x2F;google but in my experience there&#x27;s even new multi-billion dollar institutes where senior management has never even heard the term devops.<p>Most places advertise for &quot;data scientist&quot;, 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.<p>It&#x27;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.<p>This week a software engineer trying to make the switch to biotech actually DM&#x27;d me to ask why they were seeing a ton of data science &#x2F; ML job positions but no software engineering &#x2F; devops positions.<p>They were worried that these companies were trying to save on costs by forcing their data scientists to create infrastructure but it&#x27;s actually worse than that. Most of these companies aren&#x27;t even aware that there&#x27;s supposed to be infrastructure.<p>Despite all of this the future is looking better and I&#x27;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&#x27;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.
skosuriover 2 years ago
I am a founder of a startup (Octant - a16z backed) that has a small &amp; growing software engineering and data science team (see the Nov who&#x27;s hiring post). Some thoughts on some of the discussion here:<p>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&#x2F;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&#x27;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.<p>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&#x27;t think anyone has really cracked this nut yet (or if it&#x27;s even possible).<p>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 &amp; data science first startups. I think in the larger pharma&#x2F;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.<p>3. I think one important difference is the type of company. There are many software companies in healthcare&#x2F;bio that are software products supporting R&amp;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&#x27;t.<p>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).<p>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&#x27;s a pretty amazing time in biology, with a suite of new technologies to read, interpret, write, edit, deploy molecules&#x2F;DNA&#x2F;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.
AtNightWeCodeover 2 years ago
Warning sign. You can&#x27;t even select the text on the site.
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quest88over 2 years ago
Which open source projects need help, and why those?
LarsDu88over 2 years ago
I do work in genomics.
travisporterover 2 years ago
Clicking to highlight text is disabled. <a href="https:&#x2F;&#x2F;xkcd.com&#x2F;1271&#x2F;" rel="nofollow">https:&#x2F;&#x2F;xkcd.com&#x2F;1271&#x2F;</a>
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zach_garwoodover 2 years ago
Several of the job boards linked don&#x27;t have any job listings, most don&#x27;t provide a salary range, several require advanced degrees, and none specify whether remote work is possible.<p>If I can get a better salary and working conditions at some crappy no-name startup, why would I choose to work at an organization that respects my craft so little they haven&#x27;t bothered to maintain their software for a decade?
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jerjerjerover 2 years ago
Hard no.<p>Initial code would still be developed by SME, who:<p>- Don&#x27;t understand most programming abstractions<p>- Don&#x27;t see the advantage of a clean codebase<p>- Would rather go back to their code spaghetti mess, than help figure out why some corner cases behave differently in a fresh codebase<p>- Would still submit changes to their code spaghetti mess and expect you to apply them to the cleaned codebase<p>I did what the author suggested (not in genomics, but in a different research-heavy scientific field) for a while and would not recommend it to anyone.<p>And that&#x27;s not even taking compensation and work conditions into account.
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