[HN Gopher] Consider working on genomics
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Consider working on genomics
Author : clmcleod
Score : 287 points
Date : 2022-11-19 15:56 UTC (7 hours ago)
(HTM) web link (claymcleod.dev)
(TXT) w3m dump (claymcleod.dev)
| photochemsyn wrote:
| Related HN discussion (May 2022) on similar article:
|
| https://news.ycombinator.com/item?id=31577376
|
| https://www.nature.com/articles/d41586-022-01516-2
|
| > "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."
| ninala wrote:
| This does not have to be true. You can certainly pursue
| interesting biology research questions informed by a software
| engineering POV.
| jjtheblunt wrote:
| 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.
| zach_garwood wrote:
| Several of the job boards linked don't have any job listings,
| most don't provide a salary range, several require advanced
| degrees, and none specify whether remote work is possible.
|
| 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't
| bothered to maintain their software for a decade?
| clmcleod wrote:
| I think your phrase here sums up how many people feel:
|
| > why would I choose to work at an organization that respects
| my craft so little they haven't bothered to maintain their
| software for a decade
|
| This is changing in my experience, albeit slowly. And really,
| this is what I'm calling on us, as a community, to do better
| on.
|
| The reason you _would_ work at these organizations is because
| (1) the subject-matter is really interesting, (2) there are
| hard problems to be solved, and (3) you wake up every morning
| knowing that you are working on something that will have an
| impact on the lives of people around the world.
|
| At least those are my reasons :)
| rleigh wrote:
| How are we "as a community" going to be able to improve this?
|
| It's ultimately down to the cultural norms of the field, as
| well as the realities of academic funding.
|
| I was a research software engineer (RSE) for the best part of
| a decade. The best thing that happened to me was being made
| redundant when my funding ran out, and being forced to work
| in industry. What a difference (and wholly for the better).
|
| The reasons you give are all nice positives, but they all
| ultimately are very emotionally manipulative. You're asking
| people to act against their own self-interest. But this isn't
| really for the benefit of humanity. It's for the benefit of
| the PIs who run the research groups, and keeping their little
| empires running. But the cost to the individual is great.
| You're sacrificing salary, a career track, advancing your own
| skills to the full, and in many cases the opportunity to have
| a life: being able to afford a home and support a family.
|
| In retrospect I, and many others like me, do feel that we
| were taken advantage of to some degree.
|
| I spent several years on a massive grant, then several years
| on lots of small short-term grants (12 months, 6 months, 3
| months). You can't risk getting a mortgage when you have no
| guaranteed employment. And it's also very stressful not
| knowing if you'll be employed in three months time every
| three months. And unlike in a company, RSEs don't really have
| a proper career track. There's no real progression. You're a
| hired help.
|
| RSEs are not treated equally with academics. Let's be really
| honest about that. We're not. I even had a PhD in the subject
| area and you're still beneath all of the "real" academics.
| We're not "partners" in their work. We're the dogsbody's.
|
| If these people want software developers with real chops to
| work in the field then they need to pay a competitive salary,
| have a proper career track, and really fix the job stability.
| And they also need to properly respect the expertise RSEs
| bring. Unless all of those are fixed, a career in industry
| will continue to be the only rational choice.
|
| This won't happen though. Tenured academics refuse to
| consider paying the going rate because that would mean the
| "hired help" would be earning considerably more than they do.
| I had already topped out the salary band when I left, and I
| was earning more than most of the junior-mid-career
| academics. They are, of course, on fairly poor salaries. They
| too would earn vastly more in industry, but are mostly
| unwilling to consider that option as a rule. Their loss. If
| they truly respected the value they were getting, then they
| would pay for it. It will not happen though. Most of academia
| is about climbing the greasy pole and not about advancing the
| state of the art; there's just no way they'll permit others
| to sit higher on the salary pyramid than they do.
|
| At least in industry skill and competence and the ability to
| deliver are highly-valued, and companies will gladly pay for
| people who are proven to deliver. In practice the work I do
| in industry (biomedical) has far more positive impact upon
| the world than anything I did in the academic niche I used to
| occupy, and is also vastly more enjoyable, with a lot more
| responsibility and technical depth.
|
| Are you personally planning to stick it out for the whole of
| your career? Because if I could give you the advice I would
| have liked to have given myself, it's that you should
| properly think about where you want your career to go in the
| medium to long term, and decide when (not if, but when) you
| will exit to move to industry. Use it as an opportunity to
| gain some useful skills, and move on to where your skills
| will be properly valued.
| cratermoon wrote:
| I have experience working in academia. I started out working
| for a medical school in fact, on bioinformatics. It's been a
| while, so I have kind of forgotten the problems, but I'll do
| my best.
|
| 1. Academic code. Not one institution would pass the Joel
| Test[1]. You pretty much covered some key points in your
| first paragraph, so I see not much has changed. The best
| predictor of how something will perform in the future is how
| it has performed in the past. Just hiring good software
| engineers won't change the system in which they work.
|
| 2. Academic bureaucracy & administration. I've worked for
| large Fortune 500 companies with less byzantine org charts.
| I've been matrix-managed. The siloing in academia is crazy.
|
| 3. Advancement. Because it's academia, advanced degrees are
| everything. My first boss in academia had a PhD. His job? He
| ran the student computing lab. My second boss was an MD/PhD.
| Great guy, but treated everyone like a lab assistant. I went
| to graduate school for one year and realized it wasn't for
| me.
|
| 4. (added after reading other comments). Completely
| unrealistic understanding of what developing robust, complex
| software is like. You touched on this by mentioning how many
| projects have 1 maintainer. I remember seeing a doctor
| shopping around his project plan. I'd say it would be a
| challenge for a high-performing 5-person team. He thought it
| was a job for a single entry-level programmer.
|
| 1 https://www.joelonsoftware.com/2000/08/09/the-joel-
| test-12-s...
| pclmulqdq wrote:
| If you don't have a PhD, don't touch academic jobs with a
| 10 foot pole. They all got one, and they value the
| credential to a ridiculous degree.
|
| When I last worked with academia, they essentially thought
| of me as the same as the guy who maintains the lab
| equipment, not an actual collaborator on their research.
| cjbgkagh wrote:
| The academic elitism doesn't end at PhD. A friend asked a
| Nobel prize winner their thoughts of different person who
| was recently awarded a Nobel prize in the same field.
| Their response "Ah, yes that was one of the lesser
| Nobels"
| chitowneats wrote:
| Ever since the pandemic, many software engineers have become
| exactly the type of "I've got mine, Jack" people they
| typically deride.
| jwilber wrote:
| Or, and hear me out here for a second, people go where
| they're most valued. Why would someone volunteer to go work
| somewhere where they'll get less money, have less
| flexibility, be treated as second-class employees, have
| less work perks, etc. when so many alternatives exist?
| Doubly so in this economy.
|
| Maybe genetic companies should catch up in workplace
| etiquette instead of recommending that SWE's lower their
| expectations.
| cratermoon wrote:
| > be treated as second-class employees
|
| The pay isn't all that important to me, as long as I can
| live on it, but this. It was so obvious when I was
| working in academia that because I wasn't myself an
| academic that I was just lab help, no better than the
| person who washes the test tubes and beakers.
| cycomanic wrote:
| I don't quite understand this post. In my experience lab
| technicians in academia are highly valued (however I
| mostly have experience with clean room staff), however
| they are support for the researchers, who drive the
| research agenda (well actually it's the funding
| primarily). What exactly do you expect to not be what you
| call "a second class citizen"?
| rleigh wrote:
| Are you really, really serious?
|
| Academia is a hugely elitist pyramid with well-demarcated
| layers, and the lab technicians are at the very lowest
| level of the pecking order, down with the cleaning staff.
|
| They might be "needed", but by and large are they really
| "well respected" or "valued"? Not really, sad to say.
| clmcleod wrote:
| I agree. With that said, I do think we are getting there.
| The pay is becoming more comparable, and I think software
| engineers are becoming more and more valued in these
| companies/organizations.
| zach_garwood wrote:
| Haha, thanks! This is much kinder than my response was
| going to be.
| jghn wrote:
| At least one of the entities on that list is a nonprofit
| academic institution. Expecting pay equal to the standard
| software industry is misguided.
|
| Whether or not that's a tradeoff you're willing to make
| is another question.
| zach_garwood wrote:
| And three of them are FAANG. They could certainly afford
| it.
| jghn wrote:
| And they pay their standard rates.
| nine_k wrote:
| If you go to academia, you're certainly are not going for
| the money.
|
| People can work for less if they are visibly valued, or
| where they are doing some heroic stuff that appeals to
| them personally.
|
| People can for some time withstand being treated as
| second class, being overworked, etc, if they are paid a
| lot.
|
| But if it's neither, why would anyone bother?
| jghn wrote:
| > But if it's neither, why would anyone bother?
|
| Because they find it rewarding in some other way? I agree
| that that way is not the conventional wisdom, but it
| exists, it turns out that some people value doing things
| that provide a demonstrable benefit to humanity.
|
| Also he second class citizen thing has diminished over
| the years. It still exists but there are plenty of
| companies where that's no longer true. This is in stark
| contrast to when the field was getting off the ground,
| for instance it wasn't uncommon for benefits like PTO to
| be tied to your degree level & not length of employment.
| tikhonj wrote:
| The problem is that it _isn 't_ just about pay, it's
| about _everything_ : autonomy, flexibility, culture, work
| quality, respect... If an organization can reliably
| convince--show, not tell--that it will be a much better
| place to work overall, I'm certain they can hire highly
| skilled engineers even if they can't compete on pay.
|
| My experience is that most non-tech organizations can't
| or won't.
| zachthewf wrote:
| How's the startup ecosystem?
| cjbgkagh wrote:
| I charge a high rate not because I need the money but because
| I need to stop people from wasting my time. I've worked at
| these places before where they exploit your altruism and
| dedication to craft to extract more work out of you for less.
| Concretely one of the places refused to hire a frontend dev
| to help so I got stuck wasting time churning frontends.
| Charging more encourages them not to do that.
| fnbr wrote:
| Yeah. It's one thing if the only way the job is worse is in
| pay, it my experience has been that if the pay is
| significantly worse, the job is worse off in every way.
| RangerScience wrote:
| I think what I'd ask is:
|
| Will I be allowed to fix the parts that result in
|
| > an organization that respects my craft so little
|
| Like, it's one thing if they haven't - that can be fine, it's
| just more work. It's an entirely different thing if they _won
| 't_.
| clmcleod wrote:
| I think the honest answer is, it depends where you work.
| Where I work, we have that autonomy. But we also have
| leadership that understands and respects the software
| engineering craft.
| psadri wrote:
| This reads a bit like "what can this place do for me?" instead
| of "how can I make the place I work at better".
|
| High potential areas like genomics that are behind on software
| are amazing places for talented software people with a givig
| attitude to have a big positive impact.
| zach_garwood wrote:
| I can have a big positive impact and make the startups I tend
| to work for better places AND get paid well and be respected.
| It seems the "potential" here is a result of a lack of care
| and maintenance for legacy codebases, and not, say, driving
| innovation.
| jghn wrote:
| In general salaries would be lower than what you can get in a
| standard software role. Some of the ones on that list allow
| remote work, others are more limited. The tradeoff is that
| you're working towards the betterment of humanity. Whether or
| not that's worth the tradeoff for you is a personal decision.
| rleigh wrote:
| > you're working towards the betterment of humanity
|
| If only this was actually true.
|
| In reality, you're being taken advantage of and it's very
| manipulative and deceptive to make this claim.
| jghn wrote:
| Agree that not everyone will buy this. But it is why many
| people are working in positions that are otherwise worse on
| paper. It's up to them to decide if its real or not.
| bloqs wrote:
| "How high are you on trait agreeableness"
| [deleted]
| Simon_O_Rourke wrote:
| > 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't
| bothered to maintain their software for a decade?
|
| Amen, couldn't have said it better myself. I'm sure it's very
| worthy and all working on a genomics project that aims to
| eradicate some killer disease, but you need to live and provide
| for your family while you're doing it.
| rafiki6 wrote:
| It seems to me like we'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'm open to the idea if anyone wants to chat, let me
| know. I'm SWE but would want to partner with a Genomics Expert.
| lebovic wrote:
| I'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'll be paid like a researcher with the respect of a
| lab assistant - unless you have a PhD and a postdoc.
|
| That said, it's possible find work that'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'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
| (https://scholar.google.com/citations?user=RzVMRc0AAAAJ).
|
| To find those kinds of jobs, I'd try YC's Work at a Startup,
| Flagship Pioneering's portfolio companies, and emailing founders
| of companies that have a bioinformatics component (my email is in
| my profile!).
|
| I think the issues with the field are because it'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.
| ninala wrote:
| If you want to find good jobs like this, you should check out
| the monthly HN "Who is hiring" threads. There aren't that many
| biotechs, but there are a few (like ours). I agree about the
| need for better tooling. There's also a need for a stronger
| conceptual understanding of cell biology generally, and an
| ability to build an ecosystem of APIs that work well together.
| My email is in my profile if you'd like to talk more about this
| space.
| samtho wrote:
| 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.
|
| 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/yr you'd think the companies need to at least
| adjust their expectations.
| foooobaba wrote:
| Yeah, I agree, I looked into this before, and the pay doesn't
| come close to other swe jobs, as far as I have seen whenever I
| look. It is usually like 2x less, it's hard to want to choose
| that just to work on something a bit more interesting. I even
| have a background in bioinformatics, but I never found anything
| that compensates it as much as pure swe roles.
| the_only_law wrote:
| Yeah the low pay is one thing, but in my experience a lot of
| the academic jobs seem to want a domain scientist who can do
| programming, not the other way around.
| ninala wrote:
| Not always true - but finding a very good programmer who
| knows the domain well enough to make a significant impact is
| challenging.
| [deleted]
| captainoats wrote:
| If you're interested in genomics I'd recommend working for a
| commercial entity in clinical/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.
| whatever1 wrote:
| These should be separate in academia.
|
| SWEs cannot write code that maps equations that may change daily
| completely due to modeling / assumptions change.
|
| Too much focus on modularizing, premature optimization, useless
| unit testing etc. Who cares about all these if the underlying
| model is wrong?
|
| 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.
| sargstuff wrote:
| Umm..... software weather modeling systems map equations that
| may change daily completely due to modeling / assumptions
| change.
| cuttothechase wrote:
| I'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.
| rhn_mk1 wrote:
| What is the significance of that observation?
| theGnuMe wrote:
| Couple of things I know.
|
| 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...
|
| 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.
| sargstuff wrote:
| biologist / chemist will take the architecture studio approach,
| then develop math to shorten the write-up.
|
| research software engineer will develop the mathematics to
| describe things, then use the numerical system to write
| software to determine things.
| babuloseo wrote:
| 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.
| aWidebrant wrote:
| "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."
|
| Like others have pointed out, this really makes the engineer's
| end of the bargain sound like janitorial work. There'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.
| kzuberi wrote:
| > this really makes the engineer's end of the bargain sound
| like janitorial work
|
| I don't think you should interpret it that way. Another take
| would be that its like collaborating with a domain expert
| outside your specialization.
|
| Important is that your potential impact as an engineer can grow
| as you become more knowledgeable in the relevant bio. Most of
| the scientists I've worked with were happy to teach background
| (and some were just exceptional, fun times if you also found
| the field interesting as I did!). Obviously some allowance must
| be made for differences in culture from org to org, and that
| likely accounts to some of the disappointed voices - but I'm
| not convinced this is endemic to the field as opposed to
| organization specific. Just like with an opportunity with any
| particular company, do your research.
|
| Incidentally, working on a well defined
| engineering+optimization problem, if you are lucky enough to
| bump into one, is just candy for lots of engineering types. Ok
| quick & simple one: a scientist I worked with was doing some
| analysis that involved intersecting piles of genomic intervals
| with each other, which was taking many hours for a single run -
| super painful to tweak and re-execute. Our team showed them how
| to use interval-trees and made these available integrated in
| our internal tools, and the problem transformed into ~10 min
| execution runs. See, a wee a bit of comp-sci where suddenly
| you're the domain expert. And appropriately appreciated!
| sseagull wrote:
| I'm more familiar with chemistry, but a lot of times the
| scientist is the one who needs to make the first iteration to
| prove their idea. It's often the case you really don't
| understand the problem until you actually program/run the idea
| in at least a quick and dirty way.
|
| But the role of the software engineer after that is invaluable
| in making that idea accessible and reproducible.
| clmcleod wrote:
| Yeah I think this is fair enough after reading it back.
| However, that was not exactly my intention here, and I think
| this is a case of me needing to be more careful in my wording.
|
| When I said that software engineers add in the speed and
| reliability, I didn't mean they _only_ add in the speed and
| reliability: just that these two tenants of good software
| engineering where accounted for in this "correct" way of doing
| things (as opposed to the state of most genomics software that
| I described above).
|
| However, I can see how my phrasing can give the wrong
| impression about the contributions an engineer makes when the
| biologist and engineer sit down to do create the real thing
| together. In a positive environment, both sides (biologists and
| software engineers) share enough information with one another
| that the either can make contributions to the
| scientific/software engineering domain.
| sargstuff wrote:
| software engineer provides/developes the appropriate level of
| abstraction for the non-software engineer to make use of.
|
| Which if there's no standard for field, and working outside
| of a given field, makes writing grant(s) without paring up
| with someone who can develop field standards to be included
| in grant necessary. Hard to find/compete for scarce
| applicants using limited resources.
|
| aka startups vs. big company funding for pure research lab
| (bell labs, xero parc, etc)
| [deleted]
| moron4hire wrote:
| This is tangentially related to what I'm currently doing.
|
| I basically work in EdTech. The company is not an EdTech company,
| it's a education services company. I was hired on to develop
| software that we couldn't find in the market[0].
|
| I'm the process of building this _thing_ , we've been attending
| and speaking at conferences in our industry. And I'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'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).
|
| We would love to offer our software to researchers in our field.
| We've gotten feedback from several that what we are building is
| exactly the sort of thing they need. But they have _no_ money,
| and even if we were in a position to give it away for free, we
| can 't even make those connections come to fruition.
|
| So I don't know what to do. I really am thinking of starting to
| give it away for free, because at least we'd benefit from more
| research results in our field pricing the efficacy of our
| approach. But that's a really slow burn.
|
| [0] Specifics don't matter, but if you're curious, I make a VR
| environment for foreign language training emphasizing culture.
| mshockwave wrote:
| 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?
| neilv wrote:
| 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'll risk
| accidentally ending up on the other side of a distorted status
| system (not the side that normally pampers techbros).
|
| You need to feel out the particular person you'll be reporting to
| on how well they personally _respect_ and understand the role,
| and also whether they 'll have clout/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/teams with whom you'll be collaborating.
|
| You also need to check _compensation_ , so you don't wind up a
| low-paid person who later discovers they're competing for local
| house offers with others in the org who are getting big-bucks TC
| (plus consulting on the side).
|
| You also probably have to be OK with _never being the star_ (like
| you hypothetically could someday be in a software company).
| Supporting actors should still get respect and get paid.
|
| Find the right science situation, and you might have much more
| positive impact on the world than you could have in a software
| company, _while also being happy and comfortable_.
|
| Some more quick of-the-cuff comments about this (sorry for run-
| ons, but I need to get back to my weekend)...
|
| * 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'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.)
|
| (Some real-life instances of this I'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'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'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 "clean up" or "extend", 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.)
|
| * COMPENSATION -- Related to the above. If you're very
| experienced and marketable in tech, and would be making key
| enabling contributions, are you getting paid like it?
|
| (The most recent life sciences software engineering opportunity I
| talked with, with a high-profile organization, they needed FAANG-
| like Staff/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'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'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'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.)
|
| (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'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't entirely representative of the talent
| pool that included people for whom the tech company had
| showstoppers.)
| _dain_ wrote:
| your parenthetical paragraphs are bigger than your paragraph
| paragraphs
| asciimov wrote:
| Not quite a decade ago, I took some work for a lab to replace
| some aging software (circa 1990) used to do peptide synthesis.
|
| It was an enlightening experience. While I was the programming
| expert with a CS degree, I wasn't trusted for anything, because I
| wasn'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.
|
| 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.
|
| 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're not gonna be getting much money.
|
| Everybody lives and dies by the grant. If funding dries up, you
| will be out of a job.
|
| 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.
|
| Regulations, like ethics, you will have to bend to regulations.
| It's not a bad thing, just a different thing.
|
| 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.
|
| Loads and loads of ego. You will work with very smart and
| sometimes unreasonable people. Learning to navigate this with
| tact is important.
| aaauaucuggaa wrote:
| I will add Mammoth Biosciences to the list. We are looking for
| Software Engineers, Data Engineers, Data Scientists and more.
|
| https://mammoth.bio/careers/
| astatine wrote:
| I keep thinking of this space but don'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/hobby/learning mode.
| dottedmag wrote:
| This field does not _need_ software engineers.
|
| This field needs marketing, product and project managers (for-
| profit or non-profit variety) that could figure out:
|
| 1. what product to build to have the biggest impact
|
| 2. how to build it.
|
| Once 1. and 2. is clear it will be equally clear that if you have
| a bunch of scientists you won't get a great product, as nobody
| will build the product, everyone will build a prototype.
|
| 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.
| the_jeremy wrote:
| > Often, it's not required to know the domain before you join a
| group, and they will teach you on the job.
|
| I looked. There are zero full-time, remote roles that don't
| require previous genomics experience at any of the companies
| listed.
| clmcleod wrote:
| I know there are at least a few, because positions on my team
| offer remote and don't require and previous genomics
| experience.
| CoastalCoder wrote:
| Perhaps you and the GP could compare notes about where they
| searched and where you advertise.
| debacle wrote:
| Science programming jobs suck. You get all the bad parts of
| academia, including less money, plus you're seen as a janitor
| rather than an engineer, and you get to deal with scientists all
| day.
|
| Tooling roles in SWE in every other field are highly regarded.
| Why not here?
| sargstuff wrote:
| Well, math / computational power for simple, static protein
| modeling is horendus.
| tgv wrote:
| Because it's not what sells. It's literally a tool, and if you
| don't deliver the level of perfection they're used to get from
| sequencing, NMR or assay testing machines, you're the PITA. You
| really have to bring something very interesting to the table to
| earn some status, and software engineering just doesn't. It's
| too far from the core business. Think of the attitude SWEs have
| towards sales people...
| firstplacelast wrote:
| The thing is many will pay big bucks to
| contractors/consultants/IT services/LIMS systems, but if
| you're an employee, nope.
|
| They have a hard time having someone with a BS or MS making
| 50-75k more than a freshly-minted PhD.
|
| I just left a job in pharma because I cannot do it anymore
| (salary being a big one, but my experiences reflect many in
| this thread).
|
| They spent 500k on a consulting company to build a few NGS
| processing pipelines. This was built using a framework I was
| unfamiliar with. I re-factored one of them and was able to
| increase runtime by 60% in a couple weeks. I was paid in the
| low 100's.
|
| They would rather contract out the high-paid work and pay
| orders of magnitude more for it.
| convolvatron wrote:
| it depends. I've been in science support roles where people are
| genuinely grateful for the help, and its _really_ interesting
| to get to peek in on people's research.
|
| it depends on the role. it worked out really well for me when I
| got to drop in and do piece work on lots of projects in
| different fields. working on a larger software development
| project can be really painful and demoralizing because the
| people running it don't really understand how the sausage gets
| made.
| whimsicalism wrote:
| Call me when non-tech fields learn to treat engineers as equal
| partners rather than disposable labor.
|
| Academia? Yeah they're going to be one of the last to realize,
| PIs don't want to cede any power in their little fiefdom. Very
| familiar with the dynamics there.
| [deleted]
| sargstuff wrote:
| Scope of PI interest / funding defined by research grant.
|
| So, unless research is ground breaking / exploritory across
| disciplines, supporting disciplines tend to be extremely
| limited by PI research interest.
|
| aka (wording sanitized a bit) tends to come across as being
| tight wad / ham fisted
| sargstuff wrote:
| side note: Biological sciences tend to have way to many
| applicants for available positions. Typically not enough
| software engineers for available positions.
|
| Treating a position with limited available applicants as if
| there were to many available applicants is always a receipt
| for issues.
| JZL003 wrote:
| I work at the broad institute and it's a pretty cool place, can
| be long hours but they're investing heavily in software and the
| like. Can be a nice intermediate between research and
| applications
| zach_garwood wrote:
| You're not exactly selling it...
| foobiekr wrote:
| 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.
|
| 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.
|
| 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't think
| you have to to earn a good living, but you also don't have to
| work for companies that deliriously underpay you.
| JaDogg wrote:
| From what is said in the article and comments, this may be a good
| place to be if you are bootstrapping your own company.
| uvesten wrote:
| 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.
|
| 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...)
|
| 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"...
|
| Thanks, but no thanks.
|
| 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.
| rafiki6 wrote:
| Honestly, I think people like you are the right kind of people
| to start private enterprises and bring along professional
| software engineers to help you build something incredible in
| the space.
| rleigh wrote:
| There might me an opportunity for a company to enter this
| space, but then again maybe not.
|
| When everything is a mess of ad hoc Perl, Python and R
| scripts to solve unique one-off problems, you might well find
| that there isn't a sufficiently common subset of
| functionality that people are prepared to pay money for. That
| is, while the need may be there, the business case may not
| be. It might be that most of the field are quite content with
| the status quo.
|
| It's easier and cheaper to get some poorly-trained PhD
| students to wrangle badly-written and poorly-maintainable
| scripts than it is to pay a company to provide a robust and
| well-written solution instead. The "indentured labour" also
| distorts the supporting ecosystem. [I say this after having
| done a PhD in biomedical science.]
|
| I remember one of my colleagues asking me to help him getting
| some special software from a particular group working [for
| DNA methylation analysis]. They wanted paying $10K for it
| IIRC. It was a complete mess, wouldn't work, had not
| documentation, and I didn't trust it was genuinely functional
| it was just such a state. For a one-off, maybe $10K was worth
| it, but if you only have 2-3 customers worldwide who will
| pay, it's not a viable business if the product works
| perfectly, let alone if it's a fragile disaster that barely
| works at all.
| baran1 wrote:
| 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's a lot of work to be done in the area - my
| perspective is a little different. Although this doesn't apply to
| all genomics companies, I'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'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 :)
| sargstuff wrote:
| From past work experience & 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).
|
| aka need to be able to develop the dna / dna number system
| equivalent of things (aka something other than binary / punch
| card block based number system) such as:
| treesitter nyquest :
| https://en.wikipedia.org/wiki/Nyquist_(programming_language)
| slippery chicken :
| https://ccrma.stanford.edu/workshops/algorithmic-composition-
| with-slippery-chicken
|
| but wind up doing the equivalent of automated statistical
| analysis, because focus is NOT to develop software
| package/system.
|
| short broader subject take, what programming groups dont get
| about applicative programming vs. algol/block programming
| travisporter wrote:
| Clicking to highlight text is disabled. https://xkcd.com/1271/
| clmcleod wrote:
| My fault! I'll fix it when I can. Appreciate the report.
|
| Edit: fixed.
| runnerup wrote:
| I use "Stop The Madness" extension in Safari. Similar options
| available for Chrome.
|
| But this shit is so dumb.
| jerjerjer wrote:
| Hard no.
|
| Initial code would still be developed by SME, who:
|
| - Don't understand most programming abstractions
|
| - Don't see the advantage of a clean codebase
|
| - Would rather go back to their code spaghetti mess, than help
| figure out why some corner cases behave differently in a fresh
| codebase
|
| - Would still submit changes to their code spaghetti mess and
| expect you to apply them to the cleaned codebase
|
| 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.
|
| And that's not even taking compensation and work conditions into
| account.
| Raed667 wrote:
| I have a friend who works as a "make this mess a product we can
| show in conferences" engineer in a research center and it is
| literally what you described.
|
| The only reason he told me for still working there, is that:
|
| 1- the workload is fairly low
|
| 2- he has a lot of autonomy
|
| 3- he shows up every day around noon and leaves at 5PM
| [deleted]
| hrgiger wrote:
| I understand your point and you are completely right, but on
| their perspective your experience from multiple aspects of
| codebase is still valuable contribution and making a difference
| isnt it.
| wesleywt wrote:
| 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.
| zmmmmm wrote:
| yep ....
|
| One of the borderline fraudulent aspects of the field is the
| pretense that method publications are real software.
|
| That is, you come up with a break through statistical or
| algorithmic method, you get it to run exactly once based on
| whatever random walk of exploratory code got you to a result
| that looks better than competing/prior methods, and then you
| dump your workspace into a script and put it on Github and
| _pretend_ this is something anybody else could or should
| responsibly use in your Tier 1 publication. The minute the
| publication is approved there is zero benefit to the authors in
| maintaining the software, and in fact its better if nobody can
| run it because that way they can 't disprove your results. Then
| naturally nobody can get this to work afterwards and 50% of
| software engineering time and effort is trying to run code that
| can/never will work outside the context it was created in - but
| you have to try because this is now the accepted best practice
| method of doing X or Y based on its publication.
|
| The bigger problem is that this whole cycle actually shapes the
| view of software engineering by academics to the point where
| they really do think that most software engineering is a waste
| of time. A small number of 10x engineers manage to prosper in
| the environment, but it's mainly because they have the sheer
| technical capability to deal with ALL of that while still doing
| something useful, and it actually makes the problem worse
| because the academics then see that as the baseline for
| software engineering capability.
| danking00 wrote:
| I don't have any funding to hire right now, but I'm always happy
| to chat about the industry and my experience building Hail
| (https://hail.is, https://github.com/hail-is/hail), a tool widely
| used by folks with large collections of human sequences.
|
| The other posters are not wrong about compensation. Total
| compensation is off by a factor of two to three.
|
| However, it is absolutely possible to work with a group of top-
| notch engineers on serious distributed systems & 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.
|
| 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.
|
| 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.
| didip wrote:
| heh, you think scientists automatically understand computing
| nature?
|
| You'll be the janitor cleaning up their 20k LoC, one file Python
| with zero abstraction.
|
| If this is already a thing at a FAANG, it will be worse at a pure
| science shop.
| _Wintermute wrote:
| You'll be lucky if it's python, most likely thousands of lines
| of R by someone who doesn't know how to write a function or
| declare dependencies.
| sargstuff wrote:
| Ummm... messy python/R sounds lot better than messy numerical
| analysis in fortran with NO programming standards because has
| been used/modified for over 50+ years.
|
| Mainly because can find / write software to analyze &
| reorganize modern languages such as python & R into something
| human usable/readable.
| skosuri wrote:
| 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.
| thrway2342 wrote:
| > ADVANCED DEGREE HOLDING SOFTWARE ENGINEERS: consider working on
| genomics
|
| fixed the title.
| mherdeg wrote:
| What is the opportunity here -- writing new algorithms,
| implementing them accurately, optimizing them for special
| execution architectures, or just building more usable tools?
|
| I remember Manolis Kellis sprinkled some pretty interesting
| genomic questions into his Algorithm class's problem sets. There
| were a number of cool problems about optimally aligning strings,
| searching within text, etc.
|
| This was like 15 years ago and I haven't kept up with the
| discipline at all. But is there still algorithmic low hanging
| fruit?
|
| I do keep reading about an ongoing series of problems with
| Microsoft Excel distorting analysis in the scientific literature
| (https://www.nature.com/articles/d41586-021-02211-4) and
| wondering if the tooling is having trouble..?
| jltsiren wrote:
| > But is there still algorithmic low hanging fruit?
|
| Algorithmic bioinformatics has become a separate research
| field, because there are so many low-hanging fruit. Biotech
| companies create new instruments producing new kinds of data,
| researchers find new uses for the data, and new algorithmic
| problems emerge all the time. There is also a steady migration
| of people from theoretical computer science to bioinformatics,
| because it's often easier to get research funding for something
| bioinformatics-related than for pure CS.
| boldlybold wrote:
| We're only starting to see the age of genomics accelerated by
| GPUs. I think it's still early if you have the technical
| background.
| 331c8c71 wrote:
| Edico developed FPGA-based processing solution for common
| bioinformatics processing tasks (e.g. dna/rna mapping,
| variant calling) and the company was bought by Illumina.
|
| The product (Dragen) has been around for a few years and now
| will be integrated in the new generation of sequencers.
| Extremely impressive technology and a better fit for the
| niche compared to GPU-based solutions I have seen. More
| downstream processing and analytics is sometimes closer to
| traditional ML and naturally there are lots of GPU-based
| algos.
| boldlybold wrote:
| I'm more excited about NVIDIA's acquisition of Parabricks
| and the version 4.0 of the software that makes it free to
| use, than I am about DRAGEN. At the very least it's good to
| have some competition in the space, Illumina's stuff is
| always SO expensive. We'll have to see what hardware will
| win in the end.
| 331c8c71 wrote:
| > But is there still algorithmic low hanging fruit?
|
| I would say no unless looking at the frontiers of what is done
| in the wet lab which might require new analytical tools. But
| this stuff is probably much easier for and much better aligned
| with someone doing CS in academia.
|
| My impression that there is quite some space for ML-based
| approaches including DL. But even there I would not call it
| low-hanging.
| bmitc wrote:
| 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,
| 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).
|
| These organizations are also pretty traditional in their
| selection of stacks. Good luck trying to use a functional-first
| language, aside from _maybe_ 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".
|
| 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.
| laidoffamazon wrote:
| 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.
| geoffjentry wrote:
| Keep in mind that there are wetlabs with experiments being
| conducted in them. Lab techs will be coming and going at all
| hours.
| aednichols wrote:
| 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.
| hobofan wrote:
| > 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).
| geoffjentry wrote:
| > Good luck trying to use a functional-first language, aside
| from maybe Scala
|
| While they've moved away from it in the last few years, the
| Broad Institute had a huge investment in Scala. It's been in
| use there since at least 2010 and I believe longer. The primary
| software department was almost entirely Scala based for several
| years. That same department had pockets of Clojure as well.
| neilv wrote:
| > _I once saw a Python signature (function name and arguments)
| spill over 10-20 lines,_
|
| Quote I liked (can't find attribution; maybe Alan Perlis?):
|
| "If your function has 10 arguments, you're missing some."
| enraged_camel wrote:
| Yeah, I'd love to work in scientific computing and write
| Elixir, but it seems non-existent.
| faizshah wrote:
| 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.
| tdullien wrote:
| So if one was financially independent and wished to write
| something open-source in that field, where would the highest
| impact be?
| jdeaton wrote:
| Invent a new file format (or a few) for storing genomics data.
| They're all the rage in the bioinformatics field. Make sure not
| to document its semantics so that its implementation is the
| only spec.
| tejtm wrote:
| Ahh a "reference implementation" connoisseur
| raphaeljlt wrote:
| Quick plug here for Atomic AI ( https://atomic.ai/ ,
| https://boards.greenhouse.io/atomai ), 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.
|
| Shoot me a message at raphael@atomic.ai if you want to learn
| more.
| aschleck wrote:
| (chiming in here as a founding engineer at Atomic)
|
| So I spent more than 8 years as a SWE at Google, and now work
| here with both experimental biologists and machine learning
| scientists. And yes, a lot of the concerns mentioned in this
| thread are also things I have had anxiety about.
|
| Most obvious to me, being a software engineer at Google felt
| like being the center of the universe. Coming here, the focus
| is the scientific research. And yes, the scientists all managed
| to complete their PhDs so they don't necessarily need me to
| unblock them every second of their day. But contrary to my
| expectations, this has been remarkably freeing. I think one
| particularly important part of our company that makes this work
| is that, even on the science side, we're multidisciplinary (at
| a high level, emphasizing both experimental biology and ML.)
| And so engineering feeling like another arm of that multi-
| discipline nature is fairly... natural.
|
| The reason I feel it's freeing, and the reason I enjoy working
| here, is also the greatest challenge. Because the scientists
| are focused on the science, because they respect me and trust
| me to figure it out, and because they aren't constantly blocked
| by me, my job is mostly about dreaming extremely expansively
| about what I can do to reduce toil and make the scientists more
| productive. Of course they have feedback and input, but how I
| use my time and what I build is ultimately my decision because
| I am the engineer. And I have been able to do some things I am
| very proud of, like rolling out Bazel and Kubernetes and
| finding ways to seamlessly bring them into the cloud (we're
| even multi-cloud now without them even noticing!) On the other
| hand, it's very challenging because when you work on a product,
| say Google Photos, as a SWE, you always have some direct tether
| to the product ("what should we build next? ahhhh, well I guess
| we could just embed stable difficusion and a million people
| would immediately play with it".) At Atomic, my tether is very
| ambiguous. If I do my job successfully, they'll be able to do
| research more quickly (? effectively?), and eventually we'll be
| able to produce a therapeutic that hopefully changes the world.
| Identifying what I can do today to speed up that far outcome in
| the future is very challenging, but it is a far more
| interesting challenge than gluing some pre-existing software
| into my UI or running A/B tests to turn a red button blue.
|
| If, like me, you enjoy being given ownership over incredibly
| ambiguous problems, please do reach out!
|
| This role focuses on directly partnering with the biologists:
| https://boards.greenhouse.io/atomai/jobs/4726839004
|
| This role is expansive cloud infra:
| https://boards.greenhouse.io/atomai/jobs/4531035004
|
| And this role is directly partnering with the ML scientists:
| https://boards.greenhouse.io/atomai/jobs/4191285004
| ericb wrote:
| What would I need to get started on an open source genomics
| program?
|
| Where do they live? What do they do?
|
| 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'd look at to get started in AI,
| for example. But for genomics, it's a total mystery.
| hobofan wrote:
| > 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.
|
| 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'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.
|
| 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?
|
| > 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?
|
| What you propose sounds more like "hey, be the next idiot that
| commits to maintaining critical software for nothing", 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).
|
| If you want to have good software in the sciences, you first have
| to solve the OSS funding problem.
|
| PS: the `user-select: none;` on your page is really annoying
| jltsiren wrote:
| > 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 it. In
| bioinformatics, writing software is often a research activity.
| You write software to determine what the software should do,
| and then you adjust your ideas and rewrite it. The person
| writing the first version(s) of the software is a researcher -
| at least in practice if not by job title.
| hobofan wrote:
| 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, you can just stay up-to-date on ML
| trends and release a new paper that applies them every few
| years, in an almost automatable way.
| jltsiren wrote:
| 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.
| [deleted]
| LarsDu88 wrote:
| I do work in genomics.
| anonymous_bio wrote:
| The author completely neglects the downsides:
|
| - The compensation _absolutely_ 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 ( "Curing Cancer"). The role is actually
| just juggling various bioinformatics file formats.
| cratermoon wrote:
| > just juggling various bioinformatics file formats
|
| Your other points are spot on. This one I want to address
| specifically. The file formats. Academics _love_ their
| incredibly over-engineered file formats. MARC. SGML. DICOM.
| HL7. RDF. Those are just the ones I know. Universally, they try
| to cover every corner case that anyone could ever imagine.
| Academics absolutely love their ontologies. Just implementing
| one of them is a nightmare. Going from one to another is an
| exercise in the philosophies of ontologies.
| manv1 wrote:
| HL7 is't technically an academic file format, it's an
| industry standard interchange format for health data.
|
| DICOM is for radiology.
|
| RDF and SGML, well, they're from the same era as XML, so
| yeah.
| kweingar wrote:
| > Just implementing one of them is a nightmare. Going from
| one to another is an exercise in the philosophies of
| ontologies.
|
| Good thing there are lots of competing implementations! It
| would be a shame if these files were actually portable.
| zmmmmm wrote:
| Actually I think genomics / bioinformatics is a counterpoint
| there. One of the things I like about the field is nearly
| every file format is under-engineered. It's TSV all the way
| down and if you need compression gzip it. If you need to
| index that, sort it (literally often with unix sort command)
| and block-gzip it. Anything more engineered arose
| specifically because the above failed and something more is
| actually needed.
|
| The downside is it's a giant hellscape of unstructured,
| poorly specified formats where data types are barely
| specified at all or if they are most of the schema is
| published on some rambling blog post by some rando scientist.
| You will spend most of your time understanding it by
| empirical reverse engineering of the data that you are trying
| to deal with.
| boppo1 wrote:
| PIs?
| hobofan wrote:
| Principal investigator:
| https://en.wikipedia.org/wiki/Principal_investigator
|
| The person that runs a research lab, which at a university is
| usually a (tenured) Professor.
| rleigh wrote:
| Principal Investigators. Basically, the academics who get the
| grant funding and run their own research groups.
| BeFlatXIII wrote:
| - Marketing ("Curing Cancer")
|
| Nothing like putting that boilerplate pablum on research grant
| proposals. Either that or something about green energy. Some
| PIs just want to play with ligands, man.
| the_only_law wrote:
| > The role is actually just juggling various bioinformatics
| file formats.
|
| I need an advanced degree for that?
| cratermoon wrote:
| You do in academia. Otherwise you might as well be washing
| dirty labware for all the respect you get.
| tonto wrote:
| it is a meme that bioinformatics is just about converting
| different file formats but it's a shallow take
| possiblydrunk wrote:
| 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'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.
| awill88 wrote:
| > There is a significant gap between how software is currently
| developed in this space versus how it should be developed
|
| I appreciate the authors honesty. Been there, take it easy bud.
| YouWhy wrote:
| I am a career SW engineer that has worked on genomics in a
| startup. The field is genuinely exciting.
|
| 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).
| ninala wrote:
| Do you think that's true of pharmaceuticals/biotechs as well?
| Or just academia?
| tejtm wrote:
| Decades ago my very very bright HCI prof commissioned a psyc
| study for a database we were building for some biologists
| next door, you know so we could better address their needs in
| ways that would be useful to them. Details are pretty fuzzy
| anymore but they proved correct many times over.
|
| Things the study said would not work never worked i.e.
| biologists wanted "temporarily" private data, say until till
| published as psyc predicted they would never freely share it.
|
| but the biggest thing I will try to paraphrase:
|
| Biology is an observational, the work is in interpreting
| which lends to group dynamics and politics, leaders ect.
|
| Which is at odds with Math/CS which is constructive where if
| something can be proved then that is that.
|
| So when a CS person states a fact from their perspective a
| biologist might see it as just another opinion subject to
| hierarchical ranking.
|
| So I would argue it is a function the individuals
| proclivities and correlated training in the cultural
| environment they end up in.
|
| So a healthy work environment could value both fact and
| opinion where each has a complementary role whether academic
| or industry.
|
| But as a longtime academic, I am now sadly looking towards
| industry.
| elric wrote:
| Would love to, both out of interest and out of a belief that it
| might one day improve the world. But it's not happening. I have
| 20+ years of experience as a software engineer, but I don'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.
| gedy wrote:
| If you enjoy programming, don't work for fields or companies that
| view you as a cost center, it's a drag.
| spacemadness wrote:
| 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.
| metalforever wrote:
| 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'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.
| boppo1 wrote:
| Can you elaborate with some anecdotes? Why is their current
| workflow wrong? Why would an organization hire someone to build
| software if they can achieve goals with spreadsheets?
| maximus-decimus wrote:
| The fact they renamed human genes because they were importing
| it in Excel in a way it thought they were dates and was
| changing them says a lot.
|
| Can you really trust the scientific results if they depend on
| software made by people who don't care about code quality?
| boppo1 wrote:
| >renamed human genes because they were importing it in
| Excel in a way it thought they were dates
|
| Just at your shop, or the field in general?
| jghn wrote:
| Field in general [1]
|
| [1] https://www.theverge.com/2020/8/6/21355674/human-
| genes-renam...
| rleigh wrote:
| The whole field! This was actually a thing(!)
| myaccount9786 wrote:
| Why indeed.
| mdlm wrote:
| Those who are interested in the Broad Institute can reach out
| directly to me at mdelamaz@broadinstitute.org
| isoprophlex wrote:
| Do you do fully remote positions, from non-US timezones (eg.
| Western Europe)?
| lowbloodsugar wrote:
| Even large corporations in this space pay relatively little for
| software engineers, and treat them with little importance.
|
| I also experienced "software engineers" 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.
|
| To be fair, it looks like the same can be said for machine
| learning. Many software engineers I know are in the "machine
| learning space", but report that they are just operations support
| for data scientists, and don't actually get to learn about, let
| alone be involved with creating, the models they support.
|
| If you are a software engineer, work in a software company, where
| engineering is the value proposition.
| clusterhacks wrote:
| 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.
|
| There is next to zero demand for tool development internally. I
| do it _on the side of "normal" IT data management_ because I love
| high performance computing, algorithms, and multithreaded
| hackery. But even at my large, well-funded institution, there
| isn't a specific role where that is all that you do by design.
|
| I do _suck at marketing_ - 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.
|
| 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.
| sargstuff wrote:
| Ah, sounds so much like history of programming. At the 50's
| stage of straight up statistical manipulation.
|
| DNA base units not viewed as base 4 binary number system that
| can be transformed into an abstract software language, where
| can select abstraction level of choice to use. Much like
| musical notation not viewed as numeric system.
|
| Although, most software engineers don't view systems as
| numerical language development, too.
| sargstuff wrote:
| difference in view between qualatative & quantitative usage;
| NP vs. P type problem(s).
| robertlagrant wrote:
| > Of course, this would not be the fault of the individuals who
| maintain the software, who are often brilliant: it's just simply
| not fair to expect individuals to ensure this consistency using
| their own, ad-hoc processses
|
| I think this is a little generous. Engineers of all stripes
| should take responsibility for their work. If they say, "Yes I
| can add methylation analysis in three weeks," then they should
| make sure that means it's made well, with tests and all. I've
| definitely encountered people who don't communicate the scale of
| the task, and for most of them it's because they don't do
| software engineering; they do informatics scripting.
| sargstuff wrote:
| > "Yes I can add methylation analysis in three weeks,"
|
| virtual or reprogram the robotic arm?
| noname123 wrote:
| I just want to add my $0.02 to respond to the low pay and low
| respect as a Software Developer/Engineer in the genomics. This is
| 100% true and also not true [bear with me]... you get it back in
| the back end.
|
| 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 & 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.
|
| Just a data point of one, I took an online data science degree
| whilst working like 15hrs/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/automated trading. Now over the past 4 years, I'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.
|
| Now autonomy/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 "hot tech" company where I was bored out of my minds
| cranking CRUD widgets and re-learning JS frameworks every year
| and attending BS lunch n' 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's like being on the
| front-seat to a movie cinema or basketball court where the
| scientific evolution is happening. You'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'm still excited with
| the only disappointment that I will never learn it all.
|
| 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.
| bambax wrote:
| > _Google Genomics. Careers link._ > _Microsoft Genomics. Careers
| link._
|
| Google and Microsoft probably know how to make software?
|
| Side note: why does this page have user-select: none on body?
| It's annoying; what does it accomplish?
| [deleted]
| jghn wrote:
| Google Genomics is now aka Google Cloud Life Sciences. There's
| also their sister company Verily that operates in this space.
| cosentiyes wrote:
| There is also a research group: https://health.google/health-
| research/genomics/
| arnaudsm wrote:
| I hope this FAANG downturn will push software engineers to new
| industries, and bring some cross-pollination.
|
| What happens when the world's most brillant minds do something
| else than making us click on more ads ?
| zach_garwood wrote:
| If academics embraced software and software developers as
| heartily as advertisers did, you'd see that result. Until they
| do, I expect you'll continue to see a bunch of skepticism from
| developers.
| clmcleod wrote:
| Exactly my thoughts, and what I hope this post makes some
| consider.
| jesse__ wrote:
| Shameless self-promotion incoming.
|
| I'm interested in contributing to this field. I have significant
| experience in 3D graphics, game engines, compilers and language
| runtimes. I'm a competent low-level engineer.
|
| There's a lot of red-flags in this thread about adverse working
| conditions, but I'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'd love to
| hear from you.
|
| jesse@scallywag.software
|
| https://scallywag.software/resume.html
|
| EDIT: Largely interested in remote roles, but could relocate for
| the right offer.
| fastaguy88 wrote:
| 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.
|
| But I'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.
| j7ake wrote:
| 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.
|
| 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.
| iainctduncan wrote:
| 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.
|
| We had bad attrition to both more interesting and higher paying
| work. (I left for both after a year at the consultancy)
| denvaar wrote:
| I'm most definitely not an expert in this area, but I have
| recently taken interest in learning about "succinct data
| structures", which from what I understand have their place in
| bioinformatics.
|
| It'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.
|
| Normally when thinking about data structures and algorithms,
| we'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 "compressed"
| format. I think this comes in handy when doing things like DNA
| sequencing since data sets are so large.
|
| I'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's a few resources I'd recommend:
|
| Prof. Ben Langmead's YouTube channel:
| https://www.youtube.com/user/BenLangmead/featured
|
| Alex Bowe's blog has some good content:
| https://www.alexbowe.com/articles/
|
| Prof. Erik Demaine's "succinct" lectures from his adv. data
| structures course at MIT on YouTube:
| https://www.youtube.com/watch?v=3Y2weLDiUWw
|
| Edward Kmett's Haskell live coding session going into some
| details about succinct:
| https://www.youtube.com/watch?v=9MKEmNNJgFc
|
| There's also a lot of research papers, which you should be able
| to find by searching for "succinct data structures" (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.
| teekert wrote:
| 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].
|
| 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.
|
| [0] https://genomsys.com/
|
| [1] https://mpeg-g.org/
| tonto wrote:
| mpeg-g to me is probably bad for the field. sam/bam/cram is the
| way of the present and mpeg-g offers little over these formats
| and is patent encumbered. xref samtools developer blog
| http://datageekdom.blogspot.com/2018/09/mpeg-g-ugly.html?m=1
| teekert wrote:
| Hmm I agree with James. I bring the same points to my
| employer actually, they sort of listen but they like IP.
| quest88 wrote:
| Which open source projects need help, and why those?
| UncleOxidant wrote:
| 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?)
| jghn wrote:
| There are a lot more positions for people with advanced
| mathematics and/or science backgrounds with strong programming
| chops than there are typical software positions. But they do
| exist.
| jefftk wrote:
| 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
| boppo1 wrote:
| From a genomics layperson with decent dev skills:
|
| A. What are the broad and medium goals you work on?
|
| B. What are your daily activities? How do they fir into (A)?
|
| C. What does nonprofit genomics vs for profit look like from a
| revenue standpoint?
|
| D. What specific technologies/stacks are you using?
|
| E. The CRUD frontend+backend+database to serve users (and sell
| ads) is pretty ubiquitous in 'tech', with some branches. How
| does your field compare?
| jefftk wrote:
| A: The goal of my current project is to identify novel
| pandemics, even if they're caused by something we've never
| seen before, most likely by looking at growth patterns. At a
| broader scale, I'm trying to learn enough about working in
| this field that I'll be able to contribute on whatever future
| projects seem most appropriately important to me.
|
| B: unlike my previous work, I'm back to being an individual
| contributor. Very few meetings, mostly coding and analysis.
| Current thing is trying to understand what drives per-sample
| variability in wastewater sequencing data.
|
| C. Our group is currently philanthropically funded, and is
| focused on determining whether/how this is
| possible/practical.
|
| D. I'm mostly working in (bio)python, with a few bits written
| in C and gluing things together with bash.
|
| E. I was most recently working on (a) JS infrastructure to
| fetch and render ads and (b) working with browsers on
| platform features that would improve privacy, security, and
| efficiency.
| steakknife wrote:
| Are there any open source tools/projects worth contributing to
| that don't need specialized infrastructure, proprietary data,
| or a PhD in the field to understand?
| jefftk wrote:
| Almost certainly yes. For example, lots of things don't have
| tests and really should. But I'm not too sure about
| priorities, or about which projects would welcome that work.
| boppo1 wrote:
| F. The parent article mentions solutions are often custom made
| by one person. Can problems in the field be reduced such that
| extensible open-source frameworks could be applied? The way we
| have frameworks for webdev?
| jefftk wrote:
| I'm very new to this area, and am really not the right person
| to ask, but I'll try my best ;)
|
| In general you have frameworks when lots of people are trying
| to solve a large number of problems that look similar at the
| start and then will diverge. That's pretty web specific. I
| think instead in bio you mostly get (and will keep getting)
| modular tools and pipeline standardization.
| jdeaton wrote:
| 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 "all our code is
| awful- come fix it!"
| jugg1es wrote:
| I have a BS in neurobiology but have been working in software for
| 20 years. I'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.
|
| 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.
| pryelluw wrote:
| 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.
|
| PS. Feel free to reach out. Email in profile. I'll be happy to
| email around the subject.
| zmmmmm wrote:
| 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.
| mehphp wrote:
| 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.
| fxtentacle wrote:
| Google already axed all job offers, Microsoft and AWS are
| searching student interns...
|
| I used to work in genomics and computational biology. It was
| incredibly interesting. But it's university research and gets
| paid as such. 2-year time-limited contracts, lots of interns and
| students, extremely low salaries.
| cowsandmilk wrote:
| The AWS jobs aren't even related to genomics. They just have
| genomics in the description of types of workloads performed by
| customers of AWS. The jobs are hard core CS automated reasoning
| jobs.
| dankle wrote:
| > 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.
|
| True, but working in academia is very VERY different working in a
| tech/product company.
| pestatije wrote:
| > This state of affairs makes it difficult for anyone other
| than the original author to contribute to these code bases,
| further cementing the one-maintainer policy.
|
| Who wants to fix other peoples code mess? This is a no-no if
| you want to promote a job opening.
| cratermoon wrote:
| I do. It's my bread-and-butter. I call myself a code janitor.
| I live by books like "Working Effectively With Legacy Code"
| and "Kill it With Fire". But I have my limits. Academic code
| has.. coded, in the medical sense, and it can't be revived.
| Put a DNR on it.
| CoastalCoder wrote:
| I've seen this also in several software systems that started
| life in a CS grad department. (Not all the same university.)
|
| The original authors' quirks get enshrined in the code base,
| and its neigh impossible to fix until they leave the company
| that commercialized it.
| sargstuff wrote:
| sorta like the original calculus thesis.
| throwawaysleep wrote:
| 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.
| shadowgovt wrote:
| Average salary of $58k.
|
| Genomics companies: consider paying more.
| pengwing wrote:
| 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.
| whage wrote:
| I'd like to hear about this too!
| whitepaint wrote:
| This please. I would love to start working on (or create from
| scratch) some software that helps people in that field.
| 331c8c71 wrote:
| 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 breaks/fails.
|
| There are probably 100s of tools written for this but no
| clear winner so far. The traditional software engineering
| approaches like git, ci/cd seem too heavyweight (or rather
| too low-level) especially during development. IMHO there
| could be space for a fully remote/cloud solution where one
| would code/debug/deploy from the browser optimized for
| writing/maintaining pipelines.
| kzuberi wrote:
| 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?
| jinto36 wrote:
| Protein structure prediction was a huge deal, which is why
| AlphaFold received so much fanfare. It is actually pretty good.
| The next step is to predict where multi-protein complexes would
| interact- which is not just as simple as predicting the
| structure of two proteins independently and then trying to fit
| them together like a puzzle, because the the interactions can
| also change the structure. While it's not as hard as it used to
| be to experimentally determine protein targets of, for example,
| a protein kinase, it's still not an arbitrary or cheap
| experiment, and to do that for the many thousands of such
| proteins, across different conditions (stress, presence of co-
| factors, etc) and in different organisms would be rather a lot
| of work. Something like alphafold that makes reasonable
| predictions and can be used to help you focus on what's most
| likely to be relevant to your disease or process of interest
| helps quite a bit.
|
| There's also more need for integrating "multi-omics" data,
| where you have data from multiple assays (gene expression,
| phospho-proteomics, lipidomics, epigenetics, small RNA
| expression, etc etc) with the goal of somehow combining all
| these different assay results from various levels of gene
| regulation, to get closer to figuring out actual mechanism for
| complex processes. Building on that, we can also do single-cell
| multi-omics to some extent- where you have results from
| different sequencing-based assays on the level of the same
| _individual cell_. This is still pretty limited, but it 's
| exciting and advancing pretty quickly. This will eventually be
| combined with things like spatial transcriptomics, which is
| useful for mapping out what's going on in heterogeneous tissue
| samples like tumors, for example, so we'll end up with spatial
| single-cell multi-omics, at which point you're looking at 1)
| some quantitative trait for multiple genes/loci/molecules, and
| often 10k+ of such features at the same time per assay, 2)
| multiple assays, such as DNA accessibility and gene expression,
| in 3) single-cells, of which you might have 10k of in a single
| sample, 4) across a physical tissue sample where individual
| cells are spatially mapped, and where you probably want to
| figure out how cells might influence the state of those around
| them, and 5) in multiple different samples, where you might
| want to compare disease vs control, or look for correlation to
| heterogeneity of results within one group.
|
| There's a lot of public data already available for single-cell
| gene expression projects if you want to get a feel for how
| these things are structured and how (passable but not amazing)
| the existing tooling is- one of the main repositories for this
| data is the NCBI's SRA https://www.ncbi.nlm.nih.gov/sra but
| you'll quickly note that searching and browsing is not as easy
| as you might think it would be- because one of the main
| limiting factors in bioinformatics is how bad everyone is at
| keeping terminology consistent. For many bioinformaticians, a
| majority of time is spent in the data cleaning phase. It's
| awful. Sometimes the experimental parameters make it into SRA
| or GEO, but sometimes you have to read through the associated
| paper to pull that out. Often it's only large consortium
| projects like the The Cancer Genome Atlas (TCGA) or the
| Genotype-Tissue Expression project (GTEx) - which have enough
| funding for staff dedicated to data management- end up
| publishing datasets that are easy to "consume" without having
| to jump through a whole bunch of hurdles to figure out how the
| data was produced.
|
| I have a BS/MS in bioinformatics and I'm presently a PhD
| candidate in genetics and computational biology defending in
| February.
| jokethrowaway wrote:
| 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).
|
| Working in research in general doesn't seem to pay that well or
| the well paid jobs are few and far.
|
| Maybe it'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's a tangential aspect as well and
| doesn't impact much the actual business.
| joefreeman wrote:
| Thanks for posting this, and your learngenomics.dev resource
| looks great - I'm looking forward to reading this though. I
| recently started working as an engineering manager/lead in a
| genomics startup (https://www.genpax.co), and I've been picking
| this up as I go. I've also started working my way through the
| 'Micro binfie' podcast, which is great.
|
| Our company values software quality and we're very product
| focussed. We're actively hiring in London:
| https://news.ycombinator.com/item?id=33423547
| DonsDiscountGas wrote:
| I've worked on genomics, at the Broad. Can confirm there is a ton
| of toxicity. There'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.
|
| More broadly...shortages like this aren'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).
|
| 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're interested in the area.
| noname123 wrote:
| 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.
| noname123 wrote:
| 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 and I felt we were
| doin' important research - not just pipeline monkeys but
| actually performed important analysis like RNASeq
| differential analysis, ChIPSeq peak calling, metagenomics
| etc. on publications along with PhD scientists even if I
| didn't have the academic credentials. Groups within the Broad
| was running courses for Software Engineers to learn
| Biology... and you could literally take off middle of day to
| go across the street to Stata Center to attend lectures on ML
| or audit Comp Bio at MIT. Nobody would bat an eye. 75% of my
| group got a Masters degree on the job where we spent more
| time some months on classes than actual work.
|
| The culture somewhere shifted around 2018-2019... where they
| brought in new management to run DSP (Data Science Platform
| where most SWE's likely end up). The DSP management (not the
| chief guy) but lieutenants ran the "tech playbook"... get PM,
| Scrum/Agile coaches in; make software and comp biologists
| line workers.A lot of my fav. people either left or got
| pushed out. A lot of intuitional knowledge about sequencing
| and biology got lost, self-driven people left and line
| workers to work on Portal web development and Data pipeline
| management came in. To the point where I presented once to
| the software engineers of DSP and nobody in the room even
| knew the basic's like what is a long or short reads is. I
| left soon afterwards to a place where I wouldn't be silo'd. I
| wouldn't recommend the Broad to anybody now... unless you're
| working for an academic group. Avoid platform groups (DSP
| mostly; other platforms are still good) if you want to learn
| & grow.
| aednichols wrote:
| Current DSPer since 2017 and broadly agree with OP.
| bmitc wrote:
| 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.
| geoffjentry wrote:
| A really hard aspect to this is that there's a massive
| impedance mismatch between the research & production side
| of things. Working in the research side is pretty
| straightforward - although software development practices
| are going to be a lot looser & faster. Working in a
| production environment is straightforward, it's like any
| other software job. But - working at the confluence of
| those two states is incredibly difficult.
| AtNightWeCode wrote:
| Warning sign. You can't even select the text on the site.
| AtNightWeCode wrote:
| 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...
| AlbertCory wrote:
| 20 years ago I got interested in "bioinformatics." I loved
| learning something about molecular biology, after all those years
| of hearing about DNA and not understanding it. And "Molecular
| Biology of the Cell" is, hands down, the greatest textbook ever
| written.
|
| That said: a lot of the comments are spot on. You're working in a
| field where the hard scientists and business people rule and
| you're a helper. Maybe they're grateful for your help OR maybe
| they regard you as an overpaid lab assistant. After all, they
| have PhD's and postdocs, and you don't.
|
| I've never actually worked in that field. I'd guess that it might
| be very satisfying, despite the low pay. Or not.
| bluejellybean wrote:
| Molecular Biology of the Cell got me extremely excited about
| genetics and bioinformatics, highly, highly recommend this book
| to any software person I meet who is interested in biology.
|
| As to the work environment, it seems to be extremely varied
| depending on the lab and team your on. I came from a number of
| years doing web development in marketing and finance before
| joining an R1 university research lab, and in many ways the
| day-to-day is quite similar in both fields. You are not the
| 'go-to' person for most things, but with that said, even as an
| individual contributor I feel my voice is heard on technical
| decisions where appropriate. As for pay, it's the biggest
| aspect that will make me leave at some point. If you do not
| have a PhD, or even a degree in my case, you can't expect to
| get paid a lot. As to the speculation on the satisfaction of
| the work, it is indeed deeply satisfying!
|
| I got to have a conversation with one of the hero donors that
| gave a kidney biopsy after a life-saving transplant. It's hard
| to overstate just how impactful your work feels when talking to
| someone like that. Even as a small cog in the larger machine
| (our lab is around 50 strong with many people being at the top
| of their sub-fields), the end results of the effort will be
| massive improvements in individuals quality of life, this alone
| makes it quite easy to get out of bed in the morning.
| harles wrote:
| Any particular edition of Molecular Biology of the Cell you'd
| recommend? I just looked up the 7th edition on Amazon (seems
| like the latest) and it's $300 USD. Oof.
| AlbertCory wrote:
| I'm on #3.
|
| An awful lot has changed since 2000. RNA is now a Thing,
| where it was just a poor stepchild before. Protein folding,
| of course.
|
| But yeah. The pictures are shining examples of what a
| scientific diagram can be.
| rleigh wrote:
| I've still got my 3rd edition copy (from 1999 when I was an
| undergrad molecular biologist). Most of the basic
| biochemistry and molecular biology will be exactly the same
| --it hasn't changed much if at all. While there have been
| lots of additional details added over the last two decades,
| the fundamentals are unchanged for the most part.
|
| This wouldn't apply to other fields such as Immunology
| (Janeway's Immunobiology) where I have purchased multiple
| copies of the years due to the field changing so fast.
| somedudetbh wrote:
| Go on ebay and by the "international" edition
| wwweston wrote:
| What level of chemistry do you need to know in order to
| benefit from reading the text?
| [deleted]
| x0x0 wrote:
| I worked in the field. Leaving to work on ads immediately
| tripled my salary, and gave me more room to grow.
|
| Everyone who says you're the hired help and treated about as
| well as a secretary that the organization dislikes is dead on.
| At best, you're viewed as an overpaid cost center.
|
| Which is sad, because I'd love to work in these areas... but
| I'm not giving up 66% to 75% of my income to as charity to
| private corporations.
| rossdavidh wrote:
| Having worked (as a consultant/contractor) for a few businesses
| in the field, I can say that my experience was closer to
| "grateful for your help" than to "an overpaid lab assistant". I
| even recall once, in a meeting, being referred to (by a senior
| staff scientist with a Ph.D.) as "the technical guy", causing
| me to wonder at how someone who does gene sequencing thinks of
| programming as being more technical.
|
| But, YMMV.
| blep_ wrote:
| > causing me to wonder at how someone who does gene
| sequencing thinks of programming as being more technical
|
| Everything you don't understand looks complicated from the
| outside.
| tifik wrote:
| I have worked in a genomics lab after finishing a
| bioinformatics master's.
|
| It was my first fulltime job, and by far the most chill. People
| were great. The PI was laid back, the whole lab went out for
| beers every now and then - and not because of a mandatory
| startup-style 'bonding' event. We genuinely enjoyed each others
| company and hung out outside of work. I never had that in any
| other job, which were/are all commercial operations.
|
| The vibe and the power structure felt very different. More
| level. There werent any purely managerial roles, everyone was
| doing at least a bit of 'science'. And even junior ICs like me
| got to coach undergrads every now and then. Most of the
| operational budget comes from grants, on which you have to
| deliver. The pay is not amazing, so most employees really are
| in it for the science.
|
| Or I was still young and naive and was lucky all of the two
| layers of management were all nice people.
|
| Ultimately I left, as the grant money coudnt keep up with
| offers I was getting.
|
| It is still the job I am most proud of. I love talking about
| it, and it really sucks that even a well funded lab cant really
| afford market engineering rates.
| jonnycomputer wrote:
| I'm in a role that is very similar (different field though).
| However, I know enough about academia to know that alot
| depends on the culture the PI fosters. Also, I spend a lot of
| time learning the field.
| boppo1 wrote:
| >Molecular Biology of the Cell
|
| Tangential, but what are the chemistry prereqs to grasp this
| book?
| ninala wrote:
| The chemistry requirements are minimal. You should understand
| the difference between ionic and covalent bonds, how van der
| Waals forces work, hydrophobicity, solubility, and the
| effects of catalysts on reaction transition states. It will
| also be important to understand what reaction kinetics are
| and what pH means. An understanding of buffers might be
| useful.
|
| I would argue that, to understand the book, you specifically
| don't need to know electrochemistry, organic chemistry,
| analytical chemistry, organometallics, spectroscopy, or even
| physical chemistry.
| wenderful wrote:
| Fwiw, I studied humanities, do a lot of pop science reading
| in my spare time, and I'm able to appreciate it. There are
| more detailed and technical sections I skim or skip, but the
| overviews are fantastic. Incredible description of, for
| example, the sheer wonder we should all experience at the
| fact that all life starts as a single cell.
| timr wrote:
| MBC is readable by someone with an undergraduate background
| in science. You'd probably want basic knowledge of biology,
| general chemistry and organic chemistry.
|
| It's essentially an upper-level undergraduate textbook.
| AlbertCory wrote:
| I did get a book or two out of the library, plus I had Chem
| 101 in college, but really, not very much.
| tranzudao wrote:
| Probably just a college level gen chem class. Pretty
| accessible, albeit technical, textbook from what I remember
| of reading it for a course a few years ago.
| clmcleod wrote:
| > That said: a lot of the comments are spot on. You're working
| in a field where the hard scientists and business people rule
| and you're a helper
|
| This definitely was the culture when I started working in the
| field 6 years ago. However, the culture has shifted (at least
| where I work) to where biologists and engineers are equal
| partners that work together on solving these problems. For
| those organizations that are not this way, I think they're
| going to have to change if they want to innovate.
| jghn wrote:
| Agreed. Huge change over the last 10-15 years. My first job
| in the space had a view that _obviously_ a mere software
| developer wouldn 't be paid more than even a postdoc
| scientist. And as postdocs weren't paid all that well, you
| see where this is going.
|
| These days more biotech companies are
| computationally/software focused. They understand that to
| pull in strong talent they're not operating in the same
| academic science world.
| pclmulqdq wrote:
| That may be the case for engineers with PhDs and scientific
| credentials, but I'm not so sure that is true of normal
| developers who did not play the academic game. I'm not going
| to take a job based on the eventuality of a culture shift,
| and I don't think you should either.
|
| This isn't just genomics, by the way. Scientific computing
| folks are very similar.
| AlbertCory wrote:
| That's always been my impression, but it does sound like
| "software eats the world" has had some effect. At least in
| some places.
|
| Looking at it from _their_ point of view: CS people tend to
| think that "everything is just information, and _now that
| we 're here_ you're all going to be working for us."
|
| You can see why a PhD in mol bio would resent that.
| Everything is _not_ just information.
| rafiki6 wrote:
| I wish more fields would just start adopting the
| product/engineer partnership that Software companies have
| perfected. Engineers are very good at what they do. Product
| people are very good at what they do. They need each other to
| build things. Sure, engineers might know enough about product
| to get by and product people might know enough about coding to
| get by, but the reason it works is because each one is an
| expert in what they do and are equal.
|
| Its no different in finance, healthcare, genomics etc. I'd love
| to work in a setting where I'm paired with an SME product
| manager in a domain I have no clue about and they respect my
| work and I respect theirs and we are partners.
|
| This is one of the biggest factors that made software/internet
| companies explode. They respected people who build software.
| They didn't need to. A bunch of MBAs could have easily just
| decided that the best way to run the company was to treat the
| people building the product as a cost center. Many did. I think
| that's probably one of the reason for the lack of innovation
| and down fall in many old tech companies like HP/IBM.
|
| The ones that treated SWEs properly and valued them
| accordingly, did very well.
| jonathanyc wrote:
| I have heard from a friend who's a doctor that in hospitals
| there's a very adversarial relationship between doctors and
| MBAs. The MBAs see the doctors as a cost center, and the
| doctors resent people without MDs being above them.
|
| Your comment reminds me to be thankful that at many software
| companies engineering, product, and design do respect each
| other as equal partners. I totally agree that to do otherwise
| is business suicide.
| sargstuff wrote:
| to very opposing philosopies:
|
| MD's -> patient interest comes first
|
| MBA's -> company interest comes first
| olalonde wrote:
| Is it feasible to do any meaningful work in this field without
| joining a team? (e.g. as a solo hobbyist/entrepreneur)
| boldlybold wrote:
| If you have a software background and can get some basic
| domain knowledge, there's lots of open source projects that
| could use your contribution.
|
| Doing fundamental reseach is a taller order. But lots of
| software, tools, pipelines etc need maintainers,
| optimizations...
| quest88 wrote:
| Which projects? That seems like a good place to start.
| boldlybold wrote:
| I contribute to Nextflow core (https://nf-co.re/) It's
| more of a collection of pipelines than traditional
| software, but there are users all around the world and a
| good community.
|
| Most of the packages on bioconda
| (https://bioconda.github.io/) are open source. But you
| probably want to find a sub-field that interests you most
| before finding a project.
|
| In grad school, we also had an ex-google software
| engineer volunteer with us one day a week. It was very
| impactful for many members of the lab to learn good
| engineering practices, and it wasn't at all like the
| sentiment others in this thread are expressing where
| engineers were "janitors".
| attractivechaos wrote:
| Difficult but possible. For example, Robert Edgar [1] works
| alone and is one of the most productive developers in this
| field.
|
| [1] http://drive5.com
| dekhn wrote:
| I worked with Bob some ~20 years ago at Berkeley. he showed
| up one day to check out the seminars and see if he could
| "help out" after having sold his database company to Intel.
| he said he'd been trained as a physics guy in the 80s but
| there were no real jobs so he started a software company
| instead. He joined my advisor's group (it helped a lot,
| because at the time most journals wouldn't publish a paper
| submitted from a home address).
|
| He proceeded to completely understand hidden markov models
| and protein sequence alignment and was immediately hacking
| improvements to HMMER. However, Sean Eddy couldn't
| understand his optimizations (Sean has to know how HMMER
| works at all times) and so Bob went off and made his own
| tools like MUSCLE.
|
| One of the reasons he can do this is, well, he's a
| programmer/math genius, and the other reason is that HMMs
| and protein alignments are a fairly well understood and
| programmable thing these days.
|
| Still blows me away we train up all these people to be
| scientists when there are no jobs for them in that role.
| njbooher wrote:
| I don't work in this space anymore, but just want to say
| kseq (and the rest of klib) is such an awesome time saver.
| Thank you.
| d4nyll wrote:
| 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.
|
| It's the same reason why there's a lack of qualified computer
| science teachers in schools.
| dekhn wrote:
| 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).
| roughly wrote:
| I work at at a SynBio company and heartily second this. If you're
| looking for interesting work where you can make an impact, it's
| an incredible field to be in.
|
| I'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'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'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.
|
| At the same time, there'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't allow for that - everything that we'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're
| dealing with can vary from a few characters up to a couple
| megabytes (within the same represented "object"), 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've got some fiendishly
| complex problems.
|
| And at the end of all that, you'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's an incredibly exciting place to be, and I've found
| people are genuinely thrilled to have good software folks along.
| amrx101 wrote:
| 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
| Marsymars wrote:
| I left academia for that reason; there was no advancement path
| that didn't involve more advanced degrees, and that wasn't
| something I was interested in at the time.
| Cupertino95014 wrote:
| The bio & pharma & medical fields value academic credentials
| very, very highly. Too highly.
|
| That's their whole life: "where did you do your PhD? Who did
| you do your postdoc under?"
|
| Many world-class hackers would do pretty poorly on those
| questions.
| brofallon wrote:
| Most of the discussion here seems to assume bioinformatics /
| genomics jobs are academic, but I work for a clinical testing lab
| where production-quality code is a must. We're probably a 10/12
| on the Joel test.
|
| If you're into bioinformatics or genomics, but aren't excited
| about an academic setting, take a peek:
| https://recruiting2.ultipro.com/ARU1000ARUP/JobBoard/62cc791...
|
| We hire fully remote positions and starting salaries are about
| US$100k.
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