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.
Consider working on genomics
131–140 of 299 posts
Re: Consider working on genomics
#132> 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?
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Re: Consider working on genomics
#133I 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.
Re: Consider working on genomics
#134"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.
Re: Consider working on genomics
#135The 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.
Re: Consider working on genomics
#136What 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..?
Re: Consider working on genomics
#137Anecdata, 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…
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.
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.
Re: Consider working on genomics
#138Hard 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 auth…
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
Re: Consider working on genomics
#139Hard 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 auth…
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Re: Consider working on genomics
#140> 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.