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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 gen
by clusterhacks 4y ago
I work in this field at a large medical research institution. There is a significant amount of genomics analysis that occurs here on a day-to-day basis. The genomic processing pipeline work all falls directly into my group.
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 4y agoAh, 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 4y agodifference in view between qualatative & quantitative usage; NP vs. P type problem(s).
- mfld 4y agoGreat post - which contains the answer to many of the questions raised in this thread. I am working in this area as well. There is "next to zero demand for tool development" because there are great open source tools. Only in rare cases (e.g. Illumina Dragen), a commercial software adds significant value that the audience is willing to pay for.