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In a related article: "Tackling bioinformatics as a Webdev: Why is it so hard?" Maybe Webdev is just complex? But tbh, as a bioinformatician (in Next Generatio

In a related article: "Tackling bioinformatics as a Webdev: Why is it so hard?" Maybe Webdev is just complex? But tbh, as a bioinformatician (in Next Generation Sequencing mainly) I actually find Webdev easier. I mean, we face Bam files, Sam files, Cram files and annotate them with Bed files (with many different poorly documented standards) or GTF files depending on your Ensembl or UCSC references persuasion... Some file types are 0-based inclusive, some are 1 based exclusive, some call chromosome just ints (1,2, and then error when X, Y if you really assume they are ints) some call them chr1, chr2, chrX etc. We have fastq files with different quality encodings depending on their age, I recently had some strange errors, turns out the R2 of a fastq file is reverse complementary from the standard (why?!)... It's a mess and many people that spend years in the field still don't know more than just "choose one side and stick with it"... We also have a huge amount of frameworks for data analysis pipelines, Snakemake, Bpipe, Broad's WDL, etc, etc, etc. Not to mention the insance amounts of read mappers (BWA, RSEM, Tophat 1 and 2, Kallisto etc). Need I go on?

LifeIsBio 7y ago
That's super interesting. If someone asked me if bioinformatics was complex, I'd say "Yes, massively so." But then, I would take it in a totally different direction. To me, the complexity of bioinformatics come from the biology. How do you think about weird biological edge cases? What do your distributions look like and how do you choose thresholds? How do you even form a good question? Thinks like [B|S|Cr]am files are complex in their own way, but mostly they're just kinda annoying to have to figure out. You can dig in as deep as you need pretty easily. On the other hand, maybe I'm over-simplifying because I feel more comfortable in this domain, which I think is your point.
- teekert 7y ago
  Well, I come from Biology, always had Webdev as a hobby and then moved into bioinformatics which now turns towards software development. So Biology feels most familiar, but it is indeed also always complex. Btw, the files are ok and with effort can be understood and maybe some could even be considered elegant. It's just the shear amount of "standards" or rather the lack thereof.
yread 7y ago
Hah bam files are the pinnacle of engineering compared to the clusterfuck that is VCF: GT or PL? Ploidy? Enumerating all possible ALTs but some with 0 AF? And then you have mutations in cis, try to merge them. Which assembly - you can guess because it doesn't have to be specified. You also don't have to specify your transcripts and of course you have better defaults than everyone else. How many different formats for annotating mutation effects are there 10? 20? With webdev I can at least stick with jquery and do no harm
- collyw 7y ago
  > With webdev I can at least stick with jquery and do no harm The amount of time saved by doing this would be immense based on my experience inheriting maintenance projects in Anglaur / React / whatever flavour of the month framework was used. They may seem productive when developing, but trying to fix bugs in them can be an absolute nightmare.

LifeIsBio 7y ago

That's super interesting. If someone asked me if bioinformatics was complex, I'd say "Yes, massively so." But then, I would take it in a totally different direction. To me, the complexity of bioinformatics come from the biology. How do you think about weird biological edge cases? What do your distributions look like and how do you choose thresholds? How do you even form a good question? Thinks like [B|S|Cr]am files are complex in their own way, but mostly they're just kinda annoying to have to figure out. You can dig in as deep as you need pretty easily. On the other hand, maybe I'm over-simplifying because I feel more comfortable in this domain, which I think is your point.

teekert 7y ago
Well, I come from Biology, always had Webdev as a hobby and then moved into bioinformatics which now turns towards software development. So Biology feels most familiar, but it is indeed also always complex. Btw, the files are ok and with effort can be understood and maybe some could even be considered elegant. It's just the shear amount of "standards" or rather the lack thereof.

yread 7y ago

Hah bam files are the pinnacle of engineering compared to the clusterfuck that is VCF: GT or PL? Ploidy? Enumerating all possible ALTs but some with 0 AF? And then you have mutations in cis, try to merge them. Which assembly - you can guess because it doesn't have to be specified. You also don't have to specify your transcripts and of course you have better defaults than everyone else. How many different formats for annotating mutation effects are there 10? 20? With webdev I can at least stick with jquery and do no harm

collyw 7y ago
> With webdev I can at least stick with jquery and do no harm The amount of time saved by doing this would be immense based on my experience inheriting maintenance projects in Anglaur / React / whatever flavour of the month framework was used. They may seem productive when developing, but trying to fix bugs in them can be an absolute nightmare.