Comment by dekhn | Hacker News Reader

Comment by dekhn | Hacker News Reader

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Here's a link to the gene they mention: C7orf26 https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtMod...

To understand its function, it has its own wikipedia page(!) https://en.wikipedia.org/wiki/C7orf26 It's one of the remaining proteins whose "function" (to the extent that proteins can be said to have a "function") has not been reliably determined.

There are sites for protein function, my favorite is Uniprot: https://www.uniprot.org/uniprot/Q96N11

as you can see, they don't really know what it does: "Probable component of the Integrator (INT) complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing.".

The integrator complex is an important bit of machinery that helps transcript DNA to RNA on its path to protein expression: https://www.embl.org/news/science/at-the-core-of-the-integra...

In general, data presentation in biology is a pretty mixed bag. The field never attracted the level of UX investment that you see at ad-driven companies.

That’s true, software for biology tends to be terribly, almost comically bad, with one-off file formats, brittle data interchange, and impossible-to-maintain code being the norm. With user interface and ergonomics being the most neglected aspect. Why do you think that is?

Surely there is plenty of money in biology these days to hire a good designers to design good user experiences. Surely better user experience for biology software would lead to better understanding of biological systems and better outcomes in bioengineering.

Where are the polished, powerful design tools for biology like those that exist for other fields like online advertising that routinely process and distill huge amounts of lightly-structured data?

I've been trying to break into biotech for years...short answer is they want biologists, not programmers, and don't appreciate skillsets that aren't already secondary to PHD industry-relevant experience.

The reason why is it is easier to train a biologist to become a programmer than it is to train a programmer to become a biologist. Sure the quality of biologist-turned-programmer code will often not be great, but it will usually answer the question asked.

Not in my experience. The reason is because of funding. NIH grants are focused on biological discoveries and not so much around infrastructure. So you can get funding to build a tool, but not so much to maintain it. The downstream effect is that tools and websites are stuck in the era in which they were created, databases are not updated, and tools are broken because the grad student left and now there’s no one to respond to issues.

This is a seperate (important) issue.

Oh, so like Wall Street in the 80-90s, gotcha.

User interfaces for biology have drastically improved over the last 10 years.

Domain-specific tools like genome browsers, protein viewers, or phylogenetic explorers [1-3] almost all look and feel a lot better than they did in 2012.

The biggest exception here is UCSC Genome Browser, which has an old-school design and web technology stack. That said, it's steadily added features over the years, has substantially sleekened UX in its periphery, and remains widely used.

There are also bespoke visual design resources for biology applications that are good and getting better, like BioRender and PhyloPic [4-5]. There are multi-tiered packages like Dash Bio that wrap biology components together [6]. There's a Blender biology community, too!

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1. Genome browsers and components: https://jbrowse.org/jb2/, https://www.ncbi.nlm.nih.gov/genome/gdv, https://igv.org/app, https://eweitz.github.io/ideogram

2. Protein viewers: https://pymol.org/, https://nglviewer.org/ngl/

3. Phylogenetic explorers: https://clades.nextstrain.org/

4. https://biorender.com/

5. http://phylopic.org/

6. https://github.com/plotly/dash-bio, https://dash.gallery/Portal/?search=[Pharma]

The argument I've heard for such domain specific software having poor UIs is refined UIs only matter for a the first third "10,000 hours". After becoming an expert you simply become used to the software. Anybody professionally using the software would only see a _loss_ in productivity - even if the UI changes for the better.

See also Emacs, maybe?

Software quality improves once you move to older well-established problems, where developers who are not actively involved in research can contribute.

If you work with cutting-edge problems, the job of a programmer is turning vaguely expressed biological questions into software. The first attempts will inevitably fail, as they try to solve the wrong problem in the wrong way. Technical debt will accumulate at an incredible pace, as your understanding of the problem improves and the software becomes something very different from what you originally imagined.

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