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> New CRISPR-based map(ping process) ties every human gene to its function Maybe it's because I'm not in that industry, but I was looking for a graphical gizmo

> New CRISPR-based map(ping process) ties every human gene to its function Maybe it's because I'm not in that industry, but I was looking for a graphical gizmo that I could click on a gene and see functions but they mean "map" in its functional programming term Although clicking through the first link does say "Interactive Website under construction..." so maybe this was just submitted too early or something

caycep 4y ago
it seems like that is a whole other skillset vs. biology graduate students...I know the Allen Institute employs data vis people to write visualisation tools like this in d3/react or whatever the web api du jour is, but they are separate from the science folks
dekhn 4y ago
Here's a link to the gene they mention: C7orf26 https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr7%3A6593761%2D6612466&hgsid=1375192377_nrQXzaDA44NJQx2z41IdMAi7nNRU 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 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 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-integrator-complex 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.
- lysozyme 4y ago
  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?
  - Psyladine 4y ago
    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.
    - danieltillett 4y ago
      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.
      - timy2shoes 4y ago
        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.
        4y ago
popcube 4y ago
you can just try ensembl or ucsc genome browser
jhgb 4y ago
> but they mean "map" in its functional programming term We just called it "mathematical term" back in the day. :)
- aaronblohowiak 4y ago
  Paging doctor Church, paging doctor Church, your patient Turing is here to see you
hyperpallium2 4y ago
...but it's not a function function, because one gene can have many functions.
- bumby 4y ago
  For those interested in further reading: https://en.m.wikipedia.org/wiki/Pleiotropy https://en.m.wikipedia.org/wiki/Pleiotropy

caycep 4y ago

it seems like that is a whole other skillset vs. biology graduate students...I know the Allen Institute employs data vis people to write visualisation tools like this in d3/react or whatever the web api du jour is, but they are separate from the science folks

dekhn 4y ago

Here's a link to the gene they mention: C7orf26 https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr7%3A6593761%2D6612466&hgsid=1375192377_nrQXzaDA44NJQx2z41IdMAi7nNRU 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 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 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-integrator-complex 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.

lysozyme 4y ago
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?
- Psyladine 4y ago
  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.
  - danieltillett 4y ago
    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.
    - timy2shoes 4y ago
      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.
      - 4y ago

popcube 4y ago

you can just try ensembl or ucsc genome browser

jhgb 4y ago

> but they mean "map" in its functional programming term We just called it "mathematical term" back in the day. :)

aaronblohowiak 4y ago
Paging doctor Church, paging doctor Church, your patient Turing is here to see you

hyperpallium2 4y ago

...but it's not a function function, because one gene can have many functions.

bumby 4y ago
For those interested in further reading: https://en.m.wikipedia.org/wiki/Pleiotropy https://en.m.wikipedia.org/wiki/Pleiotropy