13 ms·

For everyone reading this: if you are tired of making websites and iPhone apps for people to share their cat photos, and want to do something more consequential

For everyone reading this: if you are tired of making websites and iPhone apps for people to share their cat photos, and want to do something more consequential, consider going into computational genomics. Although Sanger sequencing was/still is used sometimes, the "next-gen" sequencing methods that have become centrally important over the last decade generate massive amounts of data that require a lot of computational analysis, something that most scientists in the field could use assistance with.

thearn4 13y ago
It is kind of a sad commentary on the state of things when so many of the brightest and creative minds of a generation are squandering the most productive years of their life writing software to enhance marketing and targeted advertising. And that these are efforts valued on the order of hundreds of billions of dollars.
- dekhn 13y ago
  And yet, by doing so, large piles of rational cash can be allocated to scientific research. See, for example, Gates Foundation, Rockefellar Foundation, Calico, etc.
- kamjam 13y ago
  I'm getting a lot of this feeling these days. This is an interesting post by the OP. I am going to investigate this more, it might up some avenues to explore further.
- dnautics 13y ago
  the false assumption is that all effort in the sciences is not similarly squandered. I assure you, most of it is. At least when you're making a better platform for cat pictures, you are presumably giving someone what they want and making their life marignally lighter. So much science is basically just politically connected higher ups getting money thrown at them for pursuits that if you stopped and thought about you would realize they were not.even.worth.it, or, being chased after by the wrong researcher. And in the process, the poor grad student (or postdoc) is having the best years of their life ground down. In 97% of cases, I'd say the cat pictures are of better social benefit.
dnautics 13y ago
What we need are tools that have a lot of input from people actually doing the wet work. The basics of how to do assemblies are more or less worked out, what we need are tools that actually fit with our workflow, and don't require us to kitbash pieces from different packages and have to run perl scripts to interconvert file formats.
yread 13y ago
I agree. They also need a lot of help with basic software engineering, versioning, specifications, databases, documenting....
- w1ntermute 13y ago
  Exactly. Someone who is only considered mediocre in a software company will be seen as an amazing software engineer if they are working with scientists. Many of these scientists are not using version control. They don't have proper websites for their software. The codebases are a mess, and the software is very buggy. This is all low-hanging fruit that most software developers will be able to fix (if the scientists whose code it is are amenable to those fixes - many times they are not).
  - dekhn 13y ago
    Actually, these days, most scientists who are at the forefront of computational biology have mastered github. They use markdown for README files, and produce md5summed data sets and command lines so you can repro their work. From what I can tell, this started 3-5 years ago when the kids coming into grad school picked up what the open source hackers were doing. To be clear: none of this is properly incentivized by the funders, so there's not much selection for this behavior.
    - yread 13y ago
      What use is an MD5 of dataset if its semantics should be clear from table and column names?
      - dekhn 13y ago
        Fileset checksumming addresses a different concern from the semantic content of the data. It's merely a way to ensure that two people send the exact same input files to a routine. It's a critical control.
- a_bonobo 13y ago
  It sounds as if http://www.software-carpentry.org http://www.software-carpentry.org might be something to join for most participants in this thread - a non-profit organization that runs bootcamps for scientists to learn proper coding, version control etc. I think they're always looking for more volunteers.
bthomas 13y ago
Well said. I work in the field and am looking for more hackers to join. I'm happy to talk with anybody that might be interested - email in profile
JunkDNA 13y ago
Those iPhone apps for cat picture sharing are valued at over a billion dollars by the marketplace, so it's kind of hard for developers to ignore. Truthfully, most of us in the field of biomedical informatics would have much more lucrative careers applying our scientific skills to figuring out how to get more people to click on advertisements. It's unfortunate because as I see it, most scientific software is universally awful. It suffers from poor usability, poor maintainability, poor stability. Whole swaths of software are abandoned because they were someone's PhD thesis and that person has since moved on. Another commenter here is right: version control, bug tracking, testing, etc... are all luxuries that are seldom employed. Shameless plug: If you're a hacker and interested in this stuff and want to help, we're always looking for contributors for our open source biomedical data discovery framework: http://harvest.research.chop.edu/ http://harvest.research.chop.edu/ We're trying hard to not do all the things I listed above.
- davecap1 13y ago
  Harvest looks very interesting! I'm a computational biologist in the field working on a startup called SolveBio (https://www.solvebio.com/ https://www.solvebio.com/). We're working on making the worlds biomedical data easily accessible to programmers and scientists. You might find it interesting and useful, especially to plug into Harvest.
  - JunkDNA 13y ago
    SolveBio is exactly what I've been looking for for some other work I've been doing. We're using Harvest to build a variant filtering and reporting tool for clinical applications. We want to integrate external resources but we don't want to have to waste time writing parsers and keeping up with that public data stuff. Drop me a note (email is in my profile) if you want to talk more.
  - yread 13y ago
    That looks really cool. I'm working on tranSMART ( http://www.transmartfoundation.org/site/scientistsclinicians http://www.transmartfoundation.org/site/scientistsclinicians ) - a tool for connecting phenotypical and genetical data, perhaps it would make sense to integrate the two. Drop me a mail on j.hudecek at nki.nl. Oh and if you could find a spot for me in the private beta, that would be sweet.

thearn4 13y ago

It is kind of a sad commentary on the state of things when so many of the brightest and creative minds of a generation are squandering the most productive years of their life writing software to enhance marketing and targeted advertising. And that these are efforts valued on the order of hundreds of billions of dollars.

dekhn 13y ago
And yet, by doing so, large piles of rational cash can be allocated to scientific research. See, for example, Gates Foundation, Rockefellar Foundation, Calico, etc.
kamjam 13y ago
I'm getting a lot of this feeling these days. This is an interesting post by the OP. I am going to investigate this more, it might up some avenues to explore further.
dnautics 13y ago
the false assumption is that all effort in the sciences is not similarly squandered. I assure you, most of it is. At least when you're making a better platform for cat pictures, you are presumably giving someone what they want and making their life marignally lighter. So much science is basically just politically connected higher ups getting money thrown at them for pursuits that if you stopped and thought about you would realize they were not.even.worth.it, or, being chased after by the wrong researcher. And in the process, the poor grad student (or postdoc) is having the best years of their life ground down. In 97% of cases, I'd say the cat pictures are of better social benefit.

dnautics 13y ago

What we need are tools that have a lot of input from people actually doing the wet work. The basics of how to do assemblies are more or less worked out, what we need are tools that actually fit with our workflow, and don't require us to kitbash pieces from different packages and have to run perl scripts to interconvert file formats.

yread 13y ago

I agree. They also need a lot of help with basic software engineering, versioning, specifications, databases, documenting....

w1ntermute 13y ago
Exactly. Someone who is only considered mediocre in a software company will be seen as an amazing software engineer if they are working with scientists. Many of these scientists are not using version control. They don't have proper websites for their software. The codebases are a mess, and the software is very buggy. This is all low-hanging fruit that most software developers will be able to fix (if the scientists whose code it is are amenable to those fixes - many times they are not).
- dekhn 13y ago
  Actually, these days, most scientists who are at the forefront of computational biology have mastered github. They use markdown for README files, and produce md5summed data sets and command lines so you can repro their work. From what I can tell, this started 3-5 years ago when the kids coming into grad school picked up what the open source hackers were doing. To be clear: none of this is properly incentivized by the funders, so there's not much selection for this behavior.
  - yread 13y ago
    What use is an MD5 of dataset if its semantics should be clear from table and column names?
    - dekhn 13y ago
      Fileset checksumming addresses a different concern from the semantic content of the data. It's merely a way to ensure that two people send the exact same input files to a routine. It's a critical control.
a_bonobo 13y ago
It sounds as if http://www.software-carpentry.org http://www.software-carpentry.org might be something to join for most participants in this thread - a non-profit organization that runs bootcamps for scientists to learn proper coding, version control etc. I think they're always looking for more volunteers.

bthomas 13y ago

Well said. I work in the field and am looking for more hackers to join. I'm happy to talk with anybody that might be interested - email in profile

JunkDNA 13y ago

Those iPhone apps for cat picture sharing are valued at over a billion dollars by the marketplace, so it's kind of hard for developers to ignore. Truthfully, most of us in the field of biomedical informatics would have much more lucrative careers applying our scientific skills to figuring out how to get more people to click on advertisements. It's unfortunate because as I see it, most scientific software is universally awful. It suffers from poor usability, poor maintainability, poor stability. Whole swaths of software are abandoned because they were someone's PhD thesis and that person has since moved on. Another commenter here is right: version control, bug tracking, testing, etc... are all luxuries that are seldom employed. Shameless plug: If you're a hacker and interested in this stuff and want to help, we're always looking for contributors for our open source biomedical data discovery framework: http://harvest.research.chop.edu/ http://harvest.research.chop.edu/ We're trying hard to not do all the things I listed above.

davecap1 13y ago
Harvest looks very interesting! I'm a computational biologist in the field working on a startup called SolveBio (https://www.solvebio.com/ https://www.solvebio.com/). We're working on making the worlds biomedical data easily accessible to programmers and scientists. You might find it interesting and useful, especially to plug into Harvest.
- JunkDNA 13y ago
  SolveBio is exactly what I've been looking for for some other work I've been doing. We're using Harvest to build a variant filtering and reporting tool for clinical applications. We want to integrate external resources but we don't want to have to waste time writing parsers and keeping up with that public data stuff. Drop me a note (email is in my profile) if you want to talk more.
- yread 13y ago
  That looks really cool. I'm working on tranSMART ( http://www.transmartfoundation.org/site/scientistsclinicians http://www.transmartfoundation.org/site/scientistsclinicians ) - a tool for connecting phenotypical and genetical data, perhaps it would make sense to integrate the two. Drop me a mail on j.hudecek at nki.nl. Oh and if you could find a spot for me in the private beta, that would be sweet.