5 ms·

I can't find the concrete idea behind this project..

Zikes 13y ago
Many areas of science can be and currently are improved through computing. Folding@Home is a great example of this, as are various projects that aim to use the web to detect planets by having people analyze data for transit anomalies. Unfortunately, many areas of science aren't funded well enough to support a team of CS majors to work with the scientists, and indeed many scientists might not even be able to identify what aspects of their work could be improved through computing. This project seems to be aimed at educating scientists to overcome those hurdles.
- toufka 13y ago
  Educating us is not the problem. We know. Just not much we can do about it. We don't have funding to hire coders/developers/designers. And even if we did, we'd likely spend it on that new microscope instead. Much of what we need doesn't require computational power, but requires a good input parser, a reasonable UI, and some basic (though absolutely solid) math. And a way to change a whole host of variables used in the computations without too much effort. I have a set of a few projects that a mildly competent coder could bang out in a relatively short period of time that would undoubtedly progress the whole field in which it was aimed. But that's pretty much like 20 people. 20 grad students - their bosses don't care if they count the data by hand over a week, or have a computer do it in 2 minutes. It's not worth anyone's (unpayable) time. So I code it myself - it's crappy, it's rough, but it gets the job done. But no one will ever be able to reuse that code. You hackers want to do something good for the world? Set up a hackathon thing for your local biology/chemistry grad students. In a weekends' time you can write a few open-source apps which would rapidly and noticeably affect the pace of cancer and other basic research.
  - Zikes 13y ago
    That hackathon idea sounds great, and even makes me wonder if it should be rolled into the curriculum of the university, perhaps as an assignment of some sort to an applicable computer education course.
  - jk4930 13y ago
    > biology/chemistry What are the low-hanging fruits I can aim for to get used to the problem domain? What are the relevant pain points that justify some hard thinking and coding? In the end what I have in mind is basically this: http://biomind.com/AI_Against_Aging.pdf http://biomind.com/AI_Against_Aging.pdf
    - Zikes 13y ago
      I've known for a while that Perl is really common in biology, and some Googling led me to a project called BioPerl[1]. It might be worthwhile to port that library's functions into other languages that could be beneficial to scientists, or use them to build specialized compiled tools that don't necessitate writing any code. [1] http://www.bioperl.org/ http://www.bioperl.org/
      - jk4930 13y ago
        And there are Biopython, Biohaskell etc., but from what I saw there this is more about bioinformatics (e.g., focus on gene sequencing). I don't know whether those are the problems the parent was talking about. From my experience (interviews) with labs it's more about the workflow (often pretty pre-computer) and quick&dirty software with terrible UI.
        toufka 13y ago
        There are a lot of much more basic (far less sexy) things a basic programmer can do that don't need much power. Being able to access those Biopython/biohaskell libraries entirely from a GUI would aid so many people. If you already know how to use python/haskell/fortran, then there is far less urgency in having a good UI or even using those really basic libraries. But there are a lot of fantastic biologists/geneticists/etc. who can reprogram the genes in a living tissue with alacrity, but run in fear from a command line.
    - simonster 13y ago
      As far as neuroscience goes, we need the following: - An open source GUI for sorting spikes. When you put an electrode into the brain, you often end up recording the "sounds" of multiple neurons firing. To make sense of what's going on, you have to identify which spikes came from which neurons. While there are fully automated algorithms for spike sorting, they aren't widely used because people don't trust them to work on real recorded data. Even if you use them, you probably want to check their results later, and you need a good GUI to do so. Right now, the "state of the art" is Plexon's Offline Sorter (http://www.plexon.com/products/offline-sorter%E2%84%A2 http://www.plexon.com/products/offline-sorter%E2%84%A2), which is slow, occasionally crashes, and costs thousands of dollars per license. It's mostly a GUI, and replicating it would probably not require much domain-specific expertise. The fact that it's closed source actively prevents the development of better partially supervised spike sorting algorithms. - Better fMRI data analysis tools. See https://news.ycombinator.com/item?id=5239530 https://news.ycombinator.com/item?id=5239530 for some previous discussion. - An open source replacement for MATLAB that is familiar to users of that language and encourages modular design and has a JIT that can achieve C-level performance. I am betting that this is going to be Julia (http://julialang.org/ http://julialang.org/), but there's still plenty of work to be done before Julia is ready for people without substantial programming experience. - Better tools for visualizing high-dimensional data sets. I'm not actually very familiar with what's been done in this domain, but I feel it's something that isn't often attempted because there's little overlap between experienced graphics programmers and scientists. A good way to visualize your data can save you days spent performing statistics.

Zikes 13y ago

Many areas of science can be and currently are improved through computing. Folding@Home is a great example of this, as are various projects that aim to use the web to detect planets by having people analyze data for transit anomalies. Unfortunately, many areas of science aren't funded well enough to support a team of CS majors to work with the scientists, and indeed many scientists might not even be able to identify what aspects of their work could be improved through computing. This project seems to be aimed at educating scientists to overcome those hurdles.

toufka 13y ago
Educating us is not the problem. We know. Just not much we can do about it. We don't have funding to hire coders/developers/designers. And even if we did, we'd likely spend it on that new microscope instead. Much of what we need doesn't require computational power, but requires a good input parser, a reasonable UI, and some basic (though absolutely solid) math. And a way to change a whole host of variables used in the computations without too much effort. I have a set of a few projects that a mildly competent coder could bang out in a relatively short period of time that would undoubtedly progress the whole field in which it was aimed. But that's pretty much like 20 people. 20 grad students - their bosses don't care if they count the data by hand over a week, or have a computer do it in 2 minutes. It's not worth anyone's (unpayable) time. So I code it myself - it's crappy, it's rough, but it gets the job done. But no one will ever be able to reuse that code. You hackers want to do something good for the world? Set up a hackathon thing for your local biology/chemistry grad students. In a weekends' time you can write a few open-source apps which would rapidly and noticeably affect the pace of cancer and other basic research.
- Zikes 13y ago
  That hackathon idea sounds great, and even makes me wonder if it should be rolled into the curriculum of the university, perhaps as an assignment of some sort to an applicable computer education course.
- jk4930 13y ago
  > biology/chemistry What are the low-hanging fruits I can aim for to get used to the problem domain? What are the relevant pain points that justify some hard thinking and coding? In the end what I have in mind is basically this: http://biomind.com/AI_Against_Aging.pdf http://biomind.com/AI_Against_Aging.pdf
  - Zikes 13y ago
    I've known for a while that Perl is really common in biology, and some Googling led me to a project called BioPerl[1]. It might be worthwhile to port that library's functions into other languages that could be beneficial to scientists, or use them to build specialized compiled tools that don't necessitate writing any code. [1] http://www.bioperl.org/ http://www.bioperl.org/
    - jk4930 13y ago
      And there are Biopython, Biohaskell etc., but from what I saw there this is more about bioinformatics (e.g., focus on gene sequencing). I don't know whether those are the problems the parent was talking about. From my experience (interviews) with labs it's more about the workflow (often pretty pre-computer) and quick&dirty software with terrible UI.
      - toufka 13y ago
        There are a lot of much more basic (far less sexy) things a basic programmer can do that don't need much power. Being able to access those Biopython/biohaskell libraries entirely from a GUI would aid so many people. If you already know how to use python/haskell/fortran, then there is far less urgency in having a good UI or even using those really basic libraries. But there are a lot of fantastic biologists/geneticists/etc. who can reprogram the genes in a living tissue with alacrity, but run in fear from a command line.
  - simonster 13y ago
    As far as neuroscience goes, we need the following: - An open source GUI for sorting spikes. When you put an electrode into the brain, you often end up recording the "sounds" of multiple neurons firing. To make sense of what's going on, you have to identify which spikes came from which neurons. While there are fully automated algorithms for spike sorting, they aren't widely used because people don't trust them to work on real recorded data. Even if you use them, you probably want to check their results later, and you need a good GUI to do so. Right now, the "state of the art" is Plexon's Offline Sorter (http://www.plexon.com/products/offline-sorter%E2%84%A2 http://www.plexon.com/products/offline-sorter%E2%84%A2), which is slow, occasionally crashes, and costs thousands of dollars per license. It's mostly a GUI, and replicating it would probably not require much domain-specific expertise. The fact that it's closed source actively prevents the development of better partially supervised spike sorting algorithms. - Better fMRI data analysis tools. See https://news.ycombinator.com/item?id=5239530 https://news.ycombinator.com/item?id=5239530 for some previous discussion. - An open source replacement for MATLAB that is familiar to users of that language and encourages modular design and has a JIT that can achieve C-level performance. I am betting that this is going to be Julia (http://julialang.org/ http://julialang.org/), but there's still plenty of work to be done before Julia is ready for people without substantial programming experience. - Better tools for visualizing high-dimensional data sets. I'm not actually very familiar with what's been done in this domain, but I feel it's something that isn't often attempted because there's little overlap between experienced graphics programmers and scientists. A good way to visualize your data can save you days spent performing statistics.