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For an engineering community manager, that was an awfully rant-y way to make the point: "It's frustrating that researchers don't publish their code." Not to sa

For an engineering community manager, that was an awfully rant-y way to make the point: "It's frustrating that researchers don't publish their code." Not to say I disagree with the frustration... but it's also not something new. It's been this way for decades. I'd much rather hear about who is doing work in this space and what they're working on. Here are the ones I know of: 1. The Center for Open Science (https://cos.io https://cos.io) is one such org trying to fix this with the Open Science Framework [1]. 2. GitHub also recognizes the need for citable code and gives special discounts for research groups, in fact, Mozilla is one they work with [2]. Two smaller related startups are: 3. Datazar (https://datazar.com https://datazar.com) - A way to freely distribute scientific data. 4. Liquid (https://getliquid.io https://getliquid.io) - A scientific data management platform. Somewhat like "Excel for scientific data as a Service". Also, a related HN thread from some years ago: "We need a GitHub of Science" https://news.ycombinator.com/item?id=2425823 https://news.ycombinator.com/item?id=2425823 --- 1: https://osf.io https://osf.io 2: https://github.com/blog/1840-improving-github-for-science https://github.com/blog/1840-improving-github-for-science

asimuvPR 11y ago
Should also include Gitlab as option to Github. I have no association with them. Just a user of both platforms.
- lgas 11y ago
  Do they also give discounts to researchers or otherwise show awareness and support of this issue? Might be good to call attention to that fact.
  - asimuvPR 11y ago
    Researcher here: I Use Gitlab because I get everything for no cost as a regular user. With Github I had to pay and get limited features.
  - sytse 11y ago
    GitLab.com and GitLab CE are free to use. GitLab CE is used by many universities. If you use GitLab EE you don't have to pay for student users.
    - ptman 11y ago
      GitLab CE in almost any environment with more than one team (say uni course with many groups doing projects) would need ldap group sync.
      - sytse 11y ago
        The vast majority of universities that use GitLab use CE that has LDAP login but no sync.
nextos 11y ago
I like his rant. But at the same time, as an ex-CS grad student now doing biology, I wish my field was 1/10th as rigorous, tidy and beautiful as computer science. Code is a joke, most data is processed using "pipelines", which in reality means some irreproducible mess. People don't generally do research trying to understand how cells or tissues work, they generally write papers about "stories" they found. Only a small minority are trying to do some serious modeling using serious math.
- shanacarp 11y ago
  Now imagine being a patient reading those studies and knowing that. Struck a nerve
  - vanderZwan 11y ago
    Biology is related to medicine, but not researched quite the same way. Medicine certainly has it's own issues, but they're working on it: https://en.wikipedia.org/wiki/John_Ioannidis https://en.wikipedia.org/wiki/John_Ioannidis http://www.theatlantic.com/magazine/archive/2010/11/lies-damned-lies-and-medical-science/308269/ http://www.theatlantic.com/magazine/archive/2010/11/lies-dam... http://www.economist.com/news/science-and-technology/21598944-sloppy-researchers-beware-new-institute-has-you-its-sights-metaphysicians/ http://www.economist.com/news/science-and-technology/2159894... I mean really, the Churchill quote about democracy applies here as well: the current way of doing research is the worst possible way of doing it, except for all the other ways we've tried before.
    - shanacarp 11y ago
      I was thinking more along the lines of the Myriad Database http://www.theatlantic.com/science/archive/2015/10/filling-in-the-unknown-unknowns-of-cancer-genetic-testing/409828/ http://www.theatlantic.com/science/archive/2015/10/filling-i... VUSes that actually could be clinically significant are hoarded, and conversely, some companies claim to know that certain VUSes are not based on their own proprietary data that no one else sees/double checks. meanwhile the actual data comes from patients, who are left in the dark That's just cruel. Comparatively, at least CS gets math formulations
gautamdivgi 11y ago
I think the reason academics don't publish their code is that they don't want to get stuck into an endless discussion on the code along with people asking for "support" on it. What I have found is that if you need the code for a specific data analysis then send an email to the authors of the paper. More than ever you will be surprised. They do share code with fellow researchers. So - if you do really want code, write the email. Be forewarned though - the quality is often bad from a s/w engineering perspective and suits a very specific purpose. It will also come in a language of the authors choice (Tcl/Tk for ns2 scripts, matlab scripts, octave, etc.)
- derf_ 11y ago
  I've published code for most of my papers, and rarely, if ever, received support requests. When I have, it's usually been from someone else trying to do work with it, who asks good, intelligent questions (i.e., the requests you want to receive). Maybe that just means I don't write very interesting papers.
  - vanderZwan 11y ago
    I think you're doing pretty well if you've gotten more than zero supports requests, and they are all relevant to the topic too.

asimuvPR 11y ago

Should also include Gitlab as option to Github. I have no association with them. Just a user of both platforms.

lgas 11y ago
Do they also give discounts to researchers or otherwise show awareness and support of this issue? Might be good to call attention to that fact.
- asimuvPR 11y ago
  Researcher here: I Use Gitlab because I get everything for no cost as a regular user. With Github I had to pay and get limited features.
- sytse 11y ago
  GitLab.com and GitLab CE are free to use. GitLab CE is used by many universities. If you use GitLab EE you don't have to pay for student users.
  - ptman 11y ago
    GitLab CE in almost any environment with more than one team (say uni course with many groups doing projects) would need ldap group sync.
    - sytse 11y ago
      The vast majority of universities that use GitLab use CE that has LDAP login but no sync.

nextos 11y ago

I like his rant. But at the same time, as an ex-CS grad student now doing biology, I wish my field was 1/10th as rigorous, tidy and beautiful as computer science. Code is a joke, most data is processed using "pipelines", which in reality means some irreproducible mess. People don't generally do research trying to understand how cells or tissues work, they generally write papers about "stories" they found. Only a small minority are trying to do some serious modeling using serious math.

shanacarp 11y ago
Now imagine being a patient reading those studies and knowing that. Struck a nerve
- vanderZwan 11y ago
  Biology is related to medicine, but not researched quite the same way. Medicine certainly has it's own issues, but they're working on it: https://en.wikipedia.org/wiki/John_Ioannidis https://en.wikipedia.org/wiki/John_Ioannidis http://www.theatlantic.com/magazine/archive/2010/11/lies-damned-lies-and-medical-science/308269/ http://www.theatlantic.com/magazine/archive/2010/11/lies-dam... http://www.economist.com/news/science-and-technology/21598944-sloppy-researchers-beware-new-institute-has-you-its-sights-metaphysicians/ http://www.economist.com/news/science-and-technology/2159894... I mean really, the Churchill quote about democracy applies here as well: the current way of doing research is the worst possible way of doing it, except for all the other ways we've tried before.
  - shanacarp 11y ago
    I was thinking more along the lines of the Myriad Database http://www.theatlantic.com/science/archive/2015/10/filling-in-the-unknown-unknowns-of-cancer-genetic-testing/409828/ http://www.theatlantic.com/science/archive/2015/10/filling-i... VUSes that actually could be clinically significant are hoarded, and conversely, some companies claim to know that certain VUSes are not based on their own proprietary data that no one else sees/double checks. meanwhile the actual data comes from patients, who are left in the dark That's just cruel. Comparatively, at least CS gets math formulations

gautamdivgi 11y ago

I think the reason academics don't publish their code is that they don't want to get stuck into an endless discussion on the code along with people asking for "support" on it. What I have found is that if you need the code for a specific data analysis then send an email to the authors of the paper. More than ever you will be surprised. They do share code with fellow researchers. So - if you do really want code, write the email. Be forewarned though - the quality is often bad from a s/w engineering perspective and suits a very specific purpose. It will also come in a language of the authors choice (Tcl/Tk for ns2 scripts, matlab scripts, octave, etc.)

derf_ 11y ago
I've published code for most of my papers, and rarely, if ever, received support requests. When I have, it's usually been from someone else trying to do work with it, who asks good, intelligent questions (i.e., the requests you want to receive). Maybe that just means I don't write very interesting papers.
- vanderZwan 11y ago
  I think you're doing pretty well if you've gotten more than zero supports requests, and they are all relevant to the topic too.