5 ms·

Very cool. I think if you added a few more ways of slicing and dicing this data, you would have a decent chance at getting it accepted to a bioinformatics journ

by xaa 11y ago

Very cool. I think if you added a few more ways of slicing and dicing this data, you would have a decent chance at getting it accepted to a bioinformatics journal. For example, Oxford Journals Bioinformatics has an "Application Note" type of submission for useful programs that aren't quite original research. I work with one of the editors and he was impressed with the interface and thought it would have a good shot at acceptance. In particular I think there need to be options added to normalize the y-axis of the graph beyond raw counts to percentage of deaths by age group to control for the fact that the number of deaths per bin is not the same. It would also be nice to add a little more categorization to the causes of death, in a tree-like structure. For example, all vascular disease, with cerebrovascular disease, CVD, etc, as subtypes. Also it would be nice to be able to ask questions like, "which states have the most (or least) fraction of deaths by, e.g., CVD"? Do some states have smaller or larger gender gaps in particular diseases?

subcosmos 11y ago
I DO have a much larger viz in the works! It lets you cut down by race, year (1999-2013), and a few other metrics. I wanted to put this out first to see how it performs on various devices. Stay tuned! I come from an academic background. Made this in my PhD: amass-db.org But my core passion this days is the project that this viz is hosted at (www.infino.me). I think I can make a much bigger impact with more consumer-facing nonprofit apps than in publishing academic articles.
- xaa 11y ago
  Cool, I am looking forward to an improved version. I would be interested in your rationale behind how the public would/could use this kind of data. I think the infino.me/health seems to be an example, pointing out major risk factors behind cancer and CVD. But don't you think this is already common knowledge? Or is the primary goal to get people to voluntarily share their health and genotype data to get a big dataset for analysis, and maybe eventually provide a sort of personalized risk assessment? I wonder how the FDA views that sort of thing.
  - subcosmos 11y ago
    In short, I built a search engine for my genome. Im letting the rest of the world use it ;) I did my PhD work in diabetes genetics. It runs in my family, and Im kinda pissed that its killing off a large fraction of us. The eventual goal is to make this into some kind of communal science effort where people can contribute open source analysis pipelines. I need the right kind of organizational structure however to keep the data safe and centralized but still allow open source research. So, some kind of platform where algorithms can get in, results can get out, but raw data stays locked up. I want a world where this kind of research happens in the open, and not privately in biomedical corporations.
    - varelse 11y ago
      Type 2 is somewhat an opt-in disease, is it not? What pisses me off is how much can be done to prevent it and how little people are willing to do so, especially when their genes can tell them point blank that they really ought to be doing something and doing it right now before the very bad thing happens that will negatively impact them forever.
      - subcosmos 11y ago
        It's more genetic than people realize. In my PhD I focused heavily on the key gene responsible. Your stem cells are literally predisposed to become adipose tissue instead of muscle from the start. It sucks.
        varelse 11y ago
        So what happens when such a person eats relatively healthily and exercises regularly? Does this do any significant good or should they just accept the inevitable?
        subcosmos 11y ago
        It always helps. Some people just need to try harder. Much deeper, and more valuable, would be information on the optimal time of day to eat, exercise, etc, and more information on the specifics of the exercise needed (in terms of intensity or heart rate zones). TLDR, exercise matters, so does genome, but what we really want is more specifics. This might inform better lifestyle adjustments.

by xaa 11y ago

subcosmos 11y ago

I DO have a much larger viz in the works! It lets you cut down by race, year (1999-2013), and a few other metrics. I wanted to put this out first to see how it performs on various devices. Stay tuned! I come from an academic background. Made this in my PhD: amass-db.org But my core passion this days is the project that this viz is hosted at (www.infino.me). I think I can make a much bigger impact with more consumer-facing nonprofit apps than in publishing academic articles.

xaa 11y ago
Cool, I am looking forward to an improved version. I would be interested in your rationale behind how the public would/could use this kind of data. I think the infino.me/health seems to be an example, pointing out major risk factors behind cancer and CVD. But don't you think this is already common knowledge? Or is the primary goal to get people to voluntarily share their health and genotype data to get a big dataset for analysis, and maybe eventually provide a sort of personalized risk assessment? I wonder how the FDA views that sort of thing.
- subcosmos 11y ago
  In short, I built a search engine for my genome. Im letting the rest of the world use it ;) I did my PhD work in diabetes genetics. It runs in my family, and Im kinda pissed that its killing off a large fraction of us. The eventual goal is to make this into some kind of communal science effort where people can contribute open source analysis pipelines. I need the right kind of organizational structure however to keep the data safe and centralized but still allow open source research. So, some kind of platform where algorithms can get in, results can get out, but raw data stays locked up. I want a world where this kind of research happens in the open, and not privately in biomedical corporations.
  - varelse 11y ago
    Type 2 is somewhat an opt-in disease, is it not? What pisses me off is how much can be done to prevent it and how little people are willing to do so, especially when their genes can tell them point blank that they really ought to be doing something and doing it right now before the very bad thing happens that will negatively impact them forever.
    - subcosmos 11y ago
      It's more genetic than people realize. In my PhD I focused heavily on the key gene responsible. Your stem cells are literally predisposed to become adipose tissue instead of muscle from the start. It sucks.
      - varelse 11y ago
        So what happens when such a person eats relatively healthily and exercises regularly? Does this do any significant good or should they just accept the inevitable?
        subcosmos 11y ago
        It always helps. Some people just need to try harder. Much deeper, and more valuable, would be information on the optimal time of day to eat, exercise, etc, and more information on the specifics of the exercise needed (in terms of intensity or heart rate zones). TLDR, exercise matters, so does genome, but what we really want is more specifics. This might inform better lifestyle adjustments.