Re: Diabetes hacking (and data visualization)

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Benjamin West

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Feb 2, 2013, 5:32:46 PM2/2/13
to Jana Beck, mede...@googlegroups.com, Melissa Thielen, Bernard Farrell, Damon Muma, Aleksander Rozman
Nice.

Those sound like the right steps, I can help with both, although I'm not sure if my R installation is up to date.

I don't know when I'll be able to try running R and python; if you submit some gists with errors, I might be able to help/explain things.

For d3, I intend to get fork some of mike's boxplots and heatmaps to try and port your charts in gist/d3 soon.

Apologies, bl.ocks.org seems to be down for all examples (not just mine) ATM, as Bernard also noted.
It's not mine, it's a google app run my Mike Bostock.  It simply re-serves a gist as a pre-formatted web page.  This idiom (of re-using git-repos for other purposes, eg as the data-package for an application) is increasingly commone, ruby, node, python, et al all have package managers that intuitively deal with git-hosted repos for package management.  (I'm curious if we can create a git-phr, to manage medical records, independently of the application consuming it, and to audit what effects software has on those records.  With a git-phr, you could use a tool to compile the kind of report Jana created, and keep it around with your data, even if the app you are currently using doesn't know anything about it.  Forever.)

We do need a visualization gallery app, similar to bl.ocks.org, but focused on diabetic visualizations.  Bernard, I commend you for setting up hosting stuff.  I think github will serve most of our communication/infrastructure needs, but if you want to host bl.ocks.org for us so we at least host visualizations composed in gist or similar reliably, that might be compelling.  Or if someone wanted to come up with a gh-pages template for these visualizations, I'll port mine over and try to stub ut some more demos, and we can simply use github for this as well.

Finally, Damon, and I have begun exchanging commits to organize our efforts, so the ball is officially rolling. https://github.com/medevice-users/diabetes/tree/medevice and http://thedamon.github.com/opendatabetes/

Bernard, we will be using the materials you've collected under the diabetes wiki heavily, I suspect. :-)
Short term, I'm still scanning for people I've missed, eg, I know gcc is missing from the list (can you add it Andy?), and I'm also missing a bunch of links to things like http://www.cvast.tuwien.ac.at/projects/horizonvis and http://www.2aida.net/welcome/,

-bewest

On Sat, Feb 2, 2013 at 1:28 PM, Jana Beck <jana.el...@gmail.com> wrote:
Great! Melissa, nice to meet you! (I just followed you on Twitter too, although I'm barely on there.)

D3 is definitely my next step, and it's good to know that there are resources for help on that, as I am new to it. (BTW, I got errors on both of your demos at bl.ocks.org, don't know if that's their servers or something else.)

I've also started experimenting with hooking into R via Python here. My first effort was mostly unsuccessful (it does produce the boxplot, but efforts to hook into the ggplot2 package failed), but I talked to some of my academic colleagues who use R a lot more than I do, and they managed to dig up some more extensive sample code than what's in the RPy2 docs, so trying again is on my list of things to do.

Jana

On Thu, Jan 31, 2013 at 6:16 PM, Benjamin West <bew...@gmail.com> wrote:
Jana, your demoes are very nice.  Many of this is doable using d3.js

Have you seen the horizon charts advocated by Mike Bostock?  I keep thinking they might come in handy.

-bewest


On Thu, Jan 31, 2013 at 3:09 PM, Benjamin West <bew...@gmail.com> wrote:
The two of you may have overlapping skills that work well together.  Surprisingly few people know python.

Here's a rough outline of all my stuff:
Medevice - "github" organization for users who want medical data from the devices they own: https://github.com/medevice-users

Insulaudit is for auditing lots of devices,
the decoding-foo are each to decode that very specific type of device.

I've found gist/blocks/d3.js very useful for experimenting with d3.

Backend, wise I was thinking of having lots of daemons, communicating using json, and continuing to experiment feature by feature before attempting to tie together any monolithic web-app.

Does working altogether under the "medevice" org umbrella make sense?

-bewest

On Thu, Jan 31, 2013 at 2:46 PM, Benjamin West <bew...@gmail.com> wrote:
Howdy Jana,

You can add pcaps for the dexcom here: https://github.com/bewest/decoding-dexcom
I know python and javascript quite well.

I do javascript professionally for Meraki.com.  I've been practicing using d3.js and bl.ocks.orghttps://gist.github.com/4292338

I'm reading through your github materials.  I look forward to working together!
-bewest

On Thu, Jan 31, 2013 at 1:22 PM, Jana Beck <jana.el...@gmail.com> wrote:
Hi Benjamin,

Amy Tenderich just sent me a heads up about the Diabetes Mine piece on you today, and I was very glad to see it. I was one of the patient representatives at this year's DiabetesMine Innovation Summit, and I've been doing some hacking of my own diabetes data. My main interest is in analysis and visualization: you can see some of the charting I've done with my Dexcom data here.

I'm also working on creating an interactive visual logbook with my Dexcom data, insulin doses, meals, exercise etc. That's all in a GitHub project here, with a bit of a (messy) demo here. (My programming background is mostly Python that I use for scripting in my research as a Ph.D. student in linguistics. Now that I've been teaching myself more JavaScript and jQuery, I've got a lot of ideas for making the logbook more interactive and less messy.)

I'm following a couple of your repositories on GitHub now. Forgive me if it's on GitHub and I missed it, but is there any chance you'll be hacking the Dexcom? I am dying to get away from their Windows-only software to get my data out via their export-as-csv option.

I'm also sending you an invite to the Diabetes Hacks and Data Vis Google group I created after the DiabetesMine Summit.

Best,

Jana Beck





Bernard Farrell

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Feb 3, 2013, 5:40:52 PM2/3/13
to Aleksander Rozman, Benjamin West, Jana Beck, mede...@googlegroups.com, Melissa Thielen, Damon Muma
I've created a basic index page for databetics.org.

Tomorrow I'll add links for forums, wiki, etc to the front page. Please don't feel that you need to use this. I'm happy to add pointer to other projects.

Bernard


Diabetes questions? Diaboogle answers
  http://diaboogle.com/


On Sun, Feb 3, 2013 at 10:24 AM, Aleksander Rozman <andy....@gmail.com> wrote:
On 02/02/2013 11:32 PM, Benjamin West wrote:

Hi everybody !

Nice to see that everyone is so active on diabetes front... only problem is that I haven't received all of messegaes (actually this is the only one I received). Could we move this conversions into some list? I know that Ben opened some list on google so that we could talk?

Take care,
Andy

Damon Muma

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Feb 3, 2013, 9:09:29 PM2/3/13
to mede...@googlegroups.com, Aleksander Rozman, Benjamin West, Jana Beck, Melissa Thielen, Damon Muma
Is it possible to include the databetics website in the github repository so we can all go in and monkey with it? That would be kinda cool maybe. I only have a basic understanding of git and github, though. Is that what you were thinking for databetics Bernard or would you rather keep it as its own thing?

I like databetics.org as a name / address and I kinda like the idea of the movement having a kind of public face to direct people to an overview of what we want to do.. I can do some prettifying of it if anyone wants. Maybe not top priority, but it is a thing I enjoy doing ;)

Also is everyone on the medevice list? we could move to that from email just to have everything concentrated in one place
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