Project Notes

Jody — Fri, 12 Jan 2007 19:52:04 +0000

Semester Wrap-Up

Tam — Sun, 17 Dec 2006 19:04:01 +0000

Olga and I met yesterday. We got our survey requests for CREU so we want to make one final pass on the website and make sure it’s not too terrible. (One page somewhere still says “And it will be some text here.” Oops!)

I am not totally pleased with our progress this semester, though we did accomplish some things. I hope we have some time to work on things over the break, and I hope next semester will be a bit less hectic so we can really get somewhere.

Finals Week

Tam — Mon, 11 Dec 2006 14:53:39 +0000

It’s finals week. Normally this is a relaxing week for me because I “just” have a few tests and everything else is done. But this week I have about 15 sections of homework for my two math classes due, plus a 4-5 page paper, plus two scary tests. This is my worst end-of-semester ever.

So don’t expect much from me this week, is what I’m saying. I don’t think we’re going to meet.

Data Distribution

Tam — Fri, 08 Dec 2006 22:48:31 +0000

From today’s meeting with Olga I have a copy of a big page of handwritten notes about everything that can be measured about a patient (weight, blood pressure, etc.) and what the expected ranges might be. Olga was an endocrinologist, so she had lots of good subject knowledge, but we had to do a lot of unit conversions since she worked in Russia and they use metric there, of course.

(That sounds simple, and in some cases it is - kilograms to pounds or something. You can just type it into Google - something like “40 kg in lbs” - and get an answer. But for some things like A1C test results they really use totally different units for both numerator and denominator and the units are not common ones. It helped that we found some pages about the specific medical conversions.)

Olga doesn’t have a copier, so we had to figure out how to get me a copy of the notes. We ended up scanning them in and printing them out. It’s fun how computers are replacing all the other machines. (Olga has a lot of computers in her basement!)

Happy Birthday Tam

Tam — Sun, 03 Dec 2006 01:20:08 +0000

Today is my birthday. OK, yes, that’s irrelevant.

Last week was fall break and Thanksgiving, and I didn’t get that UML diagram done. It was kind of a pointless meeting this week for that reason. I felt bad about that. We mostly talked some more about data distributions, which I guess is going to be our next task - figuring out what data we expect so we can go write some code to put in that data, and then we’ll have data to start working with.

It’s turning into a digraph again!

Object Model

Tam — Sat, 18 Nov 2006 16:38:58 +0000

Things got a little hectic this week - next week (in other words, starting now) is our fall break (also Thanksgiving). I can’t believe the semester is so far along.

Anyway, yesterday Olga and I really hammered out our object model. It was a lot like when we did our database model - a lot of very productive arguing at the kitchen table with pencils in hand. I am going to make a UML diagram of what we came up this week so we’ll have something for Dr. Paul when we meet.

Objects, Research

Tam — Sat, 11 Nov 2006 05:45:58 +0000

Met with Dr. Paul this week. We showed him our DB model and started talking about the object model.

For doing actual intelligence stuff, of course, we want to read stuff out of the database, put it into some type of objects, and do our work with the objects. This is a big scary thing to think about (I get intimidated a bit easily sometimes), but we can try to start by designing the objects.

We also talked about needing to get some data into our system, and how we could write some software to put in fake data based on ranges & the distribution pattern of different items. (For instance, if we expect patient weights with a certain mean and standard deviation, in a normal distribution, we can build that behavior into the data-maker-upper, and that would give us better sample data than just randomizing everything.) Scary.

We also talked some about the need to do more research. I want to start by re-reading some of the sources I used in our original grant proposal; I only skimmed them when we were writing that (in kind of a hurry, as I recall).

Database Design

Tam — Sun, 05 Nov 2006 16:22:06 +0000

Olga and I met Saturday and we really did hammer out a database design. (It was more that than a data model, but it should roughly suffice for both.)

One big question between us was how to view the different pieces of patient information. Would we organize them around “visits” (like an office visit) or around individual items like tests, symptoms, etc. One thing that’s kind of difficult to remember is that you can always make it LOOK like it’s organized any way you want - you can make the user interface look like it’s organized by visit if you want, but then take the data and do whatever you want with it, and later spit it out a whole different way. Or the same way. Or a third way.

Anyway, we had a lot of arguing and I think it was really productive. (Of course by “arguing” I don’t mean that we were angry or anything like that. But for the first time we had actual real arguments about what to do, and I thought they went well, and that’s important.)

I think our database model is going to work well, at least as a start. It’s always possible we’ll scrap the whole thing later if it doesn’t work out.

Moving From Stack to Queue?

Tam — Thu, 26 Oct 2006 15:43:07 +0000

One of the things I have a problem with in projects (school, work, or personal) is when they morph into a stack data structure. For instance, if you’re thinking about something you need to do, but to do that, you first have to do another thing, and to do that other thing, you first have to do some other thing - that’s what I mean. Once the third or fourth things gets piled on top I tend to say “to heck with it” and go do something else. (Yeah, that’s not a very productive strategy, I admit.) It feels hopeless getting to the bottom.

Fortunately, one thing we do in our meetings with Dr. Paul is turn the impossible stack back into a queue - a list where it’s obvious what needs to be done next. (It’s really more of a perspective shift than anything.)

(Of course, our project is really like a tree or maybe a digraph - we could go in all kinds of directions at once. But that’s equally tricky to navigate.)

So, our next stage right now is to design the database to store our patient data. We talked with Dr. Paul about object-oriented databases but I think that might be more than we want to get into at this moment (projects within projects).

Oops, did I say database? I should have said “data model.” But as with so many things, I’ve mainly designed data models by designing databases (kind of like I’ve usually designed objects in Java by coding them first, though I can sometimes manage it the other way around).

Anyway, Olga and I are going to work on our ideas about that and then meet to hammer something out.

Subversion via CVSDude

Tam — Fri, 20 Oct 2006 18:07:36 +0000

“Subversion” sounds more interesting than it is - it’s just another cvs type of thing.

Anyway, Olga got us set up with a subversion repository on CVSDude. It looks like it’s going to be free (I don’t think we’ll need their premium services) and it seems pretty easy to use, so I think that’s going to be just great. Olga is a champ. She did that sometime this week and we worked with at her house earlier.

In one of those heart-stopping moments that sometimes happen around computers, Olga deleted some whole directory by mistake when I was at her house and for a moment it looked like we lost everything. But it had already been uploaded to the website so we were able to recover it (as is usually but not always the case with those heart-stopping computer moments). Whew.