Sunday, November 18, 2012

Setting up an RDF server in VirtualBox, part 1

VirtualBox is an open-source virtual machine that you can use on Windows, Mac OSX, or Linux to run one of the other operating systems. Here I'll be using VBox on an Ubuntu Linux desktop machine to set up an Ubuntu server machine. The point in doing that when the two operating systems are so similar is to keep the two environments separate, and to discover what I'll need when I move the server to a VPS.

I'm doing this on a laptop with a 160 gig partition with Ubuntu 10.04 desktop. I can comfortably dedicate 20 gig to the virtual hard disk image. The VM will run Ubuntu 12.04 server. No shared folders because they won't be available on the VPS.

Make sure you have a good fast Internet connection for the Ubuntu desktop machine, and download the Ubuntu server ISO. It's available as 32-bit or 64-bit. If you're not sure about your CPU, you're probably better off with 32-bit. Set up VirtualBox:
$ sudo apt-get install virtualbox-ose

Now you'll find "VirtualBox OSE" in the Applications->Accessories menu in the upper left of the screen. Click on that, and when the window comes up, click on the light blue "New" icon. Pick a machine name, and Linux/Ubuntu as the virtual machine type, and give yourself a decent amount of RAM and hard disk space. It's nice to start the hard drive with 20 or 30 gig if you can spare it. Once the VM is created, go into settings for it, click "Storage" and click the third line with the CDROM icon. To the right of "CD/DVD device" click the yellow folder icon and navigate to the Ubuntu server ISO that you downloaded earlier. Set "Network" to the "Bridged adapter" option. Under shared folders, add your home directory (read only) and give it a name you'll remember. Now it's time to start the VM and install Ubuntu server on the virtual hard disk you've created. Before I could do this on my laptop, I found I needed to go into Settings->System->CPU and enable PAE.

During the installation process, you'll be asked what kinds of servers you want to run. Select "OpenSSH server" (so you can ssh/scp into the VM) and "LAMP server" (to get Apache and MySQL) and "Tomcat Java server" (to pick up a bunch of Java stuff you'll want for Jena). If you select an empty password for the root user on MySQL, you'll need to enter it multiple times, so you may want to select something almost as trivial like "root". You don't need to worry too much about security with a VM that will only be reachable on the local subnet.

When the installation is done, the machine will reboot, and the VM window will close and re-open. Go to the "Devices" menu at the top and under "CD/DVD devices", unclick the Ubuntu server ISO.

On to Jena. Looks like there is some good advice here, but some of it is dated so I'm tweaking it a bit:

Log into the virtual machine and type:
$ sudo su -
# chmod 777 /opt
# exit
$ cd /opt
$ wget
$ wget
$ for x in *.gz; do tar xfz $x; done
$ rm *gz               
$ mv apache-jena-2.7.4 apache-jena
$ mv jena-fuseki-0.2.5 jena-fuseki
$ chmod u+x jena-fuseki/s-*

Add these lines to your .bashrc:
export FUSEKIROOT="/opt/jena-fuseki"
export JENAROOT="/opt/apache-jena"
export CLASSPATH=".:$JENAROOT/lib/*.jar:$FUSEKIROOT/*.jar"

You'll want to copy some client-side Ruby scripts from the server's Fuseki directory to your host machine. My VM is at, so on the host machine I typed:
$ scp* .
I also needed to install Ruby on the host machine.

Now you can start up the Fuseki server and load it with some data. The docs for Fuseki are here. On the server:
$ cd /opt/jena-fuseki
$ ./fuseki-server --update --mem /dataset

This starts an empty database of RDF triples. This database is in-memory and non-persistent, and will vanish when you control-C. Back on the host machine, you can enter some data into the database:
$ ./s-put default family.rdf
$ ./s-put default wares.rdf

This is a small semantic graph talking about who in my family is married and whose kids are whose. To  make sure the data was actually stored, we can query it.
$ ./s-get default

This prints out the entire database in Turtle, an update of N3. Or we can get the same thing in JSON:
./s-query --service 'SELECT * {?s ?p ?o}'

I can see that I don't have the time and energy to get everything done in one sitting that I hoped I would accomplish. So this is part 1, and a part 2 will follow later, and I'll make sure they include links to each other.

Tuesday, November 13, 2012

A Semantic Network of Patient Data

This idea has two inspirations. One is this TED talk by Dave deBronkart or "e-Patient Dave". The other is the work that has been done on the semantic web and linked data.

Dave's talk is about patients taking control of their medical records and sharing them with other like-minded patients, so that they can learn from one another's histories and experiences. Some of these patients, including Dave, had terminal diagnoses and were able to improve or resolve those conditions because of having shared data with others.

The semantic web is the idea of formatting information so that computers can do more with it than simply store it or transmit it or display it on a screen. Computers can understand the meaning of the information much as a human would, so they can reason about it and draw new conclusions that aren't already spelled out. I first learned about it in a 2001 article in Scientific American. There are some more details here. I've blogged in the past about some of the basic ideas.

In the semantic web, all "things" (nouns, basically) are assigned URIs (web addresses). Relationships between things (and relationships are also things) are represented as RDF, where every statement is a triple of URIs, being a subject, predicate, and object. These statements are often printed or transmitted in XML, but the N3 language is more readable for people. Typical relationships look something like this.
  Will, town, "Framingham MA".
  Will, name, "William Ware".
  Will, pet, cat#12345.
  cat#12345, name, "Kokopelli".
  cat#12345, birthyear, 2003.
Strings ("William Ware", "Kokopelli") and numbers (2003) can be raw data, everything else is a URI. The idea is that a URI connects you to the rest of the semantic web of meaning, so if you don't know what a "pet" is, you can follow that URI, or query other triples with "pet" in them, to find out more.

You might wonder if it's silly to have such a primitive representation for knowledge. It allows the same kinds of economies of scale that we get by representing information in a computer with ones and zeroes. Because the format is so simple and uniform, we can build processing architectures that can be very efficient, and people have been doing that for over ten years. We have scalable databases for RDF, and when we set up rules that mimic set theory, we can build reasoning engines that extract new conclusions from the data.

When data is formatted with an appropriate ontology, it can be searched in rich complex ways, and computers can look for patterns and correlations that a human might not notice. When applied to patients' medical data, the results might be new medical knowledge or new treatment options.

There are other ways to find new information hidden in patient data. Semantic web technology is great for pure logic, but for quantitative measures (a dosage increase in this medication seems to cause a decreased amount of that neurotransmitter) we can turn to machine learning, where progress in the last decade or two has been explosive, given the data available on the web and the economic rewards for finding patterns in it.

An idea I've blogged about in the past (and spoken about at a couple of very small conferences) is applying this to general scientific literature, with the goal of hastening scientific progress and in particular medical progress (since I'm an old fart now and interested in that sort of thing).

If this topic interests you and you wish to discuss it, I'm starting a Google Groups forum for that purpose.

UPDATE: I've discovered that there is a company in Cambridge, MA called PatientsLikeMe which already pools patient data into a database, and sells subscriptions to that database. I don't know if they place the same emphasis on machine-tractable formats that I've done above. But knowing that somebody is doing it on a commercial basis, I don't see much point in trying to replicate that effort in my evenings and weekends.

Thursday, November 08, 2012

Node.JS on the Raspberry Pi

Most of this procedure is taken from a posting on Github by Sander Tolsma. His post is a little bit old and some of the steps he included can be skipped because the versions of things have become better synchronized. So very briefly, here is what to do, assuming you've successfully booted into Raspbian.

$ sudo apt-get install git-core build-essential
$ # IIRC, build-essential is already present on Raspbian
$ git clone
$ cd node
$ git checkout v0.8.14-release
$ #             ^^^^^^ update to most recent stable version
$ ./configure
$ make        # this takes a while
$ sudo make install

Voila, you're done. Type "node" at the Linux prompt and you'll get Node's ">" prompt. Then you can type in JavaScript and watch it run interactively, or you can create a file of JavaScript and run it.

pi@raspberrypi ~ $ cat > foo.js
for (var i = 0; i < 3; i++)
pi@raspberrypi ~ $ node foo.js

I'd like to import events from hardware so that they can take handlers, just like DOM event handlers running on a browser. One approach would be to run an HTTP server in Node and set up endpoints for the events I want to handle. That sounds like quite a bit of overhead for hardware events.

Alternatively, I could do what looks like the right thing, involving eventfd and its cohorts. I need to dig into the Node source code to see how to do that, and do more research in general.