Summer Research

science-xkcdI’ve started a new research project this summer in Marcello Del Carlo‘s lab. Dr. Del Carlo is a new faculty member at Rush in the Department of Biochemistry. Our lab is affiliated with a clinical urologist faculty and we’re researching a urological disease called Peyronie’s Disease (PD) [Warning: male nudity]. From a biochemical perspective, we’re studying the process of growth and formation of a fibrous plaque underneath the skin of the male penis in a layer of connective tissue called the tunica albuginea. Currently, we’re analyzing both diseased and non-diseased tissue samples that have been surgically removed from patients with PD. In the future, we’ll also be working with a cultured fibroblast cell line doing similar work. So far we’re using Western Blots to identify and characterize proteins that are up- or down-regulated in diseased tissue compared to that of non-diseased. Our hope is that the studies will lead to a better understanding of PD and how the plaques form to aid in treatment.

In addition to research, Dr. Del Carlo is very interested in using FOSS as it relates to scientific research. By the time I met with him, he had already set up a database using PASSIM in order to keep track of tissue samples from patients. He also had the idea of using a WordPress blog as a sort of “online laboratory notebook”. I thought this seemed very in line with the Science Commons project, a derivative of Creative Commons. Science Commons is attempting to lower the barriers of scientific research, which is currently not nearly as “open” as it should be, considering almost all of it is funded by the U.S. Government. Most people believe that the fruits of governmentally funded projects should be available to the general public. In many cases, however, scientific research is locked down (for varying periods of time) due to copyright after being published in scientific journals. Since a scientist’s credibility is often judged by previous publications in journals, Science Commons is working to reduce the hold of copyright on this process, so that labs can publish data immediately to the web, allowing it to be indexed, freely searchable, and available immediately to anyone wanting to read it. This will continue to be an uphill battle since journals make a large amount of their money by licensing access to large academic institutions for their faculty. The idea that labs can make their data freely available on their own personal websites is being met with resistance. Still, I feel as a society we must push forward, despite the corporate interests, in order to do what’s best for the public. Plus, my thought is that journals will not suffer any major economic hardship. Their “seal of approval” by publishing the content will continue to be the scale by which research is judged. They would also continue to act as a collecting ground so that researchers looking for the latest data don’t need to worry about sorting through Google search results to find the latest findings in a field. Instead, some publishing groups have the gall to say that in order to publish in their journal you must leave the rights to your work on their doorstep, no matter who did the experiments. This will continue to be a very important issue in the scientific community in the future, and I’m hoping to gain a keener understanding of it over the next few weeks and months.

At least for now, I am the only one updating the Peyronie’s Disease Information Repository and it contains all of our experiments and results to date. Feel free to check it out, but unless it’s scientifically relevant, keep personal comments to my site.

Now with Identicons

I decided it would be a good idea to upgrade to WP 2.5.1 this morning. Unfortunately I made the mistake of not backing up all my files correctly and proceeded to delete my custom WP theme. That sucked, so I spent all day re-making it from scratch. J/k. Luckily ANhosting was able to provide me with a backup of the folder. I had one of my own but it was from a while back, so I’m glad they had a recent backup copy. In other news, I also added the new Gravatar support for Identicons to the comments. That means that now instead of the boring old “blank face”, anyone who posts a comment on my site that doesn’t have a Gravatar will be given an avatar created by running an algorithm on their IP address to generate an image of colors and shapes. See that? Pretty cool.


Lots of upgrades for me over the past 24 hours. The most relevant one is that WordPress 2.5 was officially released today, so my blog is now running on 2.5. What does this mean? Well not a whole lot for you readers unfortunately, given that the big changes occurred on the back-end (where I write my posts from). Two things you may notice are the introduction of galleries and Gravatars. I’ll try posting a bunch of photos in a gallery later.

Gravatars are “Globally Recognized Avatars”. To use them, you need to sign up for an account with Once you do that, you will need to upload an image that you’d like to use as your avatar (you can trim the image down after you upload it). Your image will be linked to your email address. A lot of websites (like this one), forums and other online services use email addresses to identify you. If they use Gravatars on their site, they’ll be able to display your image just by using your email address. Want to see it in action? Check the comments. A nice feature of Gravatar is that you can manage multiple email addresses and pictures all from 1 account, so there’s no worries if you get a new email address. Plus, if you ever want to change your picture, it gets instantly changed all over the web. Gravatars can also be integrated into email clients and more. Expect this service to take off considerably over the next few months.

The next upgrade probably won’t concern anyone, but I realized that my fonts on the new website weren’t displaying correctly on all browsers. Apparently I’ve been doing font sizes in CSS wrong for a long time. You should use pixels instead of points unless you’re designing something for print. So I changed a bunch of stuff, but hopefully for most people you won’t even notice a difference.

Finally, my big upgrade was installing Ubuntu Hardy Heron (beta) on my new Thinkpad T61 last night. Everything seems to be running super-smoothly so far; I’m really liking it. The “official” release is not scheduled to come out until April 24th, but considering how much I like Ubuntu, I thought it would be good for me to test it out and report any bugs I can find. Yeah right. This was just my excuse to install it a month early 🙂


I should be a plastic surgeon because I just gave my website a wicked face lift. This is a design I’ve been working on for quite a while now. I started it last spring/summer when I was thinking about making a blog. By the time I actually got the site up and running, school had started, and I had no time to finish the work. I just figured I’d limp along on Kubrick (the default WordPress theme) until I was able to get my design looking the way I wanted it to look.

This design is (at least in most respects) one that was started from scratch. I borrowed selected bits of code from Kubrick and elsewhere, but I have a good enough understanding of how WordPress works (or how to learn when I don’t) that I was able to just figure out what I wanted things to look like and tell WordPress what to do.

Some highlights include:

  • The theme should be ready for WordPress 2.5 (as am I :)), with support for Gravatars.
  • “Regular posts” and “Asides” are now displayed differently. Many of my posts (categorized as Attention Deficit) are what I’d consider an Aside. They’re usually short, sweet, and off-topic, and they likely contain a link and very little input by me. Regular posts are generally supposed to contain more input by yours truly (although depending on my mood, this may or may not be true). This is an example of a “Regular Post”.
  • Fancy new graphics. They’re everywhere. I’m not an artist. Sorry about that.

And there’s a little more on the way. I’ll be adding ShareThis links to every post. More importantly, I’m going to be assessing the structure of categories on the site. Personally, now that “tags” have been implemented in WordPress, categories seem more like a “post type” to me. For example, an “aside” is a type of post (as explained earlier). A “rant” is another type of post, and so is “news”. A post is “tagged” with key words pertaining to the subject of the post. Some of my categories don’t seem to fit this structure, so I’ll be working on my organizational skills to keep this place as clutter-free and logical as possible. Thanks to blogs like LifeHacker and ifacethoughts, I’ve come to understand the importance of organization and productivity in my electronic life. Now if I could only figure out the IRL version :p.

Let me know what you think of the new design. Don’t be afraid to tell me it sucks. If enough people don’t like it, I may change it back or to something else. If you don’t like all or part of it, let me know what specifically bugs you. Sometimes I feel like the design is somewhat disconnected (maybe because of the 2 ways to display posts on the front page), so this may be something I need to work on in the future as well.

If for some reason you’re interested, the source files for this design will be available on the Colophon (definition).

BuddyPress frees social networking

I’m a big fan of WordPress. It runs this blog, millions of other private blogs, and hundreds of thousands of blogs at It’s a great architecture for developing online tools and the community is one of the best around. Matt Mullenweg (lead developer of WordPress and founder of Automattic) announced today that Automattic has taken BuddyPress under its giant wing today to nurture the project into full bloom. BuddyPress is a social network based on WPMU, the framework behind It will be a social network that will connect me right where I am (this blog). And it will be FOSS that anyone can use, improve, and even create plug-ins for.

The important part of this is something I’ve felt for a long time. No offense to users of Facebook, MySpace or what-have-you, but I think this quote sums it up very nicely:

I am tired of data silos. I am tired of trying to keep up with every new site that comes along. I am tired of someone else owning my place on the internet. This is my place. This blog is me. Anyone who reads this I am sure will think I am strange that I mix my personal thoughts in with my programming frustrations. I don’t care. I write this for me because I own these bits and by hell they will do my bidding. –Justin Ball

I also enjoyed this Q & A on Techcrunch:

I asked Mullenweg if the world really needs another social network. His response:

The world doesn’t need another social network, it needs a thousand networks that let you own your data and interconnect using open standards. We invest countless hours giving our data to networks like MySpace, essentially sharecropping on their land for the privilege of being able to connect to our friends. It’s our friends, our time, our connections, our data — it should be our software.

I think only an Open Source solution can do that.

I can’t wait to see how this shapes up over the course of the next few weeks/months/years.

Moving Day

I’m moving my domain over from GoDaddy to my brand new ANhosting account. What difference does this make for you? Probably not much. I’ve been using ANhosting for a week or two with the RMstudents website and I liked them so much (and they were having such a good Halloween hosting special) that I decided to move my site over here. Plus now I can ping other websites without a problem! Namely the wonderful ping-o-matic.

WordPress 2.3 Released

WordPress 2.3 “Dexter” was released today. Despite the appeal of its new features, I’m going to wait to upgrade for a week or two until the plug-ins to get their kinks worked out. This big upgrade is part of the reason I’ve been slow to start adding features to my new blog. I think WP is going to be better than ever here in a week or so though…