Monthly Archives: December 2009

Moving Mobile Metagenomics Forward

This afternoon I began working on integrating my graph code from the proof of concept into MM-proper. As I looked through my code I noted a lot of places where there are things I’d like to clean up / reorganize / word differently throughout my code. I had been holding off on doing a lot of this because we’ve had a lot of excitement surrounding new MM features and I’ve wanted to push things forward as quickly as I could.

When I finally reached the section of code that I’ll need to change to allow for the new graphing functionality (as well as future growth), I realized that adding the code will take some significant restructuring. To that end, I’ve decided that the time for doing some spring cleaning on MM is at hand. Since I’ll be reorganizing quite a bit anyway, I may as well do my best to create code that will be as easy to understand and maintain as possible. With the completion (and impending integration) of the graph code, I’ve completed all of the functionality that has been outlined for MM so far.

Rob and I plan to have me work on the code through the end of February, and work on publishing a paper on it through March. My aim is to spend some time organizing the code so that it can be useful into the future, even if I am not working in the lab. Whether that usefulness comes in the form of being able to easily borrow code from MM for other projects or the project itself being easily extended to add other features, I want to do a good job streamlining things. Once I’ve completed that work, it should have the side effect of expediting my own efforts towards advancing MM over the next few months.

Squashing Bugs

Since getting back from our trip to the Rocky Bioinformatics conference I’ve been working on fixing up some code. There were a number of bugs that I had back-burned in favor of working on my presentation for the conference. The graphing proof-of-concept for Subsystems that I had been working on was first to hit the burner. I stopped work on that in order to get the json saves to the new server working.

The json saves were close, but not perfect when I left for Colorado. Daniel and I actually discovered a couple more weird little problems when I got back. (Luckily, he made quick work of his own OpenSocial portion of the saves, so I had a reliable place to get correct output to check against). Click the read more to hear my bug-squashing tale in all its glory!

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Biobike and Alisp

Hey, guys.

I know it LOOKS like I don’t do any work at all, and this could be true! But I have done some work recently! I currently wrote about it on the labwiki, too! You can find the current topics, there are only two, at

the How To Biobike guide is not finished, not by a long shot, but hey, at least I’m pulling a weight around here!

Back to blogging

I’ve been away from my desk (and this blog) for a while now, but thankfully all of the payroll mixups have been ironed out! I’m happy to be working on MM again, and excited to be presenting at Rocky ’09 next week. I’ve been focusing mostly on getting my presentation in shape, and have gone through several iterations of my slides already. I think  have the basic idea of what I want to say down, but I’m hoping to fine tune the delivery with Rob and everyone else sometime this week.

I’ve never given a talk at a conference, nor have I attended this particular conference, so I hope that my presentation fits in. Mentally I think I fall more on the computer science side of things, so I’m unsure of how to make my presentation appeal to both the biology- and CS-minded attendees. I’m confident that by the time I present, we’ll have all of that sorted out though!

As far as MM itself is concerned, Rob went out of his way and did a whole bunch of code to make my job easy with the new JSON storage cgi. Unfortunately, I couldn’t get his new code to agree with android (well, that’s technically a lie, I did kind-of get it working, but apparently you can’t have URLs that are thousands of lines long). Today we went back to the drawing board and did it the ‘hard way’ wherein I hand-code the cgi form with a bunch of yucky string manipulations in java. That code seems to be working nearly perfectly! 🙂

I hope to have the code fully operational within the week, but I may have to stop and prioritize the Rocky preparation. It all really depends on when and how often I work with others in the lab on my presentation. Regardless, I’m really excited to have the ball rolling again with this project. I can’t wait to see what people think of it at Rocky; I hope they’ll be impressed by what we’ve done!