Monthly Archives: July 2009

Brad Hull



Location: GMCS 429

Phone: +1 619 742-8541





Currently working on an upgrade to the BLAST Graphical Output seen on the SEED using HTML5/CSS/Javascript. Past ideas included using Perl/gd, perl/Cairo, and the GWT/Google Viz.



Bachelor of Science: Computer Science

SDSU C/O 2009

Next version of MM – Coming soon!

I’ve spent a while now working on little bits and pieces of code that I will need to eventually incorporate into Mobile Metagenomics. I’ve finally reached a point where I feel ready to move on to the next stage and start to synthesize all of these little ideas into something meaningful for MM. My goals for the next version essentially involve taking it out of a proof-of-concept stage and into a stage where it more or less ‘works’. I will probably leave the file browser and more friendly results view out, but most of the other goals from my talk should be included. I will at least establish a framework to later slot in all of the ideas that we discussed.

1. Download all 'file chunks' and display them.
2. Do this asynchronously, allowing the user to view results while work happens.
3. Split the program into a 'Search' Activity and a 'Results View' Activity.
4. Make the physical phone buttons work!
5. Eventually, code the rest of the event methods such that MM can be interrupted by a gTalk or gmail
notification and restart itself without loss of progress.

I had also been working on an app for myself after work, when I realized I was actually learning a lot of valuable things about more complex Android User Interface design. I may keep this around as a side project to work on for a few minutes here and there, when I need a quick break from MM. I think that learning some of the intricacies of Android UI will come in very handy in the future, and it will definitely help if I have a fun project as my learning platform!

Become Even More Productive – 2 New Cool Things!

Over the past couple of days I’ve been toying with a couple of neat ways to access / visualize data. Rob showed me Cooliris, which was pretty mind blowing as far as just looking like it came straight out of a sci-fi movie. More seriously, I’ve found that it is actually a pretty efficient way to do image searches. It displays images much more quickly than a simple google image search result.

The other awesome thing that I’ve found is the Compiz-Fusion suite of window management plugins for Linux. (You can download a version for your distro here). It allows you to manage a large number of extended desktops; this is particularly useful on the EEEPC netbooks which have small monitors! Other cool features worth checking out are the Ring-switch plugin ( + tab for application switches), Desktop Cube & Rotate Cube (Alt-Ctrl-Mouse button 1 click and drag). Turning transparency on the cube is actually pretty nice because it allows you to view a number of desktops all at once.

Some cool things to do just for looks are: 
Enable Skydome on the cube (use custom backgrounds while in cube view).
Try out the water plugin (ctrl + to initiate, Shift+f9 and shift+f8 for rain control).
Turn on wobble plugin for your application windows.
Check out the wiki to learn even more awesome stuff you can do!

Now that you’re all informed, install this stuff on your linux machines, go out, and be impressive!

Terminase cluster

A conserved cluster around terminase protein-encoding genes

One of the reasons terminases are interesting is that they are somehow “essential” in tailed phages. Essential is a word that should always be used with caution because such thing does not exist in phage genomes (unlike ribosomal genes and tRNA synthetases in bacteria for example).

So, here is a nice cluster around terminases… (Please click the Read more button (below)  to see it. I had to put it in another page to avoid clogging the main page)

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Phage module of the day: Phage DNA packaging

A major challenge for a bacteriophage is to quickly pack lengthy (relative to its size) DNA in newly formed phage heads (capsids). This packaging involves “pressurizing” this DNA in the available space.

A good place to start reading about it is this review by Rao and Feiss: The Bacteriophage DNA Packaging Motor (Annu. Rev. Genet. 2008. 42:647–81).

Once you get the big picture, follow these proteins in phage genomes in the Phage Packaging Machinery subsystem.

DNA packaging



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Phage of the day: Bacteriophage r1t

Why am I working on phage r1t today?

I was working on mycobacteriophages, starting with Che9d; but I found out that since Rob was working on a phage closely related to that one, we were continuously reversing each other’s annotations.

On the other hand, r1t is quite important because: 

i) I know some things about it

ii) it has been (re-)annotated by Brüssow’s group, known to be miticulous and accurate

iii) more importantly, it has multiple close relatives in my favorite organism, Streptococcus pyogenes