Monthly Archives: June 2010

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cliques clans and complexity analysis

We’ve come a long way since proteins in pools by probability. Cliques provoked research into how best to validate their worth, which led to hamming distances, densitrees, splitstrees, and more.

My latest development milestone is the first working version of the perl code I’ve written for annotating proteins with their functions. I had a version of this code previously that did so for all cliques, but this time, I wanted to only handle the cliques indicated by Jim’s MatLab code.

The script works great, and outputs all cliques by binary signature, listing proteins and functions, and outputs the list of strains. Both on Octopussy and on my netbook, execution took just over an hour.


My next undertaking will be speeding the code up as much as possible, so that when I rework it to sit on the edwards.sdsu server with form submission, it will actually be usable in speed. The move to a web-based tool will of course include some other major headaches, but task one is getting the complexity analysis done and making strides towards speeding it up. example from

Increasing Heap Size in Eclipse

Ran into the problem of running out of heap space when running my program on Eclipse the other day. It just so happens that the heap space that is allocated for my programs in Eclipse on my Mac at home is less than what is supplied for my work laptop, thus making my program crash at home and not on my laptop. When dealing with a huge amount of data and objects in a large hash array of trees, heap space can run out pretty quick. So, after digging around a bit on Google I found two simple solutions that I continued to run into. Click here or the Read More link for solutions…

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Networking Long Distance (It’s a Really Bad Idea)

Okay, guys.

If you were working in the lab on monday the 15th, somewhere around 5 or 6PM, then you noticed at somepoint that everything related to stopped working. That’s the SEED, all the websites, everything.

Yeah, that was my fault. I’m sorry!

Rob has had me working on getting DHCP working on the new server, such that we feed internet in through one ethernet port (eth0), and it subdivides it out to all the OTHER servers, which are connected on another ethernet card (eth1). Ubuntu does NOT provide good documentation for dhcp. If you know about servers or about DHCP to begin with, it’s all you need. But I’m going to admit, I knew nothing. Nothing nothing nothing. So I followed their advice to the letter, and managed to do everything wrong.

Summary: I defined eth0 as our router, on a fixed IP. (Please remember that we’re currently feeding internet IN and OUT through that.) I also defined a wireless network with two sub domains inside of it, one pointing to eth1, and the other pointing to nothing. (An important thing to note, we don’t even HAVE a wireless card.)

So I logged in monday remotely, I wasn’t able to make it to campus, it was the only day all week I wasn’t going to be in the lab, and was like, “I am confident this will work! *Networking Restart*” Shortly after, the server disappeared from the world as we know it because I had just told it to stop using eth0 for internet. Panic ensued, Rob had to stop everything he was doing to go clean up my mess because I wasn’t even on campus, and I felt terrible. But I had kept the original configuration files for EVERY file I edited, and disaster was averted via those.

So now it is Tuesday. I’m in the lab, and I have started from step zero to configure dhcp. If you take all the information Ubuntu gives you and take it out of context, only apply it to eth1 with a bit of intuitive logic, you get our current situation: which is that DHCP works! I have posted detailed information on the labwiki.

This blog post is here to admit my mistakes, and impart a very important lesson to anyone who reads this: For the love of god, always save the originals of any file you edit, and NEVER change server configuration files if you are not next to the server.

The end.

Edwards lab 2010 all-day meeting

We are now celebrating the first anniversary of Edwards labsite as we are sitting in the SDSU Coastal Waters Laboratory to plan for the coming year, and the coming summer in particular.

All lab members will now present short summaries of their work in the past few months then their plans/objectives for the following months.

New lab members will also join the labsite very soon… Stay tuned

splits trees paper

In the spirit of ample blogging, I’m posting the link for a paper the math guys and I have been fighting our way through. Enjoy!