MacBook

So, in my infinite wisdom and grace managed to slap a cup of water onto my 6-month old ThinkPad last Thursday. To say this was a bother, is well… an understatement. I did all the necessary precautionary things like shutting it down, pulling out the battery, dismantling it and generally just trying to take care of it.

However, I did need some files off of it so I let it dry out for a few hours, booted it up (was kinda surprsed it did), then proceeded to copy off those files I needed. In the mean time, I was stuck sharing a laptop with the girlfriend which was not really a good setup as I tend to customize everything to my liking.

All the while, I had been secretly wishing that I had a Mac of some sort. I’ve started to get into more development that would be made easier by using Mac, I was tired of fighting with Linux for a half-assed *nix solution on a laptop, and the Windows CLI just isn’t good enough.

Which brings us to Friday night, when I bought a MacBook. Basic White model, the new one though with 802.11 a/b/g/n and the Nvidia 9400m graphics chipset. I’m loving it. Its an excellent computer. Its nice to have a decent command line interface and now that I’ve got it configured the way I like it, I’m not sure I’ll willingly use any other hardware for laptops at least.

Hopefully though, my ThinkPad will recover and then I can give it to my dad to use. That would be nice. Hopefully

Syndicated 2009-02-10 04:04:01 from Zac Brown

Genend Update

The server that I was running the computations hard locked sometime during the winter break. Apparently it ran out of disk space while another user was running simulations on it. Wasn’t able to access the machine till I returned to Miami.

Since I had no access to machine with large amounts of memory, I spent some time trying to figure out what was wrong with the training software. Still wasn’t able to find the problem, must be missing something simple.

Upon return to Miami, did the following:

• Fixed the server, apparently it ran out of disk space from log files created from other user’s run.
• Researched building a database for taxonomies.
• Built a database using the BioSQL schema after discovering that Genbank files track phylogeny through recursive ranks.
• Wrote a Python script to fetch the Genbank file for each of the 625 fasta-format genomes and load it into the BioSQL database.
• Began revising taxonomic classifier, ~80% done.

Next things to do:

• Run the taxonomic classifier.
• While waiting for taxonomic classifier results, tear apart training classifier and figure out whats wrong.

Syndicated 2009-02-02 17:02:11 from Zac Brown

Ruby…

In the past I’ve vehemently argued against using Ruby. My encounters with it had shown a shoddy VM, decent libraries but my greatest grievance was the lack of any clear standard. It was really just whatever Matz felt like, or at least that was my understanding. Others may correct me if I’m wrong.

Despite my distaste for Ruby I always sensed that at some point I would pick it up when it became clear that the language was stabilizing, the VM was ready for the big leagues and when I actually had some time to make sure my past encounters weren’t just issues of my own ignorance (which I’m prone to as much as anyone else).

That said, I am picking up some Ruby now and am enjoying it. Unlike most these days, my primary interest wasn’t in Rails/Merb or I guess what is now “Rails 3″ but rather _why’s Shoes framework. I have long been irritated by GUI programming. In almost every language it feels incredibly… unwieldy (I think thats the word I want to use). It seemed as though no matter the language and how graceful it generally is to work with, there were always things that made its GUI toolkit interfaces ugly to work with.

Shoes on the other hand has been quite enjoyable. Its minimal and still has a ways to go but in a couple days I was able to learn enough Ruby and enough of how the Shoes framework works to write a pretty simple application to solve a long-standing issue that my mother has had with trying to copy her music to her MP3 player. She’s not well suited to navigating multiple Windows Explorer windows and copy/pasting her way to victory. With that, I wrote a really simple Shoes app that basically shows two panes, the “all the music you have” pane and the “music thats on your MP3 player” pane. It only shows files not already on her MP3 player so you just click the file you want and it will “move” the file in the window to the other pane as well as actually copying the file.

If anyone is interested in this brain dead app, I’ll post it later once I’ve attached all the license information for it, etc.

Syndicated 2009-01-14 02:18:37 from Zac Brown

Vista Media Streaming

I recently built a new media center PC. I’ve wanted one for a while along with also wanting a computer that would be capable of playing the “Latest and Greatest” computer games. The specs looks something like this:

• Processor: AMD Athlon X2 6000+ (2 x 3.10 GHz)
• Motherboard: Foxconn A7GM-S - a good motherboard, has integrated HDMI though I have a vid card with that too
• Video Card: Power Color AX4830 (ATI Radeon 4830 with 512 MB DDR3 + HDMI audio/video)
• Memory: 4 GB, soon to be 8 GB whenever I get my hands on x64 Vista or Windows 7
• TV Card: Hauppage HVR-2250 - dual digital/analog tuner with an MCE remote
• HDD: Western Digital Caviar 640GB w/ 16MB cache
• Operating System: Windows Vista Ultimate x32 using Vista Media Center to record the TV stuff. Gotta say, thats some brain dead simple software to setup with my TV card.

Obviously not the best computer on the market but it can play Fallout 3 on Ultra High settings and I can’t seem to really slow it down. I anticipate an upgrade this summer whenever the novelty of the Phenom II chip comes down a bit. This new computer fits both niches nicely though I did find an interesting caveat with streaming my recorded TV to other computers in the house.

I don’t always like to be in the study watching TV, partly because my Dad works in there as well so unless its fairly late at night I can’t watch things I’ve recorded. In these cases I head to my room with my laptop. My laptop has Vista Enterprise on it and it immediately picked up the media sharing of my desktop/htpc.

However whenever I tried to play an episode of Southpark I found I was only getting audio, no video output whatsoever. My first suspicion was that the files were to big to be transferring over wireless at a rate that would transfer video but after thinking about that a moment I realized that was idiotic as it would have shown the video in some choppy fashion.

After some cryptic searching on Google I found that I was missing the DScaler MPEG Filter for Windows Media Player. After installing this codec, I was getting video playback fine. It seems odd to me that with all this media sharing between the different computers that Vista does so well that it doesn’t include the codecs to playback the PVR files recorded by Vista Ultimate or Home Premium.

So with that, I make a humble request to the group in charge of Media Center or the Media Codecs (in fact the team I’ll be on next summer as an Intern):

Dear Future Employer:

Will you please include this codec on all versions of the operating system in the future. It would make life a lot nicer for those of us not using the same version of Windows on all our computers. Kthxbai.

With love,

Your humble (future) minion

Syndicated 2009-01-06 16:57:36 from Zac Brown

To Do for December 2008 - Revisited

This is my brief todo list for December 2008 revisited, also known as the first vacation I’ve had since I started college.

1. Build the new PC I bought and get Windows Vista Ultimate (Super Fantastic) Media Center running.
2. Turn 21 and become a drunkard overnight (hah). (T-minus 2 hours)
3. Reinstall the laptop to repartition the operating systems. In the process of this, also install Ubuntu 8.10. (Still haven’t done this… will wait till I’m done with a few things.)
4. Play a lot of video games. (Bought the two Guild Wars expansions, Factions and Nightfall)
5. Sleep… this hasn’t been consistently done in a long time. (Still need more of this)
6. Learn C++ better, especially proper template design. (Heh, this is work, haven’t started on that yet.)
7. Finish leftover things for my bioinformatics research work. That is, build a database for the organisms for doing phylogenetic classification. Maybe play more with SVM’s…  (Same as 6)
8. Sleep more. (Working on it)
9. Play more games. (Working on this too)
10. Setup the new Roku Soundbridge M1001 I bought for my parents for Christmas. (Have to return the one I ordered and wait till they have more of these available….)

There are probably other things that should be on here… like my senior project work. I suspect I’ll start that Tuesday as tomorrow is my birthday and I will be eating and drinking merrily.

Syndicated 2008-12-22 04:00:16 from Zac Brown