Older blog entries for rufius (starting at number 55)

Pinterest?

What exactly is the purpose of Pinterest? I see that people seem to use it. It’s a sort of strange mish-mash between Twitter, Tumblr, and Etsy.

Why?

Syndicated 2012-10-16 17:47:54 from Smart (sort of) Pointers

Morals, Ethics, and Religion

Thunk of the day: “While it is useful for religion to inform our morals, it is a slippery slope for it to inform a society’s ethics (and by effect, laws).”

Not profound, but relevant in a society that is vigorously debating gay marriage.

Syndicated 2012-10-15 19:06:42 from Smart (sort of) Pointers

Programming Editors (also some customer service kudos)

I’m a particular individual; a creature of habit. Especially in matters of computers, cooking, and my home, I can get a bit snippy when things do not work reliably and predictably. For the last couple years, I’ve been developing software professionally at Microsoft. The culmination of my efforts (and many others’) will be released on October 26th, 2012 to the general public as “Windows 8″, the most significant change to the flagship Microsoft product since Windows 95.

During those two and a half years, I’ve jumped around from editor to editor, trying to find one that suited my needs. I started with Emacs which I became a fan of during college as an intern at Google. After time, that wore on me as pinky cramp set in and my own inability to convince myself to learn e-lisp. Then I tried Visual Studio for a while but it has its own set of challenges with respect to developing for Windows. Additionally, I’ve never enjoyed using an IDE (as opposed to an editor) to develop C++. I find languages like C++ which were designed before the modern concept of an IDE existed tend to integrate poorly with an IDE anyway. Sublime Text 2 offered a good compromise where folders represent “projects” which worked well with the build system I am accustomed to. Unfortunately, lack of any contextual tagging (Intellisense) proved to be a hindrance as I had to continually use grep and a code indexing service to search for context and follow code flow.

The editors I iterated over earlier were just the ones I used for longer than a trial period. I also played with several commercial editors in the process but was put off by their high price. The short list of these was Lugaru Epsilon (proprietary Emacs clone), Source Insight, UltraEdit, and finally Visual SlickEdit. Most of these editors run at least $100, with SlickEdit being on the higher end at $300. Of the proprietary solutions I tried, it seemed the most promising and powerful. It was clearly designed with scale in mind but at a great cost. It is Visual SlickEdit which is the actual point of the title of this post.

As we finished up Windows 8, I decided it was time to re-evaluate my tool choice again. In reflection, I recall spending a lot of time trying to understand how various code bases worked and navigating around in a web browser to follow references was tedious. Source Insight was able to handle the huge code base that I work in, building the proper contextual tagging I needed, but received such limited updating that it was no longer able to properly cope with heavily templatized C++ code. Given this realization, I could pony up and pay for a more robust editor or continue struggling with my half-assed solution where my editor has zero contextual information about the file I’m editing.

I reinstalled SlickEdit 2012 two weeks ago, and went to work on a couple bugs. After getting it setup properly with the code base and delving into the inner workings of the OLE Clipboard code base, I was pleasantly surprised at how easy it was for me to navigate around. The first time I tried out SlickEdit, I was not working in such gnarly code and was unable to fully appreciate the depth of its power. I setup a few custom key strokes to streamline my workflow and left the remaining key commands in their default CUA-style layout.

Two weeks with the editor passed quickly, with myself feeling like I had accomplished a great deal more with it than I would have in my former workflow. SlickEdit had sold me with their trial. After receiving the courtesy reminder email from Sean (the customer service rep assigned to me), I thought briefly about it and determined that SlickEdit was worth $300. I emailed Sean, asking for a quote with a discount since I was using a competing product to theirs (Source Insight). He promptly emailed back a discounted price and offered to give me a call to settle the final details. During this exchange over roughly 18 hours, my trial license expired before the licensing department at SlickEdit had finished getting my license sorted out. Sean was kind enough to email me a trial extension license to allow me to continue working. All in all, very impressed.

The thing that really got me with SlickEdit was…

  • The non-crippleware trial period. Smaller software companies often provide a trial version of their software that is crippled, doing a disservice to their potential customers.
  • The prompt response from customer service and willingness to keep them happy. This is a fine line to walk and many retailers screw it up royally. Being pushy and persistent isn’t representative of a customer service representative actually caring or being helpful. They’re just being annoying.
  • The discount for users that are using a competing product. If you’re confident in your product, you ought to be confident enough to offer a discount to bring customers over. They’ll appreciate it and feel like you’re really trying to please them.

In traditional ebaynese review language: A++++++++++++++++++++++++ service. Fast shipping, would buy again!!!!!!!!!!

Syndicated 2012-10-15 03:35:13 from Smart (sort of) Pointers

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

To Do for December 2008

This is my brief todo list for December 2008, 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).
  3. Reinstall the laptop to repartition the operating systems. In the process of this, also install Ubuntu 8.10.
  4. Play a lot of video games.
  5. Sleep… this hasn’t been consistently done in a long time.
  6. Learn C++ better, especially proper template design.
  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… 
  8. Sleep more.
  9. Play more games.
  10. Setup the new Roku Soundbridge M1001 I bought for my parents for Christmas.

Syndicated 2008-12-05 16:36:48 from Zac Brown

Archaea Classification Continued

After having thoroughly examined the code for a couple days and tried the code with replacement of fragments, I’ve convinced myself that the code is correct. After thinking about it, it occured to me that the relative k-mer distribution profiles for larger k-mers (7,8,9) might be skewed by even very small sampling without replacement.

I went ahead and took the difference between the relative distributions for Pyrobaculum calidifontis for 4 different cases:

  • 8-mers - 100% genome vs 99.5% genome
  • 8-mers - 100% genome vs 67% genome
  • 4-mers - 100% genome vs 99.5% genome
  • 4-mers - 100% genome vs 67% genome. 
Since 4-mers showed little variation between training and full genomes, I felt that was a good base for “lack of difference” in the distributions. Here’s the data:

As can be seen, the variation in relative distributions for the 4-mers is very small, generally no larger than +/- 0.002  and thats with training 67% of the genome. Meanwhile, the 8-mers show significant variation with training 67% of the genome there is a variation of up to nearly +/- 0.2 which entirely changes a profile. Even with 99.5% training, it shows variation in the hundreths place which is enough to skew the profile. This was tested on several organisms, but Pyrobaculum calidifontis just happens to be my pick.
That to me, explains why this technique might not be applicable the way its currently designed as the profiles for the organisms don’t match as well. Of course the other side of this is since every one of the genomes’ profiles would be skewed, wouldn’t that even it out. Without some serious statistical analysis (and time), I can’t say for sure.
Here also is a comparison of distributions:
From this, it can be seen that sampling with replacement (100 pieces) is pretty close to sampling 95% of the genome with replacement. Those are two separate pieces of software which is what leads me to believe the software is written correctly.

Syndicated 2008-12-05 15:21:55 from Zac Brown

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