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• Splitting bioinformatics FASTA files
• Lecture notes on iteration

• Attracting Free Blog Traffic There are plenty of ways that you can attract free blog traffic if you know...
• Save Time, Money and Space in Over 80 Ways If you're looking for handy gadgets, tools and various items that can save you time,...

#!/usr/bin/env ruby
#
# Script: dumpseq.rb
# Description: Parses the a BLAST Fasta file and dumps each sequence to a
#              file.
# Usage: dumpseq.rb [fasta_file]

require 'fileutils'

fasta_db  = File.new(ARGV[0])

sno = 0
d = 0

file = nil

while true
  x = fasta_db.readline("n>").sub(/>$/, "")
  x =~ />(.*)n/
  if sno % N == 0 # N seqs per query
    file.close if file != nil
    dir = sprintf("D%04d000", d / 1000)
    FileUtils.mkdir_p dir
    # short filenames
    fname = sprintf "SEQ%07d.fasta", d
    d += 1
    file = File.new("#{dir}/#{fname}","w")
  end
  file << x
  sno += 1
  fasta_db.ungetc ?>
end

Its pretty hackish-looking. But then I found out that BioRuby [2] wrappers for parsing FASTA files.

[1] http://en.wikipedia.org/wiki/Fasta
[2] http://www.bioruby.org

• Design and engineering of a supply chain management system for drug delivery applications
• Unix timer utility

• FOTD: Saturday Weekend look Lancome Arbonne + more I was going for a fast, easy weekend look -- which is next to impossible...
• Don't guess on your taxes When you're filling out your taxes, it should be taken seriously.  They're not a laughing...

7th PANDA Grid Workshop, Bohol, Philippines, May 4 - 8, 2009 organised by Ateneo de Manila University Sponsored also by EPSRC, IoP, PPARC and the Royal Society of Edinburgh
The aim of the workshop is to bring together grid administrators and software developers in an informal setting, involving open discussions. The focus will include grid maintenance and monitoring and data production with PandaRoot. Organising committee: Rafael P. Saldana (Ateneo) Kilian Schwarz (GSI) Dan Protopopescu (Glasgow)	Contact person: Dr. Dan Protopopescu, University of Glasgow Glasgow G12 8QQ Scotland, UK Tel: +44-141-330-55321 Address: Holy Name University, Lesage and Gallares Streets, 6300 Tagbilaran City, Bohol, Philippines

Let’s look at the itinerary:

Tagbilaran City (May 3, 4, 5)

Metro Centre Hotel and Convention Center
Pres. Carlos P. Garcia Avenue
Tagbilaran City, Bohol
Philippines, 6300
Website: www.metrocentrehotel.com

Panglao Island (May 6, 7, 8, 9, 10)

Bohol Beach Club
Bo. Bolod, Panglao Island, Bohol 6340
Website: www.boholbeachclub.com.ph

Shet, gusto kong umuwi!!!

• Invitation to Interlinks 4.0 and Launching of the Ateneo Innovation Center
• My CodeInvaders strategy

• Development and remote installation of Java service for the Android Devices Written by: Igor Darkov, Software Developer of Device Team, Apriorit Inc. In this article I’ve...
• Internet Marketing Tweets 2009-10-13 Bet365.com sees results from a great idea. Exclusive webstream of a game for customers with...

I started using git for code produced in my work. The build was successful with a simple “./configure; make ; make install” series of steps except for supporting access to subversion repositories. It was looking for the perl module SVN::Core to be able to function successfully. Googling about it will land you to the Alien::SVN CPAN module page. Its dependencies can be installed with the standard “install Module::Name” invocation in the CPAN shell. But the main package does not properly install in this environment. It is probably because of the tarball not containing the standard Makefile.PL. It has Build.PL instead. This script generates the Build that compiles the subversion library and its bindings. Then it generates a Makefile from Makefile.PL in the src/subversion/subversion/bindings/swig/perl/native directory. Below is the output of the script:

[Alien-SVN-1.4.6.0]$ ./Build
Running make
Running make swig-pl-lib
make: Nothing to be done for `swig-pl-lib'.
Running /usr/bin/perl Makefile.PL INSTALLDIRS=site
Writing Makefile for SVN::_Core
Writing Makefile.client for SVN::_Client
Writing Makefile.delta for SVN::_Delta
Writing Makefile.fs for SVN::_Fs
Writing Makefile.ra for SVN::_Ra
Writing Makefile.repos for SVN::_Repos
Writing Makefile.wc for SVN::_Wc
Running make
gcc -c  -I/home/aespinosa/local/include/apr-0
...

The command /usr/bin/perl Makefile.PL INSTALLDIRS=site generates a build environment to install in /usr. This is not favorable for installation in userspace since you do not have permission to write on that directory. So this command will be rerun /usr/bin/perl Makefile.PL PREFIX=$USERDIR, where $USERDIR is the destination directory you want to.

Now you can successfully clone subversion repositories!

• What to do with a broken Rubik's Cube: make a fused cube
• Unix timer utility

• Are You Codependent? Quick Quiz Reveals Codependency Any relationship involves a certain degree of [tag-tec]codependency[/tag-tec]. Here is a quiz designed to find...
• Should You Invest In REIT? With the current housing market meltdown, it's hard to think about investing in real estate....

I was debugging a science application for the last several months to run on petascale (100×10^3++ processors) systems. The main goal of the domain scientist was to process hundres of thousands data sequences. I got too much carried away in the debugging to make the application work and have only looked at 3000 of the set In other words, not much *real* work has been done.

Now I should always remember when debugging, remember the scientists who took pain in measuring this data or who can’t get data. (Much like an analogy of “finish your food because there are millions of children hungry in developing countries”).

• Building a 1.2 Terabyte server
• Why do research in the Philippines?

• SEO 101: Beginning Viral Marketing We've all heard of something going viral, meaning it gets picked up quickly and spreads...
• BioTime Commences Shipment of Stem Cell Research Products to Millipore Image via Wikipedia BioTime Inc.announced today that it has initiated shipments of stem cell research...

• never sell more than one innovation - his rationale for this was that the market cannot catch-up with all of your ideas. I have not thought of this deeply because [1] I have yet to have a really brilliant idea, and [2] most busines models I saw are too caught up in selling this one unique idea that they don’t bother to look at the other types (probably they are bad ideas in the first place).
• interdisciplinary collaboration - now this is more familiar to my school of thought. As what we always say in the Ateneo Innovation Center, today’s problems are so complex that you need to apply every type of paradigm to be able to attack the problem from different angles and come up with a brilliant solution.

Adarsh also discussed four types of companies [1] wishful thinking (you have enough deep connections to get angel funding), [2] historical precedence - selling technology to improve a process, [3] intuitive jump - pure luck; with democratization of technology, YouTube and Ebay became a big thing even though video sharing and online auctions were almost non-existent web services during their time, and [4] sure technology - you know that there is a need for it in the future (e.g. Y2K “bug”).

Follow-up events to this is an Entrepenuerial Brainstorming Session with GSB and CS students and an Introduction to creating application on the iPhone. Apple’s development platform makes it so easy for anyone to distribute an app and sell it over iTunes (or AppleStore?) enabling you to earn several thousand dollars in a few months.

Oh, and they had free pizza during the talk

• On science productivity
• Where do you get good news about the Philippines?

• Tree Of Life Shadow Judaism doesn’t have any concept of hell, but the emanations in some schools of Kabbalism...
• Remembering the Lion: Communications Lessons from a Kennedy Don’t sell yourself short, believe you can do it and keep moving forward for the...

W. T. Welford, Useful Optics (Chicago Lectures in Physics). University Of Chicago Press, October 1991.

Students and professionals alike have long felt the need of a modern source of practical advice on the use of optical tools in scientific research. Walter T. Welford’s _Useful Optics_ meets this need. Welford offers a succinct review of principles basic to the construction and use of optics in physics. His lucid explanations and clear illustrations will particularly help those whose interests lie in other areas but who nevertheless must understand enough about optics to create the experimental apparatus necessary to their research. Consistently emphasizing applications and practical points of design, Welford covers a host of topics: mirrors and prisms, optical materials, aberration, the limits of image formation and resolution, illumination for image-forming systems, laser beams, interference and interferometry, detectors and light sources, holography, and more. The final chapter deals with putting together an experimental optics system. Many areas of the physical sciences and engineering increasingly demand an appreciation of optics. Welford’s _Useful Optics_ will prove indispensable to any researcher trying to develop and use effective optical apparatus. Walter T. Welford (1916-1990) was professor of physics at Imperial College of Science, Technology and Medicine from 1951 until his death. He was a Fellow of the Royal Society and of the Optical Society of America.  Link to [Amazon.com]

T. P. Hughes, Human-Built World: How to Think about Technology and Culture (science * culture).    University Of Chicago Press, May 2005.

To most people, technology has been reduced to computers, consumer goods, and military weapons; we speak of “technological progress” in terms of RAM and CD-ROMs and the flatness of our television screens. In Human-Built World, thankfully, Thomas Hughes restores to technology the conceptual richness and depth it deserves by chronicling the ideas about technology expressed by influential Western thinkers who not only understood its multifaceted character but who also explored its creative potential.

Hughes draws on an enormous range of literature, art, and architecture to explore what technology has brought to society and culture, and to explain how we might begin to develop an “ecotechnology” that works with, not against, ecological systems. From the “Creator” model of development of the sixteenth century to the “big science” of the 1940s and 1950s to the architecture of Frank Gehry, Hughes nimbly charts the myriad ways that technology has been woven into the social and cultural fabric of different eras and the promises and problems it has offered. Thomas Jefferson, for instance, optimistically hoped that technology could be combined with nature to create an Edenic environment; Lewis Mumford, two centuries later, warned of the increasing mechanization of American life.

Such divergent views, Hughes shows, have existed side by side, demonstrating the fundamental idea that “in its variety, technology is full of contradictions, laden with human folly, saved by occasional benign deeds, and rich with unintended consequences.” In Human-Built World, he offers the highly engaging history of these contradictions, follies, and consequences, a history that resurrects technology, rightfully, as more than gadgetry; it is in fact no less than an embodiment of human values. Link to [Amazon.com]

Even information can be found in the UChicago Press site.

• Introduction to SPICE: teaching demo
• ICT4Health2008: Session on Medical Imaging, Instrumentation and Informatics

• Take Advantage of Emerging Technology Services With Metro Ethernet, T1 Lines and DS3 Bandwidth There are a plethora of different telecommunications and technology services you can take advantage of....
• Fight for the right to eat bacon: Swine Flu is a PR nightmare for pork industry Yea, and the swine-workers across the nation are flying into "OMG!" mode. Yep. We're talking...

But as a metric thinking type of guy, I hate it when Google gives me the results in Fahrenheit! I did some tweaking to get the weather in the metric system while using the English language.  The simple solution is to use the EN-UK language code. Simply edit your ~/.mozilla/[profile_name]/extentions/ubiquity@labs.mozilla.com/chrome/content/builtincmds.js and modify the command “weather”:

CmdUtils.CreateCommand({
  name: "weather",
  takes: {"location": noun_arb_text},
  icon: "http://www.wunderground.com/favicon.ico",
  description: "Checks the weather for a given location.",
  help: "Try issuing "weather chicago".  It works with zip-codes, too.",
  execute: function( directObj ) {
    var location = directObj.text;
    var url = "http://www.wunderground.com/cgi-bin/findweather/getForecast?query=";
    url += escape( location );

    Utils.openUrlInBrowser( url );
  },

  preview: function( pblock, directObj ) {
    var location = directObj.text;
    if( location.length < 1 ) {
      pblock.innerHTML = "Gets the weather for a zip code/city.";
      return;
    }

    var url = "http://www.google.com/ig/api";
    jQuery.get( url, {weather: location, hl: "EN-GB"}, function(xml) {
      var el = jQuery(xml).find("current_conditions");
      if( el.length == 0 ) return;

      var condition = el.find("condition").attr("data");

      var weatherId = WEATHER_TYPES.indexOf( condition.toLowerCase() );
      var imgSrc = "http://l.yimg.com/us.yimg.com/i/us/nws/weather/gr/";
      imgSrc += weatherId + "d.png";

      var weather = {
        condition: condition,
        temp: el.find("temp_c").attr("data"),
        humidity: el.find("humidity").attr("data"),
        wind: el.find("wind_condition").attr("data"),
        img: imgSrc
      };

      weather["img"] = imgSrc;

      var html = CmdUtils.renderTemplate( {file:"weather.html"}, {w:weather}
                                        );

      jQuery(pblock).html( html );
      }, "xml");
  }
});

• What to do with a broken Rubik's Cube: make a fused cube
• AJSS: CodeInvaders!

• Veretekk Marketing System | Best Lead Generation If you truly want to learn how to market, build a massive list, use autoresponders,...
• Growing Your Business With a VoIP Solution - The Future Communication System Modern day telecommunications industry has established a new technology called VoIP - Voice over Internet...

I was hanging out with a couple of Pinoy immigrants when one of them said, “Sa Pilipinas wala nito no? (This does not exist in the Philippines, right?)” Of course there are a few grains of truth to it. But what disappointed and pierced me inside was that the tone of the voice felt like the Philippines will never rise out of its ashes. It was as if life abroad is always the best and we all came from a filthy place. I also felt very useless that even though I was involved and emotionally attached in projects and movements that I believe will change the nation, all efforts are futile.

Face it. The only time when the Philippines get featured in international news networks like CNN is when: [1] a really big storm or calamity struck us, or [2] someone from the government screwed up big time. No wonder why Filipino immigrants do not see anything good happening in the Philippines.

I firmly believe that something big is on the rise in this nation. You can’t find it on mainstream media or its equivalent websites. Big things are happening locally in small communities. But where can you know these good things happening in the country? With the advent of Web2.0 and its high democratization of user contributed content small community movements are letting themselves known throughout the world. Here are some of a few sites and blogs I frequently read that makes me proud of to be a Filipino:

• The WhyNot? Forum - inspired by TEDtalks, it is a gathering of Filipinos daring themselves to ask: Why not? Bakit hindi? Speakers share their thoughts on what we can do to put the Philippines back in the map. Their website is a bit too flashy and but you can get the latest updates and most of the videos of the last 5 forums at their Multiply page.
• Ateneo Innovation Center - a new approach in doing research in the Philippines. Doing projects relevant to be implemented in local communities. Acting like a startup to work around the big hurdle of getting funding. The site features some of the crazy projects we are doing in my old university.
• Kolektib - a group of diverse professionals seeking to create real products and inventions that solve’s a Filipino’s everyday problems.
• Game Changer - Mark Ruiz’ blog about innovating and ideas that make an impact to the world.
• Young Public Servants - a site dedicated to promoting good governance and citizenship to the youth.
• Gawad Kalinga - a worldwide movement that seeks to provide housing and nurture communities in depressed areas.
• AyalaTBI - a project of the Ayala group of companies to incubate technology startups based on great and innovative ideas. They host various events like the Innovation Forum, Kape@Teknolohiya (Coffee and Technology), and TechBootCamp.
• The Bliss Project - my sister’s project to enrich the lives of a local community in my native town. I just installed the site for her but you can also look at her blog for an initial description about the project. I’m including this in the list as a proud Kuya

Where do you go on the web to inspire you as a Filipino?

• Spreadsheet-powered Election Quickcount
• The Philippine National Public Key Infrastructure

• The new website - the new approach Hello world - anybody out there? This is my new website and the same time...
• Quick Green Reads For The Weekend Volume Eighty Seven. Damn it's cold this morning. We had to go out the other day and buy...

Mark Ruiz of Hapinoy shares some updates on their company deploying a POS system for these sari-sari store. Technology is not only a key component in streamlining systems of today’s enterprises but it is also needed by people like Nanay Delia. Below is the image from his blog post:

Nanay Delia learning a Point-of-Sale System for her Sari-Sari Store. Whatever doubts of the applicability of technology for the smallest unit of retail were laid to rest after the training session. The potential of becoming more efficient in pricing controls, inventory management, and accounting were key benefits that were very much appreciated. [description from Mark Ruiz' blog

• Invitation to Interlinks 4.0 and Launching of the Ateneo Innovation Center
• The future of public health: grid gains traction

• Options For Office Phone Systems Communicating in today's business world has never been easier with email and faxes, but one...
• Taking Showers in Your Wheelchair and Dignity When you are in a wheelchair you have lost your individual freedom and you will...