Published on
2009 December 9 in
Personal.
Effective next month, I’ll be taking down this site. Most of the content have been successfully moved to my wordpress press account. Reasons for the move include [1] saving on web maintenance costs, [2] wordpress.com now has the features I need like posting equations and code, [3] I’m too lazy to regularly the wordpress.org engine to the latest version.
Please update your bookmarks and feedreaders to http://amespinosa.wordpress.com
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I keep forgetting where my scripts were in my home directories. Below is my ruby script to split a large FASTA [1] sequence into N sequences per file:
#!/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
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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?
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The del.icio.us Firefox add-on provides very neat integration into the latest version of Firefox three. I like the synchronization between local bookmarks, shortcuts, etc. The “most visited” tab actually counts how many times you clicked a bookmark and updates the toolbar respectively. The only problem is that for private bookmarks like the ones that initiate javascript link calls do not update the bookmark counters.
One of my favorite links is the citeulike.org’s add to library shortcuts which initiates a javascript call containing the current url on your browser such as an overview page of a journal article. This frustrated me for a while but after “grep”-ing my Firefox profile directory for the name of my citeulike bookmark, I edited the citeulike entry in my ~/.mozilla/firefox/$PROFILENAME/delcious.rdf:
<NC:Bookmark RDF:about="rdf:#$iw2hg3" NC:URL="javascript:var%20pw=window.open('http://www.citeulike.org/posturl?username=aespinosa&bml=popup&url='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title),%20'citeulike_popup_post',%20'width=800,height=600,scrollbars=1,resizable=1');%20void(window.setTimeout('pw.focus()',250));"
NC:Name="CiteULike: A free online service to organise your academic papers"
NC:ShortcutURL=""
NC:Description=""
NS1:LastCharset=""
NC:PostData=""
NS2:shared="false"
NS2:localonly="false"
NS2:hash="cfbf4f27149a10bca7a44c05be12ca99"
NS2:metahash="af1dd1906f18340e4a74c20e9497ceb3">
<NS2:tag>bibliography</NS2:tag>
<NS2:tag>citation</NS2:tag>
<NS2:tag>bookmarking</NS2:tag>
<NS2:tag>research</NS2:tag>
<NS2:tag>reference</NS2:tag>
<NS2:tag>academic</NS2:tag>
<NS2:tag>tagging</NS2:tag>
<NC:VisitCount NC:parseType="Integer">300</NC:VisitCount>
<NS1:LastModifiedDate NC:parseType="Date">Tue Jul 03 07:49:43 2007 +000000</NS1:LastModifiedDate>
<NC:BookmarkAddDate NC:parseType="Date">Tue Jul 03 07:49:43 2007 +000000</NC:BookmarkAddDate>
</NC:Bookmark>
The code entry above shows the XML entry for a bookmark. Simply change the “NC:VisitCount” tag to a very high value and it will appear at the top of your del.icio.us toolbar most-visited tab.
Enjoy your new favorite bookmark!
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The past few weeks was very tight as I preparing from my resignation as an instructor in Ateneo (and attending parties). I will be joining the Computer Science Department at the University of Chicago for my graduate studies. My work will be on grid computing and distributed computing under the supervision of Dr. Ian Foster, the father of grid computing himself! He is also one of the founders of the Globus Toolkit project, the key middleware in every grid deployment in the world.
This blog site will still be up and maintained but my faculty page and ECCE wiki page will not be updated as much for the next six years. Below is my new contact information:
So if you’re around the Chicago-Hyde park area, drop me an email and let’s meet up!
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