Monday, December 22, 2008

Mac vs PC

The old battle of Mac vs PC, in this video the fight is with Transformers laptops ... cool concept.


By the way, the Linux Foundation has a contest for "I'm Linux" tv-commercial, full rules here.

Friday, December 19, 2008

Perl Life


Wednesday, December 17, 2008

PS3 cluster

So do you have some PS3 and you're boring of play and watch Blue-Ray movies?

You must know the PS3 is the most accessible CELL-based machine, why not use this computer problem in other areas beyond entrainment.

In this PS3ClusterGuide you can build step-by-step your own cluster with PS3, the receipt:

1. Take some PS3.
2. Interconnect it in a LAN.
3. Install Fedora PPC in each one.
4. Install cluster utils.
5. Learn to code in CELL-SDK for a better experience and performance.

I accept some PS3 for scientific probes ... really I just want one to play ...

Sunday, December 14, 2008

Tuesday, December 9, 2008

The Seven Deadly Sins of Bioinformatics

This presentation is a good think-deep-later for anyone in this area, some quotes are fantastic and many points are well focused, others I can't agree. Must watch and think.

Thursday, December 4, 2008

Bioinfomatic in web2.0

DNASIS SmartNote is an on-line service for bioinformatic analysis integration, currently it's like Google Docs but specific for bioinformatic, it looks good and very expandable, it includes some basic tools:

  • Blast - NCBI
  • Codon Usage
  • CpG Islands
  • DNA Stats
  • Hetero Dimer - IDT Oligo Analyzer
  • Oligo Analyzer - IDT
  • PCR Primer Stats
  • Protein Stats
  • Reverse Complement
  • Reverse Translation
  • Translate Tool - ExPASy
  • ClustalW - EBI
  • Multiple Alignment Editor - Jalview
  • Pairwise Alignment - EBI EMBOSS
  • T-Coffee - EBI
  • Blast - NCBI
  • CpG Islands
  • DNA Pattern Find
  • Fuzzy DNA Search
  • Fuzzy Protein Search
  • Neural Network Promoter Prediction
  • ORF Finder
  • Primer Map
  • Protein Pattern Find
  • Restriction Digest
  • Restriction Map
  • TMHMM Server v. 2.0
  • VecScreen - DDBJ
  • xTAG Software
  • ASPE - Probe Design Tool for ASPE
  • Hetero Dimer - IDT Oligo Analyzer
  • Oligo Analyzer - IDT
  • PCR Primer Stats
  • Primer Map
  • Primer3
  • PrimerX
  • siRNA Design - DEQOR
Check the video for a demo.

Tuesday, December 2, 2008

Advice for potential graduate students

I found this text,copy and paste because it's an advice and must be in every biological laboratory.


We currently have room in the lab for more graduate students.

But before you apply to this lab or any other, there are a few things to keep in mind. First, be realistic about graduate school. Graduate school in biology is not a sure path to success. Many students assume that they will eventually get a job just like their advisor’s. However, the average professor at a research university has three students at a time for about 5 years each. So, over a career of 30 years, this professor has about 18 students. Since the total number of positions has been pretty constant, these 18 people are competing for one spot. So go to grad school assuming that you might not end up at a research university, but instead a teaching college, or a government or industry job. All of these are great jobs, but it’s important to think of all this before you go to school.

Second, choose your advisor wisely. Not only does this person potentially have total control over your graduate career for five or more years, but he/she will also be writing recommendation letters for you for another 5-10 years after that. Also, your advisor will shadow you for the rest of your life. People will always think of you as so-and-so’s student and assume that you two are somewhat alike. Finally, in many ways you will turn into your advisor. Advisors teach very little, but instead provide a role model. Consciously and unconsciously, you will imitate your advisor. You may find this hard to believe now, but fifteen years from now, when you find yourself lining up the tools in your lab cabinets just like your advisor did, you’ll see. My student Alison once said that choosing an advisor is like choosing a spouse after one date. Find out all you can on this date.

Finally, have your fun now. Five years is a long time when you are 23 years old. By the end of graduate school, you will be older, slower, and possibly married and/or a parent. So if you always wanted to walk across Nepal, do it now. Also, do not go to a high-powered lab that you hate assuming that this will promise you long-term happiness. Deferred gratification has its limits. Do something that you have passion for, work in a lab you like, in a place you like, before life starts throwing its many curve balls. Your career will mostly take care of itself, but you can’t get your youth back.

If, after reading this, you want to apply to this lab, we would love to hear from you.

By: Sönke Johnsen is deep-sea biologist and visual ecologist at Duke University and still can’t believe that his background in math, art, and writing got him a paying job, let alone one that lets him go down in submarines. In his spare time, he takes pictures (see and works with his daughter to unlock new levels on Mariokart Wii.

Source: The Science Creative Quaterly.

Monday, December 1, 2008

Slower with age ... 4rd. part and last

I'm starting to be bored with this comparisons, I've not report the last one comparing "apples with pears" between Ubuntu vs. OpenSolaris vs. FreeBSD benchmarks, but this is a more realistic comparison, take the new shinning Fedora 10 and Ubuntu 8.10 for benchmarking, the results: nearly identical perfomance in 32 and 64 bits. Not surprises here.

Yes, U-fans claim better hardware support and more user-friendly-desktop, I don't believe that 'cause Fedora is a really good Linux distribution, I had tested and used before.

Whatever, for test and compare distros you can use the Phoronix Test Suite.

I'm still waiting openSuse 11.1 and maybe try gOS, while I'm saving for an Acer Aspire One.