Monday, June 30, 2008

Darwin Ports

Since I had started to work with Mac OS X, I feel some missing command tools in the shell, as Linux user you have some favorite commands, besides the servers runs with tcsh, not bash, so many of my bash scripts do not work. I tried to use some Perl based scripts to complement some commands, but today I found the project Darwin Ports, an OpenSource alternative to use common Unix tools from source.

Some requirements include Xcode and X11, so install it first.

First you need to download the installer from their website, it is a common .dmg package, so open and install following the screen instructions. Easy.

Next you need to open a terminal and edit the .profile in the HOME, adding the lines:
export PATH=/opt/local/bin:/opt/local/sbin:$PATH
export DISPLAY=:0.0
export EDITOR=/usr/bin/pico

After this, you require to create a new shell or simply open a new terminal. Now we check for updates with:
sudo port -d selfupdate

Now you can add new programs using port commands like:
sudo port install PACKAGE

The program and dependencies sources are downloaded, compiled and installed. Cool!

To search in the available ports:
port search PACKAGE
port variants PACKAGE

More information about a package:
port info PACKAGE

List of installed packages:
port installed

And finally if you need more information, visit their Wiki.

Tuesday, June 24, 2008

Hippocratic Oath for Scientists

When I graduate from University I recited the Engineer Oath, now, as a researcher, I consider this must be implemented in all research centers:

"I promise never to allow financial gain, competitiveness or ambition cloud my judgment in the conduct of ethical research and scholarship. I will pursue knowledge and create knowledge for the greater good, but never to the detriment of colleagues, supervisors, research subjects or the international community of scholars of which I am now a member."

A group of people at the Institute of Medical Science at University of Toronto in Canada wrote a scientist's version of the Hippocratic oath. This oath (above) was recited by all graduate students in the biological sciences at the beginning of the 2007-2008 academic year.

and must read it:

Monday, June 23, 2008

Science retreat

Last week I was in Montana, our work group have an annual sessions in the Boss' Ranch, this is an excellent way of discuss and propose new projects besides to meet people and talk about everything you want.

Some details:
- The ranch is like a hotel, but without service room and fees.
- The view was great, many snow mountains, lakes and rivers.
- You can see wild animals like deers and hawks.
- Federal highways are in good conditions and are free (not like MX)
- Food is prepared in teams, isn't easy to feed 30 people, but we had success preparing mexican food (tacos, salsa, arroz and quesadillas).
- Science sessions is prepared by teams, each team has a theme to prepare and guide a group discussion.

Maybe I put some photos.

Tuesday, June 17, 2008

Code evolution

I like computer generated graphics, but if can be generated by real data and can improve some insight I say: WOW look this!

Last day I saw Michael Ogawa's works about how some codes had an evolution, I think he is using the data captured in the CVS, parsed and input to create a really amazing animations. He worked with Eclipse, Python, PostgreSQL and Apache, which are good examples of open source projects with many releases and people coding. Eclipse required HD because the enormous data.

The videos:

From: SlashDot

Monday, June 16, 2008

License or not license ...

Last week I saw in a new project wish-list a line which is a common mistake in the understood of Open Source concept:

"All the programs are Open Source and license not required"

Many Open Source programs are free (free as freedom) and not require to buy a license (free as beer), but you already have a license to use it, maybe the author don't need you to license, because you are accepted the license when you download/install/use the code.

Do you always read the license terms? I don't, because I try to use Open Source only.

Software is like sex; it's better when it's free.
Attributed to Torvalds at 1996 FSF conference.

Tuesday, June 10, 2008


Last day, the petaflops limit is broken by the RoadRunner, the new supercomputer from IBM and owned by Los Alamos Nat Lab. The hardware is a nice mix with ~7,000 AMD Opterons and ~13,000 Cell Processors, connected by Infiniband. OS is RedHat with xCAT to control it. The cost was $133 millions USD.

Many of the applications include simulations in nuclear material aging and the sciences, financial, automotive and aerospace industries.

The RoadRunner will be soon the #1 in top500.

I want one of this!

Some links:
IBM site

IBM press release
US Department of Energy

Friday, June 6, 2008

New project start

The Institute for Systems Biology will collaborate with the University of Luxembourg to create the Center for Systems Biology Luxembourg. The Center will participate with ISB on two basic research projects designed to provide greater insight into the identification of disease and to enable more effective treatments:

--  ISB Research Project 1: The first project will include completion of a
personalized human genome sequencing map on a minimum of one hundred
subjects and development of new methods for understanding the role of
genetic variations in disease, leading to new insights into diagnosis,
treatment and prevention.

-- ISB Research Project 2: The second project is development of
integrated systems proteomics, RNA and cell analysis methodology and tools
based on ISB's groundbreaking discovery of protein blood "fingerprints" and
single-cell characteristics that can report on the physiological state of
the body's 50 major organs. The research promises to lead to powerful early
diagnostic approaches to not only treat but also predict disease and the
ability to monitor the effects of existing drugs, including both effective
responses or adverse reactions.

ISB's role will be to apply its systems biology approaches and tools to study model organisms such as mice to determine how best to interrogate and analyze human genetic data at the DNA sequence level. New computational and mathematical tools will be developed to facilitate these large-scale genome analyses and to integrate these insights with protein blood fingerprints.


Tuesday, June 3, 2008

Is God Atheist?


If a tree fall and nobody hears it, what is its sound?