Showing posts with label biology. Show all posts
Showing posts with label biology. Show all posts

Friday, December 19, 2008

A second language - and a third one!

  One and a half year ago I wanted to comment an article about a second language. Sometimes people are having hard time learning new things, and it's not just their fault, it could be literally an anomaly in the brain structure or it could be related to the level of complication of the language someone chose to learn.
  To a personal background level, I believe I used to be a polyglot, a linguist if you will. I loved to learn new languages, I started English as a second language at the age of 9 (I think), all thanks to my wish to understand how to interact with the computer and read foreign literature. From there, I followed English until the GCE O'Level certificate. In the meantime, I began French for fun, having nothing to do during long summer days. The intensive 5-hour lessons proved to be a really attractive language and I continued learning for 3 consecutive years (during July/August). Then came preparation for the medical schools, which put a stop to all my other activities. Perhaps it was my teen-hormone years or my own free will that did not pursuit my love for new languages. Nevertheless, I've learned basic Latin and still continue to perfect my knowledge in Serbian language during my medical school years - I guess I still have a crave for languages deep down under the wish for wearing a white robe. :)
  No hard feelings to anyone, but I've recently compared the Serbian language to the German. Not that I know much about the German language, but I've noticed that in German there is the possibility to mix multiple words into one. Really cool once you get to know the basics of the language, but sometimes it is really hard for new learners. Basically, the grammar and the word pronounciation can be a reason for a person to pull back and not wanting to express themselves in that language. For example, Serbians from what I know have a hard time using "th" or "th"(d) - i.e. in the words "theatre" or "the" respectively - in English, which I think is one of the reasons they prefer not to use English at all.

  The fascinating thing as a child is that you can learn more stuff than an adult person, the so called "Tabula Rasa" thesis. My opinion is that gifted polyglots (people that speak a lot of languages) should nurture their languages by daily or weekly translating/reading text of headlines, otherwise the wealth of words and phrases of a language they might once perfectly knew will definitely decrease by time without giving it adequate practice. And it doesn't stop there, listening should adopt your hearing ability in order to rapidly process verbal requests or to better interact with other people. Remember, a dialogue needs "two to tango", so it might be better to find a partner for it. Exchanging opinions about your primary language for a secondary one through "The mixxer project" may prove really helpful. I haven't tried it yet, but some of the readers may have better solutions for this. I suppose that you'll have to make remarks about the difference in slang and normal language, so.. be very careful!
  Learning languages can be compared to other learning possibilities, such as playing the piano or the guitar or even writing code in various programming languages. There's a time when you might mix up words or phrases, but the brain learns to eventually adopt while multi-processing such requests - almost similar to other mechanical functions, like driving, eating a burger, talking to the phone and switching gears at the same time (not that I recommend it).
  To sum up, comparing time required, ability to learn and grace of use, as a child you'd have better results in learning a language, provided you often practice. And do practice, because in later years it will definitely prove worthy!

Tuesday, September 23, 2008

How to install Folding@home in Ubuntu using origami

This is a quick "how to" tutorial in order to provide some of your CPU time for a good cause, which is called Folding@home. As they explain it at the F@h website:
Folding@home is a distributed computing project -- people from throughout the world download and run software to band together to make one of the largest supercomputers in the world. Every computer takes the project closer to our goals. Folding@home uses novel computational methods coupled to distributed computing, to simulate problems millions of times more challenging than previously achieved.

There are other projects out there, like BOINC. In that case, I suggest to install boinc-manager (menu Applications → Add/Remove) and check out Rosetta.

Now let's get down to business. You need to pick a name, which can be anything you like, as long as it's not taken - you can also pick a team, but that's optional. You do not need a password for a username, but you need one in order to create your own team.
Tip #1: A person is called a "Donor" in F@h.

Next is the application. Ubuntu is based on GNU/Linux, and the (good? :P) people of Stanford have created a console client. Despite the fact that we are left without a graphical interface, we can still get the client program and use it.

It's time to visit our good ol' friend, the Terminal (or Konsole for KDE users). Once you start terminal (menu Applications → Accessories → Terminal) we will install the origami package:
sudo apt-get install origami
Tip #2: Type in your password and press enter if you are asked to do so

The following step is to download and install the f@h client program.
The origami manual has several examples:
origami install -u Joe -t 45104
This example will install the Folding @ Home client to the local
machine, reporting data as the Joe user as part of the 45104
(TeamUbuntu) Team.

origami install -u Joe -t 45104 -c1
This example will install the Folding @ home client to the local
machine, reporting data as the Joe user as part of the 45104
(TeamUbuntu) Team, using the i386 Folding @ Home client and
toggling the cron option to auto-stop between the hours of 8:00am
and 5:00pm.

origami install -u Joe -t 45104 -p amd64
This example will install the Folding @ home client to the local
machine, reporting data as the Joe user as part of the 45104
(TeamUbuntu) Team, using the amd64 Folding @ Home client and
toggling the cron option to auto-stop between the hours of 8:00am
and 5:00pm.

Tip: If you are on your own and don't have a team, I urge you to join TeamUbuntu ( 45104 ) or UbuntuForums ( 45399 ).

Tip #3: Don't know whether you have a 32-bit or 64-bit operating system (OS)? If you're not sure, execute this:
uname -m
It shows whether you have 32-bit (x86/i386) or 64-bit (x86_64/amd64) OS. 64-bit users will want to fully use their processors, so they need to use the -p amd64 argument.

In short, the recommended command for 32-bit is:
sudo origami install -u YourName -t 45104 -c1
..and for 64-bit is:
sudo origami install -u YourName -t 45104 -c1

Tip #4: origami installs a crontab if you use -c1 in its own system user 'origami'. If you want to edit the hours it starts/stops (after you install it), execute: sudo crontab -u origami -e

Once your f@h client is installed, you have finished the installation! You can see how your folding process goes:
sudo origami status

Tip #5: Your origami configuration files are found in the /var/lib/origami/ folder. For example, my current CPU #1 configuration file is /var/lib/origami/foldingathome/CPU1/client.cfg

Tip #6: You can give a small boost to your folding process by making it use really low CPU instead of running when it's just idle. Execute:
sudo origami 
Wait for it to stop, then run your text editor to edit the configuration file:
gksu gedit /var/lib/origami/foldingathome/CPU1/client.cfg
Add the following at the bottom of the file:
[core]
priority=96
Save and close your text editor, and restart origami:
sudo origami start

Enjoy folding proteins folks! :) You'll actually be helping out various medical fields, such as Alzheimer's and Huntington's disease researching.

Finally, take a look at these sites:
http://en.wikipedia.org/wiki/List_of_distributed_computing_projects
http://www.gridrepublic.org/
http://game.bakerlab.org/portal/

Friday, July 11, 2008

Bos taurus gas quarantined!

The gas produced by the cows' (Geek name: B. taurus) digestive system (aka GIT, short for gastrointestinal tract) is being tested, in order to see the share of effect to the global warming problem.
See it here.

What's next? Attaching tubes on human rear ends? :)

P.P.S. I'm establishing a miniposts tag, for such small posts!

Tuesday, July 17, 2007

Biology: Mosquitoes that don't replicate virus

While a decade ago scientists announced they can use foreign genes into a mosquito genome, a year ago, scientists announced a "theory to practice" successful use of an artificial gene that prevented a virus from replicating within mosquitoes. The problem is it's one virus, not all of them (virus)!

So they replaced a gene with a fake one into a mosquito and now it can't reproduce one virus - big deal. The real problem is not one virus, it's the mosquito itself, since it carries and favours the reproduce of several bacteria as well, par exemple Plasmodium.

Modifying genetically the vectors shouldn't be even a step to take to fight a virus. Fight to kill the vector or just fight another step of the reproducting ("life") cycle, called Vogralik's chain - The steps are:
  1. Infection's reservoir (mostly humans & animals)
  2. Way of spread (of the disease)
  3. Lieu of intake
  4. Concetration and virulency of the infection agent
  5. Sensitivy of the host (how immune the host is)
If one of the above is stopped effectively, then the infection will stop reappearing. The point is that it takes a long time in order to find an adequate way of preventing/stop the life cycle of an infection, especially if the vector can carry multiple infection agents.