Tuesday, September 30, 2008

BioMath


The Defense Advance Research Projects Agency (DARPA) is offering support for resolve 23 mathematical problems, you can read the full rules here (sorry it's a DOC). This is the problems they want to solve:

  1. The Mathematics of the Brain. Develop a mathematical theory to build a functional model of the brain that is mathematically consistent and predictive rather than merely biologically inspired.
  2. The Dynamics of Networks. Develop the high-dimensional mathematics needed to accurately model and predict behavior in large-scale distributed networks that evolve over time occurring in communication, biology and the social sciences.
  3. Capture and Harness Stochasticity in Nature. Address Mumford’s call for new mathematics for the 21st century. Develop methods that capture persistence in stochastic environments.
  4. 21st Century Fluids. Classical fluid dynamics and the Navier-Stokes Equation were extraordinarily successful in obtaining quantitative understanding of shock waves, turbulence and solitons, but new methods are needed to tackle complex fluids such as foams, suspensions, gels and liquid crystals.
  5. Biological Quantum Field Theory. Quantum and statistical methods have had great success modeling virus evolution. Can such techniques be used to model more complex systems such as bacteria? Can these techniques be used to control pathogen evolution?
  6. Computational Duality. Duality in mathematics has been a profound tool for theoretical understanding. Can it be extended to develop principled computational techniques where duality and geometry are the basis for novel algorithms?
  7. Occam’s Razor in Many Dimensions. As data collection increases can we “do more with less” by finding lower bounds for sensing complexity in systems? This is related to questions about entropy maximization algorithms.
  8. Beyond Convex Optimization. Can linear algebra be replaced by algebraic geometry in a systematic way?
  9. What are the Physical Consequences of Perelman’s Proof of Thurston’s Geometrization Theorem? Can profound theoretical advances in understanding three dimensions be applied to construct and manipulate structures across scales to fabricate novel materials?
  10. Algorithmic Origami and Biology. Build a stronger mathematical theory for isometric and rigid embedding that can give insight into protein folding.
  11. Optimal Nanostructures. Develop new mathematics for constructing optimal globally symmetric structures by following simple local rules via the process of nanoscale self-assembly.
  12. The Mathematics of Quantum Computing, Algorithms, and Entanglement. In the last century we learned how quantum phenomena shape our world. In the coming century we need to develop the mathematics required to control the quantum world.
  13. Creating a Game Theory that Scales. What new scalable mathematics is needed to replace the traditional Partial Differential Equations (PDE) approach to differential games?
  14. An Information Theory for Virus Evolution. Can Shannon’s theory shed light on this fundamental area of biology?
  15. The Geometry of Genome Space. What notion of distance is needed to incorporate biological utility?
  16. What are the Symmetries and Action Principles for Biology? Extend our understanding of symmetries and action principles in biology along the lines of classical thermodynamics, to include important biological concepts such as robustness, modularity, evolvability and variability.
  17. Geometric Langlands and Quantum Physics. How does the Langlands program, which originated in number theory and representation theory, explain the fundamental symmetries of physics? And vice versa?
  18. Arithmetic Langlands, Topology, and Geometry.What is the role of homotopy theory in the classical, geometric, and quantum Langlands programs?
  19. Settle the Riemann Hypothesis. The Holy Grail of number theory.
  20. Computation at Scale. How can we develop asymptotics for a world with massively many degrees of freedom?
  21. Settle the Hodge Conjecture. This conjecture in algebraic geometry is a metaphor for transforming transcendental computations into algebraic ones.
  22. Settle the Smooth Poincare Conjecture in Dimension 4. What are the implications for space-time and cosmology? And might the answer unlock the secret of “dark energy”?
  23. What are the Fundamental Laws of Biology?. This question will remain front and center for the next 100 years. DARPA places this challenge last as finding these laws will undoubtedly require the mathematics developed in answering several of the questions listed above.
So we have 9 / 23 problems involving biology (marked in blue), I think we'll have a new age in theoretical biology in the next years, including bioinformatics, computational biology, evolution and systems biology.

Image from: http://s3.amazonaws.com/mmc-digi-beta-production/assets/201/math_teacher_626_article.jpg

Friday, September 26, 2008

Learning in the bus

Today when I was in the bus, a girl close to me was reading, she had a small block of cards, the cards had a hole in one side and a key ring attached together, simple and effective mode to keep the notes, the notes are some chemical formulas, the amino acids charts, one side was the formula, in the reverse of the card was the name, 3 letter abbreviation and the polar class.

Yes, I remember when in college I learned all this information, also I build some molecules with my atomic-kit, to see the structure, and now I just see the ACGT codes, missing the 3D beauty.

Amino Acid Short Abbrev. Side chain Polar pH
Alanine A Ala -CH3 - -
Cysteine C Cys -CH2SH - acidic
Aspartic acid D Asp -CH2COOH X acidic
Glutamic acid E Glu -CH2CH2COOH X acidic
Phenylalanine F Phe -CH2C6H5 - -
Glycine G Gly -H - -
Histidine H His -CH2-C3H3N2 X weak basic
Isoleucine I Ile -CH(CH3)CH2CH3 - -
Lysine K Lys -(CH2)4NH2 X basic
Leucine L Leu -CH2CH(CH3)2 - -
Methionine M Met -CH2CH2SCH3 - -
Asparagine N Asn -CH2CONH2 X -
Pyrrolysine O Pyl


Proline P Pro -CH2CH2CH2- - -
Glutamine Q Gln -CH2CH2CONH2 X -
Arginine R Arg -(CH2)3NH-C(NH)NH2 X strongly basic
Serine S Ser -CH2OH X -
Threonine T Thr -CH(OH)CH3 X weak acidic
Selenocysteine U Sec -CH2SeH - -
Valine V Val -CH(CH3)2 - -
Tryptophan W Trp -CH2C8H6N - -
Tyrosine Y Tyr -CH2-C6H4OH X -

Thursday, September 25, 2008

Firefox add-ons


Currently I use every day the best on the world browser: Mozilla Firefox, in all my computers (1 Linux laptop with dual Vista/Mandriva, other old laptop with Puppy Linux and 1 Mac with Leopard), some add-ons "cannot-live-without" I commonly install for Firefox are:

While Google Chrome doesn't support tools like that (and native Linux/Mac versions), I hardly change the Fox.

Monday, September 22, 2008

killer tux


Killer Tux from Cenek Strichel on Vimeo.

Thanks to Xbit for the link.

man baby



BABY(1) USER COMMANDS BABY(1)

NAME
BABY - create new process from two parent processes

SYNOPSIS
BABY sex [ name ]

SYSTEM V SYNOPSIS
/usr/5bin/BABY [ -sex ] [ -name ]

AVAILABILITY
The System V version of this command is available with the Sys-
tem V software installation option. Refer to Installing
SunOS 4.1 for information on how to install and invoke BABY.

DESCRIPTION
BABY is initiated when one parent process polls another server
process through a socket connection (BSD) or through pipes in the
system V implementation. BABY runs at a low priority for approximately
40 weeks then terminates with heavy system load. Most systems require
constant monitoring when BABY reaches it's final stages of execution.

Older implementations of BABY required that the initiating
process not be present at the time of completion, In these versions
the initiating process is awakened and notified of the results upon
completion. Modern versions allow both parent processes to be active
during the final stages of BABY.

example% BABY -sex m -name fred

OPTIONS

-sex
option indicating type of process created.

-name
process identification to be attached to the new process.

RESULT
Successful execution of the BABY(1) results in new process
being created and named. Parent processes then typically
broadcast messages to all other processes informing them of their
new status in the system.

BUGS
The SLEEP command may not work on either parent processes for some
time afterward, as new BABY processes constantly send interrupts
which must be handled by one or more parent.

BABY processes upon being created may frequently dump
in /tmp requiring /tmp to be cleaned out frequently by one
of the parent processes.

The original AT&T version was provided without instructions
regarding the created process, this remains in current implementations.

SEE ALSO
cigars(6) dump(5) cry(3)

OTHER IMPLEMENTATIONS

gnoops(1)
FSF version of BABY where none of the authors will accept
responsibility for anything.

NOTES

baby -sex F -name Samantha Lynn Garriques

Completed successfully at the St. Joseph Medical Center on
November 2, at 3:31 P.M. after about 20 hours of labour.
New Mom Lisa is doing fine and will come home in about 2 days.
More information can be gotten from Dad by e-mail or by
calling the new baby hotline @931-XXXX. Celebrations can
probably begin in about 18 years.


Sun Release 4.1 Last change: Just when I got home from the hospital.


Source: http://linuxshellaccount.blogspot.com/2008/09/baby-man-page-more-linux-and-unix-jokes.html

Wednesday, September 10, 2008

Change of role


Now I'm dad of a very cute girl, I'll be off-line the next 2 weeks.