Orhan Karsligil's Ideas, Thoughts and Collection of Resources

Technology Review: Bridging the Genomic Divide

Very interesting article on combinatorial Chemistry and drug discovery methods.

Technology Review: Bridging the Genomic Divide

That small molecules have more chance to interact with proteins and that there are only very small number of them identified is amazing. Production of small molecules is much easier and thus many more of them can be tested in a combinatorial way. The article also mentiones that NIH is planning to make the results available to public and acedemia.

Beam me to Mars, Scotty!

Interesting technology...Magnetic Propulsion

I remember that in high school I was thinking about using Bogazici channel (connects Black Sea to Marmara Sea, so it is salty water) and the earths magnetic field to generate electricity. If you calculate between the coasts of the channel there is a mV range difference in potential. If you have very large metal plates you can generate electricity. THe oposite works too : You pump electricity to those plates and with the help of the magnetic field of earth (perpendicular to earth) you can move the water.

New Category: Technology

I added a new category on Technology. I am going to add links and ideas
about computers, software, technology and science in general to that

Prisoner's Dilemma

Check this site: Prisoner's Dilemma

It is about the Prisoner's Dilemma competition. The new winner is a set of cooperating agents. Very clever. The rules are so simple but yet the results are so interesting.

First post

I am planning to use this space to write about computers, software and technology in general.

Switching off gene to stop tumor

An interesting article on this new finding. Unfortunately gene therapy is still far away from being reality, but it is interesting to play with genes in this way to prevent cancer or similar health issues. The question is though the side effects. How specific can one get in preventing cell division?

Updated the Mathematics Category

Started working on some new algorithms to test my ideas on event

identification using multiscale thresholding. Check it out at my mathematics category.


Data smoothing using multiscale thresh holding

A signal consists of multiple components occurring at different frequencies. Current analysis methods analyze signals either in time or frequency domain but not in both at the same time. Time series analysis is major topic in signal processing. Any control engineer spends endless nights studying the Fourier transformations which convert a time series into the frequency domain and you can draw fancy graphs and shape your frequency response of your controller. These methods work very nicely for linear systems, meaning if you can open a valve infinitely :).

I am interested in analyzing signals in both domains at the same time. This would enable the use of methodologies from both domains, like constrains and events in time, and data smoothing (multiband frequency filters). Wavelets provide a nice framework for this type of research.

I currently work on simple multiscale threshholding algorithms. The idea and underlying math is extremely simple:

Next steps are going to be
  • Use a moving window for the threshholding algorithm to get multiple reconstructed values for the same data points
  • Analyze these points for variance
  • Establish an event detection algorithm
I will post some of my results soon.

ScienceWorld - One of the best resources on the web

ScienceWorld is a very rich scientific treasure box. I recommend everyone to go and take a look.

Multiscale Methods to Speed up QR problems

My thesis was based on Multiscale Modelling. The building blocks of this methodology are a type of filters called Wavelets. Using wavelets it is possible to transform a first order system to time-frequency domain. In this domain the model representation is not anymore the simple linear time line but a tree structure where both time line (horizontal) and scales (frequency bands - vertical) are represented.

Once the model is transformed into this new domain it is also possible to create algorithms to solve a QR Programming problem based on this first order system. Instead of solving the problem globally it is possible to solve a subset which is a close approximation. This fast solution represents fine resolution at the beginning of the time line and a coarser resolution in the future where uncertainity in most physical systems make finer calculations obsolote anyhow.

I am going to go into more details in the comments section of this post in the next couple days. I will formulate a sample case and demonstrate the solution algorithm. I hope to have some links ready at some point too. Please send comments if you have any.

UPDATE: What is QR? (click here for the source)

The quadratic programming problem involves minimization of a quadratic function subject to linear constraints. Most codes use the formulation

where is symmetric, and the index sets and specify the inequality and equality constraints, respectively.

The difficulty of solving the quadratic programming problem depends largely on the nature of the matrix Q.