All entries for April 2005
April 27, 2005
Looking at the university from a new perspective ;-)
April 26, 2005
April 20, 2005
Writing about an entry you don't have permission to view
Working on the mathematical model of Insulin Signaling pathway by Ahmad Sedaghat, Arthur Sherman and MJ quon.
Another idea is to produce Formal method notation from given ODEs.
April 14, 2005
I have to look at the functions of Insulin in the body.
1. Understand the biology behind insulin.
2. Look at the different levels for modeling, starting from molecular level to network level.
April 12, 2005
I have been reading about Statecharts for some time and would like to mention 2 papers in particular –
N. Kam, I.R. Cohen and D. Harel, "The Immune System as a Reactive System: Modeling T Cell Activation with Statecharts", Bull. Math. Bio., to appear. (Extended abstract in Proc. Visual Languages and Formal Methods (VLFM'01), part of IEEE Symp. on Human-Centric Computing (HCC'01), 2001, pp. 15-22.)
N. Kam, D. Harel and I.R. Cohen, "Modeling Biological Reactivity: Statecharts vs. Boolean Logic", 2nd Int. Conf. on Systems Biology (ICSB 2001), California, 2001, pp. 301-310. (Also in Proc. Working Conf. on Advanced Visual Interfaces (AVI'02), pp. 345-353, Trento, Italy, May 2002.)
The focus of both of the papers is on modeling biological systems with the help of statecharts. I am writing down some of the observations that I made while reading those papers –
1. The statecharts are meant to enhance modeling styles in Object-Oriented Paradigm.
(We have our reasons to believe that why OOPs is not a right paradigm for biological modeling.)
2. They capture the dynamics of the system but not the non-deternimism involved.
(Atleast, I think this. There is a zoom-in facility but mobility is still missing. In other words,
they are still static at various levels)
3. The simulations of statecharts depend on the Rhapsody tool. The tool is essentially meant to follow object-oriented paradigm(they claim) and lacks in mechanisms for object creation and broadcasting(full/limited).
In my view, statecharts can lead us to a ODE based approach. In fact they can directly be coverted into ODEs or PDEs looking at the various levels of sub-charts but would suffer from the same problems that are existing with the conventional approaches in system biology. Is there any non-determinism in the system ? I would say no. There is coarse-graining but not the ability to change the topological arrangement. This is the point where the pi-calculus simply emerges as a much superior mechanism than other approaches.
I am yet to see as how Live sequence charts are better than the statecharts. Working on that…..
April 07, 2005
The buses run, the buses run, the buses run…..............YAHOOOOOO.
Finally the buses run acorss the LoC between Srinagar and Muzaffarabad.
One of the most wonderful things that happened recently.
Heartiest congratulations to the passengers, who showed tremendous courage and determination.
" This is the beginning of a new phase in the continuing friendship with Pakistan – Manmohan Singh, Indian PM "
I am happy and join millions who are praying towards the success of the mission.