All entries for April 2005

April 27, 2005

Ariel view of Warwick University

Looking at the university from a new perspective ;-)


April 26, 2005

My Japanese Name





My Japanese Name Is...


Haruki Shigenoi


My dying brain cells

Had a chance to experience the truth today. Yes, I am indeed loosing my brain cells. I was sitting on the second floor in the university library today. After 2 hours of brain-storming I realised that I had burnt lots of energy and my body needed something, chocolates to be precise. So I went to the ground floor to grab some chocolates keeping my laptop and books open at the table. While coming back I absolutely forgot the place I was sitting at. Instead of going to the second floor, I went to the fourth floor where I use to sit usually and started looking for my laptop and books. Not only that, I was also quite confident that there was a particular table that I had occupied 5 minutes ago.But to my horror, I found a lady sitting there with her laptop and books open. I was completely surprised. I did a quick round of the foruth floor again hoping to find my place. But no,nothing happened. I went to the lady again hoping to catch a glimpse of my jacket, book ,bag just anything and even surprisd the poor girl. She must be wondering , but didn't say anything, just gave a nice smile. I realised that I must have been sitting on the fifth floor then. Happily I ran to the fifth floor hoping to get the glimpse of my laptop and was disaapointed again.Half-heartedly I went to check the third floor to be completely dissapointed. I was quite sure that either I had lost my stuffs or had crossed into a parallel universe while coming from ground floor to the fourth floor in the lift(remember.. the Matrix). Finally, I decided to have a check at the second floor as well, though I was sure that I was not sitting on the second one. I was just dragging my feet with a long dissapointed face and eureka…........a miracle happened. I saw my laptop, my research papers, my probability book,my jacket,my bag , everything in place and at the same window which I was imagining at the fourth floor. That was the biggest relief of the day but that unrevealed the saddest truth about my brain cells as well.

April 20, 2005

ODE to Formal methods

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

Insulin for case–study

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

Statechart Analysis

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…..


Ancient civilizations on net

Good site with decent details.

Article in PNAS on gene network

Recent issue (5thapril,2005) of PNAS features on gene regulatory network. The cover article written by Levine and Davidson is very interesting and could be very useful for our work. There is a whole list of papers on gene regulatory network in the "Developmental Biology Section".

April 07, 2005

Pope reborn

The Pope is being reborn here.

The Most Important Bus Trip of Our Times

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.


April 2005

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