All 23 entries tagged Work

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July 25, 2006

Center for cell analysis and modelling

Center for cell analysis and modelling – The name is self–explanatory.

Bilnov's page is very interesting in particular. Bilnov's review of 'Rules for Modeling Signal–Transduction Systems' is published in STKE section of Science. Unfortunately I am unable to access the article because university doesn't have subscription to that section.

Bilnov seems to be a dude. They have cell signalling at LANL also.

Molecular mind maps are here . The website is also cool with loads of stuff.

September 16, 2005

AVoCS 2005

"Fifth International Workshop on Automated Verification of Critical Systems" just concluded at
University of Warwick, (12–13 September 2005). The conference was arranged by members of Formal method and Quantum processing group of Department of computer Science. The details can be found here. Don't forget to check the photographs by our in-house researcher cum photographer Nick :-)

May 20, 2005


Gave a presentation on Modelling and simulation in System Biology on 18th May,2005. Plan is to make a web-page and put the PPT slide there.

May 09, 2005

Pointillist Software

Pointillist is a collection of programs for inferring the set elements affected by a perturbation of a biological system, based on a collection of evidences. It contains four programs: Data Manager, Data Normalizer, Significance Calculator, and Evidence-Weighted Inferer. First two are for data retrieval,manipulation and normalization. The Significance Calculator is a program that can analyze the probability distribution of a set of observations, and compute the statistical signficance of each observation on the basis of the distribution.The Evidence-Weighted Inferer is a classification program that attempts to divide a set of elements into two sets, affected and unaffected. It compares multiple evidences to determine which elements of a network are most likely affected by a perturbation of a system.Overall, just another machine-learning program.

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…..

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 04, 2005

Learning Markov models

I am learning Markov models. I realized that if I want to learn Stochastic modeling, its very important to know Markov processes and Monte-carlo simulations. Almost all the examples that I have come across use Markov models, directly or indirectly. I am back to my basic statistics lessons, my knowledge of Baysian statistics is not of much use here as its quite different from that :(:( I am reading it full-time to finish the topic for once and all. I have the target of finishng it by next sunday. I am also thinking about the problem that I would like to tackle. The fore runners are –

  1. Simulating Live sequence charts.
  2. Making Self-correcting models.
  3. Process Algebra + AI (can be merged with self-correcting models)
  4. Brane calculi ?? (Yet to think over it)

April 02, 2005


Learn the fast matrix mulitiplication using wavelets. Learnt wavelets recently :)

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