Design Principles in Biology

There is nothing simple about Life. There is nothing special about Life either. The laws of nature that control inanimate objects are equally applicable to the living. But then how does the ‘Life’ emerge from the non-living? Why don’t the non-living act like the living? We believe the answers to these questions lie in the interconnected dynamic processes in a living system, either inside a cell or in an individual or among the organisms. We also believe certain universal rules control these dynamic processes. Those rules are the design principles of Life. So, we borrow ideas from Physics and Engineering and attempt to understand the Living through experiments and mathematics.

Current Research


Collective behavior

Planar cell polarity
We often imagine a cell as an individual, working alone to meet its needs. However, in reality, cells in a multicellular organism live as a community. Even many single-cell microorganisms live in a group. In a community, cells interact with each other, share resources, and perform shared tasks. Interactions among cells lead to the emergence of collective behaviors and critical phenomena. Just like cells, collective behavior can also be seen among a group of animals, like in a flock of birds or a colony of bees. Statistical physics is useful to understand interacting systems, living, or non-living. We are using statistical physics to study emergent phenomena in an ensemble of interacting cells. For example, we use a spin-based model, like the Ising model of magnetism, to understand synchronized alignment and polarization of epithelial cells. Read more on this work here

Image: Alignment of hairs on the paw of a mouse (PMID:17259302)


Dynamical Systems

Phase plane
Every biological system is dynamical. Inside a cell, the number of molecules changes with time. With time, a cell itself can change its properties and metamorphose into another cell type. Even the interactions between multiple cells also change with time. In our lab, we investigate dynamics of various biological systems using concepts of dynamical systems theory and statistical physics. One such area of our work is to understand the mechanism by which molecular signaling pathways encode and decode information. You may read our work on signal discrimination in a pathway here in this article . We are also interested in the dynamics in gene expression, cell death, and cellular differentiation. In a work on Epithelial to Mesenchymal Transition, we have developed methods to decipher the trajectory of cellular state transition and have proposed a new model to represent the dynamics of phenotypic state transition. You may read more about this work in this article .

Image: The brush strokes in The Starry Night by Vincent van Gogh is like trajectories on a phase plane of a dynamic system (image source:Wikipedia)

Software


DEBay estimates cell type-specific gene expression from qPCR data of a mixed population. DEBay calculates Normalized Gene Expression Coefficient (NGEC), which is a relative measure of the expression of the target gene in each cell type in a population.

Download DEBay

The python packages used in DEBay uses C libraries for faster computation. Therefore, a GCC would help to improve the performance of DEBay but it is not mandatory. MinGW, a complete run time environment for GCC for Windows is available

Citation information: Devaraj V., and Bose B. DEBay: A computational tool for deconvolution of quantitative PCR data for estimation of cell type-specific gene expression in a mixed population. Heliyon, 2020, 6(7), e04489.



FlowPy is a tool for Flow Cytometry data analysis. It is used for data extraction, visualization, analysis like cluster analysis and histogram subtraction. FlowPy is written in Python and free to use.

Download FlowPy

Citation information: Please cite FlowPy in publication as 'FlowPy (http://flowpy.wikidot.com)'

Credit: Soumitra Saxena, M. V. Seetha Rama Sastry, Revanth Sai Kumar, Tejas Mehta, Biplab Bose, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India



network
CorNetMap is a tool for gene expression correlation analysis. Using this you can calculate Pearson correlation and cross-correlation for multidimensional data from experiments like qPCR, microarray etc. The result can be visualized as heat-map or network diagram.

Download CorNetMap

Credit: Abhigyan Khaund, Biplab Bose, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, India

Citation information: Please cite CorNetMap as: A. Khaund, B. Bose, CorNetMap (sourceforge.net/projects/cornetmap)



state transition
Matlab codes

StateTransion: Codes for estimation of fraction of cells moving from one state to another state from discrete-time population aggregate data. Codes available at GitHub . Details in this article .

Online Courses


Online course on Systems Biology. This course focuses on computational aspects of Systems Biology - particularly, Dynamical Systems, Stochastic Processes, and Network analysis.

Course Page



An introductory NPTEL course on Dynamical Models in Biology. Focuses on concepts of dynamical systems in biology and communicates those concepts without rigorous mathematical analysis.

Course starts from 23rd August 2021. Registration is open.

NPTEL Course Page

YouTube Playlist

People


Hi!! I am Biplab. I did Ph. D in Biochemistry from All India Institute of Medical Sciences, New Delhi . Before that, I had studied M. Pharm and B. Pharm in Jadavpur University, Kolkata .

My primary interest is understanding Biology through Mathematics and Physics. I enjoy debugging codes, scribbling equations, and manipulating cells to disclose their secrets.

Apart from musing over science, I am a cycloholic and enjoy long-distance cycling . I have interests in wildlife and maintain a record on birds at IIT Guwahati .

My resume


Current members of our lab:

Ph. D students: Satendra Singh Gurjar, and Mouli Sarkar.

M. Tech student: Nirupam.

B. Tech students: Tahir.


Former members of our lab:

Ph. D students: Vimalathithan, Poulami, Namami, Mahesh, Pojul, Ashok, and Asim.

M. Tech students: Gaurav, Kamleswar, Kaushalesh, Somya, Priya, Ritika and Sahil.

B. Tech students: Himakar, Param, Vishwas, Divyanshu, Mayur, M.V.S.R. Sastry, Roxy, T.V. Revanth Sai Kumar, Digvijay, Siddharth, M.S. Sudarsan, Tejas, K. Venu, Gaurav.

For students


If you are interested in working at the interface of Mathematics, Physics, and Biology, you are welcome to join our lab. You may join as a Ph. D student/ M. Tech student / B. Tech student .


For Ph. D student: We use both wet-lab experiments and mathematical models in our work. You should be comfortable with Mathematics and Computer Programming. It would be helpful if you have exposure to experimental Biology, but it’s not essential. We also encourage students from Physics, Mathematics, and different branches of Engineering to work with us.

Twice in a year, IIT Guwahati invites applications for Ph. D programs in various departments including our department. Selection is made through written test and interview. For further information follow IIT Guwahati website


For M. Tech. students: If you are an M. Tech student in our department, you may join us for your M. Tech. project. You should be comfortable with Mathematics and Computer Programming.

(I supervise only the students of IIT Guwahati. If you are a student from another institute, you may apply for 1-2 months of summer training on Mathematical Biology. Please, do not apply for the supervision of your master's thesis/project)


For B. Tech. students: If you are a B. Tech. student of any department of IIT Guwahati, you may join us for various projects. Please note that these projects would require your involvement for at least one year. You should be strong in Mathematics and computing. Interest in Physics and Biology would be helpful. You may meet me at any time to discuss prospective projects.

(I supervise only the students of IIT Guwahati. If you are a student from another institute, you may apply for 1-2 months of summer training on Mathematical Biology.)

Resources


A shortlist of popular science books and textbooks of our interests

Popular Science Books:

Linked by Albert-lászló Barabási

Sync: The Emerging Science of Spontaneous Order by Steven Strogatz

At Home in the Universe: The Search for the Laws of Self-Organization and Complexity by Stuart A. Kauffman

What Is Random? Chance and Order in Mathematics and Life by E. Beltrami


Useful textbooks:

Biocalculus: Calculus for Life Sciences by James Stewart

Nonlinear Dynamics and Chaos by Steven Strogatz

Molecular Driving Forces by Ken Dill & Sarina Bromberg

Stochastic Modelling for Systems Biology, by Darren J. Wilkinson

Birds, Mammals & Butterflies of IITG


The lush green campus of IIT Guwahati is home to diverse flora and fauna. I have made a list of birds , mammals and butterflies that I have spotted over the last few years, here on the campus. This list is not an exhaustive one.

Please visit this page for the list


Contact


Department of Biosciences & Bioengineering, IIT Guwahati, Guwahati, 781039, India

Phone: +91 361 258 2216

Email: biplabbose@iitg.ac.in