Sitabhra Sinha
The course is called Systems Biology Across Scales: A Personal View rather than simply Systems Biology because, being a relatively new field, one course on the subject can look radically different from another in terms of content as well as treatment - and the exact structure of the course depends pretty much on who is teaching it.
The common minimum on which most people agree is that systems biology essentially seeks to figure out how to bring together knowledge about the component parts in order to understand the whole (the system). For example, if we want to understand how the cell responds appropriately (most of the time) to a wide variety of signals in an extremely noisy environment, we need to pull together our knowledge of a large number of signaling pathways which involve a wide variety of molecules. There are several systems biology courses which only deal with this aspect - and from this point of view, systems biology is all about constructing a large-scale detailed computational model that will explain how a cell functions. As such, this approach has been criticized by several scientists - including the Physiology Nobel Laureate Sydney Brenner (see his 2009 lecture at the Salk Institute).
However, other systems biologists feel that just focusing on questions at the level of the cell, is missing the whole point. For example, on generalizing the above problem, we realize that essentially the same problem is confronted by the multi-cellular organism where the nervous system somehow solves this problem. Are similar principles being used both at the level of the cell and at the level of the organism - and if so, what are these "universal" principles ? That is a systems-level question, which is different from the questions that will be asked by cell biologists or neuroscientists who are more interested in the exact "wetware" by which the problem is solved in the specific system they are interested in.
One can easily see that a host of questions one can ask at one level
of biological organization (e.g., the cell) have analogs at other
levels (e.g., the organism, the population or the food web). These
could be questions about communication efficiency, computational
capability, dynamical stability, robustness to environmental noise, etc.
of the corresponding systems. Often it is more useful to generalize
the problem from the specific biological setting and frame it in terms
of useful theoretical constructs such as networks, at other times
we may be interested in a general phenomenon such as wave propagation.
I have therefore organized the course around several such "tools
for thinking" about biological problems (to paraphrase the title of
Conrad Hal Waddington's book Tools for Thought, a must-read for
any theoretical/computational biologist) - viz.,
(i) Networks,
(ii) Oscillations (temporal patterns),
(iii) Shapes (spatial patterns) and
(iv) Waves (spatio-temporal patterns)
[Note that, networks are also "spatial" patterns - although, in general, the pattern is in a non-physical abstract space]
In the 30-odd lectures of this course, we will first introduce each "tool" and then apply it to various biological phenomena. On the way, we will look at how this perspective can help us look at certain diseases - such as cancer, epilepsy and cardiac arrhythmias - in a new light.
Class Schedule:
16/1/17: Introduction
17/1/17: Antecedents and Course Outline
18/1/17: Networks: Basic Concepts
19/1/17: Networks: Paths & Cycles
20/1/17: Networks: Degree & Reciprocity
23/1/17: Networks: Clustering & Balance
24/1/17: Networks: Models I
20/2/17: Networks: Models II
21/2/17: Landscapes
22/2/17: Proteins as Networks: Centrality & Core-periphery
23/2/17: Intra-cellular systems I: Regulatory Networks and Motifs
24/2/17: Intra-cellular systems II: Metabolism & Modularity
27/2/17: Intra-cellular systems III: Protein-Protein Interaction
28/2/17: Intra-cellular systems IV: Signal-transduction and networks
10/4/17: Brain: A network of neurons
11/4/17: Network Epidemiology
12/4/17:Interactions in Ecology
13/4/17:Food Webs and Stability of Ecological Networks
17/4/17:Temporal Patterns and Biological Oscillators
18/4/17:Biological Oscillators: Hopf Bifurcation and Glycolysis
19/4/17:Temporal Patterns: Discrete time models in biology
21/4/17:Building elements for Biological circuits
24/4/17:Spatial Patterns in Biology: Turing mechanism
25/4/17:Turing patterns in Biological systems
26/4/17:Waves in Biology: Excitable Media
27/4/17:Waves in Biology: From cells and tissues to populations
28/4/17:Waves in Biology: Cardiac Arrhythmia
1/5/17: Waves in disordered excitable media
2/5/17: Synchronization in Biology
3/5/17: Oscillation, Waves and Synchronization in Uterine Tissue
3/5/17: Special Lecture by Shakti N. Menon: Collective Motion in Living Systems
Assignments
Assignment 1 (due January 25, 2017)
Assignment 2 (first part due February 3, 2017)
Assignment 2 (second part due April 24, 2017)
Assignment 3 (second part due May 3, 2017)
Readings
Stuart A. Kauffman, "Antichaos and Adaptation", Scientific American, August 1991 (19/1/17)
Textbooks:
There is, unfortunately, no book that covers the course in its
entirety and I only mention a few below that I will use for several lectures.
For networks, we will consult
Mark Newman, Networks: An Introduction,
possibly the best textbook on the subject.
For network motifs, we will look at
Uri Alon, An Introduction to Systems Biology.
For oscillations we will use
Steven H Strogatz, Nonlinear Dynamics and Chaos.
For patterns, a very good non-technical book is
Philip Ball, The Self-Made Tapestry.
However, for the course we will use more technical books such as
J D Murray, Mathematical Biology and
James Keeer and James Sneyd, Mathematical Physiology.
For waves, we will use
Jose Jalife et al, Basic Cardiac Electrophysiology for the Clinician
(don't be fooled by the title - it is much more general than just cardiac electrophysiology and certainly will appeal to a much broader audience than just clinicians), as well as, material from our recent book
Sitabhra Sinha and S Sridhar, Patterns in Excitable Media: Genesis, Dynamics and Control.
Web resources for Systems Biology:
Uri Alon's Systems Biology course, 2014