Computational Systems

Biology
Prepared by:
Dr. H. Yohannes Alen, MSc.
Pharmaceutical Sciences
Andalas University
Indonesia

What are Biological Systems?

Popular Notion:
It is a complex system consisting of
very many simple and identical elements
interacting to produce what appears to be
complex behavior
Example: Cells, Proteins

What are Biological Systems?

Realistic Notion:
It is a system composed of many
different kinds of multifunctional elements
interacting selectively and nonlinearly with
others to produce coherent behavior.

What are Biological Systems?

Complex systems of simple elements
have functions that emerge from the
properties of the networks they form.
Biological systems have functions that rely
on a combination of the network and the
specific elements involved.

Molecular vs. Systems

Biology
Biology
In molecular biology,
gene structure and
function is studied at
the molecular level.
In systems biology,
specific interactions of
components in the
biological system are
studied cells,
tissues, organs, and
ecological webs.

From Systems Biology to

Computational Biology
Biological Systems are complex, thus, a
combination of experimental and
computational approaches are needed.
Linkages need to be made between
molecular characteristics and systems
biology results

Databases and Tools

Languages
Systems Biology Markup Language
CellML
Systems Biology Workbench

Databases
Kyoto Encyclopedia of Genes and Genomes
Alliance for Cellular Signaling
Signal Transduction Knowledge Environment

p53
Protein 53
Produces 53 proteins kiloDaltons
Guardian of the genome
Detects DNA damages
Halts the cell cycle if damage is detected
to give DNA time to repair itself

p53
If (damage equals true and repairable = true)
halt cell cycle
else
if(damage equals true and repairable = false)
induce apoptosis (suicide)

The Cell Cycle

G1 - Growth and
preparation of the
chromosome
replication
S - DNA replication
G2 - Preparation for
Mitosis
M - Chromosomes
separate

Checkpoints for DNA Double

Strand Breakage

ataxiatelangiectasiamutated

Cancer Cell Network

p53

p53

activates
p21

deactivates

No cell cycle!

CDK

p53

Cancer Drugs
Alkylating agents - interfere with cell division and affect the cancer
cells in all phases of their life cycle. They confuse the DNA by
directly reacting with it.
Antimetabolites - interfere with the cell's ability for normal
metabolism. They either give the cells wrong information or block
the formation of "building block" chemical reactions one phase of
the cell's life cycle.
Vinca alkaloids - (plant alkaloids) are naturally-occurring chemicals
that stop cell division in a specific phase.
Taxanes - are derived from natural substances in yew trees. They
disrupt a network inside cancer cells that is needed for the cells to
divide and grow.
all inhibit the cell cycle

The Cost of Robustness

Robustness is not a good characteristic
for all types of cells.
Example: The robust cancer cell!

Systems that are robust against common

perturbations are often fragile to new
perturbations (vulnerability of complex
networks)

Advantages of Computational
Systems Biology
It is highly relevant in discovering more
complex relationships involving multiple
genes
This may create new opportunities for
drug discovery
Better medical therapies for individual
treatments

Whats to come?
Current work is on small sub-networks
within cells.
Feedback circuit of bacteria chemotaxis
Circadian Rhythm
Parts of signal-transduction pathways
Simplified models of the cell cycle
Models of the Red blood cells

Whats to come?
Research has begun on larger-scale
simulations
Biochemical network level
Simulation of Epidermal Growth Factor (EGF)
signal-transduction cascade
The Physiome Project

Biochemical Networks
Problem:
The behavior of cells is governed and
coordinated by biochemical signaling networks
that translate external cues (hormones, growth
factors, stress, etc.) into adequate biological
responses such as cell proliferation,
specialization or death, and metabolic control.
Motivation:
Deep understanding of cell malfunction is crucial
for drug development and other therapies.
Available: [online]
http://www.brc.dcs.gla.ac.uk/projects/bp
s/bps_slides/bps_slides.pdf

Biochemical Networks

Biochemical Networks

Interpreting Biochemical Networks as

Concurrent Communicating Systems
Biochemical networks are analogous to
concurrent computer systems in many respects.
Concurrent systems are built up using basic
concepts such as choice, recursion, modularity,
synchronization, and mobility.
By exploiting these analogies, the existing tools
and formalisms for computing systems can be
applied to biochemical networks.

Concurrency Theory
Concurrent, communicating systems have been the
subject of intense study by Computing Scientists. Rich
theories and tools have been developed to aid in design,
analysis and verification of such systems.
Concurrent systems are inherently complex. To manage
complexity, theories and tools have been developed to
allow programmers to simulate behaviour. Simulators
allow the analysis of traces through concurrent
executions and provide a testbed for experimentation.
At a more abstract level, temporal analysis involves
proving that a concurrent system adheres to a temporal
property, i. e. it can be shown that a network protocol
always delivers data packets in the same order they
were sent.

Concurrency
A concurrent system is one where multiple processes exist at the same time. These
processes execute in parallel and potentially interact with each other. As an example of a
concurrent system, consider an internet banking site. The server and multiple client
processes exist at the same time, with interactions occurring between the individual clients
and the server.

Concurrency in Biochemical
Networks
Biochemical networks are also concurrent communicating systems. Pathways consist of
sequences of interactions which sometimes affect other parallel pathways. As an
example, consider two pathways involved in cell division. The Ras- Raf pathway which
triggers the cell division and the PI- 3K- Akt pathway which keeps the cell alive are both
triggered by the same growth factor. The sequences of interactions in both pathways run
concurrently with some interaction i. e. Akt inhibits Raf.

Complex modeling of
concurrent systems
Asynchronous circuits have been used to
simplify circuit analysis
Perhaps they could be used to examining
concurrent biological systems.