Computational Systems Biology

Prepared by: Rhia Trogo Rafael Cabredo Levi Jones Monteverde

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

ataxia-telangiectasia mutated

Cancer Cell Network

p53

p53

activates

p21

deactivates

CDK

No cell cycle!

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.