ICREA/Complex Systems Lab, Universitat Pompeu Fabra-GRIB

 

 

Main Researchers: Ricard V. Solé, Andreea Munteanu
Javier Macía
Carlos Rodriguez-Caso
& Sergi Valverde

The material contained here involves basic papers and documents related to Systems Biology/ Theoretical Biology. Some of these materials are used in ongoing undergraduate and master courses given at the Universitat Pompeu Fabra. Three basic types of material (and links) can be found: (a) introductory papers to the mathematics necessary to follow the modelling approaches (including graph theory, dynamical systems and simulation approaches); (b) papers with introductory background to relevant theoretical questions, and (c) specific examples of models of biological phenomena. Models of the immune system, cancer dynamics, genetic interactions or metabolic pathways can be found here (among other examples).


SCIENCE Special Issue on COMPLEX DISEASES

Systems Biology is a system's level approach to biological complexity aimed to provide complete understanding of those phenomena that take place in living systems beyond the molecular-level scale. In spite of the long tradition within western science of the reductionist approach, such a view has been shown to be seriously flawed in most circumstances. Reductionism is defined as the analytic view claiming that understanding a given (just) requires a detailed understanding of its components. In this view, the better the knowledge of the details, the better the understanding of the whole behavior. This view is wrong: of course the detailed knowledge of the molecular structure of a given receptor is needed, particularly when looking for therapeutic drugs. But such level of detail will seldom contribute to our understanding of high-level properties such as memory, which involves thousands of interacting cells. Contrary to our intuition, models of interacting units which ignore most details are actually enough to provide full understanding of the system's behavior, thus indicating that most details are not relevant at the higher scale. Current studies in Systems Biology are being applied to numerous areas, including the so called complex diseases.


SYSTEMS BIOLOGY links of interest:

Key papers in Synthetic Biology
systems-biology.org General information and downloadable materials
Hiroki Kitano's Lab Publications, software and projects
Adam Arkin's Lab Publications, theory, papers, computation and experiments.


NEWS
1 /1/2005    Undergraduate Course on THEORETICAL BIOLOGY at the
UNIVERSITAT POMPEU FABRA

 

 

 

GENERAL INFORMATION ON SYSTEMS BIOLOGY

TUTORIAL PAPERS:


H. Kitano, Systems Biology: A Brief Overview. Science. 295, 1662-1664, 2002.
H. Kitano, Computational Systems Biology. Nature. 420, 206-210, 2002.

They can be downloaded as PDF files from: HIROKI KITANO's TUTORIALS ON SYSTEM's BIOLOGY



GENERAL VIEWS ON SYSTEMS BIOLOGY:

CAN A BIOLOGIST FIX A RADIO?, Yuri Lazebnik, CANCER CELL September 2002



LOGIC MODELS OF MOLECULAR INTERACTIONS:

General Introduction downloadable from: Computing comes to Life, by Brian Hayes

 

 

BASIC GRAPH THEORY AND NETWORK BIOLOGY

The natural language to describe and analyse complex biological systems is provided by networks. Graphs (or networks) are defined in terms of a set of elements (proteins, genes, species, neurons) interacting through some kind of link (physical contact, regulatory interaction, mutualistic coupling, synaptic connection). A graph is a well-defined object whose properties (both local and global) can be used in order to extract valuable information (and understanding) of the system's organization, its key elements and how it might react under some types of perturbations.

REVIEW PAPERS ON SMALL WORLDS from American Scientist, by Brian Hayes:
Graph Theory in Practice: Part I
Graph Theory in Practice: Part II


An example of a graph/network: here the balls indicate units (for example, proteins) and the links among them indicate the presence of some type of interaction (such as physical contact). Here the so called p53 box is shown.