Systems Biology Short Course - June 21st - June 25th 2010
Organizers
Bernhard O. Palsson, Professor of Bioengineering and Medicine at UCSD and Adjunct Professor University of Iceland
Ines Thiele, Assistant Professor of Bioengineering at University of Iceland.
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OVERVIEW
The course targets PhD students, post-docs, university faculty and life-science researchers from various scientific backgrounds. In particular, the course is oriented towards students interested in interdisciplinary research spanning biology, mathematics, and computer science. Knowledge in these three areas is not required since the course teaches the necessary background and basic principles.
This course aims to provide hands-on experience to novices in computational systems biology by combining experimental data and mathematical modeling with emphasis on kinetic modeling of cellular pathways. The course focuses on bacteria as model systems as these are amenable to simple studies to verify predicted models. Furthermore, possible biomedical and biotechnological applications are introduced. The course will be taught by world experts in the field of Systems Biology.
COURSE CONTENT
Metabolic reconstructions are a common denominator in systems biology. They represent biochemically, genetically and genomically structured knowledge-bases that capture current knowledge about an organism. To-date, metabolic networks have been reconstructed for > 35 organisms, based on well-defined procedures. Laboratories around the world are reconstructing metabolic networks for their organisms of interest, thus, there is an increasing need of researchers being familiar with the reconstruction process. These metabolic networks can be readily converted into mathematical models and then used to investigate the genotype-phenotype relationship. Metabolic models have been successfully applied in at least 6 scientific areas: metabolic engineering, model-directed discovery, interpretations of phenotypic screens, network property analysis, drug-target identification, and studies of evolutionary processes. The course will teach the reconstruction process and different modeling techniques employed in the aforementioned areas. Recently, approaches have been developed to investigate dynamics states of genome-scale metabolic networks. Basics methods are introduced in the course.
The following 4 modules will be covered during the 5 day short course:
- High-throughput data types
- How to generate and interpret
- How to use for cellular reaction network reconstruction
- Reconstruction and model formulation
- How to reconstruct chemically and genetically structured databases
- How to represent mathematically
- Topological and steady state analysis
- How to analyze steady state network capabilities, properties, and topology
- Analysis of dynamic states
- How to determine steady state and dynamic properties of networks
- How to use of public and commercial software packages for such analysis
The course is dissected into 4 lectures (each 60 min) followed by a 3 hour practical tutorial in which the participants could apply the material under guidance of teaching assistants. At the end of the short course we offer a take-home final covering the short course material, which qualifies for 4 ETSC units. Lecture notes have been developed for these modules and some are being written up as chapters in a textbook. Instructors will discuss the latest developments in the field.
Optional Module: Primer on Linear Algebra and Matlab - This module will be offered on Sunday June 20th from 10 am until 4 pm. It includes theoretical and hands-on lectures. Please register separately for this module by sending an email to systemsbiology@hi.is with your contact information (name, affiliation, email). Note that a full course registration is required for participation at the primer.
INSTRUCTORS
Bernhard Palsson is a Professor of Bioengineering and Adjunct Professor of Systems Biology at the University of Iceland. He has been developing in silico models of cellular processes for over 20 years. He has written a text book on Systems Biology and developed a series of courses on the subject.
Ines Thiele is an Assistant Professor of Bioengineering at University of Iceland. She has participated in offering several short courses on Systems Biology where she covers network reconstruction technology, the COBRA toolbox, and computational methods.
Ronan Fleming is an independent research scientist at the Department of Applied Mathematics at the University of Iceland. His research is focused on integration of thermodynamics with constraint-based modeling of genome scale biological networks.
TEACHING ASSISTANTS
Maike Aurich is a first year PhD student in Systems Biology at the University of Iceland. Her current research effort focuses on modeling of human metabolism using gene expression data.
Steinn Guðmundsson is a postdoctoral fellow at the Center for Systems Biology. Steinn's work focuses on employing operation research approaches to molecular systems biology.
Joshua Lerman is a visiting scholar from the University of California, San Diego. He is currently working on the reconstruction of the transcriptional and translational machinery of Thermotoga maritima.
Juan Enrique Nogales is a postdoctoral fellow at the Center for Systems Biology. Juan is an experimental biologist interested in systems metabolic engineering. Juan reconstructed the metabolic network of Pseudomonas putida.
Course material:
Everyone is expected to bring their own laptops. We will provide Matlab for the duration of the course. The text book (Systems Biology: Properties of Reconstructed Networks, B. O. Palsson, 2006, Cambridge University Press) will be provided.
COURSE FEE
The registration fee of 350 EUR includes a text book and comprehensive course material. 4 ECTS Credits will be given for the Systems Biology Course for participation and successful pass of the final exam.
The fee can be paid via bank transfer to:
- Bank: NBI HF, Hagatorg, 107 Reykjavik, Iceland
- Account (IBAN) : IS94 0137 3871 0001 6001 6920 39
- SWIFT CODE: NBIIISRE
This account is in the name of:
- University of Iceland
- Sudurgata
- IS 101 Reykjavik
- Iceland
Please write as an explanation: Systems Biology Course 1518-151311.
It is also possible to pay with credit card. Then please E-mail or fax the credit card number and expiration date to Ms Edda Fridgeirsdottir, eddafr@hi.is , fax +354 525 4632.
Please fax (+354 525 4632) or email ( systemsbiology@hi.is ) a certification of the transaction. Registration is completed once payment is received.
Registration is limited to 45 participants and is on first-comes first-serves basis.
REGISTRATION & CONTACT
The course registration is here, the registration deadline is May 14, 2010. For further information contact Ines Thiele, ithiele@hi.is .
TIME & LOCATION
University of Iceland, Reykjavik June 21 - 25, 2010. We will be in Askja, the natural science building. Here is a map of the campus.
- Morning Lecture: 9.00 am - 12 pm
- Lunch: 12 pm - 1 pm
- Afternoon Lecture: 1 pm - 2.00 pm
- Computer Session: 2.30 pm - 5.30 pm
HOTEL ACCOMMODATIONS
We recommend Hotel Leifur Eiriksson or Sunna Guesthouse
Here are also some other useful links about Iceland:
Disclaimer: The content of this website includes copyrighted material and is for the sole use of students registered in the Systems Biology Short Course. These materials are intended only for the use in relationship with this course.