Resources for Teaching Systems Biology

1
Resources for Teaching Systems Biology

• SC07 Education Program
• Monday, November 12
• Jeff Krause

2
What is Systems Biology

• Biologists have been studying and modeling
  systems for decades (i.e. physiology)
• Current systems biology craze has resulted from
  recent technologies that allow for rapid or
  simultaneous measurement of large amounts of
  biomolecular data (e.g. genomics, microarrays,
  etc.)

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Two Main Parts of Systems Biology

• System identification
• What are the functionally important components of
  the system
• Which components interact, and how
• Use all available data sources
• Iterate with modeling and experimentation
• Behavior analysis
• Build and run quantitative model to test
  understanding of components and their behaviors

4
Biomolecular Networks The Big 3

• Metabolic networks workhorses of living
  systems, they provide energy and do all the
  housekeeping
• Signaling networks connect and coordinate the
  activities within and between cells
• Gene regulatory networks mediate the molecular
  composition of cells

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Efforts to Identify the Systems

• Mining existing data sources
• Text mining the previous literature
• Bioinformatic methods for annotation
• Analysis and interpretation of new
  high-throughput data
• Bioinformatic and novel approaches for mining
  large datasets

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Systems Biology Databases

• The Gene Ontology Project http//www.geneontology
  .org/
• KEGG
• http//www.genome.jp/kegg/
• Reactome
• http//www.reactome.org/
• TRANSFAC

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Modeling tools and standards

• Model formats
• SBML http//sbml.org/index.psp
• CellML - http//www.cellml.org/
• Modeling platforms
• Systems Biology Workbench - http//www.sys-bio.org
  /research/sbwIntro.htm
• BioSpice - http//biospice.lbl.gov/home.html
• BioUML - http//www.biouml.org/
• Graphical representation
• SBGN - http//sbgn.org/

8
How Can We Prepare Students?

• Teach them
• System thinking
• Change over time
• Computational tools to build, run and analyze
  quantitative models

9
Lets Analyze a Reaction Time Course in Excel

• Got to
• http//elwood.sc07.org/
• Click on Files
• Click on simple reaction
• Download simplereaction.xls

10
A Systems Dynamics Model in Vensim

• Open Vensim
• Here is their website http//www.vensim.com/
• The PLE version of their software is free for
  academic use
• Here is a terrific tutorial for modeling chemical
  reaction with Vensim that is much more detailed
  than what were doing in class
• http//www.computationalscience.org/ccce/Lesson10/
  vensim_study.pdf

11
Building a Chemical Reaction with Agent Sheets

• Agent Sheets is found on your start menu
• Youll need to get the registration information
  from the wiki at
• https//sc07.sc-education.org/wiki/
• Under Information For Instructors, click on
  Available Software
• Page down twice, under Laptops (US) The third
  bullet down has license information for Agent
  Sheets
• Enter this in the registration dialog when you
  start Agent Sheets
• Here is the Agent Sheets Online Manual
• http//www.agentsheets.com/support/manuals/index.h
  tml
• They also have tutorials and demo models online
  and that come with the model