CompCellBio Twiki

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CompCellBio Twiki
Online resource for teaching modeling and the
Virtual Cell

developing materials for

• By Khanh Nguyen and Dr. Holmes
• Center for Cell Analysis and Modeling
• University of Connecticut Health Center,
  Farmington, CT.

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Goals of this talk

• Work in progress
• Introduce you to resources that exist
• Educational, training materials
• Introduce how you can contribute
• Editing, providing content
• Looking for resources and asking questions

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Why this project

• National need for courses, content and teaching
  materials in quantitative/computational biology
• Bio 2010 (National Research Council), Math Bio
  2010 (Math. Assoc. Amer.)
• HHMI- ASCB, MAA, ASM workshops, symposia,
  reports
• Researchers looking for undergraduates with
  better training across disciplines.
• Call and need for developing resources (sites,
  content...)

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Workshop in SB seeds Twiki

• Kavli Institute for Theoretical Physics.
• Biological Switches and Clocks
• John Tyson, Albert Goldbeter, Jill Sible, Reka
  Albert, Peter Ruoff
• Theoreticians and experimentalists
• Group Discussions lead to a suggested outline
  for curricular materials.
• Today, we are looking at the framework for
  creating those materials CompCellBio Twiki
• Assumes users are primarily content developers

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Outline for Teaching Modules

• Outline
• Abstract
• Physiology
• Model Description
• Model files
• Model exercises

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Outline for Teaching Modules

• Outline
• Abstract
• Physiology
• Model Description
• Model files
• Model exercises

• Framework for development
• Form to the outline
• Means of being filled out
• Location for storage
• Easy access for editing
• Wikis, Twiki

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Outline for Teaching Modules

• Abstract
• Physiology
• Model Description
• Model files
• Model exercises

• Form to the outline
• Means of being filled out
• Location for storage
• Easy Access for editing
• Wikis, Twiki

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What is a Twiki?

• Twiki is a web-based collaboration platform
• Usage
• run a project development space
• system to manage documents
• knowledge base
• Advantage
• simple to use and you can edit and update any
  Twiki page.

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How to use Twiki

• Organized as Webs
• Create a Topic
• Copy code from Edit page section and paste into
  your own page.
• As all wikis
• Easily edit or add your own text in editable
  tables
• Provide standard formats for contents

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Implementing
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Relation

• The Virtual Cell is a web accessible modeling
  framework designed for cell biologists to examine
  hypotheses about the spatial and temporal
  dynamics of cellular behaviors.
• The Twiki supports sharing VCell models, course
  lectures, and labs from around the country.
• Growth is based on user contributions and
  assisted by us.

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What Resources Exist

• Twiki
• Classroom material
• labs, lectures, models.
• Discussion
• Attach documents
• edit anytime, anywhere.
• Development site
• New ideas from anyone
• Topics
• Software

• VCell Web Site
• Software http//vcell.org
• Documentation-
• User Guides and Tutorials http//vcell.org/login/l
  ogin.html
• Educational Pages http//vcell.org/education/index
  .html

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Twiki Pages Now Available

• VCell Web
• TCNP Web
• Sandbox
• Draft and edit pages in this playground
• Test coding creating tables, inserting images

• CompCellBio
• TeachingModules
• Cell Cycle
• FRAP
• Circadian rhythms
• VCell Exercises
• CategoryCourse
• ModelingInCellBiology
• Extra Classroom material for course at UC Davis,
  CA.

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Twiki Goals and Improvements

• Complete Teaching Modules
• VCell Exercises, FRAP
• Enhance categories for topics
• Make VCell existing resources and models more
  accessible in teaching context
• Provide clearer instructions to adding/editing
  content
• Distinguish between resources as complete, in
  progress
• Distinguish between audiences (developers,
  instructors).
• CompCellBio Twiki
• Add or Send Your Topics

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Contributions

• Khanh Nguyen
• Tom Kulangara
• Dey, Mogilner, Tyson, Sible, Watrous, Cowan
• Anyone who gave feedback on the Twiki site
• CCAM staff
• NIH TCNP and NRCAM

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Example of a Page for a Course Category

• Locate
• Edit (Table)
• Edit (Page)
• Attach
• Create New Topic
• CompCellBio
• Sandbox

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Locate the following
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Bio 2010, NRC

• Biology increasingly involves the analysis of
  complex systems Creating (or re-creating)
  function by building a complex system and getting
  it to work provides compelling proof that the
  scientist understands the essential building
  blocks and how they work in synchronyTo
  understand system function in biology in a
  predictive and quantitative fashion, it is
  necessary to describe and model how the system
  function results from the properties of its
  constituent elementsAs an example, a
  quantitative understanding of cell-signaling
  chemical network involves the concepts of
  negative feedbackand cross-talk (p39

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Other resources for educators

• NCSI Computational Biology for Biology Educators
• BioQUEST Investigative Cases

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Follow the Table Template

• Abstract
• Physiology
• Model Description
• Model files
• Model exercises