Feb 2012

Section            Subject

1                        Introduction: The PAGP and COMPASS

2                        Assumed Contributor and Assumed User

3                        Nature of a Source Case and Its Views

4                        Nature of COMPASS (Wiki)

5                        Example Source Case

6                        Main PA Genome (COMPASS) Wiki

7                        Source Case Wiki and Representation of a Variable

8                        Classification System (Ontology)

9                        Connectedness

10                     Getting Started

11                     Making a List of Variables (Operons)

12                     Making a List of Relationships (Kineses)

13                     Making and Using an Ontology (Classification System)

14                     Putting a Variable and the List All Together

15                     Making a Glossary

16                     Making a Reference List

17                     Entering a Case Ontology

18                     Making a Causal Diagram

19                     Doing a Case Summary

20                       Creating a Source Case Wiki

21                     Editing in PBWorks

22                     Creating the Pages in the Source Case Wiki

23           Creating Other View Pages

24                Wrapping It All Up

25           Relevant Reading

Appendix

    A     Template for Entering a Variable

    B     Template for Entering a Case Summary

    C     Setting Up and Accessing PBWorks Wikis