Managing Software Development CSG 110
Spring 2005
Karl Lieberherr					Due date: Feb. 3, 2005

Homework 3: Multi-Dimensional Separation of Concerns continued
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In this homework we practice schema design for biological pathway modeling.
Life sciences and computer science are important allies and here is
an opportunity to work in both areas.

Read the relevant parts of the paper:
http://www.cs.berkeley.edu/~bec/2003-pml/pml03-tr.pdf
a copy of which is also in hw/3.

A start of the class dictionary is in /pml:


Main = <s> String.
PathwayModelingLanguage =
  <domains> List(DomDecl)
  <groups> List(GrpDecl)
  <compartments> List(ComDecl).

// Domains
DomDecl = "domain" DomainId "=" DomExp.
DomExp : DomainExpression | DomainId.
DomainExpression = [Bridge] "dom" Seq(SiteId) DomDesc "init" "=" "[" Seq(RuleId) "]" "end".
DomDesc = "domdesc".
Bridge = "bridge".

// Groups
GrpDecl = "group" GroupId "=" GrpExp.
GrpExp = "grpexp".

//Compartments
ComDecl = "compartment" CompartmentId "=" ComExp.
ComExp = "comexp".

SiteId = Ident.
RuleId = Ident.
DomainId = Ident.
GroupId = Ident.
CompartmentId = Ident.

List(S) ~ {S}.
// change: sequence must have one element
Seq(S) ~ "(" S {"," S} ")".
===========================================================================

Make this class dictionary complete so that it covers the entire language described
in the paper. Turn in your class dictionary and the sentences that you used to test it.

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To learn about class dictionaries:
==================================

Browse through the DemeterJ User's Guide available from the
DemeterJ and AP-Studio Resources page
  <A HREF="http://www.ccs.neu.edu/research/demeter/DemeterJava/">http://www.ccs.neu.edu/research/demeter/DemeterJava/</A>.
Focus on class dictionaries and only a little bit on the adaptive programming language of DemeterJ.

Read the two chapters:

http://www.ccs.neu.edu/home/lieber/courses/csu670/f04/materials/to-be-distributed/list.html

Two Chapters on Class Dictionaries in AP Book (chapters 11 and 12). 

The entire book is available from 
http://www.ccs.neu.edu/research/demeter/biblio/dem-book.html

Finally work through the Laboratory Guide:

<A HREF="
http://www.ccs.neu.edu/research/demeter/DemeterJava/use/lguide/html/labguide.html
">(Lab Guide)</A>
Read and work through the Laboratory Guide using DemeterJ
and hand in all
files modified (electronically only).