Session for Polly Peptide, March 2, 2001 (T1)
Vinay Chaudri


Sample Session:

Create a concept by starting from Action
Give it a name RNA-Transcription (RNAT)
Add concept DNA
Add concept mRNA
Add concept RNA polymerase
Connect RNAT to RNA polymerase by an instrument link
Connect RNAT to DNA by an object link
Connect RNAT and mRNA by object link
Abort

Create a concept by starting from Action
Give it a name RNA-Transcription (RNAT)
Add concept DNA
Add concept mRNA
Add concept RNA polymerase
Connect RNAT to RNA polymerase by an instrument link
Connect RNAT to DNA by an object link
Add concept Make-Contact
Search for Slide
Search for and add Move-to
Search for Promoter and add 
Search for Terminator and add
Search for Terminator and add
Connect Make-contact with RNAT by a subevent link
Connect Move-to with RNAT by a subevent link
Merge promoter and DNA
Merge promoter region with object of contact
Merge object of contact with carboxyl terminal end of
Merge "thing moved" of Move-to to Terminator Region
Make transcribe a subevent of RNAT

Abort

Create a concept by starting from Action
Give it a name RNA-Transcription (RNAT)
Add concept Eucaroyatic-DNA
Abort

Create a concept by starting from Action
Give it a name RNA-Transcription (RNAT)
Add concept DNA
Search DNA
Open DNA
Select Bacterial DNA
Search and Add RNA-Polymerase
Connect RNA-T with DNA by object link
Connect RNA-T with Polymerase with instrument link
Search for Attach
Add Make-contact from history list
Connect Make-contact and RNA-polymerase by an object link
Connect Make-contact and DNA by the object link
Connect Make-Contact to RNAT by subevent link
Search for move.  Add move step.
Connect RNAT to move by subevent.
Connect object of Move to Promoter of DNA
Search for attach. Add attach.
Connect RNAT and attach by subevent link.
Connect object to RNA-polymerase
Connect object to RNA-polymerase
Search for transcribe
Add Transcribe step
Make Transcribe a substep of RNAT
Search for mRNA
Add mRNA
Make it object of transcribe
Make RNA polymerase an instrument of transcribe
Search for release
Add release step
Make Release a subevent of RNAT
Make mRNA an object of Release (this did not work due to buggy software)
Search for detach
Add Brea-Contact  
Make it a subevent of RNAT
Make terminator an object of things breaking contact
Save 

Ask question
What is RNA Transcription
Two Break-Contact subevents show up, only one was put in
Click on the instrucment of RNA Transcription
Click on the object of RNA Transcription.  Its labeled as O2.
RNA polymerase shows up as an object, but it was input as an instrument
Ask how many instruments, answer =1, correct.
Ask how many object, answer = 1, correct.
Ask how many subevents, answer = 7, correct.
Ask what role does DNA play - no answer.
Ask what role does RNA polumerase play? - no answer.
What happens to location of RNA polymerase?
  -shows 7 locations, but not very informative
What happens to location of DNA?
  -shows 7 locations, but not very informative