Cathy Codon on RNA Transcription (as witnessed by Yolanda Gil) NOTE: There are comments in the notes view of these powerpoint slides - PowerPoint PPT Presentation

About This Presentation
Title:

Cathy Codon on RNA Transcription (as witnessed by Yolanda Gil) NOTE: There are comments in the notes view of these powerpoint slides

Description:

Brings in Terminator. Goes back to RNA Transcription text description ... Make-Contact, Break-Contact, Promoter, Terminator ... Terminator & Action as it ... – PowerPoint PPT presentation

Number of Views:314
Avg rating:3.0/5.0
Slides: 56
Provided by: Gil150
Learn more at: https://www.isi.edu
Category:

less

Transcript and Presenter's Notes

Title: Cathy Codon on RNA Transcription (as witnessed by Yolanda Gil) NOTE: There are comments in the notes view of these powerpoint slides


1
Cathy Codonon RNA Transcription(as witnessed
by Yolanda Gil)NOTE There are comments in the
notes view of these powerpoint slides
2
Executive Summary
  • Entered RNA transcription 6 times (6 trials)
  • 3 times because of software problems
  • Never entered it correctly or completely
  • No Transcription subevent in 6 trials, added when
    YG hand-generated KANALs output
  • In trial 1 subject decided not to follow
    guidelines in training material
  • Trial 6 is the most representative (slides 36-55)

3
Trial 1Transcription
4
  1. Defined top-level node Transcription as a kind
    of Transcribe (I think)
  2. Brings in DNA and RNA-polym
  3. Clicks on Transcription, gets arrow
    direct-object-of-change (YG is this a bug?)
  4. Brings in Promoter
  5. Tries to unify Promoter with DNA
  6. Reads the handout with components

5
  1. Collapses all roles of Transcription
  2. Draws arrow between Transcription and RNA
    Polymerase calls it subevent
  3. Brings in Terminator
  4. Goes back to RNA Transcription text description

6
Screenshot
Direct-object- of-change
subevent
Transcription
RNA Polymerase
DNA
Terminator
Promoter
Make Contact
Break Contact
Move
7
Screenshot
Subevent arrow is hidden behind
instrument
Transcription
RNA Polymerase
Direct-object- of-change
DNA
Terminator
RNA
Promoter
Make Contact
Break Contact
Move
8
Screenshot
Subevent arrow is hidden behind
instrument
Transcription
RNA Polymerase
Direct-object- of-change
DNA
TerminatorAction
subevent
RNA
PromoterAction
Make Contact
Break Contact
Move
9
Specifies Participants in Make Contact
Subevent arrow is hidden behind
instrument
Transcription
RNA Polymerase
Direct-object- of-change
DNA
TerminatorAction
subevent
Things Making contact
RNA
PromoterAction
Move
Make Contact
Break Contact
Leaves location empty
location
10
Specifies Participants in Break Contact
Subevent arrow is hidden behind
instrument
Transcription
RNA Polymerase
Direct-object- of-change
TerminatorAction
DNA
subevent
PromoterAction
RNA
Things breaking contact
Move
Make Contact
Break Contact
Leaves location empty
location
11
  • Saves it, keeps editing
  • Collapses everything, uncollapses
  • Reorganizes things

12
1140 Collapses everything, uncollapses,
reorganizes
Transcription
DNA
Direct-object- of-change
subevent
Move
RNA
RNA Polymerase
Break Contact
TerminatorAction
PromoterAction
Make Contact
13
  • We stopped for 10min
  • User admits to NOT have followed the steps we had
    specified earlier, on purpose. User just thought
    about all the processes and all the objects, then
    connected them. User prefers to do things that
    way.
  • When using the tool, user feels as if doing a
    puzzle and not the transcription process held in
    mind

14
  • Notices PromoterAction
  • User says its an error, it should not be there,
    user just wants the label to read Promoter
  • User is happy that it is a subevent, as stated
    Because the promoter is doing things

15
1157
Transcription
instrument
Direct-object- of-change
DNA
RNA RNA Polymerase
RNA Polymerase
User wonders what it is and where it came from I
said (user) dragged it user says didnt mean
to
16
Trial 2Transcription-1
17
  1. User waits for me for 15 min, during that time
    user browses through the training material
  2. Underlines verbs in the text
  3. Defines Transcription-1 as a kind of action
  4. Brings in RNA, DNA, Promoter, Term, RNA-Polym
  5. Brings in Make-contact, Move, and Break-contact

18
Screenshot
Direct-object- of-change
instrument
Transcription-1
RNA Polymerase
DNA
Terminator
RNA
subevent
Promoter
Make Contact
Break Contact
Move
19
  • Make-contact disappears (bug)
  • Saved
  • Edited
  • Everything not connected to Transcription-1
    disappeared
  • Abort trial because of software problems ?

20
Trial 3Transcription-2
21
  • Define transcription as action, bring in all
    relevant components (steps 3,4,5 of previous
    trial)

22
Transcription-2
DNA
I notice that Make Contact and Transcription are
now unified (user probably does not know), So
Transcription-2 has all the roles of Make-contact
Wanted to define DNA as the object of
Transcription, Drew the arrow wrong, so object
was not in menu. I explain why
23
Make-contact and transcription-2 were somehow
unified, thus the roles
Transcription
The objects Making contact
DNA
TerminatorAction
subevent
RNA
PromoterAction
RNA Polymerase
Break Contact
Move
24
  • User clicks to simplify
  • System freezes
  • Abort trial because of software problems ?
  • User makes comment about liking to collapse
    things and simplify only likes to see the detail
    at times, I dont need it, but I like to see it

25
Trial 4Transcription-3
26
  • Define transcription as action, bring in all
    relevant components (steps 3,4,5 of previous
    trial)
  • User makes Move a subevent of Transcription-3
  • User collapses Transcription-3, Move is lost and
    cannot get it back
  • Abort trial
  • I explain again arrows in detail

27
Trial 5Transcription-4
28
  • Define transcription as action, bring in all
    relevant components (steps 3,4,5 of previous
    trial)

29
Transcription
RNA Polymerase
DNA
RNA
subevent
TerminatorAction
Move seems to always end up at the left hand side
(I.e., coming first)
PromoterAction
Make Contact
Break Contact
Move
30
Direct-object- of-change
instrument
Transcription
RNA Polymerase
DNA
RNA
subevent
TerminatorAction
PromoterAction
Make Contact
Break Contact
Move
31
Direct-object- of-change
instrument
Transcription
RNA Polymerase
DNA
RNA
subevent
TerminatorAction
PromoterAction
Thing moved
Make Contact
Break Contact
Move
32
  • Subject collapses Move to get rid of detail
  • For each subevent (Make-Contact, Break-Contact)
    assigns roles and then collapses
  • goes too fast to take notes
  • Looks at the screen, says Shall I test it?
  • The screen is as in next slide

33
Cmap
instrument
All the participants in the subevents are
specified
Transcription
RNA Polymerase
Direct-object- of-change
DNA
subevent
RNA
Move
Make Contact
Break Contact
TerminatorAction
PromoterAction
34
  • Instead of asking questions, subject decides to
    check knowledge by uncollapsing nodes
  • Move the thing moved-gt RNA polimerase
  • Make-contact the things mkg ctc-gt DNA and RNA
    polym
  • Break-contact the things brkg ctc-gt DNA and
    RNA-polym
  • Says actually DNA and RNA break contact,
  • Since there is no delete fn in software, wants to
    abort and make another one where Move has RNA and
    DNA as objects because RNA moves away, actually
  • Says another mistake in Break-contact, should say
    RNA and DNA

35
  • Decides to ask some questions before discarding
    this
  • Asks two questions really fast (I cannot see)
  • Says very confident I know everything I did is
    right, because the picture was the answer

36
Trial 6Transcription-5NOTE Organized in
episodes. In newer versions of powerpoint, you
can see the bullets numbered (statements made by
user, YG, or comments)
37
Define Overall Process
  • Define Transcription-5 as action, bring in all
    relevant components (steps 3,4,5 of Trial 2)
  • Defines Transcription-5 as a kind of action
  • Brings in RNA, DNA, Promoter, Term, RNA-Polym
  • Brings in Make-contact, Move, and Break-contact

38
  • User specifies participants in substeps
  • Move- the thing moved RNA
  • User says wait, RNA polym moves
  • YG says it is ok to add two moves
  • User says ok but didnt do that (user forgot?)
  • Collapses everything and then expands
  • Has the same thing as in Trial 5, but has no
    participants specified for Make-contact and
    Break-Contact (see next slide)

39
Screenshot
instrument
Transcription-5
RNA Polymerase
Direct-object- of-change
DNA
subevent
RNA
Move
Make Contact
Break Contact
TerminatorAction
PromoterAction
40
User is Ready to Test Knowledge
  1. User saves and wants to ask questions
  2. User re-reads text description of RNA
    Transcription before asking questions to SHAKEN

41
Ask Questions
  • What is the instrument of Transcription-5?
  • Ans RNA-polymerase User says it is correct
  • During Tr-5, what role does the polymerase play?
    User notes it is an important question
  • Ans In Tr-5, RNA poly plays the role
  • BUG nothing shown!
  • User tries the last item (to ask questions
    through cmaps) - BUG doesnt seem to work.

42
Ask Questions (cont)
  • How many instruments are in Tr-5?
  • Ans only 1 (yg notesystem does not say which
    one)
  • How may objects are in Tr-5?
  • Ans 2
  • Which objects are in Tr-5?
  • AnsRNA and DNA User says thats correct
  • User says what is the point of asking questions,
    it is the same as the graph.
  • YG explains

43
User Wants to Continue Asking
  1. User says there is a lot of details that she
    would normally teach
  2. User says she/he is done with the scenario and
    she wants to continue asking more questions

44
Ask Questions (cont)
  • Explain Tr-5?
  • Ans object
  • instrument
  • Subevents Move, Make-Contact, Break-Contact,
    Promoter, Terminator
  • User reads this and finds it perfectly
  • normal!!
  • She wants to bring back Transcription-1 and ask
    questions about it.
  • YG suggests to stick with Tr-5

BUG It does not say Promoter Action Terminator
Action as it did in the cmap
45
Running KANAL (YG notes the interface rendering
is unclear)
  • Summary of alternative paths in simulation
  • Move
  • Step Move
  • Checking Precondition object musnt be
    restrained succeed
  • Warning no effect was produced
  • Step Make-Contact
  • Checking Preconditions the location of O1 must
    be the location of Make Contact Failed
  • Click here for suggestions
  • Checking Preconditions the location of O2 must
    be the location of Make-Contact Failed

46
User Says It is Done!
  1. YG notes the simulation is not giving useful
    output because of a software problem
  2. User says the scenario is done
  3. YG says some things not working in software, but
    she will simulate what the system would say if it
    was working ok

47
Hand-Generated KANAL-Style Output is Presented to
User
  • YG shows Move
  • Conditions RNA is unrestrained Succeed
  • Effect no effect! ERROR
  • suggested fix specify destination of RNA
    User says cytoplasm
  • User goes to editor, adds

RNA
location
place
Here is where the user wants to say cytoplasm!!
48
User confused about Fluents
  • User brings in Cell
  • User saysthis is interesting, the system is
    asking me to edit to add more details
  • Tries to connect RNA to Cell in order to say that
    RNA moves to Cell (i.e., cell is the destination
    of Move)

RNA
location
Cell
BUG it says Place Cell
49
Adding another Move
  • User Adds another Move for RNA polym
  • Bug the two moves got disconnected somehow
  • YG said to pretend this

Transcription
subevent
Move
Move
50
Hand-Generated KANAL-Style Output is Presented to
User
  • Move
  • Conditions RNA is unrestrained Succeed
  • Effect RNA is in cytoplasm
  • YG decides to move to another error at this
    point since locations are messed up, and since
    the RNA has not been created anyway
  • YG decides to see if user realizes Transcribe
    substep is missing, i.e., there are no substeps
    to create the RNA

51
Hand-Generated KANALConfusion about Expected
Effects
  • YG asks
  • What are the expected effects of Transcription?
  • User does not understand, YG tries again
  • what is true after transcription that was not
    true before?
  • What is the expected state of the world after
    transcription?
  • User says
  • RNA is taking the message and moving to the
    location where it needs to be delivered/used
  • RNA has transferred the message from where it is
    to where it needs to be used

52
Hand-Generated KANALUser understands step is
needed to create the RNA
  • YG tries again
  • Is the DNA same? Yes
  • Is the Polymerase same? Yes
  • Is the RNA same?
  • User says RNA didnt exist before
  • ?User specifies that expected effect is RNA is
    created
  • Suggested fixes add subevent that creates RNA
  • User says RNA is created by Break-contact

53
User finally adds Transcribe substep!
  • User looks back the paper material and say maybe
    one subevent needs to be Transcribe
  • User adds Transcribe as subevent
  • direct-object DNA
  • thing-created RNA
  • instrument RNA-Polym
  • source location
  • destination location

54
Transcribe Source and Destination
  • YG asked to fill out source and destination
  • User says it is where the collision happens
  • User confused that the overall process is called
    transcribe and that the actual copy is also
    called transcribe

Source is collision site
Source is promoter
55
An Example Analogy that Did not Seem to Help
  • YG tries an analogy
  • YG says start at is promoter. User gets it
  • User explains that when we say source it seems
    to mean where the info comes from, e.g., the
    book, the DNA
  • Transcribe DNA
  • What chapter 2
  • Start at page 2
  • End at page 7
  • Location copy room

analogy
  • Transcribe DNA
  • What gene
  • Start at DNA
  • Location cell
Write a Comment
User Comments (0)
About PowerShow.com