Binhua Liang

Assignment 5---ACEDB Database

Problem:

Creat a database containing 4 classes: Pathway, Enzyme, Compound and File?


Approach:

(1). Choose a biochemical pathway with at least five enzymatic steps:

  1. Go to Saccaromyces Genome Database (http://www.yeastgenome.org/)
  2. Quick search: "lactose degradation", look at search results and choose "1 Biochemical pathways"
  3. When  Biochemical Pathways  Table  shows  up,  click "lactose degradation"  link.

(2). Save the file pathways.tar.gz in my as5 directory.
  1. gunzip pathways.tar.gz ----->tar xvfp pathways.tar
  2. go to "pathways" directory, open "pathace" file and set environment variable ACEDB to reflect my database location: setenv ACEDB /home/u2/my userid/public_html/PLNT7690/as5/pathways
  3. go to wspec/passwd.wrm, open it, and set me up as admin for access and modification of database: change 'first' to my userid

(3). Launch ACEDB (existing)
  1. type in "pathace", a popup window shows up, click "Yes" to continue
  2. ACEDB window popups

(4). Create objects for "Pathway", "Enzyme", "Compound", and "File"

    Click "Edit" ---->"Gain write acess", Then click "Edit" again---->"Add/Delete/Rename/Alias objec", a window popups, select one of classes (pathway, or enzyme, or compound, or file), click "Create", a window popups, fill in the name of object. The following objects are created:
  1. Pathway class: S.cerevisiae Pathway: Lactose degradation
  2. Enzyme class: GAL7, galactokinase, galactose mutarotase, phosphoglucomutase, UDP-glucose4-epimerase, uridinephosphoglucose pyrophosphorylase, UTP glucose-1-phosphate uridylytransferase.
  3. Compound class: a-D-galactose, a-D-galactose-1-phosphate, ADP, ATP, b-D-galactose, diphosphate, glucose-1-phosphate, glucose-6-phosphate, lactose, UDP-D-glucose, UDP-galactose, UTP
  4. File class: S.cerevisiae Pathway

(5). Add information (or items) in an empty object
  1. start with "Pathway" objects......
  2. double click any object, a object window popups......
  3. right-click at any position in the window, pull-down menu shows up, click "Update"
  4. fill in items by click once on the object item, a yellow box shows up, type in name, then click "Enter".
  5. when finished, hold down the right mouse button and choose "Save"

(6). Make a link to an exiting object
  1. follow up with (5) when fill in items in one object, don't type in name in yellow box,
  2. instead, double click on the name of an object in another window
  3. when finished, hold down the right mouse button and choose "Save"

(7). Modify Compound object by adding two Int fields to indicate the number of a compound which are consumed or produced
  1. Change the model in wspec/models.wrm by adding "MoL-Consumed Int" and "Mol_Produced Int" just under "Mol_Wt Int" of  ?Compound model.
  2. Lauch ACeDB, gain write access (Edit--->Gain write access)
  3. Read in the new models.wrm (Edit--->Read models)
  4. Fill in the fields following (5).......

(8). Create gif figure
  1. go to Terminal, type in "xv"
  2. copy and crop the image, then save as in "pathways/externalFiles" directory
  3. open "File" object, after "Pick_me_to_call", fill in "$ACE_FILE_LAUNCHER    $ACEDE/externalFiles/image_name.gif"


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