[Bio] / PyGUI / ModelEditor.html Repository:
ViewVC logotype

Diff of /PyGUI/ModelEditor.html

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.1, Tue Aug 19 16:10:52 2003 UTC revision 1.2, Tue Aug 19 16:18:42 2003 UTC
# Line 33  Line 33 
33  modification, and versioning of systems biology models. In time, these  modification, and versioning of systems biology models. In time, these
34  models will span many biophysical processes; however, at the moment,  models will span many biophysical processes; however, at the moment,
35  the editor prototype focuses on biochemistry.  the editor prototype focuses on biochemistry.
36    <P>
37    
38  The editor fits into a processing model that distinguishes between  The editor fits into a processing model that distinguishes between
39  reconstructions and models. [Replay baby-steps paper].  In brief, a  reconstructions and models. [Replay baby-steps paper].  In brief, a
# Line 47  Line 48 
48  model ultimately attempts to bridge the gap from a set of parts  model ultimately attempts to bridge the gap from a set of parts
49  to a set of dynamical variables that can be computed upon to predict  to a set of dynamical variables that can be computed upon to predict
50  the behavior of the system.  the behavior of the system.
51    <P>
52    
53  Show diagram of high level workflow:  Show diagram of high level workflow:
54    <PRE>
55      genomes -> reconstructions -> models -> dynamical data      genomes -> reconstructions -> models -> dynamical data
56    </PRE>
57  We're taling about the 2nd arrow.  We're taling about the 2nd arrow.
58    <P>
59    
60  The Monera Model Editor focuses on models, not reconstructions.  The Monera Model Editor focuses on models, not reconstructions.
61  Reconstruction typically requires extensive capabilities for  Reconstruction typically requires extensive capabilities for
# Line 59  Line 64 
64  fuction.  This is not the purpose of the editor and, thus, it  fuction.  This is not the purpose of the editor and, thus, it
65  does not provide facilities for these operations.  [But it's not so  does not provide facilities for these operations.  [But it's not so
66  cut and dried...]  cut and dried...]
67    <P>
68    
69  Instead, the Model editor focuses on information management: selection  Instead, the Model editor focuses on information management: selection
70  of reconstruction elements, hierarchical organization of a model,  of reconstruction elements, hierarchical organization of a model,
# Line 76  Line 82 
82  biochemistry already exists. [ At this early stage, this is not a  biochemistry already exists. [ At this early stage, this is not a
83  great assumption...it's where we want to end up..so don't be too  great assumption...it's where we want to end up..so don't be too
84  religious about this yet]  religious about this yet]
85    <P>
86    
87  The Editor thus works by building higher level constructs from lower  The Editor thus works by building higher level constructs from lower
88  level entities.  At each step along the way, the editor enforces a  level entities.  At each step along the way, the editor enforces a
# Line 108  Line 115 
115  now: WIT and BSS.  WIT is the WIT3 prototype database at ANL.  now: WIT and BSS.  WIT is the WIT3 prototype database at ANL.
116  BSS is the BioSimScratch prototype database used for prototyping  BSS is the BioSimScratch prototype database used for prototyping
117  this application.  At present, BSS is much better supported.  this application.  At present, BSS is much better supported.
118    <P>
119    
120  In several pages you will have the option of choosing a data sorce  In several pages you will have the option of choosing a data sorce
121  via a drop-down selector.  Thus the Model Editor allows the formation  via a drop-down selector.  Thus the Model Editor allows the formation
# Line 126  Line 134 
134  or by LIKE.  "LIKE" is a backdoor that lets you insert a valid,  or by LIKE.  "LIKE" is a backdoor that lets you insert a valid,
135  unquoted SQL clause to follow a LIKE operator.  This presumes that the  unquoted SQL clause to follow a LIKE operator.  This presumes that the
136  data source is SQL based, which may not always be true.  data source is SQL based, which may not always be true.
137    <P>
138    
139  There is an ADD button that allows you to add a metabolite to the  There is an ADD button that allows you to add a metabolite to the
140  database.  The OK button produces and immediate transaction and  database.  The OK button produces and immediate transaction and
# Line 152  Line 161 
161  enzymes. [Enzymes not supported yet].  The drop down box allows you to  enzymes. [Enzymes not supported yet].  The drop down box allows you to
162  choose three searches, INPUT, OUTPUT and FROM METABOLITE PAGE (Described  choose three searches, INPUT, OUTPUT and FROM METABOLITE PAGE (Described
163  just below).   After choosing, you hit the SEARCH button.  just below).   After choosing, you hit the SEARCH button.
164    <P>
165    
166  Like the Metabolites page, the Reactions Page has both a Search Results  Like the Metabolites page, the Reactions Page has both a Search Results
167  Table and a Selected Reactions Table.  They function just as on the  Table and a Selected Reactions Table.  They function just as on the
168  Metabolites page.  Metabolites page.
169    <P>
170    
171  The meanings of INPUT, OUTPUT and FROM METABOLITE PAGE are as follows:  The meanings of INPUT, OUTPUT and FROM METABOLITE PAGE are as follows:
172  <UL>  <UL>
# Line 197  Line 208 
208  there is branch for each data source.  If you expand a data source,  there is branch for each data source.  If you expand a data source,
209  you will see all available reconstructions and models available  you will see all available reconstructions and models available
210  from that data source.  from that data source.
211    <P>
212    
213  You may select a reconstruction or model and then hit the "Load to  You may select a reconstruction or model and then hit the "Load to
214  Navigator" button at the bottom right.   The mouse indicator will  Navigator" button at the bottom right.   The mouse indicator will
215  turn to an hour glass until the data are loaded.  turn to an hour glass until the data are loaded.
216    <P>
217    
218  The data are loaded to the Navigataor page, so you do not see a change  The data are loaded to the Navigataor page, so you do not see a change
219  on the catalog page.  This may be confusing at first.  Just hit the  on the catalog page.  This may be confusing at first.  Just hit the
220  Navigator tab after hitting the tab.  Navigator tab after hitting the tab.
221    <P>
222    
223  Note:  you may load as many reconstructions and models as you wish.  Note:  you may load as many reconstructions and models as you wish.
224  Each show up in the Navigator page as indepentend trees.  You can  Each show up in the Navigator page as indepentend trees.  You can
# Line 218  Line 232 
232  Panel. The tree navigation panel shows all of the trees loaded from  Panel. The tree navigation panel shows all of the trees loaded from
233  the Catalog Page.  You can open/close the branches to explore the  the Catalog Page.  You can open/close the branches to explore the
234  models and reconstructions.  models and reconstructions.
235    <P>
236    
237  You can select a node in any of the trees.  Doing so causes the editor  You can select a node in any of the trees.  Doing so causes the editor
238  to determine if there are any associated reactions with that node.  If  to determine if there are any associated reactions with that node.  If
239  so, the set of reactions is shown to the right in the Information Display  so, the set of reactions is shown to the right in the Information Display
240  Panel.  Panel.
241    <P>
242    
243  Within the Information Display panel, you can left-click a reaction to  Within the Information Display panel, you can left-click a reaction to
244  select it.  A right click pops up a menu that allows you to cut the  select it.  A right click pops up a menu that allows you to cut the
245  reaction, copy the reaction, or paste previously cut or copied reactions  reaction, copy the reaction, or paste previously cut or copied reactions
246  OR paste in all of the reactions from the Selected Reactions Table  OR paste in all of the reactions from the Selected Reactions Table
247  on the reactions page.  on the reactions page.
248    <P>
249    
250  When a tree node is selected (highlighted), you can use the right  When a tree node is selected (highlighted), you can use the right
251  mouse button to pop-up an edit menu.  That menu allows you to cut,  mouse button to pop-up an edit menu.  That menu allows you to cut,
# Line 240  Line 256 
256  selected node.  These operations allow you to build up the model  selected node.  These operations allow you to build up the model
257  hierarchy.  Note that when you cut/paste branches, you are doing  hierarchy.  Note that when you cut/paste branches, you are doing
258  a deep copy of the branch, including all associated reactions.  a deep copy of the branch, including all associated reactions.
259    <P>
260    
261  You can also choose Paste Reactions from the popup to paste previously  You can also choose Paste Reactions from the popup to paste previously
262  cut or copied reactions OR paste in all of the reactions from the  cut or copied reactions OR paste in all of the reactions from the

Legend:
Removed from v.1.1  
changed lines
  Added in v.1.2

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3