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1 : efrank 1.1 <HTML>
2 :     <HEAD>
3 :     <TITLE> Monera Model Editor Help </TITLE>
4 :     </HEAD>
5 :     <BODY>
6 :    
7 :     <H1> Monera Model Editor </H1>
8 :    
9 :     v0.0 <br>
10 :     19Aug03 <br>
11 :     <p>
12 :     Ed Frank <br>
13 :     Kaitlyn Hwang <br>
14 :    
15 :     <H2> Contents </H2>
16 :     <UL>
17 :     <LI> <A HREF="#Introduction"> Introduction </A>
18 :     <LI> <A HREF="#Model Editor Thesis"> Model Editor Thesis </A>
19 :     <LI> <A HREF="#Organization of the Editor"> Organization of the Editor </A>
20 :     <LI> <A HREF="#Data Source"> Data Source </A>
21 :     <LI> <A HREF="#Metabolites Page"> Metabolites Page </A>
22 :     <LI> <A HREF="#Search Results Table vs. Selected Results Table"> Search Results Table vs. Selected Results Table </A>
23 :     <LI> <A HREF="#Reactions Page"> Reactions Page </A>
24 :     <LI> <A HREF="#Catalog Page"> Catalog Page </A>
25 :     <LI> <A HREF="#Navigator Page"> Navigator Page </A>
26 :     <LI> <A HREF="#Writing Out the Editing Results"> Writing Out the Editing Results </A>
27 :     </UL>
28 :    
29 :     <A name="Introduction"></A>
30 :     <H2> Introduction </H2>
31 :    
32 :     The Monera Model Editor is meant to support the creation,
33 :     modification, and versioning of systems biology models. In time, these
34 :     models will span many biophysical processes; however, at the moment,
35 :     the editor prototype focuses on biochemistry.
36 : efrank 1.2 <P>
37 : efrank 1.1
38 :     The editor fits into a processing model that distinguishes between
39 :     reconstructions and models. [Replay baby-steps paper]. In brief, a
40 :     reconstruction catalogs the actual biophysical elements of a
41 :     biological system. A model, on the other hand, while based upon a
42 :     reconstruction, has the objective of understanding and predicting the
43 :     behavior of the biological system. It may choose to ignore portions
44 :     of the system, may choose to replace portions with analogies that
45 :     simplify the system or allow the model to focus its attention
46 :     elsewhere, and may choose to insert purely hypothetical elements.
47 :     If a reconstructions is "parts," then a model is "purpose." A
48 :     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
50 :     the behavior of the system.
51 : efrank 1.2 <P>
52 : efrank 1.1
53 :     Show diagram of high level workflow:
54 : efrank 1.2 <PRE>
55 : efrank 1.1 genomes -> reconstructions -> models -> dynamical data
56 : efrank 1.2 </PRE>
57 : efrank 1.1 We're taling about the 2nd arrow.
58 : efrank 1.2 <P>
59 : efrank 1.1
60 :     The Monera Model Editor focuses on models, not reconstructions.
61 :     Reconstruction typically requires extensive capabilities for
62 :     compartive studies, e.g, compartive analysis of the genome of the
63 :     subject organism with the genomes of others in order to assign
64 :     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
66 :     cut and dried...]
67 : efrank 1.2 <P>
68 : efrank 1.1
69 :     Instead, the Model editor focuses on information management: selection
70 :     of reconstruction elements, hierarchical organization of a model,
71 :     association of reconstruction elements within the hierarchy,
72 :     versioning [future release], association of application specific data
73 :     with a model.
74 :    
75 :     <A name="Model Editor Thesis"></A>
76 :     <H2> Model Editor Thesis </H2>
77 :    
78 :     The thesis behind the editor is that, to do this on a large scale,
79 :     models can not be completely entered by hand. They must be
80 :     constrained by accumulated information in biological databases. Thus
81 :     the editor presumes a database with reconstructions and general
82 :     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
84 :     religious about this yet]
85 : efrank 1.2 <P>
86 : efrank 1.1
87 :     The Editor thus works by building higher level constructs from lower
88 :     level entities. At each step along the way, the editor enforces a
89 :     constraint that the data exist in a backing database or datastore.
90 :     The supported hierarchy right now is:
91 :     <UL>
92 :     <LI> Metabolites and Enzymes
93 :     <LI> Reactions
94 :     <LI> Trees of sets of reactions (i.e., reconstructions and models)
95 :     <LI> Catalogs of trees (catalogs of reconstructions and models)
96 :     </UL>
97 :    
98 :     <A name="Organization of the Editor"></A>
99 :     <H2> Organization of the Editor </H2>
100 :    
101 :     The Editor is organized, visually, into a notebook of pages, each
102 :     selected by a tab at the top. There are 4 notebook pages, labeled
103 :     "Metabolite," "Reaction," "Navigator," and "Catalog." You edit
104 :     by switching between these to build up your model. The pages
105 :     are now described, lowest level to highest. First, we must introduce
106 :     the concept of Data Source.
107 :    
108 :     <A name="Data Source"></A>
109 :     <H2> Data Source </H2>
110 :    
111 :     The Model Editor works in terms of database independentend object
112 :     model that represents the hierarchy just described. Any database or
113 :     that can convert its data to this format can be supported. We refer
114 :     to these as "Data Sources" or "Foundries." Two are supported right
115 :     now: WIT and BSS. WIT is the WIT3 prototype database at ANL.
116 :     BSS is the BioSimScratch prototype database used for prototyping
117 :     this application. At present, BSS is much better supported.
118 : efrank 1.2 <P>
119 : efrank 1.1
120 :     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
122 :     of models from data accumulated over numerous databases. By extending
123 :     the architecture slightly, we will later allow the databases be
124 :     remote, network services.
125 :    
126 :     <A name="Metabolites Page"></A>
127 :     <H2> Metabolites Page </H2>
128 :    
129 :     On the Metabolites Page you can search Data Sources for Metabolites.
130 :     Metabolites have a Short name (used in printing reactions, graphs, etc.)
131 :     and Long names (more detailed biochemical names). You can search by
132 :     either, combining the search criteria by OR or AND. For each
133 :     case, you can search for exact match (EQUALS), by substring (CONTAINS)
134 :     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
136 :     data source is SQL based, which may not always be true.
137 : efrank 1.2 <P>
138 : efrank 1.1
139 :     There is an ADD button that allows you to add a metabolite to the
140 :     database. The OK button produces and immediate transaction and
141 :     commit! Added metabolits automatically are added to the Search Results
142 :     Table.
143 :    
144 :     <A name="Search Results Table vs. Selected Results Table"></A>
145 :     <H2> Search Results Table vs. Selected Results Table </H2>
146 :    
147 :     When you do a metabolite search, the results land in a table at the upper
148 :     right. Each search appends to this table, but there is a clear button
149 :     you can hit to reset the table. You can left-click rows in the table,
150 :     or Contrl-left-click to extend the selection, and then hit the SELECT
151 :     button. This copies the sub-selection of the search results down to
152 :     the Selected Results Table at the bottom of the page. This allows
153 :     you to give broad searches for metabolites and then accumulate subsets
154 :     into the Selected Results Table. The utility is explained next.
155 :    
156 :     <A name="Reactions Page"></A>
157 :     <H2> Reactions Page </H2>
158 :    
159 :     The Reactions Page allows you to find Reactions in the database. The
160 :     search is by input metabolites, output metabolites and by
161 :     enzymes. [Enzymes not supported yet]. The drop down box allows you to
162 :     choose three searches, INPUT, OUTPUT and FROM METABOLITE PAGE (Described
163 :     just below). After choosing, you hit the SEARCH button.
164 : efrank 1.2 <P>
165 : efrank 1.1
166 :     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
168 :     Metabolites page.
169 : efrank 1.2 <P>
170 : efrank 1.1
171 :     The meanings of INPUT, OUTPUT and FROM METABOLITE PAGE are as follows:
172 :     <UL>
173 :     <LI>
174 :     INPUT: You specify the metabolite Short Name, exactly. All reactions with
175 :     this metabolite as an input are found.
176 :     <LI>
177 :     OUTPUT: You specify the metabolite Short Name, exactly. All reactions with
178 :     this metabolite as an output are found.
179 :    
180 :     <LI>
181 :     FROM METABOLITE PAGE: When selected, the text entry box is disabled. When
182 :     you hit SEARCH, a window pops up that contains all of the
183 :     metabolites listed in the Selected Metabolites Table on the
184 :     Metabolite page. There is one row for each metabolite.
185 :     <p>
186 :     Each row has an INPUT column and OUTPUT column with checkboxes.
187 :     Check whether you want the metabolite to be rquired as an INPUT
188 :     or as an OUTPUT. You may check both (but see below). You may
189 :     check neither, in which case the metabolite is ignored.
190 :     <p>
191 :     There are three drop-down chooser at the bottom of the table.
192 :     One says whether to "Or together" or "And together" the Inputs.
193 :     If you choose "Or together" then any reaction with any of the
194 :     metabolites selected as inputs matches. If you choose "And
195 :     together," then only reactions with ALL of the metabolites checked
196 :     as Input match.
197 :     <P>
198 :     There is a similar box for the output metabolites.
199 :     <P>
200 :     Finally, there is and And/Or box for combining the inputs and
201 :     outputs.
202 :     </UL>
203 :    
204 :     <A name="Catalog Page"></A>
205 :     <H2> Catalog Page </H2>
206 :    
207 :     The Catalog Page shows a tree rooted with "Data Sources" under which
208 :     there is branch for each data source. If you expand a data source,
209 :     you will see all available reconstructions and models available
210 :     from that data source.
211 : efrank 1.2 <P>
212 : efrank 1.1
213 :     You may select a reconstruction or model and then hit the "Load to
214 :     Navigator" button at the bottom right. The mouse indicator will
215 :     turn to an hour glass until the data are loaded.
216 : efrank 1.2 <P>
217 : efrank 1.1
218 :     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
220 :     Navigator tab after hitting the tab.
221 : efrank 1.2 <P>
222 : efrank 1.1
223 :     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
225 :     copy/paste between the loaded models and reconstructions.
226 :    
227 :     <A name="Navigator Page"></A>
228 :     <H2> Navigator Page </H2>
229 :    
230 :     The Navigator page is split into two pieces, left and right. The left
231 :     is the Tree Navigation Panel and the right is the Information Display
232 :     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
234 :     models and reconstructions.
235 : efrank 1.2 <P>
236 : efrank 1.1
237 :     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
239 :     so, the set of reactions is shown to the right in the Information Display
240 :     Panel.
241 : efrank 1.2 <P>
242 : efrank 1.1
243 :     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
245 :     reaction, copy the reaction, or paste previously cut or copied reactions
246 :     OR paste in all of the reactions from the Selected Reactions Table
247 :     on the reactions page.
248 : efrank 1.2 <P>
249 : efrank 1.1
250 :     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,
252 :     copy, and paste tree nodes between arbitrary, loaded trees [will
253 :     change in the future so that some trees are read only]. You can also
254 :     choose "New Root Node" to create a whole new tree for a new model."
255 :     You can also choose "Add Sub Element" to add a new branch under the
256 :     selected node. These operations allow you to build up the model
257 :     hierarchy. Note that when you cut/paste branches, you are doing
258 :     a deep copy of the branch, including all associated reactions.
259 : efrank 1.2 <P>
260 : efrank 1.1
261 :     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
263 :     Selected Reactions Table on the reactions page.
264 :    
265 :     <A name="Writing Out the Editing Results"></A>
266 :     <H2> Writing Out the Editing Results </H2>
267 :    
268 :     This is where you scream. At the moment, writing is not supported,
269 :     except for writing Metabolites. We are adding this ability now.
270 :     Underlying the feature is a clear statement of deep vs. shallow copy,
271 :     the statement about the impact of a change in one tree if data are
272 :     copied to another, a clear statement about search for reactions when
273 :     they are otherwise redundant but have been deep copied between trees
274 :     and statements about versioning.
275 :    
276 :     </BODY>

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