Monera Model Editor

Ed Frank
Kaitlyn Hwang

Contents

• Introduction
• Model Editor Thesis
• Organization of the Editor
• Data Source
• Metabolites Page
• Search Results Table vs. Selected Results Table
• Reactions Page
• Catalog Page
• Navigator Page
• Writing Out the Editing Results

Introduction

The editor fits into a processing model that distinguishes between reconstructions and models. [Replay baby-steps paper]. In brief, a reconstruction catalogs the actual biophysical elements of a biological system. A model, on the other hand, while based upon a reconstruction, has the objective of understanding and predicting the behavior of the biological system. It may choose to ignore portions of the system, may choose to replace portions with analogies that simplify the system or allow the model to focus its attention elsewhere, and may choose to insert purely hypothetical elements. If a reconstructions is "parts," then a model is "purpose." A model ultimately attempts to bridge the gap from a set of parts to a set of dynamical variables that can be computed upon to predict the behavior of the system.

Show diagram of high level workflow:

    genomes -> reconstructions -> models -> dynamical data

The Monera Model Editor focuses on models, not reconstructions. Reconstruction typically requires extensive capabilities for compartive studies, e.g, compartive analysis of the genome of the subject organism with the genomes of others in order to assign fuction. This is not the purpose of the editor and, thus, it does not provide facilities for these operations. [But it's not so cut and dried...]

Instead, the Model editor focuses on information management: selection of reconstruction elements, hierarchical organization of a model, association of reconstruction elements within the hierarchy, versioning [future release], association of application specific data with a model.

Model Editor Thesis

The Editor thus works by building higher level constructs from lower level entities. At each step along the way, the editor enforces a constraint that the data exist in a backing database or datastore. The supported hierarchy right now is:

• Metabolites and Enzymes
• Reactions
• Trees of sets of reactions (i.e., reconstructions and models)
• Catalogs of trees (catalogs of reconstructions and models)

Organization of the Editor

Data Source

In several pages you will have the option of choosing a data sorce via a drop-down selector. Thus the Model Editor allows the formation of models from data accumulated over numerous databases. By extending the architecture slightly, we will later allow the databases be remote, network services.

Metabolites Page

There is an ADD button that allows you to add a metabolite to the database. The OK button produces and immediate transaction and commit! Added metabolits automatically are added to the Search Results Table.

Search Results Table vs. Selected Results Table

Reactions Page

Like the Metabolites page, the Reactions Page has both a Search Results Table and a Selected Reactions Table. They function just as on the Metabolites page.

The meanings of INPUT, OUTPUT and FROM METABOLITE PAGE are as follows:

• INPUT: You specify the metabolite Short Name, exactly. All reactions with this metabolite as an input are found.
• OUTPUT: You specify the metabolite Short Name, exactly. All reactions with this metabolite as an output are found.
• FROM METABOLITE PAGE: When selected, the text entry box is disabled. When you hit SEARCH, a window pops up that contains all of the metabolites listed in the Selected Metabolites Table on the Metabolite page. There is one row for each metabolite.

  Each row has an INPUT column and OUTPUT column with checkboxes. Check whether you want the metabolite to be rquired as an INPUT or as an OUTPUT. You may check both (but see below). You may check neither, in which case the metabolite is ignored.

  There are three drop-down chooser at the bottom of the table. One says whether to "Or together" or "And together" the Inputs. If you choose "Or together" then any reaction with any of the metabolites selected as inputs matches. If you choose "And together," then only reactions with ALL of the metabolites checked as Input match.

  There is a similar box for the output metabolites.

  Finally, there is and And/Or box for combining the inputs and outputs.

Catalog Page

You may select a reconstruction or model and then hit the "Load to Navigator" button at the bottom right. The mouse indicator will turn to an hour glass until the data are loaded.

The data are loaded to the Navigataor page, so you do not see a change on the catalog page. This may be confusing at first. Just hit the Navigator tab after hitting the tab.

Note: you may load as many reconstructions and models as you wish. Each show up in the Navigator page as indepentend trees. You can copy/paste between the loaded models and reconstructions.

Navigator Page

You can select a node in any of the trees. Doing so causes the editor to determine if there are any associated reactions with that node. If so, the set of reactions is shown to the right in the Information Display Panel.

Within the Information Display panel, you can left-click a reaction to select it. A right click pops up a menu that allows you to cut the reaction, copy the reaction, or paste previously cut or copied reactions OR paste in all of the reactions from the Selected Reactions Table on the reactions page.

When a tree node is selected (highlighted), you can use the right mouse button to pop-up an edit menu. That menu allows you to cut, copy, and paste tree nodes between arbitrary, loaded trees [will change in the future so that some trees are read only]. You can also choose "New Root Node" to create a whole new tree for a new model." You can also choose "Add Sub Element" to add a new branch under the selected node. These operations allow you to build up the model hierarchy. Note that when you cut/paste branches, you are doing a deep copy of the branch, including all associated reactions.

You can also choose Paste Reactions from the popup to paste previously cut or copied reactions OR paste in all of the reactions from the Selected Reactions Table on the reactions page.

Writing Out the Editing Results