Model DB: About Model DB

What's Model Database?

Model DB is a database of models written in insilicoML (ISML). Users can download models in the Model DB freely and use them. The models stored in the Model DB are models proposed in peer-reviewed papers published already. Currently, the Model DB contains models written in the ISML version 0.1. The Model DB will be modified very soon to deal with models with ISML1.0.

The ISML is a language that can explicitly describe the hierarchical structures of the physiological functions in the model. Taking advantage of this ISML's feature, the Model DB can show the tree structure of the model on the web browser, so that users can walk through inside of the model.

There are some ISML models which include morphological data stored in the Morphology DB at physiome.jp. In such case, users can download an archive of the ISML model with the morphology data. The details are explained below.

To add models into the Model DB, please make contact with physiome.jp administrators by email. (admin [at] physiome.jp)

Site Structure of Model DB

Content of each pages in Model DB

View Models

The list of Models in Model DB. This page is a top page of Model DB.

► Search Models

To search models, follow the following steps.

  1. Enter a search keyword at the blank box

  2. Check the ISML vesrion in the check box 0.1 1.0

  3. Select the search field from the pull-down menu

    • DBID: Search insilicoDB model ID
    • DBID track: Search insilicoDB ID tracking of all modules
    • Model Name: Search model name
    • Model Description: Search model description
    • Module Name: Search all module name in the model
    • Module Description: Search all module descriptions in the model
    • Article: Search article data in the model

  4. Select the order from the pull-down menu

    • DBID: Sort by DBID in descending order
    • Model Name: Sort by model name in ascending order
    • LastUpdate: Sort by lastupdate date in descending order

  5. Click the search button

► Model Table

Get Tree DBID Model Name ISML
Ver.
ISIDE
0.3
ISIDE
1.0
PCEnv
0.6
LastUpdate
Tree 187 Hodgkin_Huxley_1952_model 0.1 O O 2009-09-27
  • : Download button. Users can download ISML model (in XML format).

  • Tree: A link to the tree structure viewer page of the model. For details, see Tree View section.

  • DBID: A link to the model details page.

  • O: Mark of the availability of the simulation environment. "IDE" means insilicoIDE and "PCEnv" means Physiome CellML Environment. If users want to simulate the model at PCEnv, it is necessary to convert the model from ISML format to CellML format. If here is a check mark, it means that the available ISIDE can convert the model into the CellML format which can be read by the PCEnv.

View Modules

The list of Modules in Model DB.

► Search Modules

To Search modules, follow these steps.

  1. Enter a search keyword at the blank box

  2. Check the ISML vesrion in the check box 0.1 1.0

  3. Select the search field from the pull-down menu

    • DBID: Search insilicoDB model ID of the module
    • DBID track: Search insilicoDB ID tracking of the module
    • Module Name: Search module name
    • Module Description: Search module description
    • keyword: Search keyword in the module

  4. Select the order from the pull-down menu

    • DBID: Sort by DBID in descending order
    • Model Name: Sort by model name in ascending order
    • LastUpdate: Sort by lastupdate date in descending order

  5. Click the search button

► Module Table

Get Tree DBID Module Name ISML
Ver.
DBID track LastUpdate
Tree187Hodgkin_Huxley_1952_model0.11872009-03-04
Tree187Hodgkin_Huxley_1952_model0.11872009-03-04
Tree187Hodgkin_Huxley_1952_I_K0.11692009-03-04
Tree187I_K0.11692009-03-04
  • : Download button. Users can download ISML model (in XML format).

  • Tree: A link to the tree structure viewer page of the model. For details, see Tree View section.

  • DBID: A link to the model details page.

  • Module Name: A link to the module details page.

  • DBID track: A link to the model details page.

Model Details and Module Details

This page is linked from View Models page and View Modules page.

► Tree View and Download buttons

  • : Tree View button. Open the new window and display the tree structure of the model. For details, look Tree View section.

  • : Download button. Model DB creates and publishes the ISML file.

Tree View

Users can see the tree structure of the model in this page. Following is the manual.

Tree View Page Manual



Contents

1. How to Use

2. Structure of Tree View



1. How to Use

Main function is the following.

  • Click + button, then child modules are visible.
  • Click - button, then child modules are invisble.
  • Click "Module Name", then users can see the information about the clicked module in the right area.
  • Click "Change Root button", then root changes to the clicked module and Tree Type changes to the selected one.



2. Structure of Tree View

2.1. Current Root Frame (location : at the top of Tree View page)

Users can see current root information in this area.

2.1.1. Root DBID text box (location : at the left of "Current Root Frame")

This text box shows DBID of current root.

2.1.2. Root MID text box (location : at the right of "Root RMID text box")

This text box shows MID of current root.

2.1.3. Root Name text box (location : at the right of "Root MID text box")

This text box shows name of current root.

2.1.4. Root Tree Type text box (location : at the right of "Root Name text box")

This text box shows current Tree Type.

2.1.5. BACK button (location : at the right of "Root Tree Type text box")

Click this button, then display "DBID List Page".

2.1.6. HELP button (location : at the right of "BACK button")

Click this button, open new window which displays "Tree View Help Page".


2.2. Tree View Frame (location : In the center part of Tree View page)

This frame displays Tree View. Each branch describes relationships of the edges between the linked modules.

  • Include relationship
  • Constituent relationship
  • Interface relationship
  • Input relationship
  • Output relationship


2.3. Selected Module's Information Frame (location : in the right of Tree View page)

Click "Module Name" in "Treeview Frame", then users can see information about the clicked module in this frame.

2.3.1. DBID text box (location : in the top of "Selected Module's Information Frame" )

This text box shows the DBID of the selected module.

2.3.2. MID text box (location : on the right of "DBID text box")

This text box shows the MID of the selected module.

2.3.3. Name text box (location : below the "DBID text box" and "MID text box")

This text box shows the name of the selected module.

2.3.4. Module type text box (location : below the "Name text box")

This text box shows the module type of the selected module.

2.3.5. Last update date text box (location : below the "Module type text box")

This text box shows the last update date of the selected module.

2.3.6. Registration date text box (location : below the "Last update date text box")

This text box shows the registration date of the selected module.


2.4. Tree View Changer Frame(location : below the "Selected Object's Information" Frame)

Users can change root and Tree Type in this frame.

2.4.1. New Tree Type select box (location : in the center of this frame)

Users can select Tree Type at this box, before clicking "change root button". The description of each Tree Type is the following.

  • All link: Shows all linked modules and edges.
  • Interface Tree: Shows linked modules and edges whose relationships are interface.
  • Structural Tree [top down]: Shows linked modules and edges whose relationships are structural (include and constituent relationship). In this Tree Type, tree structure is top-down.
  • Structural Tree [bottom up]: Shows linked modules and edges whose relationships are structural (include and constituent relationship). In this Tree Type, tree structure is bottom-up.
  • Data Flow Tree -IO-: Shows linked modules and edges along the forward data flow. In addition, show linked modules and edges whose relationships are structural (include and constituent relationship).
  • Data Flow Tree -OI-: Shows linked modules and edges along the backward data flow. In addition, show linked modules and edges whose relationships are structural (include and constituent relationship).

2.4.2. Change Root button (location : in the bottom of this frame)

Click this button, then root changes to the selected module and Tree Type changes to the selected one showing at the "New Tree Type select box".

Model Registration

Currently, only developers can access this page.