BODB Insert Model

The form for inserting Models is shown after clicking on the “Model” link in the Insert page. Click on the “Save” button to save the Model, or the “Save Draft” button to save a draft of the present Model to the BODB database. The draft will also be available to edit at a later time and will be listed in the Workspace for convenience.

The input form for Model entries.

The input form for Model entries.


Title

The name of the Model, e.g. “Mirror Neuron System (MNS) Model”. The text field has a maximum length of 200 characters. It is very important to first search for existing Models to ensure that duplicate entries aren’t added.

Authors

Add New Author

To add an author, click the “Add new” link in the “Authors” section. The ordering of authors when the Model entry is listed can be set by setting the “Order” field of each author appropriately.

Search Authors

In order to link an existing author to the new Model entry, click on the “Search” link in the “Authors” section. An “Author Search” popup window will appear where authors can be searched by multiple fields. Click on the “Select” link next to an author to link it to the Model entry.

Author search window

Author search window


Brief Description

Start with an edited abstract of the key paper, but update it to summarize key points as you write the Narrative.

Narrative

The Narrative reviews “how the model works” and “what the model does”. It will thus refer to the diagrams associated with the model and the linked SEDs and SSRs. Note 1: Part of your success a collator here and in presenting the SEDs and SSRs is to be judicious in what you highlight and what you omit. The BODB entry is not meant to replace the article(s) which document the Model but rather to help the user assess the Model in relation to available empirical data` and modeling goals. Note 2: Insert citations of references in (Author, Year) style here (and in SEDs below) with formal bibliographic entries below. You should ensure that the reference is included in the Literature section of BODB, perhaps as a result of using the PubMed Tool.

Tags

A list of keywords associated with this Model entry.

Architecture

The Architecture section allows the user to upload diagrams of the Model as well as define Model inputs, outputs, states, and submodules.

The model Architecture section.

The model Architecture section.


Diagrams

Since the model may be hierarchical, you may choose to use several diagrams. Use at least one to present the overall structure of the Model. In some cases, a diagram will explicitly show not only the immediate submodules but also the further decomposition of some of these. In other cases, you will need a separate diagram to show how a module shown as a unit of an earlier diagram is expanded to reveal the structure of its submodules.

In order to add a diagram, click on the “Add new” link in the Diagrams section. This will open the Add Diagram window. Clicking on the “Edit” link next to a diagram already linked to the model will open the Edit Diagram window, and clicking on the “Delete” link will delete the diagram and remove it from the Model.

Inputs

The Name, DataType (i.e. Image, Vector, Scalar) and Description of all inputs to the model.

Outputs

The Name, DataType (i.e. Image, Vector, Scalar) and Description of all outputs of the model.

States

The Name, DataType (i.e. Image, Vector, Scalar) and Description of all states of the model. In general, the state of a module comprises the state of all the submodules which comprise it. It is thus a matter of judgment by the collator whether the state of a module whose decomposition is presented should be described or left implicit.

Submodules

New submodules can be added by clicking on the “Add new” link in the Submodules section. This will add a new form containing fields for the Name and Description of the submodule. Clicking on the “Expand” link next to the new submodule form will make visible the Narrative field. To delete the submodule and remove it from the model click on the “Delete” link.

Related SEDs and SSRs

Summaries of Experimental Data (SEDs) and Summaries of Simulation Results (SSRs) are documented in separate entries in BODB.

The Related SEDs and SSRs section.

The Related SEDs and SSRs section.


SEDs Used to Build the Model

When reading about a Model, you may find that some of the empirical data that are cited are not actually used either in defining or testing the model. In most cases, you will not document such data in BODB. But in some cases, you may decide that they strengthen the Model Entry by setting the scene for the actual modeling. Alternately, SEDs may support some aspect of model design, e.g., an SED showing an inhibitory connection between 2 brain regions would support the decision to constrain the connection between Model modules representing those brain regions to be inhibitory.

To link an existing SED to the model, click on the “Search” link in the SEDs Used to Build the Model section. This will open the SED Search window where the “Select” link can be used to link a search result to the current model. In this case, the user only then has to select the relationship between the SED and the model (support or scene setting). Alternately, a new SED can be added by clicking on the “Add new” link. This will add a new form to the section including fields for the SED Name, Relationship to the model, and Description. Clicking on the “Expand” link next to the new form will make visible additional fields for Tags and a Narrative.

SEDs Used to Test the Model

SEDs used to test the model’s performance can be linked to Summaries of Simulation Results (SSRs) that either explain or contradict them. Clicking the “Add new” link under the “SEDs used to test the model” will add a new row to the form with the following fields:

  • Name – The name of the the association between the SED and SSR
  • Relationship – Explanation or Contradiction
  • Description – A brief description of the association
  • SED – the SED used to test the model. Click “Search” to open the SED Search page or “Add new” to add a new SED, which inserts a new subrow with the following fields:
    • Name – The name of the SED
    • Description – A brief description of the SED
  • SSR – the model’s simuation results that explain or contradict the SED
    • Name – The name of the SSR
    • Description – A brief description of the SSR

Predictions

Predictions made by the model can be entered and optionally linked to Summaries of Simulation Results (SSRs). Clicking on the “Add new” link will insert a new row in the Predictions section with fields for the Name and Description. Clicking on the “Expand” link will display fields the Tags and the Narrative. SSRs can be added to the prediction by clicking on the “Add new” link in the SSRs section. This will open the Insert SSR window.

URLs

The model URLs section.

The model URLs section.

The URLs section allows the user to add the following hyperlinks:

  • Execution URL – A URL that points to downloadable code for the present model’s executable implementation.
  • Documentation URL – A URL that points to the present model’s documentation.
  • Description URL – A URL that points to the description of the present model.
  • Simulation URL – A URL that points to simulation results obtained with the present model’s simulation code.

Related Models

Note that Models are documented in separate entries in BODB. Your job, then, is to decide which of the available Models relate to the way the present Model works. You can search BODB for related models and link them to the current one, or add a new model. Clicking on the “Show” link in the “Related Models” section will expand the Related Models section, displaying the Models linked to the current entry and allowing the user to add new Models. After expansion, the “Show” link will turn into a “Hide” link that can be used to collapse the Related Models section.

The Related Models section.

The Related Models section.

In order to link an existing Model to the current Model entry, clicking on the “Search” link will open the Model Search window. Clicking “Select” next to one of the search results will add that Model to the current Model entry. In order to add a new Model and link it to the current Model entry, click on the “Add new” link which will open a Insert Model window. Clicking on the “Edit” link next to a linked Model will open the Edit Model window and clicking on the “Remove” link will remove that Model from the current entry.

Related BOPs

This allows listing of principles related to the present Model. Note that BOPs are documented in separate entries in BODB. Your job, then, is to decide which of the available BOPs describe general principles that help us “map” the way the present Model works. You can search for existing BOPs to link to the current Model or add new BOPs. In either case, you should explain why this BOP is relevant to the current Model in the “Relationship” field– e.g., because it applies to the operation of a specific module or set of connections. Clicking on the “Show” link in the “Related BOPs” section will expand the Related BOPs section, displaying the BOPs linked to the current entry and allowing the user to add new BOPs. After expansion, the “Show” link will turn into a “Hide” link that can be used to collapse the Related BOPs section.

The Related BOPs section.

The Related BOPs section.

In order to link an existing BOP to the current Model, clicking on the “Search” link will open the BOP Search window. Clicking “Select” next to one of the search results will add that BOP to the current Model entry. In order to add a new BOP and link it to the current Model entry, click on the “Add new” link which will add a new BOP form to the Related BOPs section. The form contains fields for the BOP name, relationship to the current Model, and description. Clicking on the “Expand” link will make visible fields for BOP parent, tags, and a narrative. The “Expand” link will then turn into a “Collapse” link that can be clicked to hide the Parent, Tags, and Narrative fields. Clicking on the “Remove” link next to a linked BOP will remove that BOP from the current entry.

Related Brain Regions

There will be one entry here for every “listed” brain structure relevant to the model. In general, a brain structure will be relevant because it is in part modeled by a module, or a group of interconnected modules, of the model. Clicking on the “Show” link in the “Related Brain Regions” section will expand the Related Brain Regions section, displaying the Brain Regions linked to the current entry. After expansion, the “Show” link will turn into a “Hide” link that can be used to collapse the Related Brain Regions section.

The Related Brain Regions section.

The Related Brain Regions section.

In order to add an existing Brain Region to the current Model, clicking on the “Search” link will open the Brain Region Search window. Clicking “Select” next to one of the search results will add that Brain Region to the current Model entry. Clicking “Remove” next to a linked Brain Region will remove it from the current Model entry.

References

References to articles, books chapters, etc., relevant to this Model. Clicking on the “Show” link in the “References” section will expand the References section, displaying Literature linked to the current entry and allowing the user to add new Literature entries. After expansion, the “Show” link will turn into a “Hide” link that can be used to collapse the References section.

The References section.

The References section.

To link an existing Literature entry to the current Model, click on the “Search” link. This will open the Literature Search window where “Select” link next to any search result can be clicked to link it to the current Model entry. To add a new Literature entry, click on the “Add new” link. This will open up the Insert Literature window. Clicking the “Edit” link next to an existing Literature entry will open the Edit Literature window, while clicking “Remove” will remove the Literature entry from the Model.