Introduction to the Library

Contents

  1. Introduction to the Library
    1. Description
    2. Getting Your Own Library
    3. Basic Structure
    4. Connecting For The First Time
    5. Searching
    6. Retrieving
    7. Depositing
    8. Versions
    9. Curation Standard
    10. Public Permissions
  2. Worked Example

Description

  • The Continuity Library is a database that has been configured to store your Continuity models. Rather than storing entire .cont6 files on your system, you can utilize the library to store only the bits and pieces you change on a consistent platform. You can then search through these models by almost any user-accessible variable in Continuity (like date of production, description, basis function, node labels, EP equation, circulation model, etc.) and retrieve whole models or specific objects. Also, you can add attributes to any model, class, object, or sub-object.
  • For example, if you are working on an electrophysiology model and you keep changing the initial conditions, every time you save you are saving the same binary file with only a few bits altered because chances are the coordinates, basis, nodes, EP solvers, and EP equations have not changed. With our library however, only the objects you change are stored and they are organized on an accessible platform where they will not get misplaced. They are more accessible because besides searching by a title or user defined description, you can search by continuity’s automatically generated metadata or by biological attributes you define (these attributes are species and organ-related labels you can assign to a model or parts of a model).
  • You can also choose to make your models publicly available or locked.

  • Our back-end database is run by the National Biomedical Computation Resource and backed up once every week.

  • On this page you will find a more in-depth explanation on how the database works and instructions on searching, retrieving, and depositing.

Getting Your Own Library

  • Our database is meant to be a place where people can share completed models. We recommend that everyone install their own Library to store working models.

  • To install your own Library, see: How to set up your own library

Basic Structure

  • The design of our database is meant to mimic the the structure of a Continuity model. At the top are owners, who can have any number of models and choose to make them public or private.
  • Each Model then has a title, description, date and time of creation, version, variation, a public/private flag, and any number of classes.
  • These Classes are any of the loadable modules on the top of the Continuity home screen. They include: Mesh, Electrophysiology, Biomechanics, Fitting, Imagiing, and Script.
  • Below classes are Objects, which contain the data you can change in the various editor forms. They include: coordinate system, basis function, elements, matCoordEquations, nodes, ionic model, fitting constraints, images, scripts, etc..
  • Some Objects (namely nodes, biomechanics initial conditions, and fitting constraints) have Sub-Objects. Each of these can have a different attribute than their parent object. For example, you can specify a nodes form for a human model with pig node fibers.
  • Every Model, Class, Object, and Sub-Object can have a different attribute (or the same one). Each attribute can be any species, organ system, organ, tissues, reference author, reference title, reference date, or reference publication you wish to specify. These can be handy if say you only want to retrieve human models from the database or just any model with a dog mesh class.

Connecting For The First Time

  1. From the Continuity home screen, go to File-->Library-->Connect...

  2. At the top is a “Login To:” radio button. Select …
    1. “Continuity’s Public Library As A Guest” if you do not have an account or you just want to search and retrieve models.
    2. “Continuity’s Public Library” if you do have an account.
    3. “Custom Library” if you have your own model library to login to.
  3. Fill out the required fields and click “Test Connection” to make sure all the information is correct.
  4. Save the profile to you hard disk (all your information is encrypted).
  5. Click “OK” at the bottom.

Searching

  1. From the Continuity home screen, go to File-->Library-->Search...

  2. A search window should pop up with all the models on the database. If you are connected to our public database you will see all the models used in the tutorials. If nothing comes up then you are connected to a different database with no models. If an error message comes up then then database you are connected to is not up and running.
  3. Select either Properties, Objects, or Attributes field to search by clicking on the drop-down menu button after the “Search” label.
  4. Select a search operation by clicking on the second drop-down menu. Some search operations cannot be applied to all fields. For example, you cannot search titles by the “greater than” operation
  5. If you selected an Attributes field, you can also specify the type of Attribute to search (species, organ system, organ, tissues, reference author, reference title, reference date, or reference publication) by clicking on the drop-down menu button labeled “Select Attribute Type”.
  6. Enter a keyword to search for. If you enter multiple keywords separated by a space or comma then Continuity will search for them independently.

Retrieving

  1. You can view a model from the results frame of the Search Form double-clicking on it. Putting the mouse over the ‘ID’ column instantly displays a model’s description. By right-clicking on a model, you edit its metadata and view its forms (Nodes, Elements, Ionic Model, etc.). There is also a list of buttons and a menu-bar in the middle of the form that does the same thing.
  2. By opening a model you will bring up the Retrieve Form showing similar to the Deposit Form except the fields are disabaled.
  3. You can select which Objects to retrieve from the model by going to the Objects Pane and selecting either ‘retrieve’ or ‘ignore’ for each object.
  4. If you click ‘OK’, the model will be loaded from the database into Continuity.
  5. If you click ‘Cancel’, you continue searching and viewing other models.

Depositing

  1. You must first be a registered user of Continuity and have a working model loaded.

  2. From the Continuity home screen, go to File-->Library-->Deposit...

  3. In the Properties Pane, fill in the various fields. All required fields are denoted by a ‘*’.
    1. Please give a description, log (what was changed), and curation level (see ‘Curation Standard’ below).
    2. Specify public permissions to your model (see ‘Public Permissions’ below).
  4. In the Objects Pane, you can select which objects to store by clicking on ‘Use Old Object’, ‘Deposit New Object’, or ‘Don’t Deposit’ for each object if you are storing a version.
  5. In the Attributes Pane, you can specify one or many attributes for the model by simply choosing the component and entering in the attribute(s). If you select the check box on the left-hand side the attribute will be assigned to any child components. For example, say you specify an attribute for a Mesh class. If you select the check box, that attribute will also be given to the coordinates, basis, nodes, matCoordEquations, and elements objects as well as the nodes sub-objects (which are all under the Mesh class).
  6. In the Links Pane, you can associate any number of links to your model. These will appear nicely formatted when ever a user clicks on your model in the Search Window.
  7. You will be storing a New Model or a Version of an existing model depending on your title. See below for more information.
  8. Click ‘OK’ to deposit.

Versions

  • Every time you deposit a model, you can store a new problem or a version of an existing problem.
  • You can store a new problem by simply specifying a unique title. If a model’s title is different than any of your models’ titles than Continuity knows to store new copies of all the objects into a brand new model.
  • You can store a version of an existing problem by specifying the title of that existing problem. Versions contain only new copies of the objects you change (a new nodes object would be stored if you change a coordinate) and it references old objects (the same basis function object would be referenced if you do not change it).

Curation Standard

  • Level 0: not curated
  • Level 1: All parameters and initial conditions are defined. Model has a simulation (script) and it runs correctly.
  • Level 2: Model satisfies biophysical constraints (conservation of mass, energy, momentum) and metadata describes these constraints. Model is also well annotated with biological attributes.
  • Level 3: Model is published, accurately represents the published model, and the publication is linked to metadata.

Public Permissions

  • Confidential:
    1. Only the owner of the model can view it, retrieve it, alter its metadata, store a new version of it, and delete it, if the model is not shared with anyone i.e. the ‘Exclusive ID(s)’ is set to None. By default the ‘Exclusive ID(s) field is set to ‘None’.
    2. The owners mentioned in ‘Exclusive ID(s)’ field will also be able to view it, retrieve it, store a new version of it. The shared users can also delete the version saved by himself and only if that is the latest version. The shared user cannot delete the whole model or any version of the model saved by others.
    3. Deposit as Shared model:
      1. This option is enabled when ever a user loads a model which is shared to him by another user. If a user loads a shared model and want to deposit under the original owners name the ‘Deposit as shared model’ should be checked. If the option is unchecked it will be saved under his own name.
      2. All other times this option is disabled in the sense u cannot check it or uncheck it
  • Available To Public: Any user can view the model and retrieve it but only the owner can alter its metadata, store a new version of it, and delete it.
  • Owned By Public: Any user can view the model, retrieve it, alter its metadata, store a new version of it, but not delete it.

Worked Example

This example uses STICH patient data initially provided as text files, and illustrates the utility of the attachment and script managers.