Merge pull request #39 from DARPA-ASKEM/Cleanup

Misc cleanup

docs/simulation/compare-datasets.md → docs/datasets/compare-datasets.md

@@ -37,7 +37,7 @@ In a workflow, the Compare datasets operator takes two or more datasets or simul
     - Perform one of the following actions:
 
         - On a resource or operator that outputs a dataset or simulation result, click <span class="sr-only" id="link-icon-label">Link</span> :octicons-plus-24:{ title="Link" aria-labelledby="link-icon-label" } > **Compare datasets**.
-        - Right-click anywhere on the workflow graph, select **Simulation** > **Compare datasets**, and then connect the output of two or more datasets or simulation results to the Compare datasets inputs. 
+        - Right-click anywhere on the workflow graph, select **Data** > **Compare datasets**, and then connect the output of two or more datasets or simulation results to the Compare datasets inputs. 
 
 ## Compare datasets
 

docs/datasets/index.md

@@ -15,7 +15,7 @@ The Transform data operator can also serve as a place to visually plot and compa
 
 !!! note
 
-    For information about uploading datasets, see [Gather modeling resources](../upload-resources/index.md).
+    For information about uploading datasets, see [Gather modeling resources](../gather-resources/index.md).
 
 ## Dataset resource
 
@@ -64,6 +64,8 @@ Hover over the output of the Dataset resource and click <span class="sr-only" id
 
     - [Transform dataset](transform-dataset.md)  
       Guide an AI assistant to modify or visualize the dataset. 
+    - [Compare dataset](../datasets/transform-dataset.md)  
+      Compare the impacts of two or more interventions or rank interventions. 
 
 -   __Configuration and intervention__
 
@@ -72,7 +74,7 @@ Hover over the output of the Dataset resource and click <span class="sr-only" id
     - [Configure model](../config-and-intervention/configure-model.md)  
       Use the dataset to extract initial values and parameters for the condition you want to test.
     - [Validate configuration](../config-and-intervention/validate-model-configuration.md)  
-      Use the dataset to validate a configuration
+      Use the dataset to validate a configuration.
 
 -   __Simulation__
 
@@ -81,6 +83,6 @@ Hover over the output of the Dataset resource and click <span class="sr-only" id
     - [Calibrate](../simulation/calibrate-model.md)  
       Use the dataset to improve the performance of a model by updating the value of configuration parameters.
     - [Calibrate ensemble](../simulation/calibrate-ensemble.md)  
-      Use the dataset to improve the performance of a model by updating the value of configuration parameters.
+      Fit a model composed of several other models to the dataset.
 
 </div>

docs/datasets/review-and-enrich-dataset.md

@@ -4,7 +4,7 @@ title: Review and enrich a dataset
 
 # Review and enrich a dataset
 
-Once you have [uploaded a dataset into your project](../upload-resources/index.md), you can open it to:
+Once you have [uploaded a dataset into your project](../gather-resources/index.md), you can open it to:
 
 - Explore and summarize its data and columns.
 - Manually add metadata that explains the data in each column.

docs/upload-resources/index.md → docs/gather-resources/index.md

@@ -13,7 +13,7 @@ Documents, models, and datasets appear in your project resources. You can transf
 
 ## Upload resources
 
-Using **Upload** in the Resources panel, you can import resources of the following types:
+Using the Resources panel, you can import resources of the following types:
 
 <div class="grid cards" markdown>
 
@@ -51,11 +51,10 @@ Using **Upload** in the Resources panel, you can import resources of the followi
 
 ???+ list "Upload resources"
 
-    1. In the Resource panel, click **Upload**.
-    2. Perform one of the following actions:
-        - Drag your files into the Upload resources dialog.
-        - Click **open a file browser** to navigate to the location of the files you want to add.
-    3. Click **Upload**.
+    1. Do one of the following actions:
+        - Drag your files into the Resources panel.
+        - Click **Upload** and then click **open a file browser** to navigate to the location of the files you want to add.
+    2. Click **Upload**.
 
 ### PDF Extraction
 

docs/get-started/using-terarium.md

@@ -66,11 +66,11 @@ The overview of a COVID-19 project. The Resources panel (left) provides access t
 
 ??? list "Create a project"
 
-    1. Perform one of the following actions on the Home page:
+    1. On the Home page, do one of the following actions:
         - To start from scratch, click :octicons-plus-24:{ aria-hidden="true" } **New project**.
-        - To copy a project, find it in My projects or Public projects and then click <span class="sr-only" id="menu-icon-label">Menu</span> :fontawesome-solid-ellipsis-vertical:{ title="Menu" aria-labelledby="menu-icon-label" } > :octicons-copy-24:{ aria-hidden="true" style="transform: rotate(-90deg);"} **Copy**.
+        - To find a project to copy, search My projects or Public projects and then click <span class="sr-only" id="menu-icon-label">Menu</span> :fontawesome-solid-ellipsis-vertical:{ title="Menu" aria-labelledby="menu-icon-label" } > :octicons-copy-24:{ aria-hidden="true" style="transform: rotate(-90deg);"} **Copy**.
         - To upload a project, click :octicons-upload-16:{ aria-hidden="true" } **Upload project** and drag in or browse to the location of your *.project* file.
-    2. Edit the project overview to capture your goals and save results over time.
+    2. In the new project, edit the overview to capture your goals and save results over time.
 
 ## Gathering resources
 
@@ -87,9 +87,10 @@ Use the Resources panel to upload and access your models, datasets, and document
 
 ??? list "Upload resources"
 
-    1. Click **Upload** in the Resources panel.
-    2. Drag in your resources or click **open a file browser** to locate them.
-    3. Click **Upload**.
+    1. Do one of the following actions:
+        - Drag your files into the Resources panel.
+        - Click **Upload** and then click **open a file browser** to navigate to the location of the files you want to add.
+    2. Click **Upload**.
 
         !!! note
 
@@ -110,20 +111,21 @@ Create a workflow to visually build your modeling processes. Each box is a resou
     2. Select a template, fill out the required fields, and then click **Create**.
     3. Use the canvas to customize your workflow:
 
-        - Drag in resources (models, datasets, or documents) from the Resources panel.
+        - Drag in models, datasets, or documents from the Resources panel.
         - Right-click on the canvas to add operators.
         - Connect resources and operators by clicking the source input ![](../img/output.png){ aria-hidden="true" class="node-icon" } and followed by the output ![](../img/input.png){ aria-hidden="true" class="node-icon" } destination. Labels show you the types of resources and operators you can connect.
 
 ## Using the library of operators
 
-Drill down into operators to configure complex scientific tasks. Each operator supports: 
+Terarium's operators support various ways for you to configure complex scientific tasks. For example, you can drill down to access: 
 
 - A guided wizard for quickly configuring common settings.
 - A notebook for direct coding.
 - An integrated AI assistant for creating and refining code even if you don't have any programming experience.
 
-??? list "Use Terarium's operators"
+??? list "Use a Terarium operator"
 
+    1. Make sure you've connected all the required inputs.
     1. Click **Open** or **Edit** on the operator node.
     2. Switch to the Wizard or Notebook view depending on your preference.
 
@@ -142,7 +144,7 @@ Drill down into operators to configure complex scientific tasks. Each operator s
         :material-github:{ title="GitHub" aria-label="GitHub" class="md-annotation__index"} [*Source code*](https://github.com/DARPA-ASKEM/model-service/blob/07ae21cae2d5465f9ac5b5bbbe6c7b28b7259f04/src/ModelService.jl#L54){ target="_blank" rel="noopener noreferrer" }  
 
     - [**Edit model**](../modeling/edit-model.md)  
-        Modify model states and transitions using a graphical template editor or an AI assistant.  
+        Modify model states and transitions using an AI assistant.  
         :material-github:{ title="GitHub" aria-label="GitHub" class="md-annotation__index" } [*Source code overview*](https://github.com/DARPA-ASKEM/beaker-kernel/blob/main/docs/contexts_mira_model_edit.md){ target="_blank" rel="noopener noreferrer" }  
 
     - [**Stratify model**](../modeling/stratify-model.md)  
@@ -158,7 +160,7 @@ Drill down into operators to configure complex scientific tasks. Each operator s
     ---
 
     - [**Simulate**](../simulation/simulate-model.md)  
-        Run a probabilistic simulation of a model under specific conditions.  
+        Run a simulation of a model under specific conditions.  
         :material-github:{ title="GitHub" aria-label="GitHub" class="md-annotation__index" } [*Source code*](https://github.com/ciemss/pyciemss/blob/main/pyciemss/interfaces.py#L323){ target="_blank" rel="noopener noreferrer" }  
     - [**Calibrate**](../simulation/calibrate-model.md)  
         Determine or update the value of model parameters given a reference dataset of observations.  
@@ -167,10 +169,10 @@ Drill down into operators to configure complex scientific tasks. Each operator s
         Determine the optimal values for variables that minimize or maximize an intervention given some constraints.  
         :material-github:{ title="GitHub" aria-label="GitHub" class="md-annotation__index" } [*Source code*](https://github.com/ciemss/pyciemss/blob/main/pyciemss/interfaces.py#L747){ target="_blank" rel="noopener noreferrer" }  
     - [**Simulate ensemble**](../simulation/simulate-ensemble.md)  
-        Run a deterministic simulation of multiple models or model configurations under specific conditions.  
+        Run a simulation of multiple models or model configurations under specific conditions.  
         :material-github:{ title="GitHub" aria-label="GitHub" class="md-annotation__index" } [*Source code*](https://github.com/ciemss/pyciemss/blob/main/pyciemss/interfaces.py#L35){ target="_blank" rel="noopener noreferrer" }  
     - [**Calibrate ensemble**](../simulation/calibrate-ensemble.md)    
-        Determine or update the value of model parameters given a reference dataset of observations.  
+        Extend the calibration process by working across multiple models simultaneously.  
         :material-github:{ title="GitHub" aria-label="GitHub" class="md-annotation__index" } [*Source code*](https://github.com/ciemss/pyciemss/blob/main/pyciemss/interfaces.py#L156){ target="_blank" rel="noopener noreferrer" }  
 
 -   __Data__
@@ -181,6 +183,10 @@ Drill down into operators to configure complex scientific tasks. Each operator s
         Modify a dataset by explaining your changes to an AI assistant.  
         :octicons-book-24:{ title="User Guide" aria-label="User Guide" class="md-annotation__index" } [*Source code user guide*](https://pandas.pydata.org/docs/user_guide/index.html#user-guide){ target="_blank" rel="noopener noreferrer" }  
 
+    - [**Compare dataset**](../datasets/transform-dataset.md)  
+        Compare the impacts of two or more interventions or rank interventions.  
+        :octicons-book-24:{ title="User Guide" aria-label="User Guide" class="md-annotation__index" } 
+
 -   __Config and intervention__
 
     ---
@@ -191,5 +197,6 @@ Drill down into operators to configure complex scientific tasks. Each operator s
         Determine if a configuration generates valid outputs given a set of constraints.  
         :material-github:{ title="GitHub" aria-label="GitHub" class="md-annotation__index" } [*Source code repository*](https://github.com/siftech/funman){ target="_blank" rel="noopener noreferrer" }  
     - [**Create intervention policy**](../config-and-intervention/create-intervention-policy.md)  
+         Define intervention policies to specify changes in state variables or parameters at specific points in time.
 
 </div>

docs/index.md

@@ -4,7 +4,14 @@ title: "About Terarium"
 
 # About Terarium
 
-Terarium is a modeling and simulation workbench designed to help you assess and contribute to the scientific landscape. Regardless of your level of programming experience, Terarium allows you to:
+Terarium is a modeling and simulation workbench designed to help you assess and contribute to the scientific landscape. New to the workbench? Check out these topics:
+
+<div class="gridcards" markdown>
+[Using Terarium](get-started/using-terarium.md){ .md-button }
+[Get started](get-started/example-workflow.md){ .md-button }
+</div>
+
+Regardless of your level of programming experience, Terarium allows you to:
 
 <div class="grid cards" markdown>
 - :fontawesome-solid-magnifying-glass:{ .lg .middle } **Extract models from academic literature**
@@ -15,18 +22,17 @@ Terarium is a modeling and simulation workbench designed to help you assess and
 
 ![The Terarium home screen with a list of projects and related papers](img/terarium-home.jpg)
 
-Need help? Check out these topics:
+Need more help? Check out these topics:
 
 <div class="gridcards" markdown>
-[Get started](get-started/using-terarium.md){ .md-button }
-[Upload modeling resources](upload-resources/index.md){ .md-button }
-
+[Gather modeling resources](gather-resources/index.md){ .md-button }
 [Build a workflow graph](workflows/index.md){ .md-button }
-[Review and transform data](datasets/index.md){ .md-button }
 
+[Review and transform data](datasets/index.md){ .md-button }
 [Modeling](modeling/index.md){ .md-button }
-[Configuration and intervention](config-and-intervention/index.md){ .md-button }
 
+[Configuration and intervention](config-and-intervention/index.md){ .md-button }
 [Simulation](simulation/index.md){ .md-button }
-[Integrated subsystems](subsystems/index.md){ .md-button }
+
+[Annotate your work](notes/index.md){ .md-button }
 </div>

docs/modeling/index.md

@@ -12,7 +12,7 @@ A model is an abstract representation that approximates the behavior of a system
 
     For information about: 
 
-    - Uploading models, see [Gather modeling resources](../upload-resources/index.md).
+    - Uploading models, see [Gather modeling resources](../gather-resources/index.md).
     - Creating models, see [Edit model](edit-model.md).
 
 ## Model resource

docs/simulation/index.md

@@ -39,10 +39,4 @@ With Terarium's simulation operators, you can:
 
     Calibrate with multiple models simultaneously to explore how different configurations collectively align with historical data.
 
--   [Compare datasets](compare-datasets.md)
-
-    ---
-
-    Compare or rank two or more interventions.
-
 </div>

mkdocs.yml

@@ -94,12 +94,13 @@ nav:
   - Get started:
     - Using Terarium: get-started/using-terarium.md
     - "Tutorial: Recreate, modify, and simulate a model": get-started/example-workflow.md  
-  - Gather modeling resources: upload-resources/index.md
+  - Gather modeling resources: gather-resources/index.md
   - Build a workflow graph: workflows/index.md
   - Review and transform data: 
     - datasets/index.md
     - Review and enrich a dataset: datasets/review-and-enrich-dataset.md
     - Transform dataset: datasets/transform-dataset.md
+    - Compare datasets: datasets/compare-datasets.md
   - Modeling: 
     - modeling/index.md
     - Review and enrich a model: modeling/review-and-enrich-model.md
@@ -121,7 +122,6 @@ nav:
     - Calibrate a model: simulation/calibrate-model.md
     - Simulate ensemble: simulation/simulate-ensemble.md
     - Calibrate ensemble: simulation/calibrate-ensemble.md
-    - Compare datasets: simulation/compare-datasets.md
   - Annotate your work: notes/index.md
   - Integrated subsystems:
     - subsystems/index.md