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51 changes: 26 additions & 25 deletions A_Getting_started/intro.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,22 +6,23 @@
:::{note} The AnyBody software comes with an inbuilt model repository - The
AnyBody Managed Model Repository (AMMR). This tutorial starts with unpacking a
local version of the AMMR. You can skip to {doc}`lesson 1 <lesson1>` if you have
already done this.
already done this.
:::

## Goals for this tutorial

This tutorial takes a top-down approach and aims to accomplish the following:

1. Create a new standing model using the Human Standing template model
2. Learn how to load & change the posture of the human model, and use
2. Learn how to load & change the posture of the human model, and use
the model view window
3. Run an inverse dynamics analysis and review the results

This tutorial relies heavily on using the AnyBody Managed Model Repository (AMMR).
This tutorial relies heavily on using the AnyBody Managed Model Repository (AMMR).
Follow the steps below to unpack a local version of the AMMR.

(SettingUpAMMR)=

## Setting Up the AMMR

The *AnyBody Managed Model Repository* (AMMR) is a comprehensive open library of
Expand All @@ -30,40 +31,32 @@ System. It allows users to configure and combine different body models, which
can be easily integrated into their own simulations and analyses.

The AnyBody Managed Model Repository (AMMR) is included with the AnyBody
Modeling System, but it needs to be manually installed or unpacked after
installing AnyBody. You can install the AMMR from the AnyBody Assistant dialog
that appears when AnyBody starts.

To get a copy of the latest AMMR files, press the Demo tab in the AnyBody
assistant dialog box. Then select the *“Install the demo repository by clicking*
*this link”*
Modeling System. You can navigate to the Demo tab in the AnyBody
Assistant dialog box.

```{figure} _static/intro/image1.png
:alt: AMMR setup
:class: bg-primary
:align: center
```

This installs a copy of the AMMR locally in your documents folder by default (e.g.
{{AMMR_DEMO_INST_DIR}}). If
there are multiple users using your computer, each of them will have to follow
this guide. It is good practice to create a second local copy of the AMMR so
that you do not overwrite the original AMMR folder by accident. There you can
initialise a git repository in which you can version you models, keep a backup,
or share them easily with the community.
In the Demos tab you will find a gallery of the example models included in the AMMR.
Following the link will take you to the application example overview page.

:::{important}
AnyBody Modelling System comes with a version of AMMR (not necessarily the
latest) placed in the installation folder of the software. Do not directly use
these files for your actual work as updates or reinstallation of AnyBody can
overwrite your changes. So always **copy the files from the AMMR folder to your**
**working folder** before using them.
:::
```{figure} _static/intro/assistant_gallery.png
:alt: AnyBody Assistant demo tab gallery overview
:class: bg-primary
:align: center
```

From here you are can browse the description of each model and open them directly in
AnyBody. The first time you open one of the models, you will be prompted to unpack the
full AMMR into your computer.

## AMMR structure

Open a file manager and navigate to the directory where you unpacked the
repository (default is your documents folder). You should see a folder structure
repository (the default is your documents folder). You should see a folder structure
that includes the following subfolders:

- **Application**: Includes demo simulations of activities such as cycling,
Expand All @@ -85,6 +78,14 @@ A closer inspection of the Application branch reveals that it has four subfolder
purposes, typically by comparison of the model predictions with experimental
measurements.

:::{important}
AnyBody Modeling System comes with a version of AMMR (not necessarily the
latest) placed in the installation folder of the software. Do not directly use
these files for your actual work as updates or reinstallation of AnyBody can
overwrite your changes. So always **copy the files from the AMMR folder to your**
**working folder** before using them.
:::

:::{admonition} **Continue**
:class: seealso

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