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PEN Quick Start Guide

by Rachelle Howell, Gregory P Rodgers, Ian Mathew


PEN Quick Start Guide

This is the quick start guide for the Project Explorer for NEES (PEN). The tutorials provided in this guide will help you with all of the major functionality of the PEN tool. The application images shown and descriptions of functionality described in this guide are for PEN versions 2.0 and higher.


About the PEN Tool

The Project Explorer for NEES (PEN) tool is used to organize files and directories for upload to or download from the NEES Project Warehouse. The primary function of the PEN tool is to facilitate the bulk upload of data into the Project Warehouse. You can use the PEN tool to organize all of your data into the Project Warehouse directory structure on your local computer and then perform a single bulk upload of the data to transfer it into the NEES Project Warehouse.


Release Notes

To see what changes and enhancements have been implemented in the latest version of the PEN tool, please check the Release Notes.

Reporting Issues

If you encounter an issue while using the PEN tool, we encourage you to log a support ticket. Even if you think the issue is minor, please report it. The NEES IT team is always happy to assist you and it is their goal is improve your NEEShub experience, which includes addressing even minor issues.

Requests for New Functionality

If you feel that the PEN tool is lacking certain functionality that may make it better or easier to use, please let us know by logging a wish. Wishes help the NEES IT team determine what functionality to add to their tools in future releases.

Requests for Changes to this Wiki

If you have a suggestion as to how we can improve this wiki, please let us know via the “Comments” tab.


The tutorials provided here are designed guide you through the basic PEN tool functionality. These tutorials have been broken up into sections. The tutorials in the Getting Started section describe the most basic PEN tool functionality. The tutorials in the File Handling section describe those actions that are specific to files. The tutorials in the Object Handling section describe those actions that are specific to objects (i.e., experiments, trials, repetitions, simulations, hybrid simulations, etc.). The tutorials in the Other Actions section describes actions that can be performed on both files and objects. Finally, the tutorials in the Exiting PEN section describe how to close out projects, log out, and exit PEN.

Getting Started

The PEN tool can be downloaded or launched from the PEN tool page

Should you download the tool or launch it within the NEEShub?
This tutorial will help you decide which option is appropriate for what you’re trying to do.

Opening a project
This tutorial will help you open your project in the PEN tool.

Opening a local-only directory.
You may want to work in a local directory and create objects, import files, etc. prior to connecting to a project. This tutorial will show you how to open a local-only directory in PEN.

Connecting a local directory to a Project
If you work with a local-only directory, there will come a time when you want to connect that directory to your project. This tutorial will walk you through that process.

Re-opening a project
This tutorial will show you how to open a project that you have already opened in the past (i.e., projects that are already connected to a local directory).

Editing tool preferences
This tutorial will show you how to edit your default directory, the handling of failed uploads, confirmation messages, and your upload preferences (i.e., upload method, upload type, and TCP settings).

Navigating the project directory
This tutorial explains how to navigate the project directory view in the PEN tool.

Object/file color coding
PEN color codes files and objects based on their status in relation to the project as it exists in the NEES Project Warehouse. This tutorial will explain what each color signifies.

File Handling

These tutorials cover the PEN functionality that is specific to files.

Importing files
Before you can begin uploading files into the Project Warehouse, you need to import them into your project at the local level.

Uploading files
Once you have imported your files, you can begin uploading them into the Project Warehouse.

Downloading files
You can download files that exist in the Project Warehouse to your local computer.

Editing file information
PEN allows you to edit the most basic file information such as title and description.

Associating data files with inDEED
In order signal to the Project Warehouse that you have an interactive data file, you need to associate your data file with inDEED.

Creating filmstrip photos
Filmstrip photos are the photos that appear at the top of the experiment page in the Project Warehouse. You can designate photos as filmstrip photos using the PEN tool.

Checksumming files
The checksum is what PEN uses to determine whether or not your local file matches the file in the project warehouse. This tutorial will show you how to initiate a checksum on selected files.

Deleting files
You can delete local files and files that exist in the Project Warehouse.

Object Handling

These tutorials cover the PEN functionality that is specific to objects (i.e., experiments, trials, etc).

Object types
This tutorial will define the different object types that exist in PEN.

Creating new objects
You can create new objects in PEN.

Uploading objects
When you create new objects in PEN, they are created locally and will need to be uploaded before they will be visible in the Project Warehouse.

Duplicating objects
You can duplicate existing objects. When you duplicate an object, the duplicate will belong to the same parent object as the original. Duplicated objects will not contain the sub-objects and files that the original object has, but they will have the same object information (i.e., description, start date, end date, etc.).

Editing object information
PEN allows you to edit the basic object information (i.e., title, description, start date, end date, etc.).

Editing materials
Materials are a special type of object and the material information will vary depending on the material chosen.

Editing simulation models – coming in release 2.3.x.

Deleting objects
You can delete objects that exist locally and in the Project Warehouse. Deleting an object requires that all of the files within the object be deleted first.

Other Actions

These tutorials cover the PEN functionality that applies to both objects and files.

Copying and pasting objects/files
You can copy and paste objects and files. Copying and pasting an object differs from duplicating an object in that you can copy and paste an object to a different parent object. Additionally, when you copy and paste an object, all files and sub-objects belonging to the original object are copied to the new object.

Ignoring objects/files
PEN allows you to mark objects and files as “ignored”. Ignored objects and files are immune to all other actions.

Viewing objects/files in the Project Warehouse
PEN proves a link so that you can view any selected object or file within the Project Warehouse (provided it has been uploaded to the Project Warehouse).

Opening objects/directories/files locally
PEN allows you to open objects and files that exist locally. Objects will open in a file browser. Files will be opened using the default program for the selected file type.

Making asynchronous changes
Asynchronous changes are changes made outside of PEN (i.e., via the file browser). This tutorial will show you how to get these changes to appear in PEN.

Expand all /Collapse all directories
PEN allows you to fully expand and collapse nodes with a single menu option.

Refreshing the project view
While working in PEN, you may need to refresh your project view, particularly if you are making asynchronous changes.

Adding default directories
When objects are created in PEN, they have contain certain default directories. This tutorial will show you how to re-add any default directories that you may have deleted or removed.

Exiting PEN

Closing a project
You can close a project without logging out of PEN or exiting the PEN tool.

Logging out of PEN
PEN will allow you to log out, which automatically closes your project, without exiting the PEN tool. This is useful if you need to change users or switch logins.

Exiting the PEN tool
When you exit the PEN tool, the state of the tool upon exit will be the state of the tool upon relaunch. For example, if you are logged in and have a project open, PEN will attempt to log you back in and re-open that project the next time you launch the tool.

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