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Project Explorer for NEES (PEN) . Rachelle Howell The University of Texas at Austin. You’ve created a project…. You’ve added your experiment(s)…. You have data, photos, and videos on your local computer. Data. Photos. Videos. You have inDEED files on the hub.

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project explorer for nees pen

Project Explorer for NEES(PEN)

Rachelle Howell

The University of Texas at Austin

how do you get all those files into your project
How do you get all those files into your project?


PEN is the Project Explorer for NEES. It is a java tool intended to run on a remote workstation or in the hub.

The primary purpose of PEN is to organize files and directories for upload and download with the NEES Project Warehouse while a project is in active development.

can t i do that with the project editor
Can’t I do that with the Project Editor ?

Yes! But with limitations….

The project editor limits the file size that you can upload to 650 MB.

The project editor also limits the number of files you can upload at one time.

(15 max)

i have a lot more than 15 files and some of them are really big
I have a lot more than 15 files and some of them are really big…

If you have a lot of files or you have very LARGE files such as movies or data files, you should use PEN to upload these files into your project.

do i want to run pen on my computer or within the hub
Do I want to run PEN on my computer or within the hub?

You will run PEN on your computer to upload the data, photos, and videos that reside on your local machine.

You will run PEN within the hub to upload files that reside in your personal workspace at NEES. For example, the inDEED files you created earlier.

running pen on your computer
Running PEN on your computer
  • Download the tool from NEES
  • Install PERL (Windows)
launching pen
Launching PEN

You will need:

Your NEES login and password

A local directory

Your project number

launching pen1
Launching PEN

Step 1: Enter your NEES login and password and click the login button.

launching pen2
Launching PEN

Step 2: Browse to a local directory and click the open button.

This directory should initially be empty. PEN will create a copy of the project structure from the Project Warehouse in this directory.

launching pen3
Launching PEN

Step 3: Enter your project number and click the connect button.

you are connected
You are connected!

Your Project Structure has been copied to your local directory

It’s the same structure you see in the File Browser tab in the Project Warehouse

uploading your files
Uploading your files

If we expand the directory structure for Experiment 1, we will see that there are no data folders. We need to create a Trial/Repetition in order to create the data folders to which we will upload our files.

Data Folders



you may notice that the trial you created is blue
You may notice that the trial you created is BLUE …

PEN uses following color codes:

GREY: The file exists at NEES but not locally

BLUE: The file exists locally but not at NEES

BLACK: The file exists locally and at NEES, and the files are the same

RED: The file exists locally and at NEES, but the files may not be the same

importing files
Importing files

Now that you have data folders, you can use the file import pane to drag and drop the data you want to upload into the project directory structure.

At this point, the files are copied

from the directory of origin to the local project directory. You now have two copies of these files on your local machine.

Drag and drop

editing metadata
Editing metadata

You can edit the basic project, experiment, trial, repetition, and file metadata from the info tab. The other metadata fields must be edited through the Project Editor.

Be sure to save your changes

the checksum
The checksum

You have the option to checksum your files before you upload them. The checksum is what allows PEN to determine if your local file matches the file at NEES. If you do NOT checksum your files, they will appear red after the upload even if your file matches the file at NEES.


When you are done dragging and dropping your files into the project, editing metadata, and checksumming the files, it is time to upload them.

Right clicking on any directory that contains blue files will result in a menu that contains an upload option.

In this example, I have right-clicked on the project directory so that all of my files get uploaded at once.

Had I right-clicked on a particular directory(e.g., Videos), I could have chosen to upload only the files within that directory.

You can upload a single file by selecting and right-clicking that file.

all my files turned black or all my files turned red
All my files turned black!!!OrAll my files turned red!!!

Your files changed color because they now reside both locally and in the Project Warehouse.

If your files turned black after the upload completed, that indicates that you have checksummed them.

If your files turned red after the upload completed, that indicates that you did not checksum them. You can checksum them later if you so desire.

great i ve uploaded my data now what about my indeed file s
Great! I’ve uploaded my data. Now what about my inDEED file(s)?

You will need to launch PEN from within the hub in order to upload files from your personal workspace.

running pen within the hub
Running PEN within the hub

Navigate to the PEN tool page and click the Launch Tool button.

how do i create a new folder in my personal workspace
How do I create a new folder in my personal workspace?

You have a couple of options:

  • Click the browse button and use the browse dialog box to create a new folder.
  • Designate a folder that does not exist and have PEN create it for you.
you are connected1
You are connected!

Your file import pane will now show the folders that exist in your personal workspace. Locate your inDEED file(s) and import it into the same directory as your associated data files. Don’t forget to upload!

all of my data is uploaded now what
All of my data is uploaded…now what?

You’re not done yet! PEN allows you to upload files, but it cannot determine settings such as whether or not a file should be opened with inDEED or if a photo should be a film strip photo. You will need to go back into the project editor to create these associations/settings.

this is great but what else should i know about pen
This is great…but what else should I know about PEN ???
  • PEN can also be used to download files.
  • PEN does not currently have the capability to delete files so be careful not to make a mistake. If you do make a mistake, contact NEES for help.
  • PEN is updated frequently. If you download PEN to your desktop, remember to check the tool page often for new releases.
how do i download a file
How do I download a file?

Let’s say you connect to a project that already has files uploaded to it. This is our project from before, but I’m connecting to it as if for the first time.

i don t see the files
I don’t see the files…

To see the files, right click on a directory and select “get file info”.


Right click on a grey file or a directory containing grey files, and select download. The files are downloaded to your local directory.

help i have red files
Help! I have red files!!

If you connect to your project, and you have red files that were not previously red, this indicates that either your local file or the file at NEES has changed. You should verify who has the correct file (either you or NEES) and update the NEES file if necessary.

help i cannot upload data download data create trials or see one of my experiments
Help! I cannot upload data, download data, create trials, or see one of my experiments!!!

Check your permissions under the Team Members tab in the Project Editor. You must have the proper rights to perform these tasks in PEN.

help something else is wrong
Help!! Something else is wrong!!!

You can log a support ticket through the support link in the upper right part of your screen. NEES customer support is VERY helpful.

i don t need help but i have feedback or a suggestion to make the tool better
I don’t need help, but I have feedback or a suggestion to make the tool better…

You can submit “wishes”, ask questions, and write reviews of PEN using the links on the PEN tool page.