Managing a
Personal Research Archive

Vicky Steeves & Nick Wolf

Basic Management Principles

• Use a file management system to annotate and locate files; use a systematic file naming system.
• Use "readme" files to annotate and explain file content.
• Use open file formats that are software agnostic.

NYU Storage Resources

Setting up a Cloud Environment:
NYU’s Google Drive

1. Download the Drive App for Desktop. This will allow you to integrate your cloud with some file managers like Zotero.
2. Know your root directory for your desktop app, e.g.:
   MAC | /users/NAME/google drive
   Windows | C:\users\NAME\google drive
3. Remember that files saved to this directory are saved locally first, and then synced with the Drive cloud as scheduled.
4. BONUS: Get phone and tablet apps to integrate with mobile data management applications like TurboScan

Zotero for File Management

1. Zotero is normally used as a bibliographic management tool.


2. But...elements in a Zotero library can be annotated with tags and text notes.


3. Zotero will also store links to files, either as a standalone library entry, or as a child element linked to a bibliographic record.

Note: NYU Libraries provides support for learning Zotero. See the Zotero LibGuide for more information.

Zotero for File Management

For example, create a “Document,” and name it after the filename you want to annotate. Enter identifying data and attach notes. Last, attach a link to the file.

Zotero for File Management

Use Zotero to manage files on Google Drive or any other cloud service by going to Preferences >> Advanced >> Files and Folders and changing the base directory:

Project Management with
the Open Science Framework

Project Management with the Open Science Framework

• Wiki: document your lab procedures, standards, etc.
• Collaborators: add collaborators of all levels, on different parts of your project
• Components: sub-projects to organize your research
• Version Control: upload files of the same name & OSF will track your versions!
• Add-Ons: use OSF to bring together tools you use | GitHub
• Registrations: when you have an unchanging version of your project, register it & get a DOI!

Managing Files:
Bulk File Renaming (Windows) using Explorer

Managing Files:
Bulk File Renaming (Windows) using Explorer

Managing Files:
Bulk File Renaming (Mac) using Finder

Managing Files:
Bulk File Renaming (Mac) using Finder

Managing Files:
Advanced Bulk File Renaming (Windows)

1. Download the rename.bat script and save it as rename.bat in the directory of files you wish rename. You may wish to try it on these sample files.
2. Go to the Windows Start Menu and type "run cmd"
3. Navigate to the directory to the folder containing the files you want to change. For example: type cd documents to change files in a folder called “documents”.
4. type rename.bat and hit enter to transform your files! (alternatively, double-click on the file).

Managing Files:
Advanced Bulk File Renaming (Windows)

Here's a few more cool scripts to do some useful bulk transformations.

1. Download renamePre.bat & renameSeq.bat


2. Stay in the command line & in the directory you want to work in!


3. type renameSeq.bat and hit enter.


4. type renamePre.bat and hit enter.

Managing Files:
More Bulk File Prefix Renaming (Mac)

1. Download the file_rename_MAC script in the directory of files you wish rename. You may wish to try it on these sample files.
2. From the Mac Launchpad, look for Terminal and open it.
3. Change working directory to the folder containing the files you want to change. For example, type cd Desktop/directory to change files in a folder called “directory” on the desktop.
4. type bash file_rename_MAC.sh

Managing Files 2:
Making a README

What is a readme file? A readme file is a .txt, .xml., or .html file that lives in a directory and explains the context and uses of each files in that same directory.

Managing Files:
Making a README

1. Open your text editor and create a new file named readme.html
2. Save the file in the directory you want to annotate.
3. Add the following to the readme.html file (or alternatively, grab the template):

<html>
<head>
<title>My Annotated File Directory</title>
</head>
<body>
<h1>My Annotated File Directory</h1>
<h2><a href="#">File Name</a></h2>
<p>This is an annotation</p>
</body>
</html>

Managing Files:
Making a README

For every file in your directory, add an annotation enclosed in the <p> tags and replace the # in the <a> tags with the full path to that filename. Replace the words File Name with the file name you wish to annotate.

Managing Files: Automating a README (Windows)

Dynamically create that readme file using a script:

1. Place the script toHTML.bat in the directory where we renamed files
2. Go to the Windows Start Menu and type run cmd Your command line should pop up!
3. Change working directory on the command line to the folder containing the files you want to change.
4. Type toHTML.bat and hit enter.

Look for that readme.html file in the directory, and change the annotation in your text editor as before.

Managing Files: Automating a README (Windows)

Let’s test out a few more cool scripts to generate readme in other formats!

1. Download toCSV.bat & toTXT.bat
2. Stay in the command line & in the directory you want to work in!
3. type toCSV.bat and hit enter.
4. type toTXT.bat and hit enter.

Managing Files: Automating a README (Mac)

Dynamically create that html readme file using a script:

1. Place the script readme_MAC_html into the folder of files you want to annotate
2. From the Mac Launchpad, look for Terminal and open it.
3. Navigate to the folder containing the files you wish to annotate by typing cd FOLDER-CONTAINING-FILES
4. Type bash readme_MAC_html > readme.html and hit enter. This examines your directory and outputs the list to a file called readme.html.

Managing Files: CSV and TXT files too (Mac)

1. To output a text file listing: readme_MAC_text
2. In your terminal, from the wanted directory type bash readme_MAC_text > readme.txt
3. To output a csv file listing: readme_MAC_csv
4. Type bash readme_MAC_csv > readme.csv

Bonus: Advanced Command-Line File Transformations for Mac/Linux

Thank you! Questions?

Email us: vicky.steeves@nyu.edu & nicholas.wolf@nyu.edu

Learn more about RDM: guides.nyu.edu/data_management

Get this presentation: guides.nyu.edu/data_management/resources

Make an appointment: guides.nyu.edu/appointment