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Manage your research data efficiently with OpenBio’s comprehensive file system. Upload sequences, structures, datasets, and documents—then reference them directly in conversations with AI for analysis and insights.
File Storage Location Each project has its own dedicated file storage. Access files through the file browser in the sidebar.

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Uploading Files

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Method 1: Upload Button

1

Open File Browser

Click “Files” in the sidebar to expand the file browser
2

Navigate to Folder

Browse to the folder where you want to upload files
3

Click Upload

Click the upload button (cloud with up arrow icon)
4

Select Files

Choose one or multiple files from your computer
  • Hold Ctrl/Cmd to select multiple files
  • All selected files upload simultaneously
Large files may take a few moments to process.

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Method 2: Drag and Drop

1

Open File Browser

Click “Files” in the sidebar to expand the file browser
2

Navigate to Folder

Browse to the folder where you want to upload files
3

Drag and Drop

Drag files directly from your computer to the file browser area

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Organizing Your Files

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Creating Folder Structure

1

Create New Folder

In the file browser, click the ”+” button in the top right corner of the sidebar
2

Name Folder

Type a descriptive name (e.g., “sequences”, “structures”, “papers”)
3

Press Enter

The folder is created in the current location
Create a logical structure for your research: 
📁 Project Root
├── 📁 sequences
│   ├── 📁 raw
│   ├── 📁 processed
│   └── 📁 reference
├── 📁 structures
│   ├── 📁 experimental
│   ├── 📁 predicted
│   └── 📁 complexes
├── 📁 data
│   ├── 📁 measurements
│   └── 📁 analysis
├── 📁 papers
│   └── 📁 literature
├── 📁 results
└── 📁 scripts

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File Operations

Moving Files:
  1. Click on the three dots next to the file
  2. Select “Copy” or “Cut”
  3. Navigate to the new folder
  4. Click on the three dots next to the folder
  5. Select “Paste”
Renaming Files:
  1. Click on the three dots next to the file
  2. Select “Rename”
  3. Type the new name
  4. Press Enter to save
Renaming files breaks existing references in chats. Consider copying files instead if you need to preserve references.
Deleting Files:
  1. Click on the three dots next to the file
  2. Select “Delete”
  3. Confirm the deletion
OpenBio can create and manipulate files in your current project. You can use this ability to ask OpenBio to organize your files, create new files, or modify existing files.

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Using Files in Chat

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Referencing Files with @

Type @ in any chat message to reference your files:
  1. Type @ in the chat input
  2. File suggestions appear automatically
  3. Type to filter or use arrow keys to navigate
  4. Press Enter to select a file
  5. File appears as a blue chip in your message
Example usage: 
Analyze the sequences in @protein_sequences.fasta for conserved motifs

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Attaching files using @ button next to the model selector

  1. Click the @ button next to the model selector
  2. Select the file from the dropdown
  3. File appears as a blue chip in your message

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Multiple File References

Reference several files in a single message: 
Compare the binding sites in @protein1.pdb, @protein2.pdb, and @protein3.pdb
OpenBio analyzes all referenced files together, providing comparative insights.

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Ask questions about a PDF file

  1. Upload the PDF file to the current project
  2. Reference the PDF file in the chat by typing @ followed by the filename
  3. OpenBio will answer your question based on the content of the PDF file

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Downloading and Exporting

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Single File Downloads

  1. Click on the three dots next to the file
  2. Select “Download”
  3. File saves to your default downloads folder

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Multiple File Downloads

Support coming soon.

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File Management Best Practices

Name files descriptively: human_insulin_crystal_structure.pdb instead of file1.pdb. Include organism, experiment type, and date when relevant.
Include dates in filenames: experiment_2024-01-15_results.csv helps track versions and chronology.
Create separate folders for different file types: sequences, structures, data, papers. This makes finding files much easier.
Monthly review: delete unnecessary files, archive completed work, and organize loose files into proper folders.
Download critical files as local backups. Don’t rely solely on cloud storage for irreplaceable data.

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Troubleshooting

Solutions:
  • Check file size (max 100MB per file)
  • Verify file isn’t corrupted
  • Check internet connection stability
Solutions:
  • Check browser download settings
  • Disable popup blockers temporarily
  • Clear browser cache and retry
  • Contact support if file appears corrupted

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Next Steps

Chat

Learn to reference files in conversations

Predictions

Use files for predictions

Workflows

Create file-based workflows

Notebooks

Take notes from conversations and workflows
Pro Tip: Create your folder structure at the start of each project. A well-organized file system makes research much more efficient and collaborative. You can also ask OpenBio to set it up for you.