Getting Started

Quickstart FaceBase Data Philosophy

Using FaceBase

Key Concepts for FaceBase Users Browsing and Filtering Data Visualizations in FaceBase Data Sharing and Citing Data Exporting Data from FaceBase Accessing Data Programmatically Using 3D Viewers Viewing NIfTI files Converting TIFF to OME-TIFF (using Bio Formats)

Controlled Access Human Data

Controlled Access Human Data - Policy and Requests A. Read and complete the Data Use Certificate Agreement (DUC) B. Complete the online Data Access Request (DAR) form (An IRB is required) C. Select the Requested Datasets D. Print, Gather Signatures and Submit the DUC and DAR forms E. Receive notification and further instructions F. Create and upload your encryption keys G. Renew access

Submitting Data - Basics

Video Tutorials for Contributors Key Concepts for Data Contributors Data Submission Process Creating a Dataset Creating Experiments, Biosamples, and Replicates Uploading Data Files Quality Control Rules Releasing Your Dataset Self-guided Tutorial

Submitting Data - Advanced

Using the Annotations Editor (2D images) Defining Surface Models (3D models) Linking Thumbnails to Files

Tools

DERIVA Tools - Bulk upload and export

Support

Getting Help FAQs

Accessing Data Programmatically

For more sophisticated users, who may need to perform complex data retrieval or searches for using FaceBase open-access data for analysis, pipelines, etc, there is a Python interface available called deriva-py.

However, you will need to understand about how the data is modeled in the underlying DERIVA system. Please reach out to the FaceBase Hub at help@facebase.org, let us know what you need and we can provide guidance to get you started.

You can find more general information about the Python interface at the following links:

Note that there is also an R wrapper available for this code.