Get Started with HISE
 | Abbreviations Key |
| AIFI | Allen Institute for Immunology |
| CertPro | Certificate of Reproducibility |
| CLI | command line interface |
| HISE | Human Immune System Explorer |
| IDE | integrated development environment |
| SDK | software development kit |
| UI | user interface |
At a Glance
The Human Immune System Explorer (HISE), an open science initiative from the Allen Institute for Immunology (AIFI), is a research hub where scientists and analysts can store, analyze and share data generated by scientists at AIFI and its partner organizations. We welcome your requests and suggestions. For questions about this guide or HISE, contact us at immunology-support@alleninstitute.org.
Overview
Navigate to HISE and sign in. To learn about billing, accounts, and notifications, view your projects, or use your folders, open your personal space by clicking your name in the upper-right corner of the screen.
Ingest Data
Each project has a Project Store in which users can save analyses and upload data that's not associated with automated pipelines. To send data to your Project Store, a designated watchfolder must be set up by a HISE administrator.
Understand Watchfolders and the Project Store
Use Watchfolders to Ingest Data (Tutorial)
Ingest Data into the Project Store (Tutorial)
Perform Advanced Searches
The advanced search functionality is the gateway to finding and accessing all your research data, including data files and human metadata.
Work with IDEs
When you create and manage Jupyter notebooks in HISE, you can store intermediate files, schedule notebook jobs, manage IDE state, and save results or visualizations.
Create Your First IDE Instance (Tutorial)
Manage Packages in HISE IDEs (Tutorial)
Use the HISE SDK to Create Visualizations (Tutorial)
Generate Visualizations
Any HISE user can contribute data visualizations to a study and share them with other researchers. You can save these visualizations using either the advanced search function or an IDE instance.
Explore No-Code Visualizations
Create Certificates of Reproducibility (CertPros)
A certificate of reproducibility (CertPro) is a detailed record of your scientific research generated in real time to foster reliable reproducibility of study results. This step-by-step trace includes your data, scientific algorithms, computational environment, tools stack, and results.
Understand Certificates of Reproducibility
Manage Certificates of Reproducibility (Tutorial)
Explore the Collaboration Space
The HISE Collaboration Space has access controls that let you work with other scientists to manage file sets, clone Jupyter notebooks, prepare and publish studies or reports and supporting visualizations, coordinate work on publications, and read or contribute to selected other documents and presentations.
Navigate the Collaboration Space
Create Data Apps
Present related reports, data files, notebooks, and visualizations together in a complete package known as a Data App.
Get Started with Data Apps (Tutorial)
Manage the Data Apps UI (Tutorial)
Use Data Apps Plugins and Other UI Components (Tutorial)
Related Resources