Last modified 2025-10-30

Release Notes

Recent Changes

Date	Change
2025-10-30	Collaboration Space UX/UI Improvements Updated Collaboration Space UX/UI for improved usability and workspace navigation Added expandable/collapsible sidebar to study workspace Simplified permissions and collaborator management section Created enhanced tagging interface with expanded view and edit capabilities Enabled editing of study details (name, description, hero image, collaborators, tags, associated projects) from Study Details tab Introduced study deletion functionality for study owners Improved document, asset, and permission management workflows Refined dialogs for creating, editing, and sharing studies/assets
2025-09-24	IDE Stacking Stacking mechanism groups related IDEs to improve visibility, findability, and provenance tracking. Stack actions are available to all collaborators, including editing stack membership, updating trace information, and managing permissions. IDE stacks can be autogenerated by using a common IDE name plus a version number (`v`) or date (`YYYY-MM-DD`). Alternatively, a user can create a stack manually. Edits are supported for IDE trace, stack membership changes, and designation of the top-of-stack IDE. Stacks can be cloned, resulting in a duplicate set of IDEs for independent use or analysis. Removal, dissolution, and permanent deletion are supported for individual IDEs or entire stacks. Traceability Traceability tab shows standalone assets attached to studies. This tab displays a graph of all data inputs and outputs for the asset. Users can click nodes in the traceability graph to view additional connected data assets or navigate to the detail page to view a selected node. Users can "walk the graph" to display and explore immediate neighbors (inputs and outputs) one step at a time, instead of rendering the entire CertPro graph at once. Backend and frontend now support partial graph fetching and incremental expansion as users interact with the traceability graph.
2025-09-17	Elimination of Lag Between File Upload and File Availability in Advanced Search After calling `uploadFiles()` or dropping files into a watchfolder, most files are now available in a few seconds, and even large data transfers take just a few minutes to become available in the Advanced Search UI.
2025-09-11	`update_sdk_version()` SDK Method Updates your Conda environment to the latest SDK version. `start_training_run()` SDK Method Launches customizable AI/ML training jobs with advanced resource options, including configuration of CPUs, GPUs, and memory. Enables distributed execution, script validation, and detailed error handling. Supports the recommended workflow of testing locally, approving or rejecting the run using the `review_training_job_run()` SDK, and monitoring the job in the AI/ML Hub. `review_training_job_run()` SDK Method Allows programmatic review and approval or rejection of AI/ML training jobs. Returns the complete job context—including audit logs, properties, metadata, output files, and file provenance. Facilitates efficient quality control and troubleshooting by providing all relevant job details in an accessible tabbed view. Quota Override Lets HISE admin users increase resource limits beyond the existing billing quota. To request an adjustment, contact Support .
2025-08-19	Billing On Personal IDE Billing tab, added bar chart comparing user's quota spend to that of the team. Throughout Billing section, standardized positioning and spacing of graphs and axes, and improved the consistency of formatting and labeling, including naming conventions, case, percentages, and dollar amounts. hisepy New method: `save_custom_conda_environment(env_name : string, description : string, language : list[str])` New method: `update_sdk_version()` NOTE: This installs only the latest hisepy SDK version–to install a different version, contact Support . Bugfix: survey results attached to output from `get_file_descriptors()` R New method: `saveCustomCondaEnvironment(envName : string, description : string, language : list)` New method: `updateSDKVersion()` NOTE: This installs only the latest R SDK version–to install a different version, contact Support .
2025-06-24	Released updated documentation: Use the Upload Files SDK Method (Tutorial) and Use the Read Samples SDK Method (Tutorial)
2025-05-19	Released updated documentation: Attach an IDE to a Study (Tutorial)
2025-05-14	Released updated documentation: Attach Metadata to Make Files Searchable (Tutorial)
2025-05-14	Released pipeline for Cell Ranger version 9.0.1 for flex RNA runs in HISE. To read the full details, review our documentation and the official 10x Genomics release notes . The previous version of Cell Ranger remains available. To continue using the previous version, keep your submission sheet as is. To update to the new version, specify `frna-v3` in the Type column of the Header tab on your Submission Sheet.
2025-04-29	Revised version of document published: Create, Edit, or Delete Metadata.
2025-04-21	Launched the Xenium pipeline, which enables spatial transcriptomics analysis within HISE, converting raw Xenium data into formats that can be analyzed, explored, and visualized. For details, see Use the Xenium Pipeline (Tutorial).
2025-03-14	Extended the IDE timeout period from 30 min to 12 hr.

Features

In the current release we added the following features:

Data Processing Space

We support adding cohort, subject, sample, demographics and other metadata for external data, such as reference data sets
As is already the case for assay data processed by automated pipelines, we now support defining and declaring assay data not processed by automated pipelines such that the data can be easily found via advanced search, the data availability dashboard and the sample status dashboard

Research Space

Enhancing the functionality of what was previously known as project folders, all HISE projects now have a project store, and all analysts have access to the files in the store.
New files destined for a project store can now be ingested along a submission sheet, declaring its associated metadata such as sample reference. Metadata declaration can also be done for already ingested files via the project store page (in your personal space). Metadata declaration ensures your data can be more easily found in advanced search by collaborators
Jupyter Notebooks now have interactive UI to facilitate storing derived data in a HISE project store or permanent store, and reference that data and Jupyter Notebook in a Study. Declaring derived data in this manner enable study collaborators to more easily find your analysis approach and results

SDK

The uploadFiles method has been extended to store data either in a permanent or project store. Data sets now need to be given a data type such that derived data can be more easily found in search.
All methods related to project folder have been deprecated and might be removed in a future release. To access project store data, use readFiles/cacheFiles instead (this requires that files have a sample reference).
Isolated files in a project store can still be deleted. Files in a project store can also be moved to the permanent store to prevent accidental deletion.
Methods to change the state of your virtual machine are now available.
- R
  - stopIDE()
- Python
  - stop_ide()

Collaboration Space

For publications, authors can now add their Orcid ID, affiliation and sources of funding.

Related Resources

FAQs and Troubleshooting Guide

Use HISE SDK Methods