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RELEASE NOTES

INFORMATION ABOUT NEW FEATURES AND BUGFIXES IN FASTGENOMICS

5.3b
(12.02.2020)

Analyses

New: Example notebook for spatial transcriptiomics using scanpy

Bugfixes & Minor Improvements

Bugfix: Scrolling in dataset overview using arrow key works properly
Improved: Easier selection of users in share dialogs
Bugfix: Interactive analyses are opened directly after copy and edit
Bugfix: Dataset usage tab shows analyses
Improved: Faster list of available datasets for analysis
Improved: Overall stability improvements

5.2b
(06.02.2020)

People

New: People-section for groups
New: Preview to our new groups feature including survey

Analyses

New: More tutorial notebooks published

Bugfixes & Minor Improvements

Bugfix: FASTGenomics reader reads Loom correctly also in Rpy2-environment
Bugfix: Emails on finished analysis are correctly encoded
Bugfix: Copying and editing analyses works correctly when there are duplicate datasets
Bugfix: Underline, strikethrough and links work correctly in dataset descriptions
Bugfix: You can now copy cell and gene numbers from clipboard to the dataset description
Bugfix: Dataset state is updated on overview page when upload finishes

5.1b
(03.02.2020)

Analyses

New: Copy an analysis to use the same workflow on different data, or to edit an analysis without modifying the original
Improved: Default titles for are shown upon creating analyses

Datasets

New: Preview for data set cards and improved overall usability
Improved: Search in all dataset metadata

Bugfixes & Minor Improvements

Improved: Logging no longer slows down the platform in extreme cases

5.0b
(27.01.2020)

Analyses

New: Hide code in read only mode to focus on analysis results
New: Preview in interactive mode
Improved: Show analysis actions also in full width analysis mode
New: Start an analysis directly from the dataset
New: Decide on the language of your new analysis without needing to fix the workflow upon start
Improved: Updated empty analysis notebooks to start from scratch
Improved: Faster start of new analyses

Datasets

New: Dataset overview on cards for a better overview
New: Filter your own datasets
New: Dataset delete
New: Data formats are automatically set upon upload

Technical

New: Restructured backend for faster development of new features and a more bug-free experience
New: Update to latest backend technoloy with performance improvements, security bugfixes, and long term support
New: Compatibility with Chrome 80 more private and secure same site policy for cookies

Bugfixes & Minor Improvements

Improved: Better overall error messages, e.g. when uploads or analyses are cancelled or on authentification issues
Bugfix: Visibility symbols are always consistent
Bugfix: Accidentally starting multiple uploads is prevented
Bugfix: Table preview can be opened and closed multiple times
Bugfix: Dataset modification date does not change if analyses on the datasets are changed
Bugfix: No more authentication issues after leaving FASTGenomics open for long idle time
Bugfix: Updated notification settings are correctly saved
Bugfix: No more errors when multiple datasets / analyses are deleted directly after another
Bugfix: No more issues on publishing a previously shared analysis

4.12b
(13.01.2020)

Analyses

New: Public analysis example using the perturbation prediction check and the scGen batch-removal example from Theis lab.
New: Public analysis example using the scVelo example: Pancreatic endocrinogenesis and the ForebrainGlut notebook from Theis lab.

4.11b
(16.12.2019)

Analyses

New: You may now publish your analyses, thus making them visible for everyone! To do so, special permissions are required. If you are interested, write an email to contact@fastgenomics.org.
New: Symbols show whether datasets and analyses are private (only visible to you), shared with or by you, or public (visible to everyone).
New: A generalized best practices pre-processing workflow based on the work by Luecken & Theis 2019.

Bugfixes & Minor Improvements

Bugfix: While you wait for your analysis, you can now use correct links.
Improved: Interactively opening analyses can now be done from our new UI with blent-in editing buttons

4.10b
(05.12.2019)

Bugfixes & Minor Improvements

Bugfix: An issue causing the login mask to appear again after logging in has been solved.
Bugfix: Anonymous users cannot access account settings anymore.
Bugfix: Listing all datasets could lead to an error in special cases, this has been fixed.

4.9b
(02.12.2019)

General

New: Re-design of FASTGenomics’ user interface

Bugfixes & Minor Improvements

Bugfix: Analysis pre-computation is up and running again

Analyses

Improved: You can now leave the analysis page without saving, still upon return your changes will be kept

4.8b
(25.11.2019)

General

Improved: Better stability and robustness for FASTGenomics, short outages will be much less likely

Bugfixes & Minor Improvements

Bugfix: Account deletion no longer results in an error

4.7b
(15.11.2019)

Analyses

New: Clustergrammer2 is now available on FASTGenomics, both interactively and as widget in read only mode

Bugfixes & Minor Improvements

Bugfix: Starting an interactive analysis will now always open the corresponding notebook
Bugfix: Widgets are now correctly rendered in read only mode
Bugfix: Analysis overview now shows the analysis creation date
Bugfix: Analysis sessions no longer run indefinitely
Improvement: Platform emails now come in the new FASTGenomics design

4.6b
(06.11.2019)

Analyses

New: Public Scanpy tutorial for 3k PBMC dataset visible for every registered user

4.5b
(29.10.2019)

Analyses

New: Overview and managing interface for your running analysis sessions
New: 
More software packages added for new analyses: Monocle (Version 2.12.0), TSCAN (commit 66d30ca), SingleCellExperiment (1.6.0)
Updated: New analyses will benefit from new packages and updated versions: R (3.6.1), Seurat (3.1.0), SingleR (commit adc4a0e), Scanpy (1.4.4.post1), anndata (0.6.22.post1), loompy (3.0.6)

Bugfixes & Minor Improvements

Bugfix: External links to profile pages will no longer result in a redirect error
Bugfix: Specifying a format for your dataset shows the correct hint

4.4b
(24.10.2019)

Analyses

New: Analyses can now be deleted

Bugfixes & Minor Improvements

Improved: Datasets up to 2 GB in size can now be uploaded
Improved: Enhanced permissions for newly registered accounts
Migration: Users from prod.fastgenomics.org have been migrated to beta.fastgenomics.org

4.3b
(16.10.2019)

Analyses

New: A data format has to be given when uploading a file to FASTGenomics
Improved: Better functionality for reading datasets out of the box

Bugfixes & Minor Improvements

Improved: Technical monitoring

4.2b
(10.10.2019)

Collaboration

New: Sharing of analyses

Bugfixes & Minor Improvements

Bugfix: Account management page no longer triggers logout
Bugfix: Anonymous login working again
Bugfix: Corrected usage count of analyses
Bugfix: Links in dataset metadata can now contain more symbols

Analyses

New: Notebooks are terminated after 48 hours
New: Notebooks are terminated after a certain time if the kernel is idle

4.1b
(20.09.2019)

Analyses

New: Select between an empty R, empty Python, or pre-defined R workflow for new analyses
New: Option to “save and quit” an interactive analysis

Bugfixes & Minor Improvements

Bugfix: Upload of an empty file no longer results in a broken dataset
Bugfix: Outdated bearer token no longer lets the system freeze
New: Technical monitoring to prevent broken analyses

4.0b
(16.09.2019)

General

New: Re-designed user interface and workflow
Improved: Performance improvements for all features

Analyses

New: Interactive data analysis using Jupyter notebooks with R and Python
New: Pre-installed Seurat and ScanPy images
New: Several datasets can be analyzed in one analysis
New: Custom and multiple batch columns can be used

3.15b
(19.08.2019)

General

Improved: New home section with information about the platform

Technical

Preparations: Backend Re-Design for FASTGenomics 4.0b

3.14b
(31.07.2019)

Analyses

New: Generalized best practices preprocessing workflow after Luecken & Theis, 2019
New: Showcase analyses of the generalized best practices preprocessing workflow on seven datasets

Datasets

New: Public dataset Haber et al., 2017

3.13b
(13.06.2019)

Bugfixes & Minor Improvements

Bugfix: Fixed a bug that prevented sharing of more than 10 datasets via the API

3.12b
(29.05.2019)

General

New: Reduced UI for better user workflow
New: Simplified start of dataset analysis with default workflow

Bugfixes & Minor Improvements

Bugfix: Issues on uploading of cell metadata fixed

3.11b
(10.04.2019)

Technical

New: Migration to new technical infrastructure

Bugfixes & Minor Improvements

Bugfix: Migration to new email infrastructure ensures all emails are properly sent
Improved: Technical monitoring

3.10b
(14.03.2019)

Security

New: Personal access token (PAT) for programmatic authorization
New: Configurable email notifications for account usage

Account management

New: Profile management in the browser
New: API token management in the browser

3.9b
(08.02.2019)

Apps

New: Apps section for browsing and viewing apps in the browser
API: App grouping via /api/v1/groups and /api/v1/group/{id}: an app group contains all versions of an app
GUI: Visual aids to highlight the current section you are in

Analyses

API: when creating a new analysis, the parameters may be set by using “TaskName”: {params} instead of “TaskId”:{params}.

Workflows

API: Listing workflows now also accepts an parameter that restricts the result to the requested workflow ids.
API: Get workflow now returns the parameters for this workflow if fullDetails=true

Bugfixes & Minor Improvements

Bugfix: Usage statistics are correctly counted in the App API
New: Apps from Docker Hub are now supported
Bugfix: Calculation logs larger than 10MB will be truncated to prevent errors in analyses
Bugfix: Dataset upload can no longer fail when preserving the original files
Improved: API performance improvements

3.8b
(23.01.2019)

Workflows

New: Exploratory workflow uses umap and Leiden algorithm

Visualizations

New: Configurable filter elements for all visualizations
New: Clustergrammer app
New: Summary shows names instead of IDs

Datasets

API upload: .gz file support

Bugfixes & Minor Improvements

Bugfix: Downloading a multi-gigabyte dataset as zip no longer results in an error.