Fastgenomics

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FEATURE ROADMAP

Learn about features in progress and request what you need

6.4b
19.05.2020

Analyses

New: Enter metadata for each analysis, e.g., description or citation
New: Modify an analysis’ title anytime
New: View and revoke shares of an analysis
Improved: Redesigned analysis detail page
New: New tutorial notebook about FASTGenomics’ directory structure
New: Download plots and other results of an analysis
New: Control which analysis results can be downloaded by other users
New: Re-run an analysis in batch mode

Datasets

New: Use drag & drop to add files to a dataset

Bugfixes & Minor Improvements

New: If you use a direct link to a certain dataset, analysis, or group, you are correctly redirected after logging in
Improved: Better overall stability for analysis sessions
Bugfix: Batch sessions are terminated correctly even if there are errors in the analysis code
Bugfix: If all shares are revoked, the dataset/analysis cards no longer say “shared with 0 users”
Bugfix: Widgets can be used in batch mode as well
Bugfix: Group names are shown on dataset and analysis detail pages

6.3b
11.05.2020

Analyses

Improved: Use better machines and analyze up to four times faster!
Update:
Jupyter lab version 2.1.2 including stability updates
New: Use Dill 0.3.1.1. in new Python / Python+R analyses
Update: Updated packages for Python analyses: Scanpy 1.4.6, Anndata 0.7.1, Plotly 4.6.0, Pandas 1.0.3, Clustergrammer 2 0.5.21 (also available in Python+R)
Update: Updated packages for R analyses: Seurat 3.1.5

Bugfixes & Minor Improvements

Bugfix: Plotly widgets are now displayed correctly

6.2b
28.04.2020

Analyses

New: More software packages added for new R analyses: AUCell, GENIE3, GSVA, RcisTarget, SCENIC (aertslab), SCopeLoomR (rbokehaertslab), UpSetR, circlize, factoextra, ggExtra, mixtools, nichenetr (saeyslab), openxlsx, pals, tidyverse, tm, useful, wordcloud, zoo

6.1b
23.04.2020

Analyses

New: Revoke the publication of an analysis, thus making it visible only to you or users in your group
New: Copy & edit copies all files from an analysis, not only the analysis notebook

Datasets

New: Download files of a dataset
New: Upload several expression and metadata files directly upon creating a new dataset

Bugfixes & Minor Improvements

Improved: Better search options in user documentation
Bugfix: Datasets without files are correctly shown as empty
Bugfix: Analyses are correctly started after copy & edit

6.0b
09.04.2020

Analyses

New: Download the result of an analysis as an HTML report
New: Analyses show warnings if their attached dataset files have been altered since the last computation run
New: FASTGenomics reader modules can handle datasets with several files
New: Revoke publication of an analysis
Improved: Faster start of analyses
Improved: Analysis cards show number of shares

Datasets

New: Add metadata files to your datasets
New: Add more expression files to your datasets or remove old ones
New: Better overview of shares and option to revoke selected or all shares
New: Color code on dataset cards indicate the state of a dataset

Bugfixes & Minor Improvements

Bugfix: Tags are searchable again also for public and group datasets
Bugfix: Anonymous user sees all public datasets
Bugfix: Prevent frequent “failed to get session state” errors
Bugfix: Show analyses shared with you on the dataset usage tab
Bugfix: “Copy & Edit” on a foreign analysis opens interactive mode while “Copy” on an own analysis just copies it
Improved: Reach our documentation anytime from the (i) menu at the top
Improved: Overall stability improvements

5.5b
25.03.2020

Analyses

New: Add or remove datasets attached to your analysis
New:
 Use Plotly in your R analyses
Improved: Updated packages SingleR 1.00, Clustergrammer2 0.5.17
Improved: Try our redesigned reader functions (also see our updated tutorials in R and Python)
Improved: show steps and time left upon analysis start

General

New: Color codes on cards indicate whether a dataset or analysis belongs to you and can be edited by you
New: Display author and date of last modification for datasets and analyses

People

New: Move datasets or analyses to groups to make them visible to all group members
New: See all datasets and analyses in a group together on a content tab
New: Remove users from group to make all group contents invisible to them
New: Group administrators can edit all datasets and analyses in their groups

Bugfixes & Minor Improvements

Bugfix: You cannot leave the user selection in the share dialog if you searched for a user who is not visible
Bugfix: All tooltips are correctly positioned
Bugfix: If you delete a dataset from an analysis, it is always the correct one
Improved: Better overall stability

5.4b
09.03.2020

General

New: Find a complete documentation of FASTGenomics’ features at https://beta.fastgenomics.org/docs/

Bugfixes & Minor Improvements

Improved: You may now upload datasets up to 10 GB in size
Bugfix: Values in dataset fields “organism” and “technology” are always saved correctly
Bugfix: You can use FASTGenomics also in Internet Explorer

5.4b
02.03.2020

Analyses

New: Metadata are always up-to-date in your analysis, even if you modify them while an analysis is running
New: Analyses overview on cards for a better overview
New: Analyses can be started without any datasets, enabling analyses on external data only

People

New: Create groups for easier collaboration
New: Add members to your groups
New: Group detail page with description and member overview
Coming Soon: Group members can see all group contents
Coming Soon: Move datasets/analyses to groups

Bugfixes & Minor Improvements

Bugfix: Whitespaces are not trimmed while you enter dataset or analysis titles
Bugfix: Clicking “edit” multiple times in a row on an analysis does not result in errors
Bugfix: Dataset tags can be entered without errors
Bugfix: Dataset modification date is always up-to-date
Bugfix: Copying & editing analyses always copies the notebook file
Improved: Better performance on dataset overview page

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

Analyses

New: More tutorial notebooks published

People

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

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

Analyses

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

General

New: Re-design of FASTGenomics’ user interface

Bugfixes & Minor Improvements

Bugfix: Analysis pre-computation is up and running again

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

Analyses

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

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

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

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

General

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

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

Account Management

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

Security

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

3.9b
08.02.2019

Datasets

New: API upload supports .gz files

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

Bugfixes & Minor Improvements

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

3.8b
23.01.2019

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

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

Analyses

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

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

Pin your favorite datasets and analyses

Mark your favorite datasets and analyses for pinning at the top of the overview pages.

Upload datasets via script

Use a programmatic API to upload datasets to FASTGenomics automatically, e.g., as a part of your sequencer postprocessing pipeline.

Reload intermediate results on analysis start

Currently, if you do not save the results of your computation to a file, you have to re-compute all intermediate results if you restart the analysis. We are working on a way to reload all of your objects back into memory when you open a saved analysis.

New and updated analysis packages

In August, we will release our next FASTGenomics images, containing new and updated analysis packages for R and Python. If there is anything you are missing, let us know and we will include it into the next update.

Use updated software in existing analyses

If there are new software packages available in FASTGenomics, you can choose to update your analysis. If you want to keep reproducibility at all cost, you can also make a copy with the updated packages and check the results first.

Use your own software environment

Instead of installing your own analysis packages over and over again, you will be able to define templates with all your favorite analysis packages. Once built, these templates can then be reused in all of your analyses.

Visual analytics

Did you ever want to browse a dataset visually without the need to write a single line of code? We are working on the integration of visual analytics into FASTGenomics, so you can concentrate on data exploration, not coding.
(Of course, you can always decide to dig deeper using your own coding skills.)

Analyze collaboratively

Currently, you can share your analyses with selected users on FASTGenomics or with a group. However, share recipients can only view your results (or make a copy and work on that for themselves). In the future, you will be able to control whether a share recipient can see, edit, or even administer your analysis.

Easier anonymous access

FASTGenomics offers many functions for registered users. However, you can also view public datasets and analyses without logging in. This access will be redesigned to be more user-friendly.

Request a feature

Is there anything you are missing in FASTGenomics? Please let me know! As a product owner, I am responsible for designing the product that you need.

  • This field is for validation purposes and should be left unchanged.

Jenny

Product Owner

Analyses are too slow / not enough RAM

We are aware that analyses on FASTGenomics can be slow – even slower than on your normal notebook! While we understand this is a major drawback, it is not really a bug. FASTGenomics beta is free, which means that all users share the same limited cloud resources. You can however get in touch with us to learn about paid plans with faster cloud resources or even our on-premise option.

Displaying analysis results takes long

If your analysis contains many plots or other large objects, it can take long to display the results. We are working on better performance.

Missing notification about computed analysis

If your analysis belongs to a group and you queue it for computation in the background, it can happen that your notification email gets lost.

Analysis session unexpectedly shuts down

There are cases where your analysis session shuts down in the middle of your work. We realize this is very frustrating and are working on a solution.

You can help us to make sure we fix all the issues by sending us an error report: please include the title or ID of your analysis (you can copy it from the URL) and the time the error occurred. Use email or our Slack channel to get in touch!

Error deleting a running analysis

If you delete an analysis that is currently running, you will see an error message.

Issue with interactive widgets

In some cases, there will be problems saving or displaying interactive widgets. We are working on a solution together with the community.

You can help us to make sure we fix all the bugs by sending an error report: please include the title or ID of your analysis (you can copy it from the URL) and the time the error occurred. Use email or our Slack channel to get in touch!

Report a Bug

Did you find a bug that is not listed here? Please let me know! As a product owner, I am responsible for keeping your experience bug-free.

  • This field is for validation purposes and should be left unchanged.

Jenny

Product Owner