Plugin releases

29

Diff Studio 1.0.10 (2024-06-10): docs

This version provides

  • two additional methods for numerical solving ODEs
  • solver management
  • max computation time control feature
1 Like
30

EDA 1.1.27 (2024-07-02)

This release complements Datagrok predictive modeling tools. High performance linear regression computation is added.

1 Like
31

SimPKPD 1.0.12 (2024-07-30)

This and the previous releases improve usability and fix issues.

Dive into pharmacokinetic-pharmacodynamic (PK-PD) modeling with Datagrok!

Check the main app: App > Model Catalog > PK-PD,
and demo: App > Demo > Compute > PK-PD modeling

1 Like
32

Bioreactor 1.1.9 (2024-07-30)

Fixed demo app issues.

Check the main app: App > Model Catalog > Bioreactor ,
and demo: App > Demo > Compute > Bioreactor

1 Like
33

EDA 1.1.30 (2024-07-30)

This release complements Datagrok predictive modeling tools with partial least squares (PLS) regression.

To apply PLS regression:

  • Open dataframe
  • Go to Top Menu > ML > Models > Train Model…
  • Specify Predict and Features
  • Select Eda: PLS Regression in the Model Engine field
  • Set Components

pls

Check interactive machine learning!

1 Like
34

EDA package 1.1.30

This release also includes Datagrok dimensionality reduction toolkit, which supports combination of multiple columns of different types (molecules, Sequences, numbers…) with corresponding distance functions and light-speed performance with use of WebGPU.
You can read more about the dimensionality reduction capabilities of Datagrok here.

To run dimensionality reduction:

  • Open dataframe
  • Go to Top Menu > ML > Dimensionality Reduction…
  • Specify Columns
  • For each column, specify distance function and weight
  • Choose desired method (UMAP or t-SNE) along with their hyper-parameters
  • Choose desired post-processing (clustering of embeddings)

umap-5-cols

1 Like
35

Hit Triage 1.2.0 (2024-07-30)

This release includes permission management capabilities for Hit Design / Hit Triage campaigns and other improvements, like direct support of compute queries/scripts, duplicate molecule detection and improved campaign/template management.

You can read more about capabilities of Hit Triage / Hit Design applications here.

1 Like
36

Peptides 1.17.24 (2024-07-29)

This release includes several new features to the viewers included shipped from Peptides package:

  • Logo Summary Table: Ability to aggregate string columns and display them as pie chart distribution
  • Invariant Map / Mutation Cliffs: Ability to select value aggregation from any column, setting color column, aggregation, scale and schema, ability to specify target column and category.
  • Most Potent Residues: Corrected way of detecting statistically most potent residue, with ability to specify activity target (high or low)

peptides-weblogo-piechart
invariant-map-colors
invariant-map-target

1 Like
37

Chem 1.9.0 (2024-03-21): docs, release notes

Features

  • #2495: Chem: MMP - initial vesrion
  • #2540: Chem | Substructure search: Add an option to toggle the realignment of molecules by molecular filter
  • #2525: Chem | Scaffold Tree: Remove the intermediate dialog before the color picker
  • #2504: Filter panel: The question mark hovering doesn’t show the filtering of the scaffold tree viewer

Bug Fixes

  • GROK-15147: Chem | Scaffold Tree: Highlighting disappears in some cases
  • GROK-15240: Chem | RGroups: Handling malformed data
  • GROK-15213: Chem | RGroups: Undo latest analysis doesn’t work when run on multiple dataframes
  • GROK-15187: Chem | RGroups: Fixed memory consumption
  • GROK-15171: Chem: Substructure filter doesn’t apply correctly after removing rows and disable
1 Like
38

Chem 1.9.1 (2024-04-12): docs, release notes

Features

  • R Group analysis: in browser R group analysis using RDKit JS, highlight of r groups, ability to define enumerated R groups in core
  • Similarity/Diversity search: ability to recalculate results on filtering
1 Like
39

Chem 1.9.2 (2024-04-12): docs, release notes

Features

  • R Group analysis improvements: ability to select ‘Only match at R groups’, saving R group user settings, small UI improvements
1 Like
40

Chem 1.10.0 (2024-06-12): docs, release notes

Features

  • Webgpu acceleration for chem space, activity cliffs, molecule generations
  • GROK-15299: Chem: Ability to save results of Chem functions to projects with and without data sync
  • GROK-15454: Chem: Similarity/Diversity search viewers: Row source property
  • GROK-15508: Chem: MMP: Generated - show what cases are actually generated
  • GROK-15501: Chem: MMPA: UI/UX improvements
  • GROK-15502: Chem: MMPA: Ability to swith activity on/off
  • GROK-15507: Chem: MMP: Control of fragments size
  • Chem: Integrate with Chemprop
  • Chem: Chemprop upgrade from version “1.6.7” to version “2.0” (reduced memory usage, improved performance)

Bug Fixes

  • GROK-15285: Chem: MMP: Error on re-run
  • GROK-15321: Chem: MMP: Error while running Close All after running MMP
1 Like
41

Chem 1.11.0 (2024-07-24): docs, release notes

Dependency: datagarok-api >= 1.20.0

Bug Fixes

  • GROK-16328: Chem: R-Group analysis: Broken styles
  • GROK-16329: Chem: R-Group analysis: Error when none R groups were found
  • GROK-16338: Chem: Chemical space: Reseting marker type to circles
  • Chem: Scaffold Tree: Fix representation when the viewers are stacked
  • Chem: Chemprop: Fix applying the model to different datasets
  • Chem: Fix substructure filter style
  • Chem: Do not render molecules with invisible width
2 Likes
42

Charts 1.3.3 (2024-08-08): docs, release notes

Bug Fixes

  • #2954: Sunburst: Unsupported columns are not filtered out in column selector
1 Like
43

Hi,
Is it possible to chemprop from datagrok for compound properties prediction?
If yes, are there any specific settings to use chemprop from datagrok?
Thanks,

Taka

44

Chem 1.11.2 (2024-08-12): docs, release notes

Features

  • Chem: Chemprop: Remove redundant calls in the core and move it fully to package
  • Chem: MMPA: Add meaningfull dataset for demo
  • Chem: MMPA: Restrictions and CPU fallback
  • Chem: MMPA: Compensate filtering by cutoff
  • Chem: MMPA: Add reflection for selection
  • Chem: MMPA: Add pairs filter, expose filters object so it can be used in any tab, minor improvements
  • Chem: Update demos in order to be shown in the Browse

Bug Fixes

  • Chem: MMPA: Fixes for cliffs tab and lines improvements
  • #2964: Scaffold Tree: ‘Selection to filter’ reset immediately for some data if scaffold tree is present
1 Like
45

Hi Taka,

Yes, Chemprop is fully available from the Chem package. To use it for compound properties prediction, follow these steps:

  1. Open the molecular dataset of your interest.
  2. Navigate to ML > Models > Train Model…
  3. Select table, column with the values you want to predict, and the feature column (in this case, it will be the column containing smiles or molblocks).
  4. You will then be presented with a list of suitable engines. Among them, you will find the Chemprop model engine.
  5. Simply choose Chemprop, configure the model settings, and run the training.

Once your model is trained, you can apply it by going to ML > Models > Apply Model….

If you have any questions, don’t hesitate to contact me :slightly_smiling_face:

Best regards,
Oleksandra

1 Like
46

EDA 1.1.34 (2024-08-19)

This release improves Datagrok predictive modeling tools:

  • Updated Multivariate Analysis
  • Improved efficiency of the PLS regression
  • Fixed the memory issue in the linear regression

Also, XGBoost is available:

  • Open dataframe
  • Go to Top Menu > ML > Models > Train Model…
  • Set Predict and Features
  • Select Eda: XGBoost in the Model Engine field
  • Tune settings to get better efficiency
  • Click on the Save button to save the trained model
  • Apply the trained model via Top Menu > ML > Models > Apply Model…

Check interactivity of Datagrok predictive tools
xgboost

1 Like
47

Charts 1.3.4 (2024-08-23): docs, release notes

Bug Fixes

  • #2994: Charts | Sunburst: Double click on the viewer resets the view
  • #2992: Charts: Sunburst does not select/filter on empty category
  • Charts: Sunburst: Update emphasis in order not to fade out other data
  • Charts: Sunburst: Use only categorical columns for building the hierarchy
  • #2979: Charts: Sunburst is showing default columns instead of selected ones after applying layaout in some cases
  • Charts: Demo: Fix globe viewer doesn’t show points
1 Like
48

Chem 1.11.4 (2024-08-23): docs, release notes

Features

  • Chem: MMPA: Filter fragments by significance
  • Chem: MMPA: Project and layout saving
  • Chem: MMPA: Demo loaded not calculated
  • Chem: Removed r-groups settings download from init

Bug Fixes

  • Chem: MMPA: Fixed property panel on cliff line click
  • #2983: Chem: Fix tooltip styles for structure columns
  • GROK-16493: MMPA: Fixed Summary viewer doesn’t show the values
1 Like