Program
BIOVIA Pipeline Pilot
Operating System
All supported operating systems
Description
We are providing this Technical Note to inform you about the release of BIOVIA Pipeline Pilot 2023 which includes the following enhancements and fixed defects:
Enhancements
This release of BIOVIA Pipeline Pilot includes the following enhancements.
Administration
Description | Areas Affected | Risk Level | Jira Issue ID |
There are now two options for the file upload restrictions in Administration portal Security > Security Configuration:
| Administration | Low | PPP-48317 |
The Credit Usage Report now uses a horizontal red line to represent the purchased credit number. | Administration | Low | PPP-47406 |
The Pro User Collections and BIOVIA Applications sections in the Server Usage Report now exclude the Mobile collection. | Administration | Low | PPP-47207 |
Server Infrastructure
Description | Areas Affected | Risk Level | Jira Issue ID |
Updated the Apache httpd server to version 2.4.54. | Server infrastructure | Medium | PPC-10743 |
The embedded Tomcat server has been updated to the latest security-fix version. | Server infrastructure | Low | PPC-10678 |
Updated OpenSSL to the latest 1.1.1 version. | Server infrastructure | Low | PPC-10765 |
The Java logging library reload4j is updated to the latest version 1.2.22 | Server infrastructure | Low | PPP-48694 |
The version of Python used in the Python (on Server) component and the built-in Python environment has been updated to Python 3.9.9. Please see https://docs.python.org/3.9/ for more information on changes to Python. Versions of the packages in Python Essentials libraries have also been upgraded. | Server infrastructure | Low | PPC-10448 |
Pipeline Pilot 2023 no longer includes an installer for MongoDB version 3.2. | Server infrastructure | Low | PPP-48613 |
Two example protocols demonstrating the new remote execution features were added under Protocols/Examples/Integration/Remote Execution, called "Top-level Remote Execution Example" and "Subprotocol Remote Execution Example". The "Remote Execution" parameter group can be copied from these protocols and applied to other protocols to run them using remote execution. | Server infrastructure | Low | PPP-46479 |
You can now add the "Remote Execution" parameter group to a protocol and cause it to run on a remote HPC cluster. The protocol does not need to be pre-installed on the remote HPC cluster. | Server infrastructure | Low | PPP-48534 |
Professional Client
Description | Areas Affected | Risk Level | Jira Issue ID |
Added Ctrl-K and Ctrl-Shift-K in the Pilotscript editor as shortcut keys for Block Comment and Block Uncomment respectively. | Pro Client | Low | PPP-47552 |
The layout of the scripting Replace dialog box has been modified to clarify the use of the option to make replacements only within selected text. It is now visually associated only with the Replace all button. | Pro Client | Low | PPP-47553 |
Updated the Pilotscript DebugBreak dialog to be resizable and scrollable. | Pro Client | Low | PPP-47643 |
Improved the behavior of Pro Client initialization when the remote servers are not operational or not compatible. In the past, the user would have one opportunity to change to a valid server, but if the secondary server was also not valid, the client would immediately exit. Now, the client only exits when the user cancels the change server dialog. | Pro Client | Low | PPP-48882 |
The toolbar icons on the Results panel of the Edit Protocol dialog now disable whenever their particular action (delete, move up, move down) is not available. | Pro Client | Low | PPP-47711 |
The Pipeline Pilot Professional Client is supported on Windows 11. | Pro Client | Medium | PPP-47651 |
Chromium Embedded Framework (CEF) has been updated to the latest available version. | Pro Client | Medium | PPP-48716 |
The Professional Client has been updated to support high resolution monitors. Fonts, dialogs, tool tips, window scaling, etc. are now dependent on the scaling of each monitor. Most dialogs and windows will scale based on their current monitor and will update when moved between monitors. | Pro Client | High | PPP-44129 |
Reporting
Description | Areas Affected | Risk Level | Jira Issue ID |
A new Stylesheet "Pipeline Pilot 2023" has been introduced which uses the HighCharts JavaScript library to render charts in reports. This provides a more modern look and provides consistency with the Dashboard collection output. Existing reporting protocols will not be affected since they are configured with an older stylesheet. While a new protocol uses the 2023 stylesheet by default, you can revert to an earlier stylesheet for any preferred options or behavior. You can find the StyleSheet setting in the Implementation tab of the protocol. | Reporting | Low | PPP-48201 |
Generic Components
Description | Areas Affected | Risk Level | Jira Issue ID |
PilotScript:Improved sorting features for PilotScript. Sort() and SortN() now support the following options: reverse sort, ignore case, sort as text with numbers, and sort as a specific type (text, numbers, date). Note that the NumberSort() function is deprecated, now that its functionality is covered by the enhanced Sort() function. | Generic Collections | Low | PPP-47548 |
The new prototype 'Prepare Data' component, offers a user-focused, interactive way to prepare and clean your data in the Pipeline Pilot Professional Client. Upon leaving the interactive mode, the cleaning and preparation steps are captured in the component, which can then be used in a protocol as a configured standalone component. Users are encouraged to provide feedback and examples to help steer the future development of this component. | Generic Collections | Low | PPP-48505 |
Web Pages
Description | Areas Affected | Risk Level | Jira Issue ID |
Links to BIOVA training information have been added to the Pipeline Pilot server home page and to the Welcome page in the Professional Client. | Web Pages | Low | PPP-48564 |
Some updates have been made to some Pipeline Pilot server web pages and web applications to adopt more standard Dassault Systèmes coloring, icons and fonts. | Web Pages | Medium | PPP-41871 |
Biology Collections
Description | Areas Affected | Risk Level | Jira Issue ID |
Updated biology collections to work with Pipeline Pilot infrastructure changes. | PBIO: Infrastructure | Low | PBIO-6673 |
Updated the list of third-party tools shipped with the Sequence Analysis Collection. | PBIO: Example Protocols | Low | PBIO-6684 |
Chemistry Collection
Description | Areas Affected | Risk Level | Jira Issue ID |
Allene-like stereo and atropisomeric stereo are now supported in ppchemapi's and PPChem SDK's SMILES reader and writer. The stereo is marked with @ or @@ on the central carbon of allene-like molecules and on the first atom in canonical order of the single bond of hindered rotation of atropisomers. The chirality center is marked with @ for P helicity and @@ for M helicity. "Parse Axial Stereo" parameter has been added to "SMILES Reader" and "Molecule from SMILES" components to specify whether to parse axial stereo in SMILES or not. "Include Axial Stereo" parameter has been added to "SMILES Writer" and "Molecule to SMILES" components to specify whether to output axial stereo or not. | PCHE: Chemical Perception | Low | PCHE-3515 |
Added PAINS Filter component to the Chemistry Collection. The new filter checks the input molecules for the presence of substructures included in the list of undesirable fragments in the publication "New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays". Jonathan B. Baell and Georgina A. Holloway. J. Med. Chem. 2010, 53, 7, 2719-2740. Added "Num_PAINS" as a calculable property in Pipeline Pilot. Added two methods in Chemistry SDK (Java, .NET and Python) MolPropCalc class to set the location of the PAINS query .sd file and calculate the number of PAINS query mapped in a molecule. | PCHE: Query Mapping | Low | PCHE-5696 |
Expanded the tautomeric atom donor perception criteria: 1. O S Se and Te atom can be a donor when their next attach atom is a SP2 tautomeric atom. 2. C atom can be a donor when it is attached to an aromatic C atom. This perception is included in the "Apply Perception Enhancements 2022" parameter of the Tautomer generation and identification components. | PCHE: Chemical Perception, PCHE: Enumeration | Low | PCHE-6587 |
New methods have been added to PPChem SDK to get atoms and bonds that satisfy a predicate. Java SDK APIs are public int[] getAtoms(Function | PCHE: PPChemAPI | Low | PCHE-6857 |
Improved the 2D layout of molecules with Markush bonds and Haptic bonds. | PCHE: Chemistry Depiction, PCHE: Pipette | Low | PCHE-6862 |
Added table with AlogP atom classification types to the help text of the "AtomAbstraction" parameter in the "Molecular Fingerprints" component. | PCHE: Property Calculators | Low | PCHE-7743 |
Added P and S atoms as a SP2 type tautomer atom when they have double bonds. Added tautomer score to PO and PS double bonds. | PCHE: Chemical Perception | Low | PCHE-7842 |
A new component, HELM to PNG, is provided as a prototype to allow server-side generation of Pipette Biosketcher monomer view images. | PCHE: Biologics, PCHE: Chemistry Depiction | Low | PCHE-7896 |
Fixed PPChem 2D-Coords clean crash with Markush bond in a structure repeat unit. | Low | PCHE-8043 | |
PPChem Python SDK wheel packages are available for both Windows and Linux systems and can be used to install the PPChem Python SDK fast and effortlessly. | PCHE: Usability | Low | PCHE-8165 |
Added support for reagents in SMIRKS strings to the Pipeline Pilot "SMIRKS Reader" and "Reaction for SMIRKS" components and to the PPChem SDK. | PCHE: File Formats | Low | PCHE-8274 |
Improved the positioning of subscripts in atom labels to reduce the spacing between the subscript number and the atom type. | PCHE: Chemistry Depiction | Low | PCHE-8386 |
Added support for "No Structure" (empty molecules) to Pipette Sketcher. | PCHE: Pipette | Low | PCHE-8407 |
Pipette now supports data sgroups for atoms, bonds and repeat units. | PCHE: Pipette | Low | PCHE-8408 |
Improved perception and depiction of RNA sense/antisense chains read from HELM strings. When possible, the complimentary bases in the two chains are properly aligned. | PCHE: Biologics | Low | PCHE-8410 |
Pipette Monomer Review now allows creation of Ribose derivatives with R4 groups. | PCHE: Pipette | Low | PCHE-8416 |
You can now specify axial stereochemistry in Pipette Sketcher. | PCHE: Chemical Perception | Low | PCHE-8417 |
Tautomer Perception and Score enhancements added in 2023
Note: Set "applyEnhancements2023" to true to use the 2023 tautomer enhancements. Set "applyEnhancements2023" to false to keep the SDK behave the same as in 2022 release and before. | PCHE: Chemical Perception, PCHE: Enumeration, PCHE: PPChemAPI | Low | PCHE-8428 |
Both the PPChem SDK and the Java FixMol example protocol will only be installed in a Pipeline Pilot server if a user has a PPChem SDK license. | PCHE: Molecular API | Low | PCHE-8445 |
A function is added to MolIO class in PPChem API and PPChem SDK to get version of OpenEye's library. The Java function GetOpenEyeVersion, C# function getOpenEyeVersion, and python function getOpenEyeVersion take no arguments and return the OpenEye library version number as a string. | PCHE: Molecular API | Low | PCHE-8446 |
Added error values for the atomic weight and the exact mass (weight of the most common isotope) to the internal elements table in PP Chemistry. Added Molecular_Weight_Error and Molecular_Mass_Error as calculable properties in the Molecular Weight component.Added apis to the Java, .NET and Python PPChem SDK to calculate molecular weight and molecular mass errors. | PCHE: Molecular API | Low | PCHE-8453 |
A new API SetChemicalNameInputLanguage (DotNet), setChemicalNameInputLanguage (Java), setChemicalInputLanguage (python) has been added to MolIO class of PPChem SDK to set input language of chemical names. | PCHE: Molecular API | Low | PCHE-8464 |
Two new Output options, MDLQueryKeys960 and MDLQueryKeys166, are added to the MDL Key Fingerprints component. They are also available as calculable properties. | PCHE: Property Calculators | Low | PCHE-8475 |
Added a set of common ring systems consisting of two rings connected by a single bond to the data file used by the "Replace Ring Assemblies" component. Added an option to allow this type of ring systems as ring replacements to the "Ring Types" parameter in the component. This new option is unchecked by default. | PCHE: Enumeration | Low | PCHE-8476 |
Implemented a new component, "Enumerate Tautomers(InChI2 Transforms)" to generate tautomers using a set of transformations described in "Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2", Devendra K. Dhaked, Wolf-Dietrich Ihlenfeldt, Hitesh Patel, Victorien Delannée, and Marc C. Nicklaus, J. Chem. Inf. Model. 2020, 60, 1253−1275. The new functionality is also available in the PPChem SDK. | PCHE: Chemical Perception, PCHE: Enumeration | Low | PCHE-8496 |
Added support for SMARTS CACTVS extensions to the SMARTS and SMIRKS readers, including:
| PCHE: Query Mapping | Low | PCHE-8497 |
Improved sketching and positioning of salt fragments in molecules and reactions in Pipette Sketcher. | PCHE: Pipette | Low | PCHE-8501 |
The zlib library in PPChem is updated to the latest version (1.2.12) in which security vulnerabilities associated with previous versions are fixed. | PCHE: OpenEye | Low | PCHE-8502 |
Improved Pipette Biosketcher to allow entering a sequence in the form of a string with residue letters. | PCHE: Biologics, PCHE: Pipette | Low | PCHE-8520 |
Improved salt depiction in Pipette Sketcher. They are now stacked vertically to optimize use of space. | PCHE: Pipette | Low | PCHE-8542 |
Improved Pipette Biosketcher sequence view to show reaction components horizontally instead of vertically. | PCHE: Biologics | Low | PCHE-8543 |
Added support for pasting reaction RXN files with sequences represented by Full CTAB expanded residues in Pipette Sketcher | PCHE: Pipette | Low | PCHE-8545 |
Added full CTAB molfile support to the Pipette Biosketcher when using SCSR monomers. | PCHE: Pipette | Low | PCHE-8546 |
Improved the Generate Scaffold Tree component to preserve stereochemistry at attachment points when R alpha atoms are added to track where substituents were removed from the parent molecule. | PCHE: Chemical Perception, PCHE: Enumeration | Low | PCHE-8556 |
Fixed the conversion of HELM strings containing terminal CHEM monomers to SCSR to avoid perceiving the terminal CHEM monomers as starting a new peptide chain. Now they are included in the same peptide chain where they appear as a N-terminal or C-terminal residue. | PCHE: Biologics | Low | PCHE-8565 |
Added a new parameter, Set SCSR Leaving Atom Coordinates With R Atom, to the HELM Monomer to SCSR Template component. When True, the component uses the HELM monomer R atom coordinates as the explicit leaving group atom coordinates. The default is False, where the leaving atom coordinates are generated automatically, the same as in earlier versions. | PCHE: Chemistry Depiction, PCHE: Hub Monomer Libraries | Low | PCHE-8576 |
The OpenEye MetaChem library is updated to version 1.6.0. | PCHE: OpenEye | Low | PCHE-8594 |
Updated the Search Library By Property protocols with new Search Entries by Names (PLP) and Search Entries by Names (HUB) components to enable optional parameters searching for HUB and PLP libraries. Added Search Results Output parameter to the Search Library By Property and Search Library By substructure protocols to write out the search results to an SD file. | PCHE: Hub Monomer Libraries | Low | PCHE-8598 |
Updated criteria for enclosing text fields within double quotes when writing in V3000 molfiles when any of these characters appear anywhere in the text: space, quote, double-quote, equal sign, left parenthesis and right parenthesis. Harmonized behavior with BIOVIA Draw and Pipette Sketcher. | PCHE: File Formats | Low | PCHE-8647 |
Added three new parameters to Replace Ring Assemblies component.
| PCHE: Enumeration | Low | PCHE-8674 |
Optimized the 2D oordinates of molecules with Markush bonds and Haptic bonds. | PCHE: Chemistry Depiction | Low | PCHE-7728 |
Updated Pipette Sketcher to version 3.7.3. Features and fixes included in this release:
| PCHE: Pipette | Low | PCHE-8719 |
Made changes in the PP Chemistry V3000 SD Reader and SD Writer to make sure that the Chiral flag in the M V30 COUNTS line is consistent with the stereo collections present in the molecule. The Chiral flag is set to one if the molecule has absolute chirality as indicated by the presence of only one stereo collection of type STEABS. In all other cases (AND Enantiomer, OR Enantiomer or Mixed stereo) the chiral flag is set to zero in V3000 mol files. Before these changes, V3000 mol files for molecules with Absolute stereo (as indicated by the STEABS collection) had the chiral flag in the M V30 COUNTS line set to zero. Note: the counters and chiral flag in the fourth line in the header of V3000 mol files (0 0 0 0 0 999 V3000) are always set to zero and ignored when reading the file. | PCHE: Chemical Perception, PCHE: File Formats | Medium | PCHE-8593 |
Take into account relative stereo groups (enhanced stereo) in the perception of meso symmetry. Molecules that would have been classified as meso are no longer perceived as meso if they have enhanced stereo. This change affects the Meso Chirality component and PPChem SDK meso APIs, as well as the chiral labels display in molecular depictions. | PCHE: Chemical Perception | Medium | PCHE-8597 |
Take into account relative stereo groups (enhanced stereo) in the perception of meso symmetry. Molecules that would have been classified as meso are no longer perceived as meso if they have enhanced stereo. This change has implications for Exact and Flexmatch searches that take into account stereo, as molecules with enhanced stereo that were perceived as meso before are now considered chiral and might not match similar molecules with different stereo. | PCHE: Chemical Perception | Medium | PCHE-8619 |
Documents and Text Collection
Description | Areas Affected | Risk Level | Jira Issue ID |
Added a new component parameter to the PDF Reader component, Output Format, with default Text only (old behavior) and new option Text with layout. Text with layout generates text with spaces and newlines added to approximate the spatial layout of the text in the PDF. | TXT: Readers | Low | TXT-1065 |
MEDLINE XML reader documentation updated to state that it handles both old MEDLINE and newer PUBMED format. | TXT: Readers | Low | TXT-1066 |
Imaging Collection
Description | Areas Affected | Risk Level | Jira Issue ID |
Deprecated the "Python Imaging Script" component that uses Python 2.7. It will be removed in a future release. | IMG: Components | Low | IMG-2911 |
Added new prototype component "Optimize Component Parameters" for tuning hyperparameters. | IMG: Components | Low | IMG-2962 |
Updated Pipeline Pilot Imaging collection to work with Pipeline Pilot infrastructure changes. | IMG: Readers/Writers, IMG: Example Protocols, IMG: Components | Low | IMG-3006 |
Deprecated support for storing images from the Pipeline Pilot Imaging collection in MongoDB. This functionality will be removed in a future release. | IMG: Readers/Writers | Low | IMG-3025 |
Improved architecture of the Pipeline Pilot Imaging deep learning components. | IMG: Readers/Writers, IMG: Infrastructure, IMG: Learners, IMG: Components | Low | IMG-2938 |
Materials Studio Collection
Description | Areas Affected | Risk Level | Jira Issue ID |
Pipeline Pilot Materials Studio Collection now includes components and protocols that help in generating Mesostructures using Martini 3 coarse grain model. The dedicated components and protocols also provide customised MS Martini 3 forcefield specialized in defining valance and non-bonded interactions in Mesostructure to be directly used in Mesocite simulations. | MSC: Documentation, MSC: Examples, MSC: Installation, MSC: Polymer Properties | Low | MSC-6065 |
A new Edit Sets component allows you to create and manipulate sets. | MSC: Application | Low | MSC-6118 |
You can use the new protocol, CCT Diagram (PhaseField), to calculate continuous cooling transformation (CCT) diagrams. The CCT data can be used to predict the critical cooling rate for the alloy. The protocol can use CALPHAD thermodynamic database and can make use of ThermoCalc or OpenCalphad package. | MSC: Phase Diagrams | Low | MSC-6123 |
The TTT Diagram (PhaseField) protocol now fits and returns the Johnson-Mehl-Avrami (JMA) coefficients for each simulation temperature. The JMA model describes how solids transform from one phase to another at a constant temperature. | MSC: Phase Diagrams | Low | MSC-6128 |
Previously deprecated protocols for cluster expansion based on the ICVM package are no longer included in the installation. | MSC: Phase Diagrams | Low | MSC-6138 |
A new protocol allows you to calculate core-level XPS spectra and absolute electron binding energies. | MSC: Application | Low | MSC-6197 |
Solvation Chemistry Collection
Description | Areas Affected | Risk Level | Jira Issue ID |
Enhanced usability of the COSMOtherm mixture core component. As an alternative to text-based \$PHASE input of the phase definitions in"Property Options", you can now use a parameter setting for the phases. The phase input keywords are set automatically in this case, further simplifying the input of COSMOtherm phase screening jobs. | SOLCHEMC: COSMOtherm | Low | SOLCHEMC-169 |
Added COSMOperm example protocols that demonstrate the use of protonation states and compound lists. | SOLCHEMC: COSMOplex | Low | SOLCHEMC-173 |
Added a protocol to support Morphology Solvent Screening that computes the crystal surface activity coefficients of a given set of crystal surfaces and a set of solvents with COSMOtherm. | SOLCHEMC: COSMOtherm | Low | SOLCHEMC-181 |
Added two protocols to support Morphology Solvent Screening that compute the morphology of a given crystal structure, and the periodic crystal surface COSMO files applying the Growth Morphology, and DMol3 protocols from the Pipeline Pilot Materials Studio Collection. | SOLCHEMC: COSMOtherm | Low | SOLCHEMC-182 |
Added a protocol to support Morphology Solvent Screening that analyzes the crystal surface activity coefficients for a given set solvents using the Hierarchical Clustering method. | SOLCHEMC: COSMOtherm | Low | SOLCHEMC-183 |
Fixed Defects
This release of BIOVIA Pipeline Pilot includes the following fixed defects.
Administration
Severity | Description | Areas Affected | Risk | Defect |
Minor | Updated the configutil usage help text to use uppercase for the gridtype options, since only uppercase values are actually allowed. | Administration | Low | PPC-10209 |
Minor | Fixed a bug preventing the generation of server usage reports from a remote Pipeline Pilot server running on a Linux machine. | Administration | Low | PPC-10487 |
Minor | Fixed an issue where the Admin Portal Setup/Server Configuration and Security/Security Configuration pages would not notify the administrator when settings that require a restart of the Apache and Tomcat PLP services are changed. | Administration | Low | PPP-47452 |
Minor | When installing a third-party package using pkgutil, the conversion of any pdf help document to html would fail with an error message due to trying to use an incorrect pdfbox library type. | Packaging | Low | PPP-47520 |
Minor | The scigridsetup script, which is a script used for setting up nodes for grid integration, no longer will throw an error due to an incorrect path if the answer to "Install the boot script?" is Yes. | Installation | Low | PPP-47603 |
Minor | Fixed an issue where attempting to log into the server as scitegicadmin before the admin password was properly set would result in an entry into the log files of the form "Invalid User Storage". | Administration | Low | PPP-47985 |
Minor | Fixed an issue where removing all users from the Admin Portal Security/Users page when the server is configured for external authentication would result in valid external users failing to log in. | Administration | Low | PPP-47986 |
Server Infrastructure
Severity | Description | Areas Affected | Risk | Defect |
Minor | Parallel subprotocols now work correctly for SAML Web SSO based sessions when connecting to server "localhost" (the same Pipeline Pilot server where the host protocol is executing). However, when the server specified in the subprotocol is a remote Pipeline Pilot server, SAML Web SSO based sessions cannot be delegated. | Server Infrastructure | Low | PPC-10499 |
Professional Client
Severity | Description | Areas Affected | Risk | Defect |
Minor | Eliminated the flicker for the tooltips that appear for the Professional Client status bar icons. | Pro Client | Low | PPP-32878 |
Minor | Fixed a long standing issue when using the Pilotscript DebugBreak(message) function, the message specified in the function would not appear with the Professional Client's resume dialog. | Pro Client | Low | PPP-45695 |
Minor | Fixed an issue in the Professional Client where the protocol errors dialog was incorrectly positioned when displayed on a secondary monitor. | Pro Client | Low | PPP-47653 |
Minor | Fixed an issue in the Professional Client where the help text at the bottom of the Server File Browser would not move when the dialog was resized resulting in the text possibly overlapping other controls within the dialog. | Pro Client | Low | PPP-47656 |
Minor | Fixed an issue where cancelling a client update when connecting to an incompatible server, then connecting to a new valid PLP server would result in an "Invalid Session. Probably Not Logged In." error during Pro Client initialization. | Pro Client | Low | PPP-47669 |
Minor | Fixed a problem with the synchronization of the Next and Previous buttons within the Promote tab of the protocol/subprotocol editor dialog. | Pro Client | Low | PPP-47678 |
Minor | Update the Create Protocol Link dialog so that controls are correctly disabled when they are not applicable. | Pro Client | Low | PPP-47731 |
Minor | Fixed an issue evident following a hot fix update to the Pipeline Pilot server. In some cases, in the Professional Client version dialog, the server version would still show the non-hotfix version of the server. | Pro Client | Low | PPP-47996 |
Minor | Fixed an issue where using replace all in the Professional Client script editors could cause the client to crash if the replacement text also contains the original search text. | Pro Client | Low | PPP-48287 |
Minor | Fixed an issue where an error would occur when applying changes from a dialog while any component's display name is currently being edited. | Pro Client | Low | PPP-48414 |
Minor | Fixed an issue where the prompt text in the Rename dialog when importing an existing component or protocol item was not fully displayed. | Pro Client | Low | PPP-48556 |
Minor | Fixed an issue where opening a script editor from within a secondary dialog such as the Protocol Link dialog would occasionally result in the client crashing. | Pro Client | Low | PPP-48599 |
Minor | Fixed an issue in script editors where multiple replacements within selected text could miscalculate which text was to be replaced, when the length of the replacement text was different from the replaced text. | Pro Client | Low | PPP-48610 |
Minor | The port filter in the Auto Watch panel has been updated, resulting in some small visual changes. | Pro Client | Low | PPP-48622 |
Minor | Fixed an issue where the Data Record Tree Viewer and Global Data Tree Viewer components would not preserve their position when last shown on a second monitor located to the left or above the primary monitor. | Pro Client | Low | PPP-48627 |
Minor | Fixed an issue where the Protocol and Component Explorer tabs would unnecessarily refresh when an import operation failed or was cancelled. | Pro Client | Low | PPP-48919 |
Trivial | Fixed an issue in the Professional Client that first appeared in version 2021 where moving a sticky note and saving the protocol or subprotocol would not preserve the new position of the note, unless also changing the text content, color, or gradient setting of the note. | Pro Client | Low | PPP-47672 |
Reporting
Severity | Description | Areas Affected | Risk | Defect | |
Minor | Fixed a bug in the Searchable List Box Reporting component when initialized with multiple items selected, but the first data record was not one of the selected items. | Reporting | Low | PPP-26985 | |
Minor | Fixed an issue with running the HTML5 Elements PDF Viewer and PDF to Text components on RHEL 8 by upgrading the deployed PhantomJS library. | Reporting | Low | PPP-47312 | |
Minor | The deployed Highcharts library is updated to version 10.2.1 | Reporting | Low | PPP-48685 | |
Minor | An encoding bug is fixed to support the inclusion in reports of SVG images containing Unicode text. | Reporting | Low | PPP-49133 | |
Minor | Fixed a bug in the Reporting collection's File Chooser component where a successful file upload would result in an ambiguous message implying both failure and success. (Fixed in Pipeline Pilot 2022 SP1) | Reporting | Low | PPP-49179 | |
Trivial | Fixed an issue with the XY Chart component with multiple data series. Property names for the X axis are now case-insensitive to avoid the use of multiple labels differing only by case. | Reporting | Low | PPP-27419 |
Generic Components
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Minor | JDBC data sources: Fixed an issue where a string literal that looked like an oracle comment marker led to false parameter number results. | Generic Collections | Low | PPC-10271 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Minor | Fixed a bug in the Properties to Leaf Nodes component. When Move MetaData to Properties was enabled, the non-metadata properties were erroneously cleared. | Generic Collections | Low | PPP-36472 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Minor | Fixed an issue where the Excel Viewer component fails to open the spreadsheet correctly when the PLP server is set for Restricted job directory web access. | Generic Collections | Low | PPP-47384 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Minor | Fixed an issue for Impala data sources where the SQL Builder dialog displayed tables in the form Generic Collections Low PPP-47451 Minor JSON Writer component: Mime type appropriately set when uploading to S3. Generic Collections Low PPP-48253 Trivial International characters are now better supported in Jupyter Notebook. Generic Collections Low PPP-47164 Trivial Fixed a broken link in the Perl Component API reference page. Documentation Low PPP-47761 PilotScript Severity Description Areas Affected Risk Defect Minor Fixed a specific crash bug with the LIKE conditional operator where the compared value is a single % character. PilotScript Low PPP-41664 Web Port Severity Description Areas Affected Risk Defect Major Fixed an issue when running Web Port when Pipeline Pilot is configured to use BIOVIA Foundation authentication. In some cases, jobs run in Web Port were not displayed in the job history. Web Port Medium PPP-47736 Analytics and Machine Learning Severity Description Defect Minor The R Robust Dose Response Fit component can become stuck in an infinite loop in cases when no or poor initial coefficient estimates are provided for the Initial Coefficients Property parameter. In such situations, use the Robust IRLS option of the Least Squares Curve Fit to perform a robust fit of dose-response data. PSM-2369 Biology Collections Severity Description Areas Affected Risk Defect Major Removed Variant Calling for Region (GATK), Joint Variant Calling for Region (GATK), Recalibrate Base Quality Score (GATK), Recalibrate Variant Quality Score (GATK), Run GATK Tool, and the GATK Best Practice examples. PBIO: Analysis Medium PBIO-6715 Minor Added a new parameter, "IMGT Version", to the "Annotate Antibody Domains" component to provide variations of IMGT antibody numbering. PBIO: Annotators Low PBIO-6562 Minor Improved help text of the "Add Numbering Property" parameter on "Annotate Antibody Domains". PBIO: Annotators Low PBIO-6604 Minor Corrected a typo in the Bioutilities package.conf file. PBIO: Infrastructure Low PBIO-6674 Minor Updated biology collections to work with Pipeline Pilot infrastructure changes. PBIO: Analysis Low PBIO-6708 Minor Updated GATK to version 4.2.4.1. PBIO: Analysis Low PBIO-6711 Chemistry Collection Severity Description Areas Affected Risk Defect Critical Fixed Perceive Sequence From Structure to avoid running into infinite loops for unusual use cases, such as trying to perceive the sequence for small molecules with no known residues. PCHE: Biologics, PCHE: Chemical Perception Low PCHE-8658 Critical Fixed Perceive Sequence From Structure to avoid running into infinite loops for unusual use cases, such as trying to perceive the sequence for small molecules with no known residues. PCHE: Biologics, PCHE: Chemical Perception Low PCHE-8659 Major Removed eMolecules from the list of public websites used to convert names to structures in the "Molecule from Name" component. The site cannot be access for this purpose without a valid account. The component now contains only DiscoveryGate, NCI/CADD, ChemSpider and PubChem as available sites to select. PCHE: Chemistry Content Low PCHE-8375 Major Fixed a problem calculating coordinates for expanded granular RNA residues in Clean SCSR Sequence. Added options to Expand SCSR Sequence to clean the sequence after the expansion. PCHE: Biologics, PCHE: Chemistry Depiction Low PCHE-8443 Major Perceive Sequence from Structure. Fixed the logic to identify LGRP SUP groups to make it more general and cover more use cases. The code was missing cases of Oxygen atoms attached to AA sidechains other than the natural residues D and E. PCHE: Biologics, PCHE: Chemical Perception Low PCHE-8472 Major Fixed the inconsistency by correcting initialization in the code. (The observed inconsistency is because the first molecule has an atropisomer which caused the 2nd molecule to crash) PCHE: Chemical Perception Low PCHE-8485 Major GetChemicalName of MolIO class in PPChemSDK returns empty chemical names for molecules with 1000 or more heavy atoms. This limit of number of heavy atoms is added to avoid rare crashes of the Java method on Linux systems for large molecules. PCHE: Molecular API Low PCHE-8551 Major Fixed an issue where exact structure matching in Pipeline Pilot or Direct, in certain cases, matched a structure that specifies a mixture of stereoisomers with a query that specifies a single stereoisomer. These cases involve meso or pseudochiral structures such as 1,4-cyclohexanes. PCHE: Chemical Perception, PCHE: Query Mapping Low PCHE-8552 Major Added a new parameter to the Generate Scaffold Tree component to control whether fused aromatic rings should be split into smaller rings. PCHE: Enumeration Low PCHE-8555 Major PPChem SDK Python API references in Pipeline Pilot server are working now. PCHE: Documentation Low PCHE-8570 Major A problem perceiving aromaticity of six-member rings containing atoms such as sulfur or phosphorus with alternating single and double bonds has been corrected. In previous releases, the perceived aromaticity could depend on the positioning of the double bonds. Now, the aromaticity is perceived identically, regardless of their positions. A previous fix in the 2019 release has a partial fix for the same issue. PCHE: Chemical Perception Low PCHE-8589 Major Improved the way COUNTS lines are written for reactions in V3000 RXN and RD format. Long lines with NAME and/or COMMENTS that need continuation lines are formatted to make sure they do not exceed 80 characters, with the continuation symbol always in the 80th position in the line. PCHE: File Formats Low PCHE-8590 Major Made changes in the PP Chemistry V3000 SD Reader and SD Writer to make sure that the Chiral flag in the M V30 COUNTS line is consistent with the stereo collections present in the molecule. The Chiral flag is set to one if the molecule has absolute chirality as indicated by the presence of only one stereo collection of type STEABS. In all other cases (AND Enantiomer, OR Enantiomer or Mixed stereo) the chiral flag is set to zero in V3000 mol files. This change addresses inconsistencies in the treatment of stereo information by some PP Chemistry manipulator components. PCHE: Chemical Perception, PCHE: File Formats Low PCHE-8617 Documents and Text Collection Severity Description Areas Affected Risk Defect Major Fixed an issue where all searches with "Search US Patents" were failing since USPTO no longer supports PATFT search. Now switched to use switch to Patent Public Search. TXT: Search Online Low TXT-1071 Minor Fixed an issue with the Download NIH Grants example protocol. TXT: Tutorials Low TXT-1072 Minor The new Patent Public Search does not support a deep linking capability to individual patents. Created a new Web Service "viewpatent" protocol to display the patent. TXT: Search Online Low TXT-1073 Imaging Collection Severity Description Areas Affected Risk Defect Minor Learn CNN Image Classifier now handles parameters with whitespaces. IMG: Learners, IMG: Components Low IMG-2872 Minor Improved augmentation and randomization in Learn CNN Image Classifier. IMG: Learners Low IMG-2939 Minor Improved the handling of large TensorFlow data records in Learn CNN Image Classifier. IMG: Learners Low IMG-2941 Minor Improved performance of Learn CNN Image Classifier by reducing the size of the shuffle buffer. IMG: Learners Low IMG-2942 Materials Studio Collection Severity Description Areas Affected Risk Defect Major The study table validation stage in the Reaction Pathway Display protocol no longer produces inappropriate error messages. MSC: Application Low MSC-6355 Minor Corrected capitalization for minimum and maximum composition settings phases in the phase field input file. The input settings had the wrong capitalization and were not recognized by the file reader; phase field protocols used default values for these parameters instead. MSC: Phase Diagrams Low MSC-6158 Minor VAMP component solvation parameter options have been reviewed and updated so that they are consistent and applicable. MSC: Application Low MSC-6195 Minor The Synthia components in the Chemistry and Polymer Properties collection now test the correct license key. MSC: Polymer Properties Medium MSC-6222 Minor In the TTT Diagram (PhaseField) protocol the Interface Energy column in the temperature specific study table, incorrectly reported zeros for all time steps. It now reports the correct energy value. MSC: Phase Diagrams Low MSC-6249 Minor The Mass and Charge Transport Protocol now throws an error on an incorrect input document. MSC: Application Low MSC-6293 Minor Clarified the "Minimum Energy Path" tutorial in DFTB+ and DMol3. MSC: Documentation Low MSC-6358 Minor Corrected unit for nucleation density parameter in PhaseField protocols from cm{^}-3{^} to mm{^}-3{^}. MSC: Phase Diagrams Low MSC-6415 Trivial Improved error message returned by VAMP in MSC. MSC: Application Low MSC-6049 Trivial The capitalization of the "If Available" option for the "Use GPU" help text is now consistent with the value for the parameter itself. MSC: Application Low MSC-6088 Trivial The Random Alloy Properties (Quasirandom Structures) protocol no longer submits the Run DFT component to the queue even if the DFT Task is None. Now, when DFT is not used, the post-processing is part of the main protocol. MSC: Phase Diagrams Low MSC-6093 Solvation Chemistry Collection Severity Description Areas Affected Risk Defect Minor Fixed an issue where the Pure COSMOtherm Property component of COSMOtherm as used in the Pure COSMOtherm Properties Example protocol did not recognize inert compounds such as water, and computed a finite Flash Point temperature. Water and other inert compounds are now recognized, and the Flash Point temperature is given as "NA" on output. SOLCHEMC: COSMOtherm Low SOLCHEMC-175 BIOVIA Pipeline Pilot 2023 was released in December 2022 and is available for download at https://software.3ds.com under BIOVIA products and can be found under: Product line: Lab, Scientific and Content Solutions Release: BIOVIA 2023 Level: BIOVIA 2023 Golden Fixes for this level: - If you have any questions, please contact BIOVIA Support |