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 2025 which includes the following enhancements and fixed defects:
Enhancements
This release of BIOVIA Pipeline Pilot includes the following enhancements.
| Description | Areas Affected | Risk Level | Jira Issue ID |
|---|---|---|---|
| The expat XML parser library is updated to the latest available version (2.6.2). | PPC: Third Party Libraries | Low | PPC-11525 |
| The lz4 compression library is updated to the latest version as of July 2024. | PPC: Third Party Libraries | Low | PPC-11635 |
| The internal SQLite drive is now the latest version. | PPC: Third Party Libraries | Low | PPC-11664 |
| The libssh was updated to the latest available version. | PPC: Third Party Libraries | Low | PPC-11681 |
| The version of Openssl was updated to 3.0.15. | PPC: Third Party Libraries | Low | PPC-11682 |
| The expat XML parser library is updated to the latest available version (2.6.3). | PPC: Third Party Libraries | Low | PPC-11689 |
| The Highcharts library has been updated to version 11.4.8. | PPP: Third Party Libraries | Low | PPP-52397 |
| The embedded Tomcat server is updated to version 9.0.95 | PPC: Third Party Libraries | Low | PPC-11708 |
| The Java runtime environment included with Pipeline Pilot is upgraded to Java 17. | PPC: Third Party Libraries | Medium | PPC-11503 |
| The Global properties that can be viewed or edited in the Setup > Global Properties page of the Admin Portal are now sorted intuitively (text with numbers) by property name. | PPP: Administration | Low | PPP-18798 |
A log of some administrative events can be enabled by running the command: configutil -au <admin_user> -ap <admin-password> -set -r AuditTrailPersistence -v File The log can be found in the folder <install-root>/logs/messages/admin. In this release, the administration log support focuses on general configuration settings. It also includes any specific changes to authentication settings and user management. Changes to groups or permissions are also captured, if the changes are made with the configutil command line tool. | PPP: Administration | Low | PPP-47478 |
| The Apache Httpd service has been rearchitected and moved to its own package named scitegic/apache. Configuration files have been separated from the package location into the config/httpd folder. This is to facilitate any future security updates of Httpd from BIOVIA without the need for a full service pack upgrade. | PPC: Server Infrastructure | High | PPC-4562 |
| The Cache Reader and Join Data from Cache components include a new parameter, If Cache Does Not Exist, which can be set to "Generate Error" (default) or "Do Nothing". For the Cache Reader component, if the cache does not exist and the parameter value is “Do Nothing”, no data records are output. For the Join Data from Cache component, if the cache does not exist and the parameter is “Do Nothing”, all data records are output to the Fail Port. | PPP: Generic Components | Low | PPP-16701 |
| The Prepare Data component can act as a filter to remove certain rows and it now has a Fail port to allow it to work as a filter. | PPP: Generic Components | Low | PPP-50616 |
| The Prepare Data component has been moved out of the prototypes folder. | PPP: Generic Components | Low | PPP-52296 |
| The PDF to Text component has an additional parameter Retain Layout. This provides the option of text output that adheres to the existing text layout (past and default behavior) or to ignore layout and focus solely on text content. | PPP: Generic Components | Low | PPP-52386 |
| The vestigial SharePoint Bridge package is not in the release, as it depends on unsupported versions of SharePoint. | PPP: Reporting | Low | PPP-52306 |
| The JavaScript intellisense used within the JavaScript text editor dialogs of the Professional Client now uses the latest standards. | PPP: Professional Client | Low | PPP-51241 |
| Python has been updated to version 3.9.19 | PPC: Component SDKs, PPC: Integration, PPC: Third Party Libraries | Low | PPC-11476 |
| The deprecated MongoDB package shipped with Pipeline Pilot has been slimmed down to remove the old copy of the MongoDB server that was for potential use in prior releases of BIOVIA Insight. Although any MongoDB components in existing protocols will continue to work for now, the components will not show in the Professional Client explorer tab. | PPP: Packaging | Low | PPP-52273 |
The AppCatalog index and search system has been replaced in this release, due to the age of the Solr-based architecture. The new Index and Search system aims to be significantly simpler than the AppCatalog and to provide coverage for a broader range of protocols. However, it does not yet support all the capabilities of the App Catalog, especially for the history of protocol execution. We plan to roll those features into the next release. Unicode text search is supported, but word separation for indexing of Asian character sets is still lacking. Important: If you are upgrading an existing Pipeline Pilot server and want to index documentation of the existing protocols and components authored and published on that server, refer to the information in the Administration portal, on the page Maintenance > Manage Search. There are specific instructions for Windows and Linux servers. The indexing is achieved by running the "scitegicutil -zx" command line followed by the category of XMLDB tab to be updated. This can be one of:
Authoring users may also index or reindex documentation of items in their user tab by running the "Index My User Tab" protocol. Any new protocols or component saved after the installation of Pipeline Pilot 2025 will be automatically indexed for documentation or component usage search. | PPP: Help Center | Medium | PPP-51151 |
| You can now to add a service account as tagged resource to connect to the 3DX platform, which allows you to integrate your protocols with 3DX services. | PPP: Integration | Low | PPP-52178 |
The on-prem SharePoint components have been deprecated and moved to a deprecated folder (Database and Application Integration/Utilities/Deprecated/Sharepoint)
| PPP: Integration | Low | PPP-51339 |
| The PilotScript Avg(), Sum(), Min(), and Max() functions now take arrays as parameters and additionally can take an arbitrary number of parameters. For example, Avg(Array(1,2,3,4,5), Array(6,7,8,9,10)) now returns "5.5". Additionally a new PilotsScript math function "Median()" is available, which returns the arithmetic median of the parameters provided. | PPP: PilotScript | Low | PPP-18915 |
Biology Collections
| Description | Areas Affected | Risk Level | Jira Issue ID |
| JalView2 is upgraded to 2.11.3.3 and the component is restored. | PBIO: Annotators | Low | PBIO-6736 |
| The list of Sequence Analysis third-party tools has been updated. | PBIO: Analysis | Low | PBIO-6775 |
| The database information for EBI components is updated. | PBIO: Online Components | Low | PBIO-6804 |
| Kent Utilities is upgraded to version 470. | PBIO: Analysis | Low | PBIO-6800 |
| GATK is updated to 4.6.0.0 and related components and protocols are restored. | PBIO: Analysis | Medium | PBIO-6730 |
| Updated biology collections to work with Pipeline Pilot infrastructure changes. | PBIO: Analysis | Medium | PBIO-6788 |
| BLAST+ is upgraded to 2.16.0. | PBIO: Analysis | Medium | PBIO-6805 |
Chemistry Collection and SDK
| Description | Areas Affected | Risk Level | Jira Issue ID |
|---|---|---|---|
| When creating chain annotations in Draw, the depiction of biological sequences honors the colored chains with sequence breaks sketched in BIOVIA Draw. | PCHE: Biologics, PCHE: Chemistry Depiction | Low | PCHE-7319 |
| The identification of molecules with Markush system crossing a repeat unit was added, so that a molecule of this type will pass unchanged from the PP Chem "2D Coords" component. | PCHE: Chemistry Depiction | Low | PCHE-7570 |
| The perception and depiction of pairs of sense/antisense RNA chains is now improved, especially in cases where there is only partial complementarity between the two chains. The calculation of the structure view layout for granular RNA/DNA residues now includes more homogeneous spacings and better alignments, especially in the case of sense/antisense chains with Hydrogen bonds. | PCHE: Chemistry Depiction | Low | PCHE-7922 |
| * A PP component now suggests the Natural replacement Code for a HELM Monomer using molecular substructure mapping and molecular similarity searching. * A Webport protocol now suggests the Natural replacement code for a HELM monomer sd file. * The "Modify Entry In Library(PLP)" Webport protocol now suggests a natural Replacement Code when a HELM monomer or SCSR Template is being modified in the centralized library. You can now refer to the suggestions when entering a Natural Replacement Code. | PCHE: Biologics, PCHE: Hub Monomer Libraries | Low | PCHE-8998 |
| A Pipeline Pilot Server Webservice is now available to provide configuration files. | PCHE: Hub Monomer Libraries | Low | PCHE-9234 |
| There is now an option in the "Enumerate Tautomers (InChI2 Transforms)" component to output the number of non-overlapping substructures in the input molecule mapped by the tautomer transformation reactions, without doing the full enumeration. This can be helpful to avoid enumerating tautomers for molecules with many mappings, which can potentially generate a very large number of tautomers and take significant computational time. There is also a new API to the PPChem SDK (Java, Python and .NET versions) to calculate this new counter. | PCHE: Chemical Perception, PCHE: Enumeration | Low | PCHE-9269 |
| It is now possible to create configuration files from multiple centralized libraries. | PCHE: Hub Monomer Libraries | Low | PCHE-9309 |
| siRNA and display of antisense chain now show Hydrogen Bonds in Pipeline Pilot Chemistry Collection and SDK. | PCHE: Chemistry Depiction | Low | PCHE-9344 |
| The Replace RIng Assemblies component was improved to better handle molecules with rings embedded in macrocycles. | PCHE: Enumeration | Low | PCHE-9347 |
| Substructure and exact mapping of molecules with bond enhanced stereo now behaves as expected in the Pipeline Pilot components and in the PPChem SDK. | PCHE: Chemical Perception | Low | PCHE-9385 |
| New rings were added to the "Replace Ring Assemblies" component obtained by processing data from the publication "Database of 4 Million Medicinal Chemistry-Relevant Ring Systems", Peter Ertl, Journal of Chemical Information and Modeling 2024 64 (4), 1245-1250. New parameters are now available to control the use of these rings. | PCHE: Enumeration | Low | PCHE-9386 |
| Add support for dropping skc files into Pipette Sketcher | PCHE: Pipette | Low | PCHE-9405 |
| Stereocenters present in the original molecule are now persevered in favor tautomers containing nitro groups in the calculation of the tautomer score, and storing the original molecule as the first tautomer if it has tautomers. A new PPChemSDK API now clears the data structures in C++ that store the information for previously generated tautomers (smiles, scores, transformations, ...). This api doesn't reset the loaded tautomer reactions in the tautomer enumeration engine. | PCHE: Chemical Perception, PCHE: Enumeration | Low | PCHE-9414 |
| A new function, CustomDataSetPlacement(), is now available in the PilotScript Molecular Toolkit that sets placement of custom data. | PCHE: Molecular API | Low | PCHE-9420 |
| An SCSRUtils class was added to the Pipeline Pilot Chemistry Python and Java SDK. | PCHE: PPChemAPI | Low | PCHE-9425 |
| A new method SetCTABReaderMaxNumberAtoms(int maxNumberAtoms) is now in the MolIO Class in PPChemSDK to set the maximum allowed number of atoms when reading the V3000 mol file. | PCHE: PPChemAPI | Low | PCHE-9433 |
| A new method SetMaxNumberOfAtoms(int maxNumberOfAtoms) is now on the ExpandSCSRTemplates Class in PPChemSDK to set the maximum allowed number of atoms when expanding a SCSR sequence. | PCHE: Molecular API | Low | PCHE-9434 |
| The system now checks that the number of atoms in the input molecule is smaller than a specified maximum, before proceeding with the tautomer enumeration. | PCHE: Enumeration | Low | PCHE-9436 |
| The system now checks that the number of atoms in the input molecule is smaller than a specified maximum, before proceeding with the tautomer enumeration. | PCHE: Enumeration, PCHE: Molecular API, PCHE: PPChemAPI | Low | PCHE-9449 |
| The system now handles reading and writing of antisense strand SEQID's consistently. | PCHE: Pipette | Low | PCHE-9489 |
| Crossed bonds now behave as unknown and consequently you cannot add AND, OR or ABS labels. The tool tip for crossed double is changed from "Double Either" to "Unknown Double". The tool tip for either wedge is changed from "Either" to "Unknown". | PCHE: Pipette | Low | PCHE-9537 |
| Pipette sketcher now marks centers with a unknown stereo single bond 'U' when displaying labels | PCHE: Pipette | Low | PCHE-9553 |
| The Sequence view in Pipette now displays the sequence chain details. | PCHE: Chemistry Depiction, PCHE: Pipette | Low | PCHE-9608 |
| Access control to the PLP Platform based centralized library is now available. The Shared scope supports a user group access control when the library is created. The Shared scope without a defined user group replaces the "All Users" scope. | PCHE: Hub Monomer Libraries | Medium | PCHE-8846 |
Documents and Text Collection
| Description | Areas Affected | Risk Level | Jira Issue ID |
| New US Patent Search API supports deep link to a PDF version of the patent. | TXT: Search Online | Low | TXT-1074 |
| Search US Patents component uses new US Patent Office search API to perform searches. | TXT: Search Online | Low | TXT-1076 |
| The Wikipedia page title is extracted more accurately from the Wikipedia search results. | TXT: Search Online | Low | TXT-1093 |
| UTF-8 formatted files are now read correctly by these reference file readers. | TXT: Other | Low | TXT-1097 |
| When exporting features of a Word DOCX file, you may now choose to only export bookmarks. | TXT: Applications | Low | TXT-1102 |
Imaging Collection
| Description | Areas Affected | Risk Level | Jira Issue ID |
| Updated imaging collection on Windows to work with Pipeline Pilot infrastructure changes. | IMG: Infrastructure | Medium | IMG-3175 |
Laboratory Analytics Collection
| Description | Areas Affected | Risk Level | Jira Issue ID |
| The Analytical Instrumentation components are moved to a Deprecated folder in the Pipeline Pilot 2025 release. BIOVIA plans to withdraw the Analytical Instrumentation collection in an upcoming release. If you actively use these components and plan to use them in the future, contact BIOVIA Customer Support to communicate your concerns. | AIC: AIC | Low | AIC-1473 |
Materials Studio Collection
| Description | Areas Affected | Risk Level | Jira Issue ID |
| CASTEP energy component can be used now to calculate optical properties using TD-DFT formalism | MSC: Application | Low | MSC-3828 |
| The dilatometric chart as output by the Calculate Glass Transition Temperature protocol has been improved. | MSC: Examples | Low | MSC-6032 |
| A protocol for querying OPTIMADE databases of calculated material properties is added to the Materials Studio Collection for Pipeline Pilot. | MSC: Application | Low | MSC-6056 |
| A new protocol Build Mesoscale Membrane and a new component Build Mesoscale Template are added to Materials Studio Collection. The protocol generates and equilibrates a bilayer membrane using ready mesoscale lipids and solvents based on Martini 3 models including Martini 3 forcefield customized to the mesostructure. The protocol also allows production dynamics run using the output equilibrated mesostructure. The new component creates mesoscale template documents using Pipeline Pilot and can be used together with Build Mesostructure from Template component to generate mesostructures. MaterialsScript also allows Mesostructure Template builder be accessed using scripting at Materials Studio. | MSC: Other | Low | MSC-6169 |
| The Calculate Glass Transition Temperature protocol and the Calculate Yield Stress and Critical Distortional Strain protocols can now be run with study table input. | MSC: Examples | Low | MSC-6179 |
| The Materials Studio collection now provides a new component for the creation of a crystal graph that you can use in Morphology calculations. A new example protocol demonstrates this workflow. | MSC: Examples | Low | MSC-6592 |
| Calculate Stress-Strain Curves and Calculate Surface Interaction Energies protocols are updated to have parallelization options for both thread-based and 3DExperience Platform grid-based submissions including GPU support. | MSC: Other | Low | MSC-6820 |
Notebook Collection
| Description | Areas Affected | Risk Level | Jira Issue ID |
| A custom image can be provided as preview when creating or editing an Excel section. This preview replaces the automatically-created preview, which is still the default option. | ANC: API | Low | ANC-269 |
Fixed Defects
This release of BIOVIA Pipeline Pilot includes the following fixed defects.
| Severity | Description | Areas Affected | Risk | Defect |
|---|---|---|---|---|
| Minor | The Pipeline Pilot Professional Client installer application title now displays the application name as expected. | PPD: Client Installer | Low | PPD-2918 |
| Minor | The shortcut created on the desktop once you install PP 2024 Client, now displays a tool tip when you hover over it. | PPD: Client Installer | Low | PPD-2945 |
| Minor | In the Details and Instructions for changing the Jobs Directory on the "Folder Locations" page in the Administration Portal, there is now information on restarting the Jupyter Notebook Server after making a change. | PPP: Administration | Low | PPP-45509 |
| Trivial | The confusing term "Login Name" in the Server Information page of the Administration Portal has been renamed and the Help text updated accordingly. | PPP: Administration | Low | PPP-51322 |
| Minor | Updated guidelines and instruction for the operation of the Pipeline Pilot server on a single port. | PPP: Documentation | Low | PPP-51478 |
| Trivial | Updated port reconfiguration guidelines to handle scenarios involving the Jupyter Notebook server. | PPC: Documentation | Low | PPC-11509 |
| Minor | When an array of strings that look like datetimes, are input to the Clean Data component, it works as expected. | PPP: Generic Components | Low | PPP-51004 |
| Minor | Component Reader: When SourceIs=Directory, the Component Reader now correctly finds both .xml and .ppxml files. | PPP: Generic Components | Low | PPP-51282 |
| Minor | Component Reader: When SourceIs=Directory or File, the component reader now correctly parses File URIs such as "shortcut:", "job:", "pkg:", etc. | PPP: Generic Components | Low | PPP-51314 |
| Minor | If the remote proxy server times out during an http connect operation, the http connector behaves as expected. | PPP: Generic Components | Low | PPP-51797 |
| Minor | Performance is improved for UTF8 Auto Detect of both compressed (.zip, .gz) and non-compressed files. | PPP: Generic Components | Medium | PPP-51978 |
| Minor | The Clean Data component no longer incorrectly converts certain strings to DateTimeValues and determines whether a value is a DateTimeValue in a way that is more consistent with the PilotScript IsDate function. | PPP: Generic Components | Low | PPP-52052 |
| Minor | The error message text is formatted correctly after a failed communication to a remote XMLDB server to resolve an xmldb(s) URI. | PPP: Web Services | Low | PPP-51891 |
| Minor | The legend item color for XY charts that show lines but no symbols, displays correctly. | PPP: Reporting | Low | PPP-49429 |
| Minor | If you change the symbol and fill to ExpressionType parameters, the symbol and fill options now display as expected. | PPP: Reporting | Low | PPP-52035 |
| Minor | For XY charts that show lines without symbols, the legend shows the correct colors. | PPP: Reporting | Low | PPP-52404 |
| Minor | In the Professional Client, when adding a protocol database, the Network tab displays and is active. Additionally, if the requested database is already connected within the Network tab, an alert dialog no longer displays. | PPP: Professional Client | Low | PPP-44351 |
| Minor | When the Professional Client authentication dialog displays because of an expired session, a non-functional help button no longer displays. | PPP: Professional Client | Low | PPP-50937 |
| Minor | In the Professional Client Explorer tab search bar, if there are no items in the tab and the search string is empty, the bar no longer appears orange (invalid). | PPP: Professional Client | Low | PPP-50939 |
| Minor | Switching back and forth between the protocol diff view and the protocol editor from within subprotocols, works as expected. | PPP: Professional Client | Low | PPP-51455 |
| Minor | In one of its modes of operation, the RunProtocol command line can be used to execute a protocol stored on the local file system. In Pipeline Pilot 2025 , this particular use of RunProtocol now requires a user who is configured as an Author for the target Pipeline Pilot execution server. This is because the operation is running a protocol that is not registered on the server, and this is considered equivalent to the authoring process and should require the same privilege level. This does not affect the more general use of RunProtocol to execute a protocol already installed or saved to the server. | PPP: Professional Client | Low | PPP-52232 |
| Minor | If you save a protocol after moving a component with an attached sticky note now, the sticky note's location saves as expected. | PPP: Professional Client | Low | PPP-52103 |
| Minor | If the Professional Client's Pipeline Pilot.exe process crashes or is otherwise killed, the PPBrowser.exe Chromium subprocess exits as expected. | PPP: Professional Client | Low | PPP-52414 |
| Minor | The styling of asterisks on required protocol parameters was modified to prevent them from moving while the parameters tab is resized. | PPP: Web Port | Low | PPP-50496 |
| Minor | Reporting charts using the 2023 reporting stylesheet now render correctly when viewed in Web Port. Chart axis labels and numbering were previously overlapping. | PPP: Web Port | Low | PPP-50747 |
| Minor | Custom styling on a list box component, works as expected. | PPP: Web Port | Low | PPP-51646 |
| Minor | When opening certain protocols, the help text displays as expected. | PPP: Web Port | Low | PPP-51922 |
| Minor | Radio buttons are now properly aligned in reports output by a job run from Web Port. | PPP: Web Port | Low | PPP-52085 |
| Minor | Web Port performance is now improved when the user retains a large number of jobs. | PPP: Web Port | Low | PPP-52087 |
| Minor | You can now customize the submit button style. | PPP: Web Port | Low | PPP-52102 |
| Minor | Help text displays as expected for checkboxes in forms. | PPP: Web Port | Low | PPP-52208 |
| Minor | When opening Web Port in container mode, the parameters tab is now collapsed by default and the size of the results tab is now correct. | PPP: Web Port | Low | PPP-52433 |
| Minor | Legacy client SDK libraries will now function correctly when the Protocol Parameter Injection Handling setting is upgraded to the "Restrict" level. | PPP: Client SDK | Medium | PPP-49272 |
| Minor | The defineHashTableProperty method on a PropertyCollection in the Python (on Server) component allows a Python dictionary with values that are lists of simple scalars (for example, a list of strings). Each list will be converted to a ValueArrayValue in the Pipeline Pilot HashTableProperty. | PPP: Component SDKs | Low | PPP-52038 |
| Minor | You can now use the Python Jupyter Notebook component on Windows, when the Jobs Directory is a UNC path. | PPP: Component SDKs | Low | PPP-52312 |
| Minor | If you leave the script editor of a Python Jupyter Notebook component open for over 10 minutes in a protocol that you have never run before, it runs as expected with no error or loss of data. | PPP: Component SDKs | Low | PPP-52321 |
| Minor | The Stock Statistics example now works with a new Yahoo Finance API. | PPP: Examples | Low | PPP-52205 |
| Minor | The XY Scatter Plot Utility example has been modified to allow it to run successfully, even when the Restrict mode of parameter injection analysis is in force. | PPP: Examples | Low | PPP-52287 |
| Minor | The JMP Custom Script and JMP Viewer prototype components now work with the latest syntax required by JMP. | PPP: Integration | Low | PPP-52007 |
| Minor | When reading a file from 3DDrive after making a connection using the 3DX Service Connector, if the file does not exist, an error message is shown. | PPP: Integration | Low | PPP-52251 |
| Trivial | The implementation for specifying the number of GPUs when running on LSF has been updated to adapt to changes to LSF command-line options. | PPC: Integration | Low | PPC-11426 |
| Minor | International (Unicode) characters are now correctly handled when parsing dates in PilotScript date functions, such as isDate() and DateProposeFormat(). | PPP: PilotScript | Low | PPP-52036 |
| Minor | Note the reported change in behavior: The PilotScript Min() and Max() functions now follow section 9.6 of the IEEE 754-2019 specification for "Minimum and Maximum Operations" with regards to NaN values as described for "minimum" and "maximum". The following describe the new logic for both functions:
| PPP: PilotScript | Low | PPP-52228 |
| Minor | In PilotScript, Fixed the weekday name to day of week mappings when parsing several non-English locales for the Date() function. | PPP: PilotScript | Low | PPP-52480 |
Analytics and Machine Learning
| Severity | Description | Areas Affected | Risk | Defect |
| Minor | If there is an error when an R Statistics component is running in Web port, the error messages no longer refer to R stdout. | PSM: R Statistics | Low | PSM-2513 |
| Minor | For R versions greater than or equal to R 4.3.2, warning messages correctly state the supported R versions. | PSM: R Statistics | Low | PSM-2514 |
| Minor | On Linux, if the car package does not install on the first attempt and the installed Matrix version is less than 1.6, the Check R Installation protocol now attempts to install the R package Matrix version 1.6-5. | PSM: R Statistics | Low | PSM-2520 |
Biology Collections
| Severity | Description | Areas Affected | Risk | Defect |
|---|---|---|---|---|
| Major | "Find Proteolytic Cleavage Sites (ExPASy PeptideCutter)" is updated. | PBIO: Online Components | Low | PBIO-6799 |
| Minor | URL encoding in "List DAS Data Sources" is fixed. | PBIO: Online Components | Low | PBIO-6707 |
| Minor | Parameter help is added to "Annotate Antibody Domains". | PBIO: Documentation | Low | PBIO-6718 |
| Minor | BLAST+ databases generated on Windows can be moved and still searched. | PBIO: Annotators | Low | PBIO-6739 |
| Minor | Component help text links are updated. | PBIO: Documentation | Low | PBIO-6754 |
| Minor | Examples are updated to be compatible with Pipeline Pilot and online resource changes. | PBIO: Example Protocols | Low | PBIO-6768 |
| Minor | The database information for EBI components is updated. | PBIO: Analysis | Low | PBIO-6772 |
| Minor | Updated biology collections to work with Pipeline Pilot infrastructure changes. | PBIO: Analysis | Low | PBIO-6777 |
| Minor | Entrez EGQuery is no longer supported by NCBI and has been removed from the Entrez components. | PBIO: Online Components | Low | PBIO-6818 |
| Minor | WormBase example protocols use HTTPS instead of FTP. | PBIO: Online Components | Low | PBIO-6819 |
| Trivial | Title of List MSP Third-party Software Tools report displays as expected. | PBIO: Analysis | Low | PBIO-6771 |
| Trivial | Input sequences to "Align Sequences (Muscle)" are no longer sent out the fail port. | PBIO: Calculators | Low | PBIO-6817 |
Chemistry Collection and SDK
| Severity | Description | Areas Affected | Risk | Defect |
|---|---|---|---|---|
| Critical | The QT libraries in the Pipeline Pilot Chemistry collection and SDK are now at version 5.15.17. | PCHE: Chemistry Depiction | Low | PCHE-9402 |
| Major | The conversion of granular RNA SCSR representation to HELM strings now avoids using SMILES to represent granular nucleotides that are missing a base because the sugar has only two attachment points to phosphates. | PCHE: Biologics, PCHE: File Formats | Low | PCHE-9246 |
| Major | The SMARTS Reader correctly parses two-character elements in which the second character is 'e', 'r' or 'a'. This list includes Na, Ca, Ba, Ra, Ga, La, Ta, Pa, Be, Ce, Re, Fe, Ge, Se, Te, Xe, Ne, He, Fr, Sr, Zr, Ir, Er, Ar, Kr, Lr, Cr, Pr, Br. The SMARTS reader was parsing the second character as a special case of CACTVS extensions. | PCHE: Chemical Perception, PCHE: Query Mapping | Low | PCHE-9252 |
| Major | The aromaticity perception now takes into account the coordination (dative) bonds connected to Nitrogen atoms in rings. | PCHE: Chemical Perception | Low | PCHE-9291 |
| Major | An option to determine bad stereo using either IUPAC convention or BIOVIA chemical representation now exists. The default is the BIOVIA chemical representation. | PCHE: Chemical Perception, PCHE: Molecular API | Low | PCHE-9452 |
| Major | You can now draw RNA sequences in Pipette edit mode for a base and then create a complementary strand for another part of the sequence as expected. | PCHE: Pipette | Low | PCHE-9516 |
| Major | A parameter: "Maximum Number of Atoms" is now on the Reader and Writer. The default is not set and there is no maximum. | PCHE: File Formats | Low | PCHE-9547 |
| Minor | The editing and display of complementary RNA strands in Pipette Biosketcher and the conversion to SCSR format for display in applications such as Insight and Biological Registration is now fully supported. | PCHE: Pipette | Low | PCHE-7454 |
| Minor | Using AtomSetXYZ() or AtomSetStereo() of the PilotScript Molecular Toolkit to change stereochemistry of a stereo center, now updates wedge bonds located at the stereo center as expected. | PCHE: Molecular API | Low | PCHE-8838 |
| Minor | Adding data Sgroups through CustomDataAttachToAtom() of PilotScript Molecular Toolkit now works as expected. | PCHE: Molecular API | Low | PCHE-9114 |
| Minor | A Base/N and RNA/N monomer template now exists in the default configuration files. A perceiving SCSR sequence and creation of HELM string using them, was added as well. | PCHE: Biologics, PCHE: Hub Monomer Libraries, PCHE: Office Chemistry Sketcher, PCHE: Pipette | Low | PCHE-9285 |
| Minor | The aromaticity perception now allows imidazole-like rings with the Nitrogen atom connected to a metal atom by a single bond to be perceived as aromatic, even when the sum of the bond orders exceeds 3. | PCHE: Chemical Perception | Low | PCHE-9322 |
| Minor | Chain color information for SCSR files now displays in Pipette. | PCHE: Pipette | Low | PCHE-9390 |
| Minor | When trying to create a bond for the same two atoms, the system now connects attachments to the new scaffold to avoid pathological cases where the atoms to connect are the same. | PCHE: Enumeration | Low | PCHE-9400 |
| Minor | The protocol name for "View and Copy Configuration Files" is now "View and Get Configuration Files". You can now select the source folder and target file name. | PCHE: Hub Monomer Libraries | Low | PCHE-9401 |
| Minor | There is now a new option to use either the IUPAC rule or the BIOVIA Chemical Representation rule. The Default is BIOVIA rule. | PCHE: Chemical Perception | Low | PCHE-9426 |
| Minor | The Pipeline Pilot LogD component now handles pH values that use comma as decimal point correctly. When specifying multiple pH values in the component, pipe symbol is now used as separator between values. | PCHE: Property Calculators | Low | PCHE-9430 |
| Minor | Chains that have an attachment atom(s) can now be replaced in Replace Chain Assemblies. | PCHE: Enumeration | Low | PCHE-9465 |
| Minor | The transformation types that load are now based on the selected values for the "Tautomer Transformations" parameter in the "Enumerate Tautomers (InChI2 Transforms)" component. Previously, all three transformation types loaded, irrespective of the selected values in the parameter. The tautomer enumeration now skips tautomers created by reversing a Ring-Chain transformation immediately after applying the transformation in the opposite direction. | PCHE: Enumeration | Low | PCHE-9476 |
| Minor | There is no longer a R1006 regression dependency on the speed of the running machine. | PCHE: QA | Low | PCHE-9487 |
| Minor | The Pipeline Pilot Chemistry SDK now performs as expected when reading invalid SMILES strings. | PCHE: Molecular API, PCHE: PPChemAPI | Low | PCHE-9495 |
| Minor | Pipeline Pilot Chemistry SDK performs as expected when reading invalid SMILES strings. | PCHE: Molecular API, PCHE: PPChemAPI | Low | PCHE-9496 |
| Trivial | Molecules with multiple aromatic rings and different kekule forms, now provide the same IUPAC names. | PCHE: OpenEye | Low | PCHE-8528 |
| Trivial | The labels for examples of ladder-type polymers in the Chemical Representation Guide now correctly use the term "head-to-head." | PCHE: Documentation | Low | PCHE-9293 |
Documents and Text Collection
| Severity | Description | Areas Affected | Risk | Defect |
| Minor | The Search US Patents component now uses the new US Patent Office search API to perform search. | TXT: Search Online | Low | TXT-1103 |
| Trivial | Example protocol now runs in more restrictive security environments. | TXT: Applications | Low | TXT-1099 |
Materials Studio Collection
| Severity | Description | Areas Affected | Risk | Defect |
|---|---|---|---|---|
| Major | Run Monte Carlo Reactive Molecular Dynamics protocol now clears pattern Substructures at input source structure to prevent interference with reaction process. | MSC: Other | Low | MSC-7044 |
| Major | A trajectory frequency output issue with Run Monte Carlo Reactive Molecular Dynamics protocol has been resolved | MSC: Other | Low | MSC-7086 |
| Minor | The Fit VDW protocol now tolerates an occasional failed simulation run. Such a failure can happen if the fitting algorithm chooses a particularly poor set of trial force field parameters. The protocol now continues and avoids those parameters in subsequent trials. | MSC: Other | Low | MSC-6121 |
| Minor | For the Polymer and Battery protocols, you can now use the "Other" keyword to specify grid options in the form of a command line for the queuing system. | MSC: Polymer Properties | Low | MSC-6850 |
| Minor | The process to count counter ions at the Run Monte Carlo Reactive Molecular Dynamics protocol now controls whether the counter ion setting is available. | MSC: Other | Low | MSC-6917 |
| Minor | MD stages of Run Monte Carlo Reactive Molecular Dynamics not only provide looped attempts to continue MD but also include timestep reduction for a safer MD start after each reaction is performed. | MSC: Other | Low | MSC-6918 |
| Minor | Run Monte Carlo Reactive Molecular Dynamics improved to also output intermediate reaction cycles. | MSC: Other | Low | MSC-6928 |
| Minor | The 'Molecular Dynamics (LAMMPS)' component now supports recent versions of LAMMPS. | MSC: Examples | Low | MSC-6981 |
| Minor | Run Monte Carlo Reactive Molecular Dynamics protocol has now safer MD steps that can reduce the timestep o continue MD steps. The protocol is also enhanced to have better error output on each cycle when reaction cannot be performed. | MSC: Other | Low | MSC-7030 |
| Minor | The charge assignment in the ReactionFinder is now more stable. | MSC: Application | Low | MSC-7045 |
| Minor | Run Monte Carlo Reaction Molecular Dynamics protocol has now Random Seed choice to reproduce a specific run and outputs for testing protocol. | MSC: Other | Low | MSC-7073 |
| Minor | Manage Reaction Mechanisms protocol now returns the zipped study table with the correct path for Create and Extend processes. | MSC: Application | Low | MSC-7098 |
| Minor | Issue where Phase Field results could be missing field trajectories, when run on Windows server, have been corrected. | MSC: Phase Diagrams | Low | MSC-7107 |
| Trivial | The Fit VdW Parameters protocol no longer fails with reports of a Java out-of-memory error while generating the heat map charts in the output report. The protocol now continues, but omits the heat maps from the report. | MSC: Other | Low | MSC-6891 |
| Trivial | To avoid 'Error compressing LZ4 stream' in the protocol "Calculate Yield Stress and Critical Distortional Strain", the trajectory analysis is now performed inside the parallel subprotocol. | MSC: Examples | Low | MSC-7002 |
| Trivial | The Fit Valence Parameters protocol now only performs constrained optimization when you use the Scan configuration method. | MSC: Examples | Low | MSC-7037 |
| Trivial | Forcite components now disable the Charge Assignment and Summation Method parameter groups for forcefields for which they are not relevant, including EAM and MACE. | MSC: Application | Low | MSC-7057 |
| Trivial | An issue with 14-scaling in periodic systems containing 5-membered rings has been resolved. | MSC: Examples | Low | MSC-7085 |
Notebook Collection
| Severity | Description | Areas Affected | Risk | Defect |
| Minor | The component will not report errors related to an unknown package global variable anymore. | ANC: API | Low | ANC-294 |
Resolution
BIOVIA Pipeline Pilot 2025 was released in November 2024 and is available for download at https://software.3ds.com under BIOVIA products:
Product line: Lab, Scientific and Content Solutions
Release: BIOVIA 2025
Level: BIOVIA 2025 Golden
Fixes for this level: -
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