2007 Aaps - Poster - Bioanalytical Manager
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Bioanalytical Manager: A Workflow-Based Approach to Bioanalytical Informatics 1
1
2
2
1
John P. Walsh , Charles E. Taylor , Qiner Yang , Robert Beltran and Robyn A. Rourick 1
2
Kalypsys, Inc. Pharmaceutical Sciences Department, Informatics Department 10420 Wateridge Circle, San Diego, CA 92121 Abstract Purpose Bioanalytical laboratories in Drug Discovery are resourced to support activities from all stages of Research. A server-based tool was deployed to allow complete visibility of the Bioanalytical process by all departments and interested parties within the company. The initial deployment of this system was designed to improve the sample handoff process and seamlessly collect metrics on the Department for sample and study metrics. Further utility is being added for the Bioanalytical staff by automating the sample preparation, sample analysis and study reporting to increase the efficiency of the Department.
Bioanalytical Department Needs:
During implementation of the system, several fields and features were added to make the system usable on a company-wide scale
Ability to assign personnel to specific tasks so everyone knew each others obligations Knowledge of certain study parameters relevant to Bioanalytical
The data fields were broken up to easily allow storage and query within a database
Number of samples Species of subjects
Incorporation with a Freezer or Vivarium management system was left for future development
Matrices of samples Urgency of results
Collection of data points was refined to better capture the workflow
Point-of-contact for any questions Methods The typical progression of an in vivo study was dissected into several linear stages: planning and protocol development, in vivo, bioanalytical analysis and report generation. At the creation of a study, the compounds to be tested are associated to the entry and all relevant fields for each stage of the process are created. As the study progresses through the stages, stage appropriate information is associated to the study, including files and notebook references, so that the finalized study has a full data history. This information, along with system timestamps, allows for the rapid metrics analysis. Further development of the system is focusing on tools to help the analysts with laboratory work; freezer sample management integration, liquid handler script generation, LC/MS sample list creation and automated PDF report generation.
Track and calendar the historical context of the department to better make decisions in the future
System-generated timestamps are used for milestones (study creation, stage transition, etc.)
A centralized repository for all study communication to dissect the analysis performed Project Team & Company Needs: Association of all bioanalytical data to a compound and project Tracking of all notebook entries Migration of all data into a location that can be mined for SAR information Automatic notification of study stake holders of important events and updates A centralized repository for all study communication
Selection from lists was strongly preferred over free user entry
Figure 1. Homepage view of the Bioanalytical Manager. Each row displayed represents a study in the currently selected stage (Bioanalytical Analysis stage, in this case). Notice the tabs that denote the separate stages to which a study may belong. Navigation to each stage is accomplished by clicking on the stage name. The user interface was designed to integrate well with the look-and-feel of the rest of the company intranet sites.
Check boxes are used for multiple selection opportunities
Release 1:
Drag-and-drop area for file capture was added
Feasibility of a company-wide bioanalytical collaboration tool was deployed as Release 1
Any file type can be added to the system
The workflow-management aspect of the system was refined prior to new functionality
Indexing and backup is accomplished through a Windows directory backend
Application of business rules to the system was required to allow complete adoption Results The ability to attach files has allowed other groups to use the Manager for study planning and management with the side benefit of all parties being informed. Metrics collected on the department have supported crucial business decisions concerning investment in resources. Bioanalytical processing tools and freezer management integration are in betatesting and are proving the concept of a fully integrated bioanalytical laboratory. Conclusions The deployed Bioanalytical Manager server-based application has been successful in streamlining the activities of the deliverables from the Department. Crucial and relevant information is captured on each study and serves a useful perspective in the planning and recreation of work. Bioanalytical processing tools in development and testing show enormous potential to impact the routine resource demands.
Introduction
Results
Decisions were being made without a comprehensive understanding of the departmental obligations The informal nature of the process created an environment for the potential of misinformation or mishandling of samples Study progress was best monitored through one-on-one interactions with scientists
Registration Stage Assignee
Several study parameters are required for creation, including Project Compound(s)
(Based on Study Type) Email Notification Study Director Registration Assignee
Study Type (i.e. PK, Pharmacology, TK, etc.)
Assessment of feasibility and impact to the project Approval of internal and external resources prior to initiation of the study
In Vivo Assignee(s)
(Based on Study Type) Email Notification Study Director BioA Assignee(s)
The study is currently in its dosing and samples collection stage
Report Gen Assignee
Samples are received and appropriately logged
Overall System Requirements: A centralized, comprehensive display of all current and upcoming studies Ability to track study progress in and out of the bioanalytical department Automatic notification of study stake holders of important events and updates An open architecture to evolve with the process and the department
Sample Dropoff Date, Sample location, Priority, Notebook Ref., etc.
Interpretation of all study findings Generation and analysis of any pharmacokinetic parameters, if appropriate A detailed Study Report is issued describing the conclusions of the study
The workflow is automated through integration with the laboratory systems Using the platemap and selection of an appropriate calibration curve, a Tecan executable file is generated in the system The injection plate is registered in the system after correlation with the Tecan error log An LC/MS/MS injection list is generated for easy transport of the samples to the system
Figure 5. Schematic of the added functionality for Bioanalytical Manager Release 2
Conclusion
Input Study Relevant Information:
The Bioanalytical Manager has been successful in streamlining the activities of the Bioanalytical Department
Number of sample analyzed, Number of standards prepared, Notebook Ref.
Stage: Study Report Generation
Important and relevant information on each study is captured and archived for data mining
Associate stage contact for conduct of study
The implementation of the tools of Release 2 are showing great promise towards the increased efficiency and quality of the Department
Interpret bioanalytical and in vivo findings
Acknowledgements
Email Notification
Study Report Generation:
Free text entry for any observations, anomalies and conclusions from the study
Number of standards run per study as referenced by study type
(Based on Study Type)
Study Director
Association of information from the study to the report (i.e. Instrument, Matrices, etc.)
Impact on the department as assignable by project
Default Report Gen Assignee
A detailed Bioanalytical Analysis Report is issued describing all analyses performed
Intuitive and customizable user interface
Input Sample Relevant Information:
Figure 3. Study Detail page listing all of the fields that a user has access to view and edit. The attached files section has drag-and-drop capability for any type of files to be associated with the study.
Author and attach a final Study Report
Bioanalytical preparation and quantitation of all study samples
Data from the database inserted into specified portions of an XML document
Extract and analyze all samples
(Based on Study Type)
Study Director
Incorporation of Report Generators to facilitate the ease and quality of distributed reports
Number of samples run per week
Associate stage contact for conduct of study
Default Report Gen Assignee
Email Notification
Integration with the department’s Freezer Management System for sample tracking
Number of studies run per week
Author and attach an Analytical Report
Number of study samples requiring bioanalytical analysis are inputted
Allows integration with all platemap based utilities
Stage: Bioanalytical Analysis
Observations and study notes are collected
Bioanalytical Analysis:
Start & End Date, Priority, Outsourced Vendor, Protocol, Notebook Ref., etc.
Perform and note any findings from study
Ordering and quarantine of the appropriate subjects prior to the first dosing In Vivo Study Conduct:
Input Study Relevant Information:
Associate stage contact for conduct of study
Default Analysis Stage Assignee
Reserves a location in the database for association of data to each sample
Useful reports can be generated to better make decisions on the resources of the department
Stage: In Vivo Study Conduct
Protocol development of the in vivo portion of the study
Registration of the platemap for all study plates
Number of standards required for analysis captured by the scientist
Approve study and protocol for execution
Email Notification Study Director
Study Number, Title, Type, Project & Compounds, etc.
Collect all information prior to study initiation
(Based on Study Type)
Registration:
Input Study Relevant Information:
Stage: Registration
Default In Vivo Stage Assignee
Automatic requesting of powder from the Compound Management Group for instrument tuning and standard preparation
Notebook references entered by the users are referenced to a PDF of the notebook page during the periodic imaging process
Study Creation
Every idea for a study is entered into the database to assess feasibility
Background: Bioanalytical workload was performed in non-inclusive meetings, by email and primarily through the use of a centrally located whiteboard
Bioanalytical Manager Release 1
Study Creation:
Functionality was designed to increase the productivity of the department
All study relevant files and communications are expected to accompany a study
The system had to adopt to several different study varieties to remain effective
The lifeline of a study was broken up into several high-level “stages”
Release 2:
The authors would like to acknowledge the contributions of all the Bioanalytical Group members for their patience and diligence through the testing and implementation process. Their continued sacrifices are the inspiration for all the hard work invested.
Finalized
Figure 2. Functional schematic of a typical study progression for the initial Bioanalytical Manager. Each stage has certain properties and actions associated to it. This diagram describes the most common modifications made to the study at each stage.
Figure 4. An example of the department metrics available in ready queries from the database. In this case, the graph depicts the number of studies that progressed out of the “Analysis” stage, by week of 2007.
Poster Contact
Email
John P. Walsh
[email protected]
1
2
2
1
John P. Walsh , Charles E. Taylor , Qiner Yang , Robert Beltran and Robyn A. Rourick 1
2
Kalypsys, Inc. Pharmaceutical Sciences Department, Informatics Department 10420 Wateridge Circle, San Diego, CA 92121 Abstract Purpose Bioanalytical laboratories in Drug Discovery are resourced to support activities from all stages of Research. A server-based tool was deployed to allow complete visibility of the Bioanalytical process by all departments and interested parties within the company. The initial deployment of this system was designed to improve the sample handoff process and seamlessly collect metrics on the Department for sample and study metrics. Further utility is being added for the Bioanalytical staff by automating the sample preparation, sample analysis and study reporting to increase the efficiency of the Department.
Bioanalytical Department Needs:
During implementation of the system, several fields and features were added to make the system usable on a company-wide scale
Ability to assign personnel to specific tasks so everyone knew each others obligations Knowledge of certain study parameters relevant to Bioanalytical
The data fields were broken up to easily allow storage and query within a database
Number of samples Species of subjects
Incorporation with a Freezer or Vivarium management system was left for future development
Matrices of samples Urgency of results
Collection of data points was refined to better capture the workflow
Point-of-contact for any questions Methods The typical progression of an in vivo study was dissected into several linear stages: planning and protocol development, in vivo, bioanalytical analysis and report generation. At the creation of a study, the compounds to be tested are associated to the entry and all relevant fields for each stage of the process are created. As the study progresses through the stages, stage appropriate information is associated to the study, including files and notebook references, so that the finalized study has a full data history. This information, along with system timestamps, allows for the rapid metrics analysis. Further development of the system is focusing on tools to help the analysts with laboratory work; freezer sample management integration, liquid handler script generation, LC/MS sample list creation and automated PDF report generation.
Track and calendar the historical context of the department to better make decisions in the future
System-generated timestamps are used for milestones (study creation, stage transition, etc.)
A centralized repository for all study communication to dissect the analysis performed Project Team & Company Needs: Association of all bioanalytical data to a compound and project Tracking of all notebook entries Migration of all data into a location that can be mined for SAR information Automatic notification of study stake holders of important events and updates A centralized repository for all study communication
Selection from lists was strongly preferred over free user entry
Figure 1. Homepage view of the Bioanalytical Manager. Each row displayed represents a study in the currently selected stage (Bioanalytical Analysis stage, in this case). Notice the tabs that denote the separate stages to which a study may belong. Navigation to each stage is accomplished by clicking on the stage name. The user interface was designed to integrate well with the look-and-feel of the rest of the company intranet sites.
Check boxes are used for multiple selection opportunities
Release 1:
Drag-and-drop area for file capture was added
Feasibility of a company-wide bioanalytical collaboration tool was deployed as Release 1
Any file type can be added to the system
The workflow-management aspect of the system was refined prior to new functionality
Indexing and backup is accomplished through a Windows directory backend
Application of business rules to the system was required to allow complete adoption Results The ability to attach files has allowed other groups to use the Manager for study planning and management with the side benefit of all parties being informed. Metrics collected on the department have supported crucial business decisions concerning investment in resources. Bioanalytical processing tools and freezer management integration are in betatesting and are proving the concept of a fully integrated bioanalytical laboratory. Conclusions The deployed Bioanalytical Manager server-based application has been successful in streamlining the activities of the deliverables from the Department. Crucial and relevant information is captured on each study and serves a useful perspective in the planning and recreation of work. Bioanalytical processing tools in development and testing show enormous potential to impact the routine resource demands.
Introduction
Results
Decisions were being made without a comprehensive understanding of the departmental obligations The informal nature of the process created an environment for the potential of misinformation or mishandling of samples Study progress was best monitored through one-on-one interactions with scientists
Registration Stage Assignee
Several study parameters are required for creation, including Project Compound(s)
(Based on Study Type) Email Notification Study Director Registration Assignee
Study Type (i.e. PK, Pharmacology, TK, etc.)
Assessment of feasibility and impact to the project Approval of internal and external resources prior to initiation of the study
In Vivo Assignee(s)
(Based on Study Type) Email Notification Study Director BioA Assignee(s)
The study is currently in its dosing and samples collection stage
Report Gen Assignee
Samples are received and appropriately logged
Overall System Requirements: A centralized, comprehensive display of all current and upcoming studies Ability to track study progress in and out of the bioanalytical department Automatic notification of study stake holders of important events and updates An open architecture to evolve with the process and the department
Sample Dropoff Date, Sample location, Priority, Notebook Ref., etc.
Interpretation of all study findings Generation and analysis of any pharmacokinetic parameters, if appropriate A detailed Study Report is issued describing the conclusions of the study
The workflow is automated through integration with the laboratory systems Using the platemap and selection of an appropriate calibration curve, a Tecan executable file is generated in the system The injection plate is registered in the system after correlation with the Tecan error log An LC/MS/MS injection list is generated for easy transport of the samples to the system
Figure 5. Schematic of the added functionality for Bioanalytical Manager Release 2
Conclusion
Input Study Relevant Information:
The Bioanalytical Manager has been successful in streamlining the activities of the Bioanalytical Department
Number of sample analyzed, Number of standards prepared, Notebook Ref.
Stage: Study Report Generation
Important and relevant information on each study is captured and archived for data mining
Associate stage contact for conduct of study
The implementation of the tools of Release 2 are showing great promise towards the increased efficiency and quality of the Department
Interpret bioanalytical and in vivo findings
Acknowledgements
Email Notification
Study Report Generation:
Free text entry for any observations, anomalies and conclusions from the study
Number of standards run per study as referenced by study type
(Based on Study Type)
Study Director
Association of information from the study to the report (i.e. Instrument, Matrices, etc.)
Impact on the department as assignable by project
Default Report Gen Assignee
A detailed Bioanalytical Analysis Report is issued describing all analyses performed
Intuitive and customizable user interface
Input Sample Relevant Information:
Figure 3. Study Detail page listing all of the fields that a user has access to view and edit. The attached files section has drag-and-drop capability for any type of files to be associated with the study.
Author and attach a final Study Report
Bioanalytical preparation and quantitation of all study samples
Data from the database inserted into specified portions of an XML document
Extract and analyze all samples
(Based on Study Type)
Study Director
Incorporation of Report Generators to facilitate the ease and quality of distributed reports
Number of samples run per week
Associate stage contact for conduct of study
Default Report Gen Assignee
Email Notification
Integration with the department’s Freezer Management System for sample tracking
Number of studies run per week
Author and attach an Analytical Report
Number of study samples requiring bioanalytical analysis are inputted
Allows integration with all platemap based utilities
Stage: Bioanalytical Analysis
Observations and study notes are collected
Bioanalytical Analysis:
Start & End Date, Priority, Outsourced Vendor, Protocol, Notebook Ref., etc.
Perform and note any findings from study
Ordering and quarantine of the appropriate subjects prior to the first dosing In Vivo Study Conduct:
Input Study Relevant Information:
Associate stage contact for conduct of study
Default Analysis Stage Assignee
Reserves a location in the database for association of data to each sample
Useful reports can be generated to better make decisions on the resources of the department
Stage: In Vivo Study Conduct
Protocol development of the in vivo portion of the study
Registration of the platemap for all study plates
Number of standards required for analysis captured by the scientist
Approve study and protocol for execution
Email Notification Study Director
Study Number, Title, Type, Project & Compounds, etc.
Collect all information prior to study initiation
(Based on Study Type)
Registration:
Input Study Relevant Information:
Stage: Registration
Default In Vivo Stage Assignee
Automatic requesting of powder from the Compound Management Group for instrument tuning and standard preparation
Notebook references entered by the users are referenced to a PDF of the notebook page during the periodic imaging process
Study Creation
Every idea for a study is entered into the database to assess feasibility
Background: Bioanalytical workload was performed in non-inclusive meetings, by email and primarily through the use of a centrally located whiteboard
Bioanalytical Manager Release 1
Study Creation:
Functionality was designed to increase the productivity of the department
All study relevant files and communications are expected to accompany a study
The system had to adopt to several different study varieties to remain effective
The lifeline of a study was broken up into several high-level “stages”
Release 2:
The authors would like to acknowledge the contributions of all the Bioanalytical Group members for their patience and diligence through the testing and implementation process. Their continued sacrifices are the inspiration for all the hard work invested.
Finalized
Figure 2. Functional schematic of a typical study progression for the initial Bioanalytical Manager. Each stage has certain properties and actions associated to it. This diagram describes the most common modifications made to the study at each stage.
Figure 4. An example of the department metrics available in ready queries from the database. In this case, the graph depicts the number of studies that progressed out of the “Analysis” stage, by week of 2007.
Poster Contact
John P. Walsh
[email protected]
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