Utilizing the BIOVIA ELN with Pipeline Pilot to Enhance R&D


November 1, 2019

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The BIOVIA ELN is a crucial technology that works with Pipeline Pilot in a seamless fashion.  Modern laboratory technologies such as Electronic Laboratory Notebooks (ELNs) and LIMS have made enormous amounts of data available to scientists in life science laboratories. Scientists that are recording, managing and archiving research data in paper notebooks and performing tasks manually simply cannot keep up with this deluge of data. These paper-based methods lead to scenarios where much collected data is siloed and never analyzed, while many experiments end up being needlessly repeated.

Electronic Laboratory Notebooks (ELNs) are rapidly becoming a fundamental part of every laboratory operation in industries from pharmaceuticals, to chemicals, to academia, consumer goods and more. By facilitating the storing, accessing, analyzing, reporting and sharing of critical research data, ELNs help to create an effective knowledge base for your organization, streamline the documentation and protection of intellectual property, and help scientists collaborate in increasingly global and networked activities from discovery to manufacturing. That said, implementing an ELN is really just the first step in the information management journey necessary to optimize R&D discovery and development.

Faced with intense pressure to control costs and get more out of R&D investments, many life science companies have turned to outsourcing and contract research to stimulate pipelines. As a result, industry-leading pharma companies are focused on implementing R&D informatics collaboration platforms with integrated ELNs in order to aggregate data and drive research decisions.

While entering new data in their ELN experiments, scientists have to couple the data with results coming from their lab’s instruments, and also record source material ID from their inventory for traceability. They also have to add reference to previous experiments, owned by their company or created by third party labs (CRO, university research, common references such as ACD, etc.). Scientists usually know the source of the external data, but they are missing technical IT expertise to add it to their experiment in their ELN. This blog will illustrate how Pipeline Pilot acts as a bridge to combine the new experiment data and external data.

BIOVIA Workbook

By effectively managing the flow of information, materials and tasks among scientists, instruments and software both within and between labs, BIOVIA Workbook delivers an industry-leading, enterprise ELN for life science companies. More than a simple replacement for paper notebooks, Workbook is a highly adaptable and flexible solution that helps transition from tedious paper and manual processes to a highly efficient and integrated electronic environment in non-GxP and GxP labs.

Workbook can be used across multiple scientific disciplines enabling scientists to create experiment templates based on their specific research needs. Experimental data from different domains can then be consolidated into versioned, shareable and searchable documents that are controlled by document workflows with electronic signatures and audit trails for regulatory compliance. Data can also be captured and viewed in a variety of ways – text, tables, spreadsheets, graphs, charts and more – and can be exported to third-party systems and applications.

Compared to other ELN applications, BIOVIA Workbook allows a quick and smooth interaction with the experiment data. Scientists can rapidly switch between different views of the experiment. It can be configured to add complex rules to verify the data entered in the experiments. In addition, Workbook has strong chemistry capabilities like sub structure search support for synthetic chemistry computation, or structure enumeration.

Key benefits of BIOVIA Workbook include:

  • Efficiency improvement through laboratory automatization and acceleration of data entry, processing and reporting
  • Advanced searching and browsing capabilities
  • Minimization of data errors
  • Protection of intellectual property (IP)
  • Gain operational and experimental insight through improved knowledge management
  • Integrate and automate instrument data capture and processing
  • Streamline regulatory compliance
  • Implement consistent processes across organizations
  • Extensible and customizable

Using Workbook with Pipeline Pilot

Digitalized scientific laboratories are generating more data than ever before, but in order to generate insights from this data, it needs to be examined effectively using accessible tools with advanced analytics. BIOVIA Pipeline Pilot is a graphical scientific authoring application that optimizes the research innovation process, increases operational efficiency and reduces costs for both research and IT. Pipeline Pilot automates the scientific analysis of data, enabling users across the enterprise to rapidly explore, visualize and report research results.

Pipeline Pilot offers a rich and intuitive way to access data from different data sources. It also comes with a lot of different existing Pipeline Pilot example protocols, ready for production use. Scientists or IT personnel can easily build or modify Pipeline Pilot protocols to access their own data or implement custom business rules. In addition, Pipeline Pilot offers a simple way to generate reports.

Pipeline Pilot allows you to:

  • Complete projects faster by leveraging existing research and intellectual property and automating routine data gathering and analysis processes
  • Uncover knowledge hidden in your data by quickly aggregating and processing massive volumes of structured and unstructured data from multiple disparate research areas
  • Encapsulate and deploy best practices to ensure compliance and enable collaboration across your research and development organizations
  • Reduce direct research costs

Some BIOVIA products like ChemReg, BioReg, or Insight are directly built on top of Pipeline Pilot. ChemReg or BioReg enables registration of new compounds with corporate specific metadata and rules. You could leverage these rules by invoking ChemReg or BioReg from Workbook, based on the same framework of Workbook and Pipeline Pilot integration. Insight allows you to quickly isolate a subset of your data and visualize it with different dashboards to make decisions. Workbook data can be accessed from Insight.

BIOVIA Pipeline Pilot together with BIOVIA Workbook can dramatically enhance scientific discovery and innovation for your organization. With BIOVIA Workbook, you will get, out of the box, classes and python code to call Pipeline Pilot protocols from Workbook. They can be utilized to add extra buttons to the experiment toolbar to read data from Workbook, pass it to a specific Pipeline Pilot protocol, execute the protocol, and import the results of the protocol execution back to Workbook experiment.

Pipeline Pilot flexibility allows Workbook to provide a wide range of benefits:

  • Optimization of Scientifically Aware Data Analysis – Pipeline Pilot allows operators from any programing level to tackle the most complex data processing and analysis tasks. Pipeline Pilot protocols are built using simple drag-n-drop boxes representing processing nodes. These nodes can be data readers, filters, pivoters, etc. and connection between two nodes will translate into data flow. Simply connect the nodes to complete the whole process. By calling such protocol from Workbook, you could easily compute extra properties and add the results to your original experiment.
  • Utilize Over 1000 Validated Scientific Components – Pipeline Pilot is the most scientifically-aware visual programming solution on the market. Its library of validated scientific components and best practice workflows cover a broad range of scientific disciplines and provide data management, analysis and reporting capabilities for text, numeric and complex scientific data, including chemical structures, biological sequences and scientific images. This will add extra validation on top of the already rich data constraint available from Workbook.
  • Operationalize Scientific Intelligence – Pipeline Pilot’s open and extensible integration framework seamlessly integrates in-house or third-party databases, applications and algorithms. It effortlessly fits into your unique IT environment, securely connecting both on-prem and cloud systems to generate enterprise-wide scientific intelligence. Pipeline Pilot makes it practical to insert instrument data like NMR or chromatography data into your Workbook experiments.
  • Leverage Analytics – Pipeline Pilot provides a comprehensive suite of scientifically-aware modeling tools, statistical filters and clustering components for scientific predictive analytics. It helps you go beyond typical data processing and analysis to gain a competitive advantage in today’s data-driven world. Workbook data, across experiments, could be accessed as a data pool, then analyzed and reported though Pipeline Pilot protocols.
  • Accelerate the Research Innovation Cycle – Pipeline Pilot protocols can automatically encapsulate and annotate your organization’s best practices. Users can share and re-use processes via web services across your organization to simplify business process automation and standardize operations on an enterprise level.

In addition, Pipeline Pilot can enhance other BIOVIA applications, including, but not limited to, Workbook, Insight, Registration, Discovery Studio, and ScienceCloud. Using specifically designed extension points, Pipeline Pilot can automatically provide computational services, create charts or full reports, be used to load data from files, databases and online resources, and integrate with other applications and instruments to create a unified IT infrastructure.

Beyond Pipeline Pilot Integration

A common, uniform way to access data is through micro webservices. These external webservices often provide an API to perform CRUD operations using ReST technology, with JSON to serialize and deserialize data. Pipeline Pilot already provides components to connect to such webservice endpoints, and translate JSON data packets into and from Pipeline Pilot data. On top of that, Pipeline Pilot protocols can also be configured to behave as ReST entrypoints. These protocols can then be called by external applications to process and produce JSON data packets. Many BIOVIA web applications use this method to submit requests in their javascript implementation.

The same type of interaction can be achieved from Workbook. Using a different set of wrapper classes, from Workbook libraries, you can interact with Pipeline Pilot protocols. This will allow your organization to reuse existing Pipeline Pilot protocols, and access additional resources in the same uniform way, through ReST entrypoints. Some data aggregation may be done in Workbook instead of Pipeline Pilot, with lighter data packets, more control on how data is manipulated in Workbook, better feedback to the end-user, and some performance improvements.

BIOVIA Workbook, Foundation-Hub, and Pipeline Pilot would work well for this type of interaction. They all use the same authentication framework, with a single token per user. Workbook can communicate to Foundation-Hub to get user information or instrument metadata. It could verified the data before passing it to Pipeline Pilot protocol. Pipeline Pilot protocol could process the data, build PDF report, add the report to Foundation-Hub, and provide a link to the report back to Workbook. All these interactions could be done with a common pattern using ReST entrypoints. Such implementation should be easy to maintain and extend. The ReST entrypoints should represent stateless webservices, thus reducing coupling between the different pieces integrated inside Workbook.


Electronic Laboratory Notebooks are key component of a digital laboratory environment that helps scientists execute faster, more informed, high-quality science. In this context, BIOVIA’s Workbook provides a highly adaptable and flexible solution that is configurable for use across multiple scientific disciplines. When deployed properly, Workbook can significantly improve data management, collaboration, IP protection, productivity and process efficiency across your organization.

BIOVIA’s Workbook capabilities can be significantly extended and enhanced when utilized with Pipeline Pilot – a graphical scientific authoring application that provides a comprehensive environment for the design, training, validation, and deployment of virtual models utilizing advanced analytics. The Pipeline Pilot platform supports a wide range of analytics capabilities, component collections, and domain-specific functionalities to support a full battery of scientific tasks for your organization.

To get the most out of your Workbook and Pipeline Pilot investments, it is important to work with a quality informatics consultant who understands the platform, your applications, and your scientific domain, and will work with you to complete the necessary business analysis and requirements gathering. Astrix has an experienced team of Workbook and Pipeline Pilot experts that can provide services for all your support needs including implementation, instrument and system integration, workflow and application authoring, custom reports, user training and more.

As the premier BIOVIA Services partner, Astrix provides increased value to customers through cost effective design, implementation and/or integration services leveraging BIOVIA applications and software. If you wish to learn more about Astrix services, or if you wish to discuss your overall laboratory informatics strategy with an Astrix expert, please don’t hesitate to contact us.


Contact us today and let’s begin working on a solution for your most complex strategy, technology and staffing challenges.

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