February 1, 2006 (Vol. 26, No. 3)

Maximizing Efficiency across Drug Discovery Workflow with Benchware Notebook

Todays demanding drug discovery environment requires close collaboration within and between multidisciplinary groups of scientific teams and necessitates that individual research efforts are maximally leveraged. These teams need access to experimental work and results in real-time, while individual team members demand technologies that support complex scientific workflow and enable research collaboration.

Electronic systems, specifically electronic laboratory notebook (ELN) applications, currently exist to lend scientific support and fuel innovation in such environments. Historically, the cost and labor necessary to integrate such electronic systems into already complex informatics infrastructures has been prohibitive. Tripos (www.tripos.com) Benchware Notebook is designed specifically to combat this problem, with enterprise-wide integration and deployment.

Based on the requirements of drug discovery scientists, Benchware Notebook supports research operations at large, multisite pharmaceutical organizations as well as small, single-site biotechnology companies. In addition to workflow-enhancing features, Benchware Notebook provides an open, service-oriented architecture that is designed to integrate with existing enterprise systems, including Laboratory Information Management Systems (LIMS), compound registration, and inventory tracking systems, to support seamless user workflows.

From the outset, Benchware Notebook was designed to support the needs of both scientists and IT professionals.

Reactions are imported, reagent amounts entered, and yields automatically calculated in Benchware Notebook

Enterprise Integration in Mind

Benchware Notebook was designed to allow a variety of systems to be easily tied together into seamless workflows for discovery scientists, while at the same time providing a flexible integration framework. The system uses open technologies, versus proprietary web-service protocols, to create a set of well-defined application program interfaces (APIs) and web services. Using the included Software Development Kit, informatics managers can connect Benchware Notebook to other existing enterprise systems and/or desktop tools, and modify these connections over time to meet changing business needs.

This services-oriented integration framework, designed as part of a web-services and product development initiative Tripos refers to as Service Oriented Informatics (SOI), allows informatics managers to exploit legacy resources, such as native LIMS systems and compound databases, and anticipates that scientists within the organization may require integration of new technologies and data sources as they become available and are adopted into the research organization.

The out-of-the-box integration framework offered by Benchware Notebook also provides flexible options for developing, deploying, integrating, and accessing discovery informatics technologies from within the Benchware Notebook environment, resulting in a more productive use of existing resources and greater rates of end-user adoption.

Implementing an electronic laboratory notebook system based on a services-oriented integration framework leads to potential costs savings. Without an open integration framework, the task of integrating a variety of tools and external systems could turn into a costly and time-consuming endeavorone that may require modifications to core product code.

Accordingly, the application and data-integration costs associated with many ELN implementations may exceed software license costs and extend project timelines. Such modifications to core product to support enterprise integration may also introduce numerous challenges with long-term maintenance, and may require ongoing integration work long after the initial deployment. Benchware Notebooks open architecture was designed to minimize such costs and challenges.

Drug Discovery Workflows

Benchware Notebook is specific to the area of early-stage drug discovery. A generic electronic laboratory notebook application, one meant to be applied equally across all disciplines comprising the pharmaceutical value chain, ranging from early-stage discovery to manufacturing, does not effectively serve the specialized needs of the discovery chemist or biologist.

To gain a better understanding of how Benchware Notebook affects research efficiency and innovation for scientists in an enterprise setting, we can look at its real-life use within a global drug-discovery organization.

Case Study

The deployment of Benchware Notebook to several hundred global users at Schering (www.schering.com) took place in the context of a larger informatics solution, the Enterprise Chemical Information Management System (ECIMS).

Built on the Benchware Notebook platform, the ECIMS solution provides support for planning and synthesis of compounds and handles the logistics of compound management through additional compound registration, inventory, and ordering functionality. ECIMS allows researchers to share critical research data and manage research projects.

To enter a new experiment in Benchware Notebook, a Schering user starts with a template notebook page. The components of the template page can be dictated by business rules, and dynamically customized and repositioned by the user to suit individual workflows. New customized page components can also be defined and added by a system administrator, and can be created to be domain-specific to areas such as medicinal chemistry, parallel chemistry, high-throughput chemistry, genomics, screening, ADME, and toxicology. Auto-calculation functionality within a Benchware Notebook page allows Schering chemists to determine experimental factors such as stoichiometric amounts and molecular weights (Figure).

In addition to using Benchware Notebook to plan and document experiments, Schering scientists take advantage of features within the application to collaborate with colleagues throughout the organization.

With all entered data stored in an underlying Oracle database, Benchware Notebook users are able to dynamically search notebook pages across the organization. Searches can be done by using conventional alphanumeric search terms as well as by using more complex chemistry-centric search terms, allowing users to search by compound structure.

Researchers at Schering use these features to study reactions produced by colleagues to gain new insights into their own plans, thereby saving valuable time and sparking innovation.


In the drive to increase research productivity, drug discovery organizations are focusing on extracting the maximum value from the intellectual capital of the organization through the creation of enterprise-wide knowledge bases.

Benchware Notebook is unique in its use of an open service-oriented architecture that is scalable, readily integrated with legacy informatics systems, and extensible to future research needs and capabilities. This architecture gives the system flexibility in accommodating the diverse needs of informatics managers and scientists and enables the creation of an enterprise-spanning knowledge base that meets the needs of individual scientists, research teams, and the enterprise as a whole.

Finally, Benchware Notebook was designed to support and mirror workflows specific to the disciplines involved in early-stage drug discovery. Applications that closely fit end-users needs and workflows may more readily be adopted enthusiastically and completelya requirement for successfully supporting collaborative discovery environments.

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