Dotmatics R&D Innovation For IT Organizations

Manageable R&D IT – infrastructure that makes a difference

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The right infrastructure at the right level of effort

A solid IT infrastructure is an assumed requirement for all R&D organizations. Now that digitalization has become embedded  in corporate strategies such as data-driven innovation, IT organizations need to ensure that scientists have the flexibility to capture and utilize data efficiently. Scientists rarely work alone: therefore, infrastructure needs to span departments, disciplines, and geos while at the same time supporting collaborative efforts and outsourcing. These infrastructures are often exceedingly complex, either because they have grown from isolated efforts at the department level, are amalgamated through acquisitions, or are part of legacy systems that are beyond their life expectancy.

R&D IT systems come with significant associated costs, and it is the job of the IT organization to design and select the best possible infrastructure by considering all contributing fees; licensing, maintenance, deployment, customization, and implementation.

Your challenges

Wondering how to

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Provide scalable infrastructure?

Deal with the challenges of deploying on premises, on the cloud or moving to SaaS. Support collaboration and outsourcing efforts. Consolidate vendors and avoid patchwork systems.

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Be flexible while minimizing cost?

Minimize customizations. Implement new workflows and roles using existing infrastructure. Support data-driven research from hard-to-access data silos. Evolve systems to support new science.

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Consolidate complex landscapes while retaining functionality?

Avoid rip-and-replace yet eliminate technical debt. Phase out legacy systems while providing scientists access to the data stored in them.


With Dotmatics you can

icon Reap the benefits of the unified platform approach

Dotmatics makes good on the platform promise for R&D IT, allowing you to deploy flexible, configurable workflows and roles. As it’s an open platform you can federate data sources, standardize data against a common data models, and apply security schemes that allow you to secure IP without hindering knowledge exchange and collaborations. Our platform supports these efforts via configurations, not customizations, resulting in an infrastructure that is easier to maintain and service.

icon Minimize TCO – do more with less

The Dotmatics platform can be deployed on prem, in private cloud, or as a SaaS infrastructure. Since each scenario utilizes the same codebase, you are never locked into a specific deployment scenario which means your infrastructure is future-proofed for company changes in direction such as a move from on-prem to the cloud or vice versa. Upgrades are greatly simplified since Dotmatics supports all customers via configurations of a single code base, not customizations.

icon Simplify deployment and maintenance

While many organizations are increasingly trying to move IT infrastructure into the cloud, options for R&D IT are limited, creating unique challenges in terms of interoperability, scalability, availability, and latency.

Dotmatics solves this problem with the option to run a Dotmatics supported AWS instance as a SaaS system. We have over 8 years of AWS presence, run over 300 single-tenant customer instances, manage 180+ TB of data. More than half of our new customers choose to run their systems as SaaS configurations.


icon Avoid customizations and complex multi-vendor landscapes

One of the major challenges in R&D IT is how to support complex scientific data and application requirements. Whether companies respond by allowing individual departments to pick “best-of-breed” applications, or engaging in customization projects, the burden for IT departments is generally considerable.

Within the Dotmatics platform, applications have access to all connected data sources, native Dotmatics, in-house developed, or third-party – including web sources.     The application tier also allows connections to third-party applications to allow for integrated workflows and seamless data exchange.

icon Avoid rip-and-replace

R&D IT infrastructures are rarely designed from scratch but need to find strategies to deal with legacy applications and data. Even if technically feasible, a rip-and-replace strategy can create serious change management challenges.

The Dotmatics platform solves these challenges by putting a data intelligence infrastructure on top of existing systems. This federates and contextualizes scientific data and to support scientific data mining and data-driven R&D, including machine learning (ML) and artificial intelligence (AI) applications. Data federation also allows IT departments to implement systems that help smoothing out transitions from legacy systems to modern infrastructure.

icon Keep up with new science

By its nature, science is ever evolving. Consequently, scientists will always require new functionality and data access options to be incorporated into their R&D IT systems.

Dotmatics was founded on the idea that scientists should have access to all of their data, all the time. Data federation and data visualization are core components of our strategy, complemented with a full suite of lab automation and role-based workflow capabilities. We partner with our customers to continuously innovate, recent examples include metadata frameworks, entity creation/registration for biologics and non-specific entities, support for multiple assays within a single experiment as well as graph analysis for mining reaction pathway information.


This solution consists of:

iconDotmatics Browser

Dotmatics Browser is a powerful web-based search and reporting solution that provides federated searching across Dotmatics and third party research databases, enabling research scientists to access all of their data whenever they need it, irrespective of where it is stored.

  • Provides scientific search, such as chemical substructure and similarity.
  • Manages project level and personal search forms and views, queries, lists and reports.
  • Powerful scientific data visualization as forms, tables and charts.

iconDotmatics Cloud

The Dotmatics Platform on the cloud allows the integration of multiple, diverse systems and data sources. Organizations can now securely access all of the Dotmatics solutions, using a web browser, on their own dedicated instance running in the cloud. This provides users with an all-encompassing view of relevant information, enabling better informed science and business decisions. The Dotmatics Platform in the cloud is powered by Amazon Web Services™ (AWS). Data security is guaranteed when using the gold standard AWS infrastructure. Dotmatics’ solutions are installed in Amazon-controlled data centers around the world thus ensuring that data is housed at the user’s preferred location. The Dotmatics Platform provides a single point of access to all science data and functions across multidisciplinary groups. The flexibility enables scientists, collaborators and partners to instantly interact with the same data via the cloud regardless of location and time zone, fulfilling the promise of real time research.

What it does:

  • Each customer’s data is held in a separate dedicated instance
  • Access to your instance is controlled by two layers of firewall and user authentication
  • All traffic to/from the instance is HTTPS/SSL encrypted

At the heart of collaborative research

  • Dotmatics Cloud in combination with the Dotmatics Platform revolutionizes the way that collaborative research is done
  • Dotmatics’ flexible and comprehensive platform offers secure access to users per project
  • Not just simple file sharing, but true idea generating solutions
  • Internal and external R&D teams across the world can share data and generate new discussions leading to the creation of innovative ideas and IP

Protect and control your database with single tenancy

  • A separate instance of the Dotmatics Platform and its supporting infrastructure is available to each customer, which provides significant capability to easily configure the system to mirror the requirements of each team
  • For example, R&D teams can adapt features such as additions to individual modules to various internal databases and external partner databases

Secure access from users’ preferred device

  • Simply set up new collaborative projects with multiple teams and start sharing data promptly with no extra training required for users with computers or mobile devices
  • Data from collaborators can be accessed in real time by all members of a project, enabling around-the-clock global research
  • The Dotmatics Platform is hosted within the secure and private AWS infrastructure
  • Amazon’s servers are supported by ISO 27001 certification and have successfully passed multiple SAS70 Type II audits

iconDotmatics Platform

The Dotmatics Platform is the common framework that supports the Dotmatics web-based scientific applications and allows them to work together to provide users seamless end-to-end workflows. The Platform supports managed deployments in the Cloud or self-supported deployments on premise. An open architecture enables workflows to include third-party software integration. When used together with Dotmatics Browser the Platform allows federated data access across corporate and external research data.The Dotmatics Platform is completely unified – it provides common data models, code and architecture to support business workflows that span the capabilities of the individual applications. This is important for enterprise enablement of research organizations, providing ease of maintenance and development. It gives the lowest possible total cost of ownership compared to platforms that support their applications with less tightly integrated collections of multiple technologies and/or architectures with multiple development histories.

  • Provides the framework that supports all Dotmatics web-based scientific applications and allows them to work together to provide seamless workflows.
  • Portal for administrators to manage users and groups, applications and configurations
  • Provides APIs for automation and integration with 3rd party software
  • When used in conjunction with Dotmatics Browser provide access to data from across an organization and externally

iconDotmatics Studies Notebook

Dotmatics Studies Notebook is an Electronic Laboratory Notebook (ELN) with flexible templating to capture, store and search experiments from all scientific disciplines.

  • Flexible protocols (implemented as templates) allow the single ELN to accommodate highly structured experiments such as synthetic chemistry and protein purifications, as well as more ad hoc experiment types often useful for target identification and discovery biology experiments. Ad hoc experiments are also often used to support a transition from paper based notebooks
  • Dotmatics Studies Notebook allows for collaboration on experiments by multiple scientists within or between organizations

iconDotmatics Studies

Dotmatics Studies is a highly flexible, innovative screening data management solution to capture and analyze all types of screening experiments from high content (HCS) and high throughput (HTS) to dose-response and DMPK studies.

  • Defines analysis protocols for plate and non-plate based assays
  • Provides out-of-the-box and custom assay protocols, curve fit calculations, plate readers, and plate layouts captured and stored for re-use
  • Supports very high data volume assays
  • Defines business rules for very automated classification of results
  • Manual or automated processing allows screening scientists to apply the screening protocols to process raw instrument and validate the results, or experiment creation and processing to be driven via an automation layer.
  • Once completed and validated, screening results are immediately available via Browser to the project team

iconDotmatics Cascade

Dotmatics Cascade manages the requesting and assignment of laboratory tasks, and tracking the progression of samples, across multiple teams within an organization or across a collaborating network.

  • Dotmatics Cascade allows organizations to define available services, such as assay execution or analysis and the associated scientific team
  • Scientists create requests for services and submit compounds Service managers manage, group and assign requests for execution
  • Service team scientists accept requests, create and auto populate experiments to execute them
  • Teams can see request status and monitor compound or sample progression

iconDotmatics Chemselector

Dotmatics Chemselector manages very large chemistry datasets with fast search and trivially simple maintenance/update. It has a modern user interface focused on browsing and filtering for molecule, reagent and sample selection. The available eMolecules+ for Chemselector dataset provides access to highly curated eMolecules sourcing data.


  • High performance chemical searching, filtering and selection designed to support critical medicinal and synthetic chemistry workflows including:
    • building block selection
    • fragment set design
    • screening molecule selection for scaffold hopping
    • chemical series validation for hit to lead campaigns (“SAR by catalog”)
  • Uses Dotmatics provided datasets such as eMolecules+ for Chemselector and ChEMBL for Chemselector, or datasets built in-house from corporate or public databases

eMolecules for Chemselector

  • A sourcing dataset of over 20 million compounds and 8 million unique chemical substances with availability, pricing and packaging information from hundreds of suppliers using data curated by eMolecules
  • Provides additional information to the eMolecules source data to enhance searching, including deprotected structures, calculated physicochemical properties and structure classes
  • Simple monthly updates provide the latest eMolecules supplier and catalog data

iconDotmatics for Office | D4O

Dotmatics for Office makes Microsoft™ Office® applications such as Excel®, PowerPoint®, Word, OneNote and Outlook® chemically aware.

  • Adds live chemistry to documents, emails, spreadsheets and presentations
  • Works with Dotmatics Browser to retrieve chemistry and associated scientific data from databases directly into Microsoft Office applications
  • Provides property calculations, searching, enumeration and r-group analysis on the live structures in Excel

iconDotmatics Elemental

Dotmatics Elemental is a chemical sketcher that enable scientists to draw, edit and save structures and reactions, and calculate properties.

  • Sketch molecules, reactions and structure queries
  • Calculate chemical properties
  • Available as a fully-featured desktop application, iOS app or lightweight JavaScript plugin for sketching in-line in webpages

iconDotmatics Gateway

Dotmatics Gateway is a scientific document management solution that serves as a central place to share project documents and associated information across an internal or externalized team. It provides discussion threads and project events feeds.

  • Stores and shares project documents such as reports, presentations and literature
  • Provides news feeds detailing the latest documents and project results
  • Provides discussion threads associated with documents and project events
  • Complements structured project databases such as the molecule registry or assay results databases

iconDotmatics Inventory

Dotmatics Inventory is a fully searchable sample and materials inventory that tracks chemicals, biologics, instruments and associated data across a hierarchy of locations and manages the dispensing and plating workflows, as samples are moved through an R&D process.

  • Defines a hierarchy of storage locations for an organization
  • Track samples in containers such as bottles and plates in those storage locations
  • Manages research materials, reagents and assets
  • Manages the aliquoting and dispensing workflows to distribute samples for testing
  • Maintains a full audit trail
  • Allows for searching and reporting on inventory information alongside other corporate data

iconDotmatics Nucleus

Dotmatics Nucleus is a straightforward solution for importing flat files, such as spreadsheets, into a database.

Easily upload data from a variety of sources ready for query and reporting in Dotmatics Browser.

iconDotmatics Pinpoint

Dotmatics Pinpoint is a chemical cartridge for indexing and searching chemistry within Oracle databases.

Pinpoint enables indexing of chemical structures, calculations of physical chemical properties and substructure searches within an Oracle database. It is used to support structure searching with Dotmatics Browser, check for structural uniqueness and register molecules in Dotmatics Register, and store and search chemical reactions in Dotmatics Studies Notebook.

iconDotmatics Reaction Workflows

Reaction Workflows is a graphical environment that enables scientists to build and execute data processing workflows to perform common cheminformatics tasks, such as library enumeration, structure normalization and compound profiling. Users build workflows in a drag-and-drop environment by selecting and connecting nodes that provide inputs (e.g a list of reagents) and outputs (e.g. view in Dotmatics Vortex) or perform actions (e.g. perform a reaction), configuring them with data and then executing the workflow to produce results. Many different tasks can be configured including:

  • Synthetic library enumeration for an ELN experiment
  • Virtual library enumeration and profiling for virtual screening
  • Structure normalization for registration
  • Idea generation via lead hopping or to avoid liabilities
  • Chemistry file clean up

iconDotmatics Register

Dotmatics Register is a web-based compound and batch registration system used to maintain corporate chemical registration and reagent databases.

  • Captures chemical structure and associated data for newly synthesized or acquired compounds
  • Determines uniqueness and assigns new corporate IDs and/or new batch/lot IDs
  • Allows for single compound or batch registration
  • Allows registration from its own UI or from an ELN (Dotmatics or third party)

iconDotmatics Vortex

Dotmatics Vortex is an interactive data visualization and analysis solution for scientific decision support. Building on and extending the spreadsheet paradigm, it provides the data manipulation, statistical analysis and sophisticated plotting capabilities required to explore and understand any complexity and size of data. Vortex is also scientifically aware providing native cheminformatics and bioinformatics analysis and visualizations.

  • Allows users to understand, refine and select from large and/or complex data sets
  • Allows teams to collaborate on scientific analysis through shareable workspaces and reusable templates
  • Understands numeric, textual, image, chemical structure and biologic sequence data
  • Generates high performance, interactive visualizations, including charts and tables
  • Handles very large datasets – e.g. tables of millions of compounds by thousands of descriptors or cells containing whole genome sequences
  • Has inbuilt data mining, statistical, cheminformatics and bioinformatics analysis functions
  • Loads data from many types of file or when used in conjunction with Browser, directly from databases

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