Dotmatics for Data Intelligence Software

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Making data-driven R&D a reality

As R&D teams are pressed to accelerate the pace of innovation while facing stagnant or shrinking budgets, the promise of data-centric R&D models seem irrefutable. Whether organizations are aiming to increase the reuse of existing knowledge, implement data-driven decision making, or are working towards new R&D models based on artificial intelligence (AI) / machine learning (ML), two prerequisites are often neglected: Data needs to be readily available and the context of these data needs to be understood.

Data together with context is data intelligence, and therefore should be viewed as foundational for any data-centric R&D effort.

Your Challenges

Do you need

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The right data for AI/ML?

Data-scientists need accurate and reliable R&D that correctly reflect experimental context, without having to worry about their sources, i.e. departments, disciplines, and collaborations.

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The right data for decision support?

Research managers need clear line-of-sight into how their projects are progressing with up-to-date dashboards and update reports that are easy to compile.

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The right data to plan your next experiment?

Scientists need to learn from past successes and failures. They need to understand what worked before and what steps lead to success.


With Dotmatics you can

icon Contextualize data via workflows and roles

Why is it so difficult to gain value from R&D data? After all, many organizations in life sciences and chemicals/materials research have invested in digital infrastructure designed to capture and manage R&D data. However, when it comes to retrieving data out, the situation is often less than ideal, because the wider experimental context is lost.

Dotmatics resolves this challenge with a unified, data-centric platform approach that integrates the different data types which make up the experimental fabric. This capability also allows tailoring of permissions, based on roles For example, lab technicians may only see the data relevant to a specific test, while scientists can analyze the totality of data that makes up a specific experiment.

icon Query data for complex experiments

Given access to all data connected to a given experiment, scientists can explore data in ways that they otherwise couldn’t. Dotmatics experimental workflows are configured to include all relevant data in one place without overburdening the user with data that aren’t relevant to their analysis.

Whether experiments are highly standardized, such as antibody screening workflows, or highly diverse such as in materials science applications, Dotmatics provides a flexible framework to give a holistic view onto your research data, allowing you to cross reference chemistry, biology, formulation, process and analytical/physical characterization data.

icon Extract knowledge

While it is incredibly powerful being able to access all relevant data for an experiment in one place, Dotmatics can take advanced knowledge extraction one step further. Oftentimes, researchers need their analyses to span series of experiments, whether to analyze a multi-step reaction with all their intermediates, or to understand how a series of experiments resulted in a successful outcome. Or, when project requirements are close to prior work, relevant experiments need to be aggregated to create the best possible starting point. Without Dotmatics’ data intelligence solutions these efforts often become insurmountable, resulting in the duplication of costly experimentation.

icon Visualize data and create decision support

Data visualization is a key activity within data intelligence: the process of turning data into knowledge. Unlike others who see data visualization as an endpoint, Dotmatics’ Vortex is an integral part of the data lifecycle, allowing scientists to feed their insights back into the platform. This enables decision support or creates the basis of new projects. Or, selections of relevant experiments within the design space may be fed into other applications, creating an open environment for innovation.

icon Be flexible in your platform design

The Dotmatics unified platform can be deployed either standalone or as a solution to integrate various transactional systems (e.g. LIMS and/or ELN) to help you turn your research data into valuable assets to accelerate innovation. Integrations can be implemented to tie various data silos together or to span a variety of disciplines (e.g. chemical synthesis, formulations, process and analytical/physical characterization). Other integrations at the application level allow for the streamlining of workflows (e.g. for instrument data acquisition and preprocessing).


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.


Blueprint is a web-based visualization and scientific analytics application. It is designed to help project scientists working on small molecule discovery projects to visualize and analyze their data, and to help them to design their next set of compounds to make.

  • Simple guided web user interface designed for bench scientists who are not data analysis experts and may not spend all day, every day in data analysis tools
  • Interactive visualization of scientific data with charts, tables and grids designed to explore molecular datasets
  • A carefully curated set of the more important workflows for chemistry calculations and cheminformatics analytics to understand SAR data sets
  • Enables communication through shared workspaces
  • Seamless integration to the Dotmatics suite:
    • Browser to assemble project data
    • Reaction Workflows to design libraries and chemical series
    • Vortex to enable deeper ad-hoc analysis

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 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

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 Cloud

Mobile technology offers a unique opportunity to collaborate, access data and make decisions on the go, increasing throughput and reducing time consumed by review processes. 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.

  • 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 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 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 autopopulate experiments to execute them
  • Teams can see request status and monitor compound or sample progression

iconDotmatics Reaction Workflows

Dotmatics 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 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 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 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 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)