Dotmatics Solutions for Research Collaboration Software

Making External Collaborations Work

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Optimizing Data Efficiency in Cross-Company Research Projects

Today’s research projects are often carried out across collaborative networks of pharma, biotechs, CROs and academics. Projects vary from fee-for-service to joint IP discovery to large consortia.  Many companies have made large investments in these projects but face challenges optimizing information flow across the network. Too often work requesting and results sharing are manual, using email, file shares and reports.  This can lead to lengthy delays in turn-around time, as well as errors in data transcription and interpretation. This slows innovation and adversely impacts the expected return on investment of the move to external collaboration.

The Dotmatics solution for collaborative network research can help ensure success whatever the externalized project. It provides real-time scientific data exchange, informed project management and, when appropriate, shared scientific decision making across the partners.

Your challenges

Do you need to optimize

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Data sharing and security

Every project should have a single source of truth for scientific project data. Every member of the project team should have access to all the data for which they have permission, irrespective of which partner generated it. This ensures that they can make the best-informed decisions about project progression.

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Data exchange and requests

Requests for work and exchange of scientific results should be in real-time and remove the need for manual parsing. This will accelerate cycle times and improve accuracy

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Project provisioning

Discovery projects are dynamic with partners added and removed as their expertise dictates. Provisioning and deprovisioning partners should be simple and real-time

IP protection

Legal arrangements and IP ownership of project results can be complex, but copying and sharing data in email and reports makes it almost impossible to track and secure IP.   All project actions should be capture in an audit trail, IP should be safeguarded during the project and easy to distribute at the end

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Decision support

Joint discovery projects require that partners across the network make decision together. These must be based on common views to the project data, and common analytics to ensure consistent decision making

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Project management

Project managers need to have real-time access to work status and project progression. Only with this can they understand progress and make timely decision to prioritize future work


With Dotmatics you can

icon Have a Hosted Collaboration Platform

The Dotmatics solution is hosted securely in the cloud and so can be accessed by all partners outside their firewalls. Project members can be spun up and down quickly and no partner requires VPN access to another’s servers. Data and experiments can be synchronized into a company’s existing informatics applications (e.g. legacy on-premise ELN) if required

icon Use Realtime Scientific Data Exchange

The solution provides a scientifically-aware data repository that handles molecules, sequences, assays, experiments and scientific images as well as text and data. This provides a single source of truth for each type of data within the project

Security defines each partner’s granular access to data and all partners can access all data to which they are entitled in real time.

Data can be synchronized to internal systems on a schedule or as IP is distributed at the end of a project.

icon Allow Cross-Partner Scientific Workflows

The Dotmatics applications within the suite can capture experiments, molecular and biologics entities, samples and assay results directly to the shared repository. A wide range of therapeutics research is supported from small molecules to peptides to antibodies as well as conjugates and engineered biologics

Work-requesting capabilities and experiment transfers allow work to be requested from one team to another.

Shared decision support tools allow common analytics and visualizations to drive cross-team decision making.

icon Manage Projects and Monitor Their Performance

Project managers can assign work, track the status of work requests, and monitor progress with experiments. With access to real-time project status they can make timely decisions to drive the direction of a project more efficiently

icon Automate Your Data

When the Dotmatics platform is used in conjunction with Dotmatics’ BioBright solution, files can be uploaded from partners directly to a shared secure data lake. They can be automatically parsed to extract data and metadata, and validation rules can be run. Data can be then be sent automatically into ELN or assay experiments, or added directly from the lake by the ELN user later


Antabio Implement Web-Based Informatics Solution

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This Solution Consists of

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 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

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 Register

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

  • 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 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 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 Blueprint

  • 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: 

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 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 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