Dotmatics for IT Organizations

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

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

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

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.

Chemselector

• 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

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

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

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

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

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.

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.

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

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)

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