Genedata Biologics

Learn why Crescendo Biologics describes Genedata as a single source of truth for all their biopharma research data.

Genedata Biologics® is a first-in-class biologics workflow management platform covering the full biopharma R&D process. With extensive built-in business logic, it works out-of-the-box to support diverse biologics discovery processes. The platform enables fully automated, high-throughput biopharmaceutical discovery workflows and can directly interact with laboratory instruments and robotics equipment. The complex information for each individual sample of every biologics drug candidate is made accessible, editable, and transferrable from one scientist to another and from one R&D site to another. By increasing throughput, minimizing data handling errors, and ensuring consistently high quality standards, Genedata Biologics makes the discovery and development of novel protein-based therapeutics more efficient and helps companies bring better products faster to market.

Biologics Registration
Central registration engine for large molecules

Genedata Biologics® is built on a central registration engine for all categories of biologics entities, including antibodies such as IgGs and bispecifics, non-antibody proteins, plasmids and DNA, cell lines, and other biological samples. The system provides specific capabilities for registration of modified proteins such as antibody drug conjugates (ADCs), PEGylated, glycosylated, or otherwise modified molecules (e.g., de-tagged molecule versions). Genedata Biologics performs automated molecule uniqueness checks, generates unique identifiers for molecules and associated batches, annotates domains such as binding-relevant domains as well as chemical liabilities (e.g., undesired PTMs), and calculates physicochemical and other relevant molecule properties. Molecular ancestries are fully documented, enabling tracking from early discovery (e.g., phage display screens, engineered variants) to fully re-formatted IgGs in downstream testing. Analogous to sub-structure searches for small-molecules databases, Genedata Biologics provides built-in query and reporting tools specifically tailored for large-molecules. The platform’s registration engine is key to managing data and material handovers along the biologics R&D process, and helps to eliminate duplication of work. In addition to therapeutic candidates, the system can register molecular tools and materials (e.g., antigens, tool proteins, related vectors, inserts, developed cell lines, stable pools), which are necessary for full documentation of the biologics discovery and production process protocol.

Integrated Sequence Management & Analysis
Storage, annotation, visualization, and analysis of protein and DNA sequences

Genedata Biologics is built on a comprehensive sequence management platform for storing and referencing all biomolecular sequences, for both protein and nucleotide sequences. Typical stored molecules include biotherapeutics candidates such as antibodies and therapeutic proteins, as well as molecular tools such as vector and insert sequences for molecular biology support. The underlying relational sequence database is optimized for scalability and can deal with millions of antibody and protein sequences. The system includes a sequence annotation pipeline which automatically annotates all registered sequences according to pre-defined annotation rules. Antibody sequences are scanned for CDR and Framework segments and sequence motifs relevant for post translational modifications such as glycosylation, deamination, or oxidation sites. Similarly, DNA sequences are scanned for relevant restriction sites, codons, or trimming sites for vector design and automated expression construct generation. The annotation rules can be configured to incorporate customer-specific Standard Operation Procedures to reflect specific antibody library designs or cloning strategies. Built-in tools enable the interactive analysis and visualization of sequences and their annotations, for individual sequences as well as for large sets, such as those derived from screening, engineering, or maturation campaigns.

Screening Isolate Tracking & Plate Management
High-throughput laboratory logistics and plate-based sample handling

Genedata Biologics provides integrated screening isolate tracking tools to support microtiter plate-based screening, affinity maturation, and engineering campaigns. Isolate tracking is tightly integrated with the system’s plate management and laboratory instrument integration infrastructure. Genedata Biologics supports registration and barcoding of all microtiter plates (MTPs) types, either directly from agar plates produced by colony picking devices or by re-arraying or re-formatting from existing plates. The system directly interacts with laboratory equipment such as colony pickers, liquid handling systems, and pipetting robots. Supporting all plate formats including 96-, 384-, and 1536-well formats, Genedata Biologics can be configured to handle different plate layouts for different purposes (e.g., reserving specific wells for negative, blank, or stimulator controls).  Pre-configured arraying protocols streamline laboratory operations and automatically record plate genealogy and plate isolates (e.g., re-arraying according to defined filling patterns, or reformatting from four 96-well plates to one 384-well plate). All isolate tracking is supported by a central and automated bookkeeping mechanism that registers all master and daughter plates with their isolates (e.g., assay plates, sequencing plates), minimizing laborious and error-prone manual interactions. Plate barcoding facilitates inventory management of master plates and isolates. The system also supports low- and medium- throughput processes, and manual workflows (e.g., clone re-streaking).

High-throughput Antibody Screening
Supporting fully barcoded and automated discovery processes

Genedata Biologics has been designed to support fully automated high-throughput antibody screening and engineering processes. The system’s tight integration with robotics systems for plate management, liquid handling, and screening readers enables fully automated and truly high-throughput processes. Genedata Biologics helps to eliminate bottlenecks by supporting all steps in the discovery process, from streaking on agar, colony picking, plating, plate barcoding, and generation of master-, culture-, assay-, and re-array plates, to downstream interactions with pipetting instruments and reader equipment. Automation support can be configured to work with high-throughput phage or yeast display technologies, B-cell cloning or hybridoma processes, and other antibody discovery technologies. The system is fully scalable and can process hundreds of thousands of screening isolates at a time. Bulk upload facilities enable the simultaneous import and processing of relevant assay and sequence data. The system’s two-way integration with laboratory instruments facilitates data exchange and instrument operation, such as through the system’s ability to process and interpret instrument output files, and by producing instrument control files.

Integrated Assay Data Management & Hit Selection
Identifying the most promising screening hits

Genedata Biologics comes with a database for the storage of all relevant biologics screening assay data. Assay data can be imported in bulk via standard templates, which is particularly useful for data derived from high-throughput, plate-based campaigns. The system can be flexibly configured to process and store assay data derived from different assay types (e.g., ELISA, FACS, FMAT, Biacore), different antigens (e.g. human and murine or coated antigen variants), different plate formats (e.g., 96-, 384-, 1536-well plates, flexible filling patterns), and different pre-processing steps (e.g., S/B or more complex data aggregation involving positive and negative controls). Aggregated assay data is stored in a shared database and automatically referenced against appropriate screening isolates using the Genedata Biologics isolate tracking mechanism. Integrated barcoding helps to track relevant microtiter plates and required assay reagents (e.g., antigens, panning outputs). All assay data for a given isolate can be queried and is automatically reported. Integrated tools for hit selection allow the identification of the best hits based on multiple criteria (e.g., cross-assay analyses combining ELISA and FACS readouts, and HCDR3 sequence properties). The system also supports hit list management.

Library Management & V-Region Discovery
Flexible platform for supporting diverse antibody discovery technologies

Genedata Biologics is technology-agnostic, supporting all major antibody discovery technologies and documenting all relevant experimental protocols, parameters, and results. For phage display approaches the system enables registration of the applied selection techniques (e.g., immunotube or cell-based), panning strategy, input and output titers, and hit rates, and combines this with all library-relevant information. Panning and selection outputs are tracked and documented together with relevant antigens (e.g., human, murine, rat; coated/truncated versions) and selection strategies. Genedata Biologics is agnostic to the applied discovery technology and can work with various display systems (e.g., yeast display), as well as animal-based antibody discovery technologies (e.g., hybridoma, B-cells, SLAM). The Genedata Biologics platform provides a structured way to store, reference, and query all critical experimental parameters. This also includes sophisticated antigen management and specialized functions to register focused maturation libraries.

Integrated Vector Management
Management of constructs, plasmids, and other molecular biology data

Genedata Biologics comes with a built-in database for backbone vectors, cloning and expression constructs, and corresponding vectors maps. All vectors are centrally stored, together with their DNA sequences and annotations, such as promoters, leader peptides, resistance cassette, and cloning strategy. Vectors may encode therapeutic antibodies, proteins, or tool proteins, such as antigens or drug targets. A vector registration engine checks for vector uniqueness to avoid entry duplication. All vector sequences, annotations, and references are managed within a single system. Vectors can be organized and queried according to various criteria such as encoded proteins, contact person, or relevant project. The system stores vectors according to encoded protein ancestries, which makes it easy to link vectors that are used in a specific scientific context, e.g., molecular biology efforts organized by related proteins such as full-length wild-type proteins, catalytic domain expressions, truncations, and mutated variants. Typical applications for tool proteins and reagents include assay development for MTS/HTS, structural biology and X-ray studies, and co-crystallization studies with antibodies or small-molecule compounds. Genedata Biologics supports DNA synthesis workflows by performing automated quality checks to ensure correctness of the encoded protein after codon-optimization. The system includes explicit data organization models for multi-vector expression systems, which is of critical importance when working with multi-chain proteins such as antibodies (e.g., IgGs, bispecifics).

Bulk Cloning & Molecule Re-formatting
Alleviating bottlenecks in molecular biology via in silico cloning tools

Genedata Biologics provides specialized tools for automation and scale-up of vector design. This is particularly useful if larger sets of inserts or variable regions, such as those derived from high-throughput antibody screening campaigns, need to be cloned into a backbone vector to produce full-sized IgG molecules. The system provides flexible tools for automating the bulk generation of new antibody and non-antibody vector maps and encoded protein molecules, based on selected backbone vectors and desired cloning strategies (e.g., Gateway Cloning). Specific functionalities enable automated antibody re-formatting (scFv or Fab to IgG) and isotype switching. The system also enables rapid expression vector optimization by simultaneously cloning inserts into different backbone vectors carrying different combinations of modules of interest (e.g., cleavage sites, tags, leader peptides). All resulting vectors are auto-referenced to the proteins they encode. Auto-generated expression vectors are centrally stored in a common vector repository and can be queried according to their specific properties such as used promoters, leader peptides, resistance cassettes, tags, Kozak, isotype, and constant region sequences.

Protein Expression and Purification Workflow Support
Facilitating complex workflows in a division-of-labor environment

Protein expression and purification workflows require different teams, such as molecular biologists, cell biologists, protein scientists, and analytics personnel to collaborate. Genedata Biologics supports such division-of-labor processes by enabling central registration, naming, and tracking of all relevant biomaterial samples (e.g., vector, cell line, protein expression and protein purification batches) and providing immediate central access to every molecule (e.g., sequence, physical-chemical properties) as well as to process information at any time throughout the expression and purification process. Registered samples are related to their molecules and experimental protocols, including used expression constructs, host cell lines, media, and bioprocess protocols and purification procedures. The system can work with diverse expression systems, including mammalian, bacterial, yeast, or insect. Protein expression batches may be derived from  high- or low-volume expression campaigns (e.g., tubes, shake flasks, wave reactors). Bulk upload functionalities facilitate registration of larger numbers of expression batches (e.g., derived from parallel production in 24- or 96-well plate tube fermentors). Genedata Biologics stores all relevant data for protein expression experiments such as host cell lines (e.g., HEK293, CHO, Sf9, etc), expression protocols (e.g., specific vectors used, transfection conditions, transient or stable pools, baculovirus infection, co-expression), and process parameters (e.g., temperature, induction conditions, growth media). For the downstream purification process, the system stores all relevant purification results and underlying protocols. Similarly to expression batches, Genedata Biologics supports high- and low-volume purification processes (e.g., parallel test purification in 96-well plate gravity flow columns), use of different purification equipment (e.g., such as IMAC, SEC, RFC, HIC, IEX, etc), and product modifications (e.g., de-tagging, buffer optimization). Genedata Biologics further supports users by providing tools for concrete laboratory operations, such as sample pooling, sample splitting, and individual sample processing, as well as protocol management (e.g., protein modifications such as antibody drug conjugation). Genedata Biologics consistently documents all process parameters and uniquely aggregates the data contributed by different groups along the full protein production process, providing critically important input for bioprocess development.

Analytics and QC Data Management
Capturing, reporting, and interpreting protein analytics and quality data

Analytics and QC data for protein expression and purification samples are easily reported in Genedata Biologics. Standard data submission templates enable reporting of results derived from diverse analytics instruments. Typical analytics parameters include yield, purity, stability, activity, solubility, and typical analytics technologies include SDS-PAGE, SEC, SLS/DLS, MS, and SPR. Other quality parameters, critical for biologics, are endotoxin and aggregation levels and melting temperatures. Genedata Biologics analytics data entry forms can also be configured to reflect corporate-specific analytics and quality control processes and standards. The system provides a flexible mechanism for managing all relevant analytics, QC and biophysical data, with automatic linking of reported data to the relevant protein sample. The system calculates biophysical properties such as molecular weight, isolectric point (pI), molar extinction coefficient, and absorbance as well as potential post-translational modification sites (PTMs) for use in performing the actual analytics experiments. Genedata Biologics provides single-point and automated generation of sample and analytics quality reports (e.g., Certificate of Analysis, CoA) for handover of quality-checked samples to requesting groups and departments. The integrated nature of the data management platform enables easy tracking of analytics and QC parameters. Integrated tools help eliminate protein productivity or quality bottlenecks by identifying the optimal combinations of host cells, vector backbones, tags, leader peptides, and expression and purification protocols.