Define Your Assays

Within AssayBase, details of a specific assay are defined as a "Protocol." A fundamental element of the application, a Protocol, along with its associated Result Template, defines a test by a number of parameters, conditions, activity measurables and results. Basically, they establish how the raw data and conditions of a test are used to calculate results, and which of these results are stored in the database.

Protocol parameters are user-definable, giving you maximum flexibility to meet changing experimental requirements.

AssayBase maintains complete details of the history and development of all Protocols, allowing previous versions to be used if required. You can also store and keep track of associated Protocol documentation, such as an SOP describing the assay procedure.

Result Templates are defined in Excel as Worksheets. They describe how the raw data should be transformed to obtain results and how the results should be presented.

A single Protocol can have any number of different Result Templates, which may relate to different Plate Formats, throughputs or methods of calculation. Results Templates can also contain macros or user-defined functions, and can utilize add-ins such as XLfit to provide powerful curve-fitting routines for dose-response or pharmaco-kinetic tests. AssayBase stores only essential (prime) results; the raw data is held in protected Excel format associated with the main ActivityBase database and can be viewed at any time.

Run Tests

AssayBase lets you run and collect data from testing either manually or automatically.

To manually record data from individual tests runs, simply select the Protocol and Result Template that you will use for testing, assign samples to test and calculate results using a customised session of Excel. Prime results are then passed back to the database, from where they can be assessed, verified or rejected before completing the test.

Recording data and calculating results from automated assays such as HTS is just as easy. In fact, the main difference is that the procedure is better suited to the massive volumes of data generated in automated assays, such as UHTS, HTS and high volume FLIPR assays. AssayBase places no limit on the number or size of plates you can manage.

Data Capture and Analysis

Raw data can be entered manually or imported directly from instruments or robotic systems using AssayBase's extensive data import options. Imported data can also be matched directly to a specific plate format, allowing easy cross-referencing of the results back to the original assay plate.

A personal digital assistant (PDA) such as a PalmPilot™ can also be configured to capture data into ActivityBase. Download more information.

AssayBase provides a graphical interface to define how a particular type of raw data file should be interpreted and imported into the result calculation process.

These options provide a means of importing data with the minimum of effort; they also allow the user to build up a list of reusable data import definitions.

During the data import operation, you can specify which cells on the Result Template worksheets can, and cannot, be changed; for example, the method used to calculate results can be protected to ensure protocol integrity. AssayBase also makes sure that all summary results are passed back to the database after finishing with the results-entry worksheet

Test results are calculated in AssayBase using Excel Result Templates. The full functionality of Excel is basically unchanged; however, many additional tools are provided to simplify the creation of templates.

Familiar, standard Excel functions, formulas and formatting can be utilized to describe how experimental results should be calculated from the raw data. Worksheets can also contain VBA macros, user defined functions or specific Excel add-ins such as XLfit. In addition, ActivityBase can easily be integrated with industry standard data and statistical analysis packages such as SAS.

Once results have been calculated and returned to the database, they can be reviewed, and either verified or rejected, along with any comments that you may wish to record. During the verification process, you can view the raw data and associated calculations; compound structures and all other related test data (such as images, chemical structures, etc.) together on the desktop.

AssayBase provides many features for the quick identification of "hits" during the data analysis process, including extensive charting and visualization options, de-convolution of pooled plates and verification across multiple tests at the same time.

To assist with GLP compliance and to provide a defensible audit trail, all decisions made during result analysis can be traced to their originator.

Automated Testing

Within AssayBase, the Testset option is used to record data and calculate results from plates or lists of samples run in automated assays, such as HTS and UHTS. To monitor workflow, specific actions can be recorded against a Testset and reviewed, added to or completed.

AssayBase provides extensive search tools to aid the optimisation of plate selection for Testsets by priority, expiration date, freeze/thaw cycle, etc. Workflow can be managed and tracked by adding specific actions to the Testset prior to its release.

Once Testsets have been released, they can be reviewed by members of the screening team and prioritised for testing. Once accepted, individual actions can be completed and dilution files can be produced for a robotics system.

Once the automation has been started, AssayBase waits for the appropriate data files to be written to disk and then processes these for each Testset. All events during automation are logged to ensure that no information is lost should your robotics system, network, or other hardware fail during the assay.

All of the data capture is automatic and requires no further user interaction, allowing assays to be run unattended.

Download HTS and UHTS customer case studies, Cytokinetics, NV Organon, from IDBS' Discovery Magazine

Sample Management

Along with ActivityBase's associated Chemistry and Natural Products components you can register any type of sample, including discrete compounds, combinatorial libraries, mixtures/formulations, natural substances, enzymes, cell lines, DNA sequences, etc.

Samples can be registered individually or in batches using the ObjectManager utility. Chemical structures are registered using StructureBase. You can clean and novelty-check the structure and generate unique sample and batch identifiers according to your organisation's own business rules.

A wide variety of information can be associated with a sample. For example:

Physical properties (molecular weight, structures, LogP, Solubility, etc.)

Structure (incl. Mol files, Smiles and ISIS integration)

Spectra (incl. NMR, HPLC and mass spec)

Documents (e.g., gel images, cell profiles, etc.)

Sample Location (incl. historical tracking)

Inventory information (current quantities, volumes, etc.)

Plate Management

AssayBase provides extensive plate management options for defining the layout and detail of master plates. Details such as the supplier, plate group, freeze and thaw cycles and expiration date can all be stored with the unique plate identifier. Flexible import options also allow the details of plates and the compounds or other test objects on them to be imported directly from text files or automation systems.

The ObjectManager utility lets you easily generate daughter or assay plates, re-map plates to different formats (96-well to 384, 1536 or 3456, and vice versa), and create pool plates. In addition, you can easily create text files that can be passed to automation systems to physically create the plates.

AssayBase allows you to add your own business rules to the system to automatically keep plate data current; for example, to decrement volumes for plates when tested or when generating child plates in order to monitor quantities and volumes on plates at a plate or well level.

Managing Projects and Workflow

Within AssayBase, you can schedule and request tests, as well as plan testing for the day, week or month. You can also request another group in your organisation to carry out tests on specified samples.

AssayBase is completely configurable to the workflow and business rules of your organisation. The powerful desktop interface lets you monitor all test workflows, including HTS campaigns, secondary testing or complex pharmacological scenarios. It also makes it easy to identify and correct bottlenecks.

Searching, Querying and Reporting Data

To facilitate records searching, all ActivityBase modules provide the same simple, powerful form-based query tool.

Once found, individual items can be dragged and dropped onto the desktop or onto other ActivityBase forms for further processing. For example, hits from a screening assay can be found by a form-based query and then dropped into a secondary assay or confirmation plate for testing. You could also drop the hit list into ObjectManager to create new plates for follow up testing.

For structure activity reporting or other more extensive database queries, you can use IDBS' flexible SARgen application, or any other end-user report or query tool compatible with Oracle.

Managing Documents

AssayBase lets you attach documents such as NMR spectra, Microsoft Word documents, Excel Graphs, chromatograms, and images to any form.

You can also view associated documents from anywhere within AssayBase where a list of objects is displayed, for example in the Object form. This feature is especially useful for viewing NMR and IR spectra alongside other sample data.