Method and apparatus for automated cellular bioinformatics

Abstract

An automated system that conducts, monitors, and validates a cell-line-based biological experiment including one or more treatment compounds or other external stimuli. In one preferred embodiment, the system comprises two principal subsystems, and optionally accessory subsystems. A first principal subsystem is an automated laboratory experiment manager for designing the biological experiment, for constructing an assay plate used to conduct the biological experiment, and for managing one or more of the processes that constitute the biological experiment. A second principal subsystem is an automated data analysis manager for analyzing images, for instance produced by the image production system, to detect image data including biological markers and objects, for analyzing the resulting image data to produce biological data, and for analyzing the biological data to produce biological phenotypes and treatment compound signatures.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application is a continuation of and claims priority from U.S. patent application Ser. No. 10 / 467,183, filed Jan. 12, 2004, which was the National Stage of International Application No. PCT / US02 / 05266, filed Feb. 20, 2002, which claims priority under 35 USC §119(e) from U.S. Provisional Patent Application No. 60 / 270,314, filed Feb. 20, 2001. These applications are incorporated herein by reference in their entirety and for all purposes.COPYRIGHT NOTICE [0002] A portion of the disclosure of this patent document contains material that is subject to copyright protection. The copyright owner has no objection to the facsimile reproduction by anyone of the patent document or the patent disclosure, as it appears in the Patent and Trademark Office patent file or records, but otherwise reserves all copyrights whatsoever. FIELD OF THE INVENTION [0003] The present invention relates to computer-automated cellular biological systems. More partic...

AI Technical Summary

Benefits of technology

[0026] The present invention provides a flexible and easy-to-use system for the design of cell-line-based biological experiments on specific biological markers. It provides tools that allow a designer to design an experiment that combines cell lines, marker sets, and treatment plates into a collection of assay plates. These tools also permit the full specification of the experimental process through a process model that generates a process, or collection of tasks. The system's process modeling features provide the designer the ability to specify the structure of the experimental process. The system then generates processes and tasks for each experiment that automate the process where possible. Automated milestones including but not limited to barcode scanning, and task completion updates, provide tracking capabilities that give users the ability to get experiment status and to intervene in the process where required, preferably through remote interfaces.

[0027] The system enables users to plan for and maintain adequate experimental infrastructure, including but not limited to hardware, software, reagents, treatments, and maintenance processes for planned experiments. The system tracks the infrastructure of experiments by tracking the individual hardware systems, software systems, reagents, treatments, and maintenance processes. Reports provide planning tools for users that help them to keep adequate supplies and systems on hand and in good repair.

[0030] The system includes an information system that lets users, applications, and database servers create and track system failures. The invention also provides applications that enable management to plan improvement work based on prioritization of the failures and to understand the current situation with respect to the life cycle of failures in the overall system. Managers can also use this system to improve the visibility of failures within the organization and to improve communication with respect to failures.

[0031] To create reusable information or feedback about opportunities to improve the system, it builds an information system that enables users to suggest and track improvement opportunities. It also provides applications that enable management to plan improvement work based on prioritization of the opportunities. Managers can also use this system to improve the visibility and communication of progress in realizing opportunities within the organization. The system also enables users to make comments on operational systems, and provides applications that enable management to plan improvement work based on prioritization of the comments.

[0032] The system enables users to create reusable information or feedback about systems' defects that is useful for improving the system. It builds an information system that lets users, applications, and database servers create and track system defects. The system further provides applications that enable management to plan improvement work based on prioritization of defect fixing and to understand the current situation with respect to the life cycle of defects in the overall system. Managers can also use this system to improve the visibility of defects within the organization and to improve communication with respect to defects.

[0035] The system permits easy modification of the algorithm structure and easy control of runtime processing. Developers are able to add new analytical transactions to the system quickly and easily, and operators are able to control and prioritize analysis jobs using the running system.

Problems solved by technology

Each of these steps is exacting, repetitive, and many of them require significant amounts of time from highly trained experimenters to complete.

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