NSF ITR Project Fall 2004 ABSTRACTION HIERARCHY MODELING OF HIGH-THROUGHPUT SCREENING LINE AUTOMATION. David B.Kaber & Steffen Junginger

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1 NSF ITR Project Fall 2004 ABSTRACTION HIERARCHY MODELING OF HIGH-THROUGHPUT SCREENING LINE AUTOMATION Overview: David B.Kaber & Steffen Junginger This document presents abstraction hierarchy (AH) models of the automated control systems used by operators to manage processing equipment on a high-throughput screening (HTS) line for molecular compound testing for drug discovery. The modeling work was completed as part of a larger cognitive work analysis (CWA) on biopharamacologist planning and execution of high-throughput molecular compound screening and analysis of resulting data. The CWA includes a goal-directed task analysis (GDTA) of operator behavior and additional AH modeling of the actual processing equipment. AH models are hierarchical, structural models consisting of multiple levels of abstraction. Rasmussen (1985) applied AH models in work domain analysis. At the highest level of abstraction, the models define the purpose of automation in the work domain. The lowest level of an AH model represents the physical components of the system. In between are the generalized functions of the automation. Linkages among the levels represent how the purpose of the automation is implemented through specific devices and they provide an explanation of why certain components are needed to achieve a system purpose (Rasmussen, Pejtersen & Goodstein, 1994). An AH model is typically presented using a grid of 3 columns and 5 rows (see Figure 1). The columns (from left to right) present decomposition of the automation (control software), as a whole, to presentation of specific functions. The rows (from top to bottom) present functional decomposition of the software from the overall purpose through generic control functions to the software options and settings supporting the functions. Although the lower rows of AH models are typically used to present the physical components of a system supporting functions, instead of identifying software subroutines and the inner-workings of computer code as a basis for control function explanation, from a user perspective, it is more meaningful to reveal the humaninterface display features and options through which the subroutines of the software are made accessible to the user. This also ultimately allows for a clearer integration of the AH automation models with equipment/devices models from an operator perspective. Means-ends connections are also presented across the rows. Automation Models: Appendix A presents AH models for HTS line automation used in a highly automated enzymebased (e.g., Trypsin) assay of organic compounds for the potential to serve as bases for new drug development. The automation includes: control software for a pipetting robot, an optimized chemical analysis robot (ORCA), and a plate reader integrated in the screening line. Although, we have developed AH models of bar coder and incubator equipment as part of the overall CWA (devices that are also integrated in the HTS line), this equipment has no proprietary control

2 software. The labeling of micro plates and the time to incubation as part of an assay, are merely controlled by action/configuration dialogs presented through an assay method programming application/interface used to control the entire screening line (SAMI). Consequently, AH models for the bar coder and incubator automation are not included in this document. (We present models for the action/configuration dialogs, as part of SAMI, later in this document.) All of the software applications used to control the screening line, including the SAMI, are linked to a central process control system (SILAS) that manages communication between a process scheduling system and the line devices, as well as among the devices (e.g., robot and automated pipetting system). Each independent control software application is proprietary to the manufacturer of the device that it controls. Goal or purpose of software Highest level of abstraction in model Option level (refers to options in descriptions) Abstract functions of software (physical processes controlled by software) Generic functions of software Abstract function level Generalized function level (Includes identification of software controls and system components.) Subroutines of software required to achieve functions Physical function level (Includes identification of software options.) (Describes how options of software relate to controlling devices/processes.) Figure 1. General from of Abstraction Hierarchy model for automation. One of the models presented in Appendix A is that of the control software for the plate reader. The highest level of the model presents the general purpose of the software; that is, to control the plate reading process. Directly below this level, the abstract function of the plate reader, to optically measure the state of a sample, is identified. In the context of the Trypsinbased enzyme assay currently conducted at CELISCA, the objective of plate reading is to detect the amount of yellow product resulting from conversion of an enzyme substrate (e.g., BAPNA) through the addition of Trypsin to the reaction.

3 Below the abstract function level, the generic functions of the control software are identified, including: test type selection and parameter setting; real-time measurement control; internal incubation unit control; control of the plate position within the reader; and hardware configuration. At the same generalized function level in the model, the generic control processes of the automation are broken down into component functions. For example, the test specification function involves identifying the type of plate to be processed, defining the plate layout, and defining injection and shaking processes. Although the plate reader is capable injecting liquid into plates and performing shaking of plates, these component control functions are not used in the current enzyme-based screening tests at CELISCA. Other component functions, associated with measurement, incubator and plate position control, are identified in the model. At the next lower level in the model, the interface display features and options, made available to users through the plate reader control software, are identified. For example, the options required to specify the plate layout (as part of defining the test) are listed. They include choosing from defined testing options (or default plate layouts), allowing users to define new or custom plate layouts for measurement purposes, and allowing for specification of how the wells of a plate should be indexed or counted during measurement. The level of detail of the model in representing the software is limited based on the expert and analysts determination of what interface feature and option knowledge may be critical for operators to: (1) understand how the automation functions; and (2) be able to diagnose and correct potential system faults, etc. Beyond the elements of the software/automation model, means-end connections are presented among the generic and component functions, and the component functions and interface features. Following the links (lines) from the top of the diagram down to the bottom, an operator can discover how each automation function is implemented through the software. This provides a process-oriented perspective on the detailed aspects of automation/software (i.e., the functions of the process are related to software options). Following the links from the bottom of the diagram to the top, an operator can learn why the various interface features/options exist as part of the software. This examination of the model provides a device-oriented perspective on how a screening process is implemented. Action/Configuration Dialog Models: In order to represent the automated control of those devices on the HTS line for which there is no proprietary software, we also used the AH modeling approach to represent the action/configuration dialogs included in the SAMI for specifying device operational parameters (see Appendix B). The models of the dialogs present the general purpose and functions of the software. They identify the general functions included in the dialogs and the options that can be selected; however, specific operational settings of the software are not specified. It is important to note that in addition to the action/configuration dialogs of the SAMI, there are also other dialogs associated with device representations, including micro-plate source configuration interfaces and dialogs for defining consumables to be used by line devices (e.g., pipetting tips to be used by the pipetting robot). Figure 2 shows the dialogs and options available for micro-plate source configuration through the SAMI software and Figure 3 presents the options for defining consumables.

4 SAMI Source Configuration Transport data - Name source - Select home stations - Select type plate Lids - Select has lid - Select discard lid Groupings - Force transport group - Identify plate locations to be used in source? Label - Select generate automatically - Use transport name - Use station (This information is displayed in the SAMI static scheduler.) Figure 2. Source configuration options in SILAS method editing software. SAMI Consumable Configuration Consumables Input values for each: - Quantity - Disposal location - Home position - Trash (yes/no) - Hot trash (yes/no) Figure 3. Options for defining consumables through the SILAS method editor. The dialogs and options presented in Figure 2 can be used to configure sources of deep well plates, and sample and test plates. They may also be used to configure tip box sources for the pipetting robot system. The options for consumables in Figure 3 are strictly associated with devices integrated in the HTS line.

5 Results: In general, the AH models developed on the HTS line automation can be used to support development of future operator training programs, or user manuals. The AH models can serve as a basis for educating operators on connections between automated control functions and software system functions as well as interface features and options in order to promote operator ability to potentially recover the system from error conditions. The combination of the AH models with the results of the GDTA on biopharamacologist planning and execution, and analysis of HTS operations is expected to provide a meta-method for understanding of how HTS operator needs are currently addressed (or not) by existing automation and information display technologies. This approach is expected to be superior to using GDTA alone for identification of existing system shortcomings and future design needs. Specifically, the integration of the results of the AH and GDTA methods will allow for relation of a biophramacologists goal structure and critical decisions (as part of the assay process) to the purpose of automated systems on the HTS line and functions and components. The approach is expected to identify which components of existing systems may be unnecessary or inadequate for operator system state/situation awareness and decision making processes. The results of the combined analyses may also serve as bases for formulating future automation design guidelines. References: Rasmussen, J. (1985). The role of hierarchical knowledge representation in decision-making and system management. IEEE Transactions on Systems Man and Cybernetics, 15, Rasmussen, J., Pejtersen, A. & Goodstein, L. (1994). Cognitive Systems Engineering. New York: Wiley.

6 APPENDIX A: Abstraction Hierarchy models for HTS line automation (proprietary device control software).

7 Control mechanisms of Biomek (Part I) States, operational conditions, and specific settings of Biomek control software Note: Identifies a software function or component that is not regularly used in the assay process. Control liquid transfer and plate handling System configuration Scripting utility Select comm. port Define ports for Biomek devices Record movement patterns (using manual controls) Identify available hardware Diagnostics component (for maintenance) Workstation server Test all machine parts of Biomek Establish comm. between Bioworks & PC Teaching of bench layout and tools Definition of labware Test all (perform tests automatically Identify serial port Bioworks software Select parts to be tested (gripper (angle, width), bridge (coords.), vacuum valve, peristaltic pump) Use move macro recorder interface Use X, Y ctrl. (bridge) Use Z ctrl. (bridge) Select aspirate/ disperse (tip) Define move increment size Define speed increment size Input baud rate Click connect (used for manual work only). Use teaching tool to align coordinates (x, y, z) for base module, and left and right side modules Select position calibrate (along axes, incremental sensors) Use software controls to perform movement of teaching tip tool Select existing labware or enter new (reservoirs, racks) Define features of labware in program (plate height). Use gripper teaching plate (calibration block) Place gripper in labware position Access and lift labware with gripper Confirm grip (identify max. plate width) Select work surface modules (left mod., right mod., washing tool, and value) Select options (vacuum manifold, add. lab sources, plate reorder)

8 Control mechanisms of Biomek (Part II) Control liquid transfer and plate handling Note: Identifies a software function or component that is not regularly used in the assay process. Note: See next sheet for detail on functions/options. Editing module (program methods) Lab book manager Run module (real-time control - exec. of methods) Overall help utility, run & edit Define workbench layout or initial setup (when starting new method) User identification Selection of method Editor (new methods/ modify existing methods) Ensure/verify work bench layout Execute method Bioworks software Select/identify positions for labware (use drag & drop utility to move specific labware to positions on bench (A1 A6, B1 B6)) Select default configuration of workbench for method Select clear layout Select method to edit Define initial system configuration Select method steps Configure steps (using function palette) Setup profiles ( lab notebook ) Select desktop (file locations) File retrieve & load Use dialog to confirm workbench layout Select start Select stop View elapsed time File directories (defaults for method files) States, operational conditions, and specific settings of Biomek control software

9 Control mechanisms of Biomek (Detail) Control liquid transfer and plate handling Editing module (program methods) Select method to edit Define initial system configuration Select method steps Configure steps (using function palette) - assoc. techniques with labware Bioworks software Select New Select Open Select plate type, tips, tubes, devices. Place labware icons on virtual work surface layout Select Bulk Dispense Select Change Tips Select Reset Tips Select Move Labware Select Serial Dilution Select Pipette States, operational conditions, and specific settings of Biomek control software Select Tool Type Set internal delay. Define tip handling method (aspirate excess, tip touch). Identify destination for dispensing (e.g., A2 ) Specify volume, rate and height of tip. Specify range of action on labware (physical area). Select options. Select return to rack. Select dispose. Specify plate location (e.g., B3), label and name. Identify/select tool for use (e.g., 200 ml pipetter). Input transfer volume/tip (ml). Input aspiration height and rate. Input dispense height and rate. Specify source location and destination Identify number of tips used (e.g., 0-96). Specify gripper start point and destination (e.g., move plate lid from B2 to B3) Select mix solution (cycles of aspirate/dispense and locations). Select tip touch. Define labware action - pattern of movement of pipetter over wells. Set internal delay. Specify tip handling (no change, after transfer, after each column) Describe source labware Input location, label and name Define aspiration Define liquid levels Select tip actions Define source action (range/pattern of movement, direction, and event at end of motion). Specify tool type (200 ml, multi-head) Input dispense volume (ml/tip) Input # of reps. Set internal delay Define tip handling (no change, after transfer, after each column) Select Discard ID tip source (name) Describe destination labware Input location, label and name Define dispense Select tip actions (blowout, tip touch or mix). Define destination action (range/pattern of movement, direction, and event at end of motion).

10 [ORCA NT]

11 Control of plate reading processes Note: * identifies a function that is not regularly used in the assay process. Optical measurement of sample state Test parameter setting & test selection/control Identify plate type Define plate layout Define light exposure Define injection* Define filter setting Define shaking* Measurement (realtime) control Incubator control Plate position control Ensure position of plate shuttle (automated detection) Setting and activating plate chamber heat Execute/initiate read Select plate holder state Hardware setup* Configure reader, micro-plates, filters and file paths* Select among plate options Plate reader control software Choose from defined testing options Define new (i.e., identify position to measure and well contents) Establish system pattern of counting wells Select measurement state ( start, stop ) Select incubator state (on/off) Input incubator temperature (10-60 deg. C) Select load / unload Select wave length of excitation filter Select wave length of emission filter Input gain setting (intensity of light) States, operational conditions, and specific settings of plate reader control software Select number of cycles Select number of flashes Establish pattern of well measurement (rows, columns) Input cycle times Select type of measurement (absorbance, fluorescence) Identify plate manuf., dimensions, etc. Identification of filter wavelengths and locations Enter data file locations

12 APPENDIX B: Abstraction Hierarchy models for action/configuration dialogs of SILAS method editor.

13 Control mechanisms of bar coder Label and read micro-plates Define global operation of device Printing control Select (global) action Select type of bar code Store type of bar code Define content of bar code Reading control Label and apply control Select label position on microplate Select plate position for reading Set offsets for label height (relative to top/bottom of plate) Set parameters for addressing reading errors Set frequency of bar code verification (or none) Set parameters for verification errors (reading previously labeled plates) Select among action options (Automation, Read, Manual Use) Select among label format options (Code 128, Code 39, text only) Select Update option Manual string entry Read strings from file Print and apply device software Select among Read or No-Read options Manual entry of position of code on label (in mm) Select among options for plate sites (A, B, C, D) Manual entry of label prefix and suffix with auto indexing of string Elect use of internal SILAS transport ID Manual entry and store number of read periods Select among reading error handling options (log error, flag error and stop) States, operational conditions, and specific settings of bar coder control software Select among verification error handling options (i.e., errors during verification of bar code on plate against SILAS ID - Ignore, or log and stop)

14 Control of plate liquid content Preparation of sample plates Device configuration Select test method Select Bioworks pipet tip handling method Present workbench layout Get time estimate Read from Bioworks Manual entry Options for Bioworks tip handling ( yes/no ) SAMI action/config. dialog for BIOMEK 2000 Options in list of test names Definition of layout based on selection of test method States, operational conditions, and specific settings of Biomek control software

15 Control of plate microenvironment (incubation) Preparation (heating) of sample plates Device configuration Input/select minimum time Input/select maximum time Manipulate module (manual control) Select autorun SAMI action/config. dialog for incubator Select options to define plate position (number of hotels, shelves in hotels, etc.) Input time estimate (manual entry) Select action (load, unload, initialize) States, operational conditions, and specific settings of incubator control software Identify plate position (hotel, shelf, index)

16 [ORCA]

17 Control of plate reading processes Optical measurement of sample state Device configuration Select manual action control Select test type Select options Get test names Get time estimates Open/close Initialize (verify connection with control system) Set temperature Get test names SAMI action/config. dialog for plate reader Run Select defined methods in plate reader package Select pump config. Select incubator config. Enter value (used by static scheduler) Identify file locations for methods (names are included in Keeper registry of SILAS) Read from Keeper registry (based on tests). States, operational conditions, and specific settings of plate reader control software