Description

Index file

The diversity of instrumentation, spotting pins, and reagents available, mean that production environment differences exist between microarray facilities. Whilst user-configurable files enable SimArray to model these differences, SimArray needs to accommodate for the configuration files themselves being stored in different locations and with different names. SimArray achieves this with index files, which can be edited by each user to record the configuration files locations and names (example).

Configuration files

Tool

Print tools are composed of spotting pins that are arranged in pre-defined plate-format-specific configurations (Fig. 1). Each user records the pin configurations that are available to them by adding their robotic spotter's list of options to the tool file (example). Pin configuration directly affects source visit number and maximum meta-grid area (Fig. 1).

Pins

Achievable spot densities vary according to the production environment, i.e., spotting pin, spotting buffer, substrate, temperature, relative humidity, etc. Each user should record the pins that are available to them and their achievable spot densities by editing the pins file (example). This data will directly affect selection of the sub-grid dimensions, i.e., the number of spots that the user would like to print in the x- and y-axis.

Time

Print time is dependent on a range of instrument and user-defined parameters. To estimate the print time, each user should record the time it takes to perform a single print cycle for a given print set-up by editing the time file (example). Single print cycle duration is best measured by recording how long it takes to perform a full print-run (under defined conditions) and then dividing by the number of the print cycles. Estimated print time is limited by the user-specified print cycle times.

First run:

An example first and second run can be found here

Probe Number

You must type the number of probes or wells that need to be printed, including all controls. SimArray will check that the entered value is an integer, i.e., not a decimal number because it is not possible to print fractions of a well. There is no maximum limit to the number of probes that can be entered.

Plate format

SimArray examines the tool configuration file and extracts a list of plate formats that are compatible with your robotic spotter. You will then be asked to select a plate format from the list, by entering an index key. If the key you have entered does not correspond to the list provided, you will be asked to try again.

Tools available

SimArray examines the tool configuration file and extracts all pin configurations that are compatible with the previously specified plate format. You will then be asked to select a pin configuration from the list, by entering an index key. If the key you have entered does not correspond to the list provided, you will be asked to try again. Maximum meta-grid area is calculated by simply multiplying the number of pins in each axis by the pin tool's pre-defined pin pitch (Fig. 1).

Source visits

SimArray prints a source visit list file and exits the first run. A source visit is defined as a single pin loading (Fig. 1). The printed file contains the following data:

• Header: summary of your inputs, and column headers
• Plate: microtitre plate number
• Source: pin loading that is to be printed
• Replicates: number of times that the source is to be printed (default is once)

Users can edit the replicate column to record how many times each source visit is to be printed. Source visits with zero replicates are ignored, and will be omitted from the final design.

The header and the other columns should not be modified.

Second run:

An example first and second run can be found here

Required spot density

SimArray counts how many spots need to be printed per sub-grid. This information is provided to help with the following step.

Pins available

SimArray examines the pins configuration file and displays all pins and the number of spots that can be printed per sub-grid. You will then be asked to select a pin from the list by entering an index key. If the key you have entered does not correspond to the list provided, you will be asked to try again.

Evaluate pin selection

SimArray compares the selected pin's achievable spot density to the required spot density for this array design. If there isn't a problem, a standard message is displayed and SimArray continues with the next step. SimArray terminates and an error message is displayed, if the selected pin is incompatible with the proposed target spot number.

Compute spots_x and spots_y

SimArray computes and displays the sub-grid dimensions that fall between the target spot number and a user-specified upper limit. The upper limit is the target spot number plus the user-specified 'spot number margin'. SimArray prevents users from selecting grid dimensions that are incompatible with the spotting pins maximum achievable spot density. If, however, the selected grid dimension permits more spots to be printed than required, additional spot locations are flagged to become blanks by assigning them a source visit number of zero, i.e., not printed. You will then be asked to select a grid dimension from the list by entering an index key. If the key you have entered does not correspond to the list provided, you will be asked to try again.

Compute print time

SimArray examines the time configuration file and displays all of the print set-ups. You will then be asked to select one condition from the list by entering an index key. If the key you have entered does not correspond to the list provided, you will be asked to try again. Estimated print time is calculated by multiplying the number of pin loadings by the duration of a single print cycle. Estimated print time is limited by the accuracy of the user-specific print cycle times.

Summary report

The summary report is printed by SimArray and contains the randomised source visit map along with a summary of the users responses, an estimated print time, and the estimated maximum meta-grid area. The user can specify a comma-, tab, or space-separated source visit map with the command line keys -C, -T, or -S (default), respectively. The source visit map can then either be directly uploaded to instruments that accept either comma-, tab-, or space-separated values source files, or manually entered. New array designs are appended to an existing report. You are therefore able to perform multiple 'simulated print runs' under different conditions. Each array design contains a date and time stamp.