This software module is designed for the development of MicroArray slide maps and is written in Perl. It provides a convenient and efficient way to generate these maps.
The SlideMap Perl module enables easy creation of slide maps for MicroArrays. With SlideMap, you can create a row/col to plate/well mapping of a microarray slide through a simple module import. You can create the map object based on input parameters to the module. As the module doesn't support annotation data yet, it simply creates an ordered list of spots that references anonymous arrays containing array_row, array_col, plate_alias, and well.
SlideMap supports 5 types of arrayers, including IAS (default), MD, MD3, Lucidia, and Stanford. The module also provides two methods for converting spots to wells and vice versa based on the instantiated parameters.
The main parameters of the module are machine, x_pin, y_pin, x_spacing, y_spacing, x_repeat and y_repeat. The machine parameter specifies the type of array printing machine used (IAS is the default). The x_pin and y_pin parameters indicate the number of print head pens in the 'X' (plate_row) and 'Y' (plate_col) dimensions respectively. The default values are x_pin=2 and y_pin=6.
The x_spacing parameter specifies the number of spots in one row of a block on the array and y_spacing is the number of spots in one column of a block on the array with default values of x_spacing=24 and y_spacing=25. The x_repeat and y_repeat parameters specify the number of repeated blocks in the 'X' and 'Y' dimensions respectively with their default values being 1.
Using the SlideMap module is straightforward. After importing the module, you can create a slide map object and initialize it. You can also fill the map and obtain a reference to the created map using the getMap method. SlideMap also provides several methods for setting and getting attribute values. For example, you can set the print head using the setPrintHead method and get the print head using the getPrintHead method. Other provided methods include setNoComplement, setRepeats, setFormat, setPrintDirection, and setPlateOrder.
SlideMap also provides useful diagnostic capabilities through the diagnostics method. You can choose to print spots or wells using the print_spots and print_wells methods respectively. The module also enables you to view the conversion of spots to wells using the showConvertWell method or the conversion of wells to spots using the showConvertSpot method.
SlideMap supports 5 types of arrayers, including IAS (default), MD, MD3, Lucidia, and Stanford. The module also provides two methods for converting spots to wells and vice versa based on the instantiated parameters.
The main parameters of the module are machine, x_pin, y_pin, x_spacing, y_spacing, x_repeat and y_repeat. The machine parameter specifies the type of array printing machine used (IAS is the default). The x_pin and y_pin parameters indicate the number of print head pens in the 'X' (plate_row) and 'Y' (plate_col) dimensions respectively. The default values are x_pin=2 and y_pin=6.
The x_spacing parameter specifies the number of spots in one row of a block on the array and y_spacing is the number of spots in one column of a block on the array with default values of x_spacing=24 and y_spacing=25. The x_repeat and y_repeat parameters specify the number of repeated blocks in the 'X' and 'Y' dimensions respectively with their default values being 1.
Using the SlideMap module is straightforward. After importing the module, you can create a slide map object and initialize it. You can also fill the map and obtain a reference to the created map using the getMap method. SlideMap also provides several methods for setting and getting attribute values. For example, you can set the print head using the setPrintHead method and get the print head using the getPrintHead method. Other provided methods include setNoComplement, setRepeats, setFormat, setPrintDirection, and setPlateOrder.
SlideMap also provides useful diagnostic capabilities through the diagnostics method. You can choose to print spots or wells using the print_spots and print_wells methods respectively. The module also enables you to view the conversion of spots to wells using the showConvertWell method or the conversion of wells to spots using the showConvertSpot method.
What's New
Version 1.2.2: N/A