OMERO.editor Field Types

OMERO.editor allows users to specify different fields in the Protocol "template", to store experimental parameters. These field types are shown in the following figure and listed below, along with a short description of each.

• Protocol Title. This field is automatically created at the top of any protocol. It will display the name of the current file and a button to allow the expanding or collapse of all fields in the protocol.

• Fixed. This field type does not store any experimental variable. It can be used for describing an invariant part of a protocol / template, such as a procedure or background information that rarely changes.

• Text (single line). This field can be used to store a single line of text. For example, a gene or protein name, a primer sequence etc.

• Text Box (multi-line). Use this field to store longer pieces of text that are different for each experiment, such as comments or a description.

• Drop-down menu. This field is for choosing between a fixed number of text options, one of which may be selected as the experimental variable. The list of options is defined in the editor panel as part of the protocol template, and a default option can also be specified.

• Check Box. A simple check box for recording a true / false experimental parameter.

• Number. This field is for storing a numerical variable. Units and a default value can be specified. Values stored in this field can be multiplied using the "Maths" button in the main tool bar, allowing a group of selected Number values to be (for example) doubled to make 2 volumes of reagent mixture.

• Date & Time. The Date/Time field is designed to help with planning experiments on future dates, as well as providing a history of past experiments. It contains a date-picker for choosing a date (eg 28th April 2008). Once saved, files that contain date fields can be viewed in the calendar by clicking the calendar icon in the tool bar, or Menu > Calendar > Show Calendar. It is also possible to specify an alarm time (in the panel to the right) which will cause a reminder of an event to pop-up, as long as the application is running. As an alternative to picking a specific date, this field can be used to define a date that falls a number of days after a previous date. For example, a field called "Trasfect Cells" could be specified as "2 days" later than a previous date field called "Seed Cells". In this case, a different date could be specified for "Seed Cells" and the date of "Transfect Cells" would always be 2 days later. In this way, multiple Date/Time fields (and reminders) can be set for a single protocol and all can be re-scheduled by simply changing the first date (via date-picker).

• Time. The time field can be used for storing a period of time as hours, minutes and seconds. This field can also be used as a timer, allowing a count-down of the specified time.

• Link. Use this field for linking to another file on your computer, or a URL. Once specified, the link will become active and clicking it will open the URL in a web browser, or open the document in a suitable application. If the link is to another OMERO.editor file, clicking the link will open it in OMERO.editor. NB. When choosing the link, it is possible (at the bottom of the file chooser) to specify that the link is a "relative" link, from one document to the other. Therefore, if the two files are in a common folder that is subsequently moved to a new location, the link will be maintained.

• Table. This is a simple table that can be used to store tabular data. The column names must first be specified in the right hand editor panel.

• Image. This field is a link to a locally saved image, which is then displayed in the field. The size of the image can be changed using the zoom button beside the image.

• Ontology Term. A term can be chosen from ontologies in the OBO format. First choose the ontology, using the first drop-down menu on the left of the field. Now start typing a term name in the adjacent text field. After 3 letters, this will provide auto-complete options from matching terms in that ontology. This feature requires an internet connection.

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