At the left of the web page there is a list with the names of all the EMBOSS programs. They are organised into menus and submenus, which you can expand/compress one at a time by clicking with the mouse. There is also (at the bottom of the list) an ALPHABETIC LIST OF PROGRAMS. When you mouse over the name of a program a one-line description appears in a pop-up text box. If you do not know either the name or the group of the program you need there is a Search for programs function (it searches for words in the explanatory texts of the programs and pops up a window with program names sorted according to the number of occurrences; however programs that have the words in their one-line description are grouped at the top). You can access a page for a program by clicking on the name. Remember that you can always go back to the Project Management page by clicking on the PM button at the top.
The page for each program contains a number of boxes where you can type text, use radio buttons and selectors that allow you to select one option, and use selection boxes that allow you to select any number of options (using the mouse and the <Shift> and <Ctrl> keys). For the handling of sequences, see below. The pages are "alive" thanks to JavaScript. At the top of the page there is a Hide optional/Show optional button to switch between a version of the page showing only the Standard parameters and one that also shows the Additional and Advanced parameters. Parameters are intentionally not displayed when (in the context of the choice of other options) they are not applicable. You can access an online explanatory page using the Manual button.
Both at the top and at the bottom of the page a Run xxx button lets you start the program. You can start the program in Email mode (see below, time consuming programs) or interactively. When it has finished the output will appear in a separate window that shows all the output files in the results. There is a right click to save locally button: you can click with the left mouse button to obtain a window with just the text of that file or click with the right mouse button to perform a Save Link Target As operation. For certain filenames wEMBOSS will, when you click with the left button, allow you to save the file or view it using a plug-in (see below, plug-ins). Output that, in a terminal session, would have been sent just to the screen will appear in a pink Warning box at the top of the page. A green box at the bottom contains the exact EMBOSS command line generated by wEMBOSS.
Output files are stored on the server, just as if you had run the program in a terminal, and remain there as long as you do not explicitly decide to delete them (unless the manager of the site has implemented an automated delete procedure). So, if you want to look at an old result, do not run the program a second time, rather go to the Project Management page!
All the output files of a single program run are stored inside a "hidden" directory inside the current project. In the Project Management page you can see at the right hand side a PROJECT RESULTS area with a list of outputs, sorted according to date & time of run. With the Sort by name button you can switch to an alternative display where the outputs are first sorted alphabetically by program name. A simple click will open an output page identical to the page shown at the end of the run (see above).
It is common to provide the output of one EMBOSS program as the input to another one (e.g. prophecy output can be given to prophet or emma output given to prettyplot). To do that you must first copy the output file to your project so that it becomes available as data file; therefore you must click on the Files button to obtain a COPY FILES option at the bottom of the page. If you do not need the output from any old program runs, it is recommended that you save disc space by deleting them. You can select/deselect items with the check boxes at the extreme right of the page and then Del selection.
When you look back at the list of outputs in a project, it can be a hurdle remembering which was what, certainly if the list is long. As an aid, each item is preceded by a small icon in the shape of a sheet of paper. When you do a mouse-over on this, some text appears and clicking on it allows you to add or modify the text.
If your job is likely to take a long time to finish then, before you click on the run button, you can first fill in an E-mail address in the box at the bottom of the page. A new window will appear, telling you that the job has been started. You can go on with other work or just stop your WWW client; your program is actually running "in the background". When the program has finished an E-Mail is sent to notify you. You can then pop up the output from the Project Management page or, if your E-mail client is HTML compliant, from the E-mail itself.
