MOBY is a Web protocol developed
by bioinformaticians, standardizing how to execute analysis on
remote servers. No more fill in various HTML forms, and cutting,
pasting and reformatting data!
MOBY clients like this one give you a standardized interface and common
input/output formats. MOBY also provides a yellow pages (lookup) service
so possible analysis options are presented to you automatically.
Data that can be used as input to analysis will be hyperlinked (underlined).
After clicking on a hyperlink, a popup menu will appear (this may take several
seconds depending on the service lookups required). If you hover over a menu
item for several seconds, a tooltip describing the data or service in more
detail will appear. Clicking on a service menu item will send the data to the
remote server and execute the analysis described in the tooltip.
Services that specify more user input (a.k.a. "Secondary Inputs") have an ellipsis ("...")
on their end. Clicking one of these services will launch a window with the
input options.
The easiest way to create data is to simply drag a file, text selection, or Web link onto the Seahawk interface. Seahawk will try to display the data you drop.
Click the folder/Web icon on the bottom toolbar will give you the option of loading data from a local file, or a remote Web page. To open the document in a new tab, hold down Shift while making your selection. In either case, if the specified document is HTML, RTF, or MOBY XML, the formatted data will be displayed. Any other data will be displayed as plain text, e.g. a FastA file. Highlighting a portion of the document will give you MOBY service options as described below.
With the mouse, you can highlight arbitrary sections of text in the Seahawk display. Clicking within selected text will raise a popup menu showing MOBY service options. Seahawk will try to determine the type of data highlighted are potentially show services for the selection as a, among other things:
Try highlighting all or part of the data below, then click in the highlighted region:
>gi|15898412 Glycerol kinase (EC:2.7.1.30) for Sulfolobus solfataricus P2 (a.k.a. SSO2133) MPGGFILAIDEGTTSARAIIYNQDLEVLGIGQYDFPQHYPSPGYVEHNPDEIWNAQMLAI KEAMKKAKIESRQVAGIGVTNQRETTILWDAISGKPIYNAIVWQDRRTSNITDWLKENYF GMIKDKTGLIPDPYFSGSKIKWILDNLPNVRSKAEKGEIKFGTIDTYLIWKLTNGKIHVT DYSNASRTMLFNINKLEWDREILELLKIPESILPEVRPSSDIYGYTEVLGSSIPISGDAG DQQAALFGQVAYDMGEVKSTYGTGSFILMNIGSNPIFSENLLTTIAWGLESKRVTYALEG SIFITGAAVQWFRDGLRAIDASDDIEPLAASVPDTGGVYFVPAFVGLGAPYWDPYARGLI IGITRGTTKAHIARAILESIAYQNRDVIEIMEKESGTKINILKVDGGGAKDNLLMQFQAD ILGIRVVRPKVMETASMGVAMLAGLAINYWNSLNELKQKWTVDKEFIPSINKEERERRYN AWKEAVKRSLGWEKSLGSK
When Seahawk is embedded in another application, such as Bluejay, the main application can programmatically send data to Seahawk for display. In Bluejay, clicking graphical representations of gene features will launch Seahawk's service selection interface for that gene's data.
By default, new analyses launched from within a tab replace the existing data. Like in a Web browser, you can navigate back and forward through your analysis chain using the buttons at the bottom of the window. To launch an analysis in a new tab, hold down Shift button while clicking on the service menu item. To close tabs, right-click on the tab label for options. Note that the Clipboard tab cannot be closed, and always launches services in a new tab.
According to the MOBY protocol, service providers must have valid default values
for all secondary inputs. In practice, some time they do not. To attempt to
execute a service that ends in "..." without being prompted for more
information, hold down the Control key while clicking on the service
menu item.
If some default parameters weren't properly given by the service
provider, you will be warned and the secondary input window will be displayed
for further manipulation.
Using the disk icon at the bottom of the screen, you can save the data shown in the displayed tab, in either native MOBY format (for use in another MOBY application), or in HTML (for presentation purposes).
Now, the first time Ahab was perched aloft; ere he had been there ten minutes; one of those red-billed savage sea-hawks which so often fly incommodiously close round the manned mast-heads of whalemen in these latitudes; one of these birds came wheeling and screaming round his head in a maze of untrackably swift circlings. Then it darted a thousand feet straight up into the air; then spiralized downwards, and went eddying again round his head.
But with his gaze fixed upon the dim and distant horizon, Ahab seemed not to mark this wild bird; nor, indeed, would any one else have marked it much, it being no uncommon circumstance; only now almost the least heedful eye seemed to see some sort of cunning meaning in almost every sight.
"Your hat, your hat, sir!" suddenly cried the Sicilian seaman, who being posted at the mizen-mast-head, stood directly behind Ahab, though somewhat lower than his level, and with a deep gulf of air dividing them.
But already the sable wing was before the old man's eyes; the long hooked bill at his head: with a scream, the black hawk darted away with his prize.
An eagle flew thrice round Tarquin's head, removing his cap to replace it, and thereupon Tanaquil, his wife, declared that Tarquin would be king of Rome. But only by the replacing of the cap was that omen accounted good. Ahab's hat was never restored; the wild hawk flew on and on with it; far in advance of the prow: and at last disappeared; while from the point of that disappearance, a minute black spot was dimly discerned, falling from that vast height into the sea.