1. A method of providing a graphical user interface comprising:
partitioning a graphical user interface into a plurality of regions;
setting a focus to one of the regions;
changing the focus between the regions responsive to user input signals; and
automatically selecting the region having the focus after a predetermined period of time in which no user input signals are received.
2. The method of claim 1 further comprising partitioning the selected region into a plurality of sub-regions.
3. The method of claim 2 further comprising setting the focus to one of the sub-regions.
4. The method of claim 3 further comprising changing the focus between the sub-regions responsive to user input signals.
5. The method of claim 4 further comprising automatically selecting the sub-region having the focus after a predetermined period of time in which no user input signals are received.
6. The method of claim 5 further comprising setting the focus to an object in the selected sub-region, wherein the selected sub-region includes a plurality of objects.
7. The method of claim 6 further comprising changing the focus between the objects responsive to user input signals.
8. The method of claim 7 further comprising automatically selecting the object having the focus after a predetermined period of time in which no user input signals are received.
9. The method of claim 8 further comprising restarting the predetermined timer after each selection.
10. The method of claim 1 wherein partitioning a graphical user interface into a plurality of regions comprises providing a visual overlay on the graphical user interface.
11. The method of claim 10 further comprising partitioning each region into a plurality of sub-regions with the visual overlay on the graphical user interface.
12. The method of claim 10 wherein the visual overlay comprises a grid.
13. The method of claim 1 further comprising automatically selecting a representation of a keyboard displayed on a display.
14. The method of claim 13 wherein the representation of a keyboard comprises a subset of the keys available with a full-size keyboard.
15. The method of claim 1 wherein changing the focus between the regions responsive to user input signals comprises indicating which region is receiving the focus to the user.
16. The method of claim 1 further comprising generating the user input signals responsive to the user’s aspirations.
17. The method of claim 13 further comprising generating the user input signals responsive to the user’s touch.
18. A method of providing a graphical user interface comprising:
partitioning a graphical user interface into a plurality of hierarchical levels, wherein each hierarchical level includes one or more selectable objects;
setting a focus to one of the selectable objects within the scope of a first level;
automatically selecting the object having the focus after a predetermined period of time in which no user input signals are received; and
transitioning from the first level to a second level.
19. The method of claim 18 further comprising setting the focus to one of the selectable objects within the scope of the second level.
20. The method of claim 19 further comprising automatically transitioning from the second level to a third level after a predetermined period of time in which no user input signals are received.
21. The method of claim 18 further comprising navigating between the one or more selectable objects responsive to user input signals.
22. The method of claim 21 wherein navigating between the one or more selectable objects comprises changing the focus between the one or more selectable objects if the user input signals are generated before the predetermined period of time expires.
23. The method of claim 18 wherein a first level is partitioned into one or more regions.
24. The method of claim 23 wherein the regions are selectable objects in the first level.
25. The method of claim 23 further comprising displaying a grid overlay that defines the boundaries of the regions in the first level.
26. The method of claim 23 wherein a second level below said first level is partitioned into regions, and wherein the regions in the second level for sub-regions within the regions at the first level.
27. The method of claim 26 further comprising displaying a grid overlay that defines the boundaries of the sub-regions in the second level.
28. The method of claim 26 wherein the sub-regions are selectable objects in the second level.
29. The method of claim 26 further including a third level having a plurality of desktop level objects.
30. The method of claim 29 wherein subsets of the desktop level objects are included in each sub-region of the second level.
31. The method of claim 18 further comprising transitioning back to the first level from the second level responsive to user input.
32. The method of claim 18 further comprising generating user input responsive to the user’s aspirations.
33. The method of claim 18 further comprising generating user input responsive to the user’s touch.
34. An electronic device comprising:
a display to display a graphical user interface; and
a controller communicatively connected to the display and configured to:
partition the graphical user interface into a plurality of objects;
set a focus to one of the objects;
change the focus between the objects responsive to user input signals; and
automatically select the object having the focus after a predetermined period of time in which no user input signals are received.
35. The device of claim 34 wherein the controller is further configured to provide a visual overlay on the display to define the boundaries of the objects to the user.
36. The device of claim 35 wherein the visual overlay comprises a grid.
37. The device of claim 34 wherein the controller is further configured to change the focus between the objects if the user input signals are generated before the predetermined period of time expires.
38. The device of claim 34 wherein the objects are associated with one or more functions executable by the controller.
39. The device of claim 34 wherein the objects comprise regions.
40. The device of claim 34 wherein the objects comprise sub-regions.
41. The device of claim 40 wherein the sub-regions are within the scope of the regions.
42. The device of claim 34 wherein the objects comprise desktop level controls.
43. The device of claim 42 wherein the desktop level controls are within the scope of the sub-regions.
44. The device of claim 34 further comprising a port communicatively connected to the controller to receive the user input signals.
45. The device of claim 44 wherein the port comprises a wireless interface.
46. The device of claim 34 wherein the electronic device comprises a computing device.
47. A system comprising:
a user input device to generate user input signals;
an electronic device to receive the user input signals;
a display associated with the electronic device to display a graphical user interface; and
a controller communicatively connected to the electronic device and the display, and configured to:
partition the graphical user interface into a plurality of objects;
set a focus to one of the objects;
change the focus between the objects responsive to the user input signals; and
automatically select the object having the focus after a predetermined period of time in which no user input signals are received.
48. The system of claim 47 wherein the user input device comprises a hands-free input device that generates the user input signals responsive to a user’s aspirations.
49. The system of claim 48 wherein the controller cycles focus between the objects in a clockwise direction responsive to a user’s aspirations.
50. The system of claim 48 wherein the controller cycles focus between the objects in a counter-clockwise direction responsive to the user’s aspirations.
51. The system of claim 48 wherein the speed of movement of a cursor is proportional to the force with which the user aspirates into the user input device.
52. The system of claim 47 wherein the user input device comprises a hands-free input device that generates the user input signals responsive to a user’s touch.
53. The system of claim 47 wherein the user input device comprises a microphone that generates the user input signals responsive to a user’s predetermined voice command.
54. The system of claim 47 wherein the user input device comprises a remote control.
55. The system of claim 47 wherein the controller is further configured to change the focus between the objects if the controller receives the user input signals before the predetermined period of time expires.
56. The system of claim 47 wherein the controller is further configured to vary the predetermined period of time according to user customizations.
57. The system of claim 47 wherein the electronic device comprises a port communicatively connected to the user input device and the controller.
58. The system of claim 57 wherein the port comprises a wireless transceiver that communicates with a corresponding wireless transceiver associated with the user input device.
59. The system of claim 47 wherein the on-screen keyboard includes one or more keys and a word prediction section, wherein the keys and the word prediction section are partitioned into groupings of selectable objects.
60. The system of claim 59 wherein the controller permits substantially simultaneous focus between the on-screen keyboard and an application object displayed on the graphical user interface.
61. The system of claim 59 wherein the on-screen keyboard includes a plurality of layouts, and wherein the controller switches between different on-screen keyboard layouts responsive to user input.
62. The system of claim 59 wherein the controller alters the degree of transparency of the on-screen keyboard responsive to user input.
63. The system of claim 59 wherein the controller moves the position of the on-screen keyboard on the graphical user interface responsive to user input.
The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.
1. A method for detecting a plurality of target nucleic acids from a nucleic acid sample, comprising:
a) contacting a DNA array-bound probe with:
(i) a DNA interrogation probe, and
(ii) an RNA nucleic acid sample comprising at least one target nucleic acid,
wherein the array-bound probe and the interrogation probe hybridize to the target nucleic acid such that the 3\u2032 end of the array-bound probe and the 5\u2032 end of the interrogation probe are directly adjacent to one another and ligatable by DNA ligase, and wherein the interrogation probe contains a detectable label;
b) adding an effective amount of ATP to a solution of at least two different DNA ligase enzymes, thereby charging the at least one of the at least two different DNA ligase enzymes to form a DNA ligase-AMP intermediate complex,
wherein the at least two different DNA ligase enzymes comprise at least a first ligase which when charged to form a DNA ligase-AMP intermediate complex possesses activity to form a 5\u2032 to 5\u2032 pyrophosphate bond on the interrogation probe 5\u2032 terminus, and at least a second ligase which is a mutant ligase unable to form a DNA ligase-AMP intermediate complex, but which possesses an activity of forming a covalent phosphodiester bond from the 5\u2032 to 5\u2032 pyrophosphate bond of the interrogation probe and the 3\u2032 hydroxyl terminus of the array-bound probe;
c) depleting ATP from the solution of at least two different DNA ligase enzymes;
d) adding the solution of at least two different DNA ligase enzymes to step a), thereby ligating the 3\u2032 end of the array-bound probe to the 5\u2032 end of the interrogation probe; and
e) detecting the ligated product.
2. The method according to claim 1, wherein the second ligase is E. coli NAD+-dependent ligase LigA which comprises a point mutant or an amino terminal truncation.
3. The method according to claim 1, wherein the second ligase is an E. coli NAD+-dependent ligase LigA mutant selected from the group consisting of: Y22A, D32A and D36A.
4. The method of claim 1, wherein ATP depletion is accomplished by adding an effective amount of apyrase.
5. The method of claim 1, wherein ATP depletion is accomplished by adding an effective amount of hexokinase.
6. The method of claim 1, wherein ATP depletion is accomplished by adding an effective amount of apyrase and hexokinase.
7. A method of detecting a plurality of target nucleic acids from a nucleic acid sample, comprising:
a) contacting an open circle DNA probe with an RNA nucleic acid sample comprising at least one target nucleic acid, wherein the open circle probe comprises a 5\u2032 end and a 3\u2032 end, and wherein the open circle probe contains a detectable label;
b) adding an effective amount of ATP to a solution of at least two different DNA ligase enzymes, thereby charging the at least one of the at least two different DNA ligase enzymes to form a DNA ligase-AMP intermediate complex,
wherein the at least two different DNA ligase enzymes comprise at least a first ligase which when charged to form a DNA ligase-AMP intermediate complex possesses activity to form a 5\u2032 to 5\u2032 pyrophosphate bond on the interrogation probe 5\u2032 terminus, and at least a second ligase which is a mutant ligase unable to form a DNA ligase-AMP intermediate complex, but which possesses an activity of forming a covalent phosphodiester bond from the 5\u2032 to 5\u2032 pyrophosphate bond of the interrogation probe and the 3\u2032 hydroxyl terminus of the array-bound probe;
c) depleting ATP from the solution of DNA ligase-AMP intermediate;
d) adding the solution of DNA ligase-AMP intermediate to step a), thereby ligating the 5\u2032 end of the open circle probe to the 3\u2032 end of the open circle probe; and
e) detecting the ligated product.
8. The method according to claim 7, wherein ATP depletion is accomplished by adding an effective amount of apyrase.
9. The method according to claim 8, wherein the effective amount of apyrase is about 10 mU apyrase per \u03bcl.
10. The method according to claim 7, wherein ATP depletion is accomplished by adding an effective amount of hexokinase.
11. The method according to claim 10, wherein the effective amount of hexokinase is about 0.4 U hexokinase per \u03bcl.
12. The method according to claim 7, wherein the DNA ligase is T4 DNA ligase.
13. The method of claim 7 wherein the concentration of ATP in the ligase charging mix is between 200 and 500 mM.
14. The method of claim 7 wherein the concentration of ATP in the ligase charging mix is between 100 and 1000 mM.
15. The method of claim 7 wherein the concentration of ATP in the ligase charging mix is between 0.1 and 200 mM.
16. The method of claim 7 wherein the concentration of ATP in the ligase charging mix is between 10 and 100 mM.
17. The method of claim 7, wherein ATP depletion is accomplished by adding an effective amount of apyrase and hexokinase.
18. A method for detecting a plurality of target nucleic acids from a nucleic acid sample, comprising:
a) contacting a DNA array-bound probe with:
(i) a DNA interrogation probe, and
(ii) a DNA nucleic acid sample comprising at least one target nucleic acid,
wherein the array-bound probe and the interrogation probe hybridize to the target nucleic acid such that the 3\u2032 end of the array-bound probe and the 5\u2032 end of the interrogation probe are directly adjacent to one another and ligatable by DNA ligase, and wherein the interrogation probe contains a detectable label;
b) adding an effective amount of ATP to a solution of at least two different DNA ligase enzymes, thereby charging the at least one of the at least two different DNA ligase enzymes to form a DNA ligase-AMP intermediate complex,
wherein the at least two different DNA ligase enzymes comprise at least a first ligase which when charged to form a DNA ligase-AMP intermediate complex possesses activity to form a 5\u2032 to 5\u2032 pyrophosphate bond on the interrogation probe 5\u2032 terminus, and at least a second ligase which is a mutant ligase unable to form a DNA ligase-AMP intermediate complex, but which possesses an activity of forming a covalent phosphodiester bond from the 5\u2032 to 5\u2032 pyrophosphate bond of the interrogation probe and the 3\u2032 hydroxyl terminus of the array-bound probe;
c) depleting ATP from the solution of at least two different DNA ligase enzymes;
d) adding the solution of at least two different DNA ligase enzymes to step a), thereby ligating the 3\u2032 end of the array-bound probe to the 5\u2032 end of the interrogation probe; and
e) detecting the ligated product.
19. The method according to claim 18, wherein the second ligase is E. coli NAD+-dependent ligase LigA which comprises a point mutant or an amino terminal truncation.
20. The method according to claim 18, wherein the second ligase is an E. coli NAD+-dependent ligase LigA mutant selected from the group consisting of: Y22A, D32A and D36A.
21. The method of claim 18, wherein ATP depletion is accomplished by adding an effective amount of apyrase.
22. The method of claim 18, wherein ATP depletion is accomplished by adding an effective amount of hexokinase.
23. The method of claim 18, wherein ATP depletion is accomplished by adding an effective amount of apyrase and hexokinase.