All The Claims

1. A distributed BLAST processing system, comprising:
a pre-processing system coupled to a BLAST sequence database and configured to generate a plurality of data segments, each segment including a portion of the BLAST sequence database, and configured to determine a sequence correlation term based upon properties of the BLAST sequence database; and
a server system configured to communicate with a plurality of distributed client systems, the server system further being configured to send data segments, query sequences, and the sequence correlation term to the distributed client systems and to receive BLAST result data from the distributed client systems without requiring the distributed client systems to access the BLAST sequence database; and
a plurality of distributed client systems configured to communicate with the server system through a network, each client system further being configured to receive at least one data segment and the sequence correlation term from the server system and being configured to conduct BLAST processing on the data segment utilizing the sequence correlation term without requiring access to the BLAST sequence database,
wherein the server system is further configured to send a client agent component and a BLAST work engine component to the plurality of distributed client systems, and
wherein the pre-processing system is further configured to determine a number of preceding wildcard basepairs associated with each data segment, wherein the server system is further configured to send a preceding wildcard number along with each data segment, and wherein the BLAST work engine comprises a wildcard basepair replacement routine that utilizes the preceding wildcard number to choose where to start in a predetermined string of replacement basepairs.
2. The distributed BLAST processing system of claim 1, wherein the BLAST result data comprises expectation values.
3. The distributed BLAST processing system of claim 2, further comprising a post-processing system configured to receive and compile the BLAST result data.
4. The distributed BLAST processing system of claim 1, wherein the network comprises the Internet.
5. The distributed BLAST processing system of claim 1, wherein the BLAST work engine comprises a checkpointing routine that causes progress information to be stored during BLAST processing.
6. The distributed BLAST processing system of claim 1, wherein the plurality of data segments are stored as data files having an identical size, except for a final file that is partially filled with sequence data, the final file being updated with new sequence data as such data is added to the BLAST sequence database.
7. The distributed BLAST processing system of claim 1, wherein the pre-processing system is further configured to recalculate the sequence correlation term when updates to the BLAST sequence database occur, and wherein the server system is further configured to send the updated sequence correlation term to the distributed client systems.
8. A method for distributed BLAST processing, comprising:
generating a plurality of data segments from a BLAST sequence database, each segment including, a portion of the BLAST sequence database;
calculating a sequence correlation term based upon properties of the BLAST sequence database;
communicating with a plurality of distributed client systems to send data segments, query sequences and the sequence correlation term to the distributed client systems;

receiving BLAST result data from the distributed client systems without requiring the distributed client systems to access the BLAST sequence database;
receiving, with each of a plurality of distributed client systems, at least one data segment and the sequence correlation, conducting BLAST processing on the data segment utilizing the sequence correlation term without accessing the BLAST sequence database, and sending BLAST result data back to a server system;
sending a client agent component and a BLAST work engine component to each of the plurality of distributed client systems for operation on the distributed client systems; and
determining a number of preceding wildcard basepairs associated with each data segment, sending a preceding wildcard number along with each data segment, and utilizing a wildcard basepair replacement routine within the BLAST work engine to choose where to start in a predetermined string of replacement basepairs.
9. The method of claim 8, wherein the BLAST result data comprises expectation values.
10. The method of claim 8, further comprising utilizing a checkpointing routine within the BLAST work engine to store progress information during BLAST processing.
11. A method for distributed BLAST processing, comprising:
generating a plurality of data segments from a BLAST sequence database, each segment including a portion of the BLAST sequence database;
determining properties of the BLAST sequence database needed for calculating a sequence correlation term for the BLAST sequence database;
communicating with a plurality of distributed client systems to send data segments and the calculation properties to the distributed client systems;
receiving BLAST result data from the distributed client systems without requiring the distributed client systems to access the BLAST sequence database; and
determining a number of preceding wildcard basepairs associated with each data segment, sending a preceding wildcard number along with each data segment, and utilizing a wildcard basepair replacement routine within the BLAST work engine to choose where to start in a predetermined string of replacement basepairs.
12. The method of claim 11, wherein the BLAST result data comprises expectation values.
13. The method of claim 11, further comprising, with each of a plurality of distributed client systems, receiving at least one data segment and the calculation properties, calculating the sequence correlation term, conducting BLAST processing on the data segment utilizing the sequence correlation term without accessing the BLAST sequence database, and sending BLAST result data back to a server system.
14. The method of claim 13, further comprising sending a client agent component and a BLAST work engine component to each of the plurality of distributed client systems for operation on the distributed client systems.

The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.

What is claimed is:

1. A method of compensating for variations in the track pitches of optical discs in a data processing apparatus using an optical pickup, comprising the steps of:
activating a focus servo to trace tracks of an optical disc and generate a traverse signal, and inactivating a tracking servo so as not to trace the tracks of the optical disc, while a pickup assembly is transferred;
transferring the pickup assembly across the optical disc to generate the traverse signal caused by differences between the amounts of light reflected by the tracks of the optical disc and the other portions of the optical disc, while the optical disc is rotated;
shaping the traverse signal into a pulse wave, and counting the number of pulses of the traverse signal;
measuring and storing the rotation number of the optical disc while the pickup assembly is transferred to measure a track pitch;
calculating the track pitch of the rotating optical disc using the measured number of pulses of the traverse signal and the actual distance the pickup assembly is transferred; and
calculating a target track number using the calculated track pitch, and performing a seek operation using the calculated target track number.
2. The method according to claim 1, wherein the track pitch is calculated using the following equation,
2
S
N
T

–

R
N
E
=
P
where P is the track pitch, NT is the total number of pulses of the traverse signal, NE is the number of pulses of the traverse signal resulting from eccentricity of the optical disc, R is the rotation number of the optical disc, and S is a actual distance the pickup assembly is transferred.

1. A method for monitoring performance of an optical communication link, said method comprising:
obtaining an optical signal including a plurality of wavelength channels from said optical communication link;
passing said plurality of wavelength channels of said optical signal through a polarization beam splitter to separate two polarization components;
measuring a signal indicative of differences between said polarization components; and
determining whether there has been a failure of said optical communication link responsive to said signal indicative of said differences between said polarization components.
2. The method of claim 1 wherein obtaining said optical signal comprises:
tapping off said optical signal from said optical communication link as a monitor signal.
3. The method of claim 1 wherein said failure determining step comprises:
counting zero crossings of said signal indicative of said differences between said polarization components for a predetermined time interval.
4. Apparatus for monitoring performance of an optical communication link, said apparatus comprising:
a tap to obtain a monitor signal from said communication link;
a polarization beam splitter that isolates two polarization components of said monitor signal;
a differential amplifier that amplifies a difference of electronic signals derived from said two polarization components; and
a component responsive to an output of said differential amplifier to determine a failure of said optical communication link from zero crossings at said output.
5. The apparatus of claim 4 wherein zero-crossings in output of said differential amplifier indicate presence of signal on said optical communication link.
6. The apparatus of claim 4 wherein said monitor signal comprises multiple wavelengths carried by said optical communication link.
7. The apparatus of claim 4 wherein said component comprises a counter to count said crossings.
8. The apparatus of claim 4 wherein said component comprises an analog to digital converter to determine said failure digitally.
9. Apparatus for monitoring performance of an optical communication link, said apparatus comprising:
means for obtaining an optical signal including a plurality of wavelength channels from said optical communication link;
means for passing said plurality of wavelength channels of said optical signal through a polarization beam splitter to separate two polarization components;
means for measuring a signal indicative of differences between said polarization components; and
means for determining whether there has been a failure of said optical communication link responsive to said signal indicative of said differences between said polarization component.
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. An implantable pressure monitor comprising:
a substantially rigid chip including:
a proximal end and a distal end;
pressure sensors exposed on a first surface of the chip in a sensor region of the distal end;
signal processing circuitry receiving pressure-indicative signals from the sensors and producing pressure-indicative output signals; and
a chip electrical connector in the proximal end communicating the output signals;

a substantially rigid substrate that:
is spaced apart from the chip;
faces the first surface of the chip;
is connected to the chip electrical connector in the chip’s proximal end by a substrate electrical connector;
defines an aperture positioned over the sensor region of the chip’s distal end, thereby exposing the pressure sensors; and
covers the distal end of the chip except for the sensor region;

a flexible filler material located throughout space between the chip and the substrate except beneath the aperture, thereby leaving the pressure sensors exposed, such that (a) the flexible filler material connects the chip to the substrate, and (b) the distal end of the chip is connected to the substrate by only the flexible filler material;
a wire that:
extends from the substrate;
is electrically connected to the substrate electrical connector;
communicates the output signals; and
is not connected to the chip;

a biocompatible sheath that encapsulates the chip, substrate, filler, and wire, and is sufficiently flexible to transmit pressure exerted on the sheath exterior through the sheath; and
a pressure-transferring medium extending from the sheath, through the aperture, and to the pressure sensors, thereby transferring pressure exerted on the sheath exterior to the pressure sensors.
2. The implantable pressure monitor of claim 1, wherein the sheath has a curved shape to reduce or eliminate hydrodynamic forces.
3. The implantable pressure monitor of claim 1, wherein the substantially rigid substrate extends proximally from the chip to a proximal end which comprises an anchor.
4. The implantable pressure monitor of claim 3, wherein the anchor comprises a transversely extending flange that forms suture wings.
5. The implantable pressure monitor of claim 1, further comprising a holder that fixedly receives the chip and the substantially rigid substrate and extends proximally to a proximal end which comprises an anchor.
6. The implantable pressure monitor of claim 5, wherein the holder further comprises a distal end cap protecting the chip and the substantially rigid substrate.
7. The implantable pressure monitor of claim 1, wherein the flexible filler material comprises silicone.
8. The implantable pressure monitor of claim 1, wherein the flexible filler material holds the chip and the substrate together in a fixed relationship.
9. The implantable pressure monitor of claim 1, wherein the substantially rigid substrate extends distally from the chip to a distal end which comprises a barrier wall protecting a distal end of the chip.
10. The implantable pressure monitor of claim 9, wherein the barrier wall forms an end cap at the distal end of the chip.
11. The implantable pressure monitor of claim 10, wherein the barrier wall extends in a direction substantially perpendicular to a plane of the substrate and to a height such that a top of the barrier wall is at or above a top of the chip.
12. The implantable pressure monitor of claim 9, wherein the substantially rigid substrate further extends distally from the barrier wall to a tapered front portion.
13. The implantable pressure monitor of claim 1, wherein the sheath comprises a one-piece, seamless silicone covering.
14. The implantable pressure monitor of claim 13, wherein the flexible filler material comprises silicone.
15. The implantable pressure monitor of claim 1, wherein the substrate is sufficiently rigid such that it cannot be folded or rolled up.
16. The implantable pressure monitor of claim 1, wherein the substrate is sufficiently rigid to protect the pressure sensors from damage as a consequence of contact with a surgical instrument during implantation and from mechanical damage during use.
17. The implantable pressure monitor of claim 1, wherein the substrate is sufficiently rigid to avoid twisting of the chip due to turbulent blood flow.
18. The implantable pressure monitor of claim 1, wherein the substrate is rigid.
19. The implantable pressure monitor of claim 1, wherein the substrate is mechanically inflexible.