Verinata Health, Inc.

Hewlett-packard Development Company, L.p.

Dell Products Inc.

Sun Microsystems, Inc.

Hui Huang

John P Burke

Erich D Blume

David Dice

Goutham Rao

Murali Bashyam

Eric Brueggemann

Christian Friedrich Beedgen

Mark Taylor

Ankur Lahoti

Mingyao Yang

Disclosed are methods and tools for rapidly aligning reads to a reference sequence. These methods and tools employ Bloom filters or similar set membership testers to perform the alignment. The reads may be short sequences of nucleic acids or other biological molecules and the reference sequences may be sequences of genomes, chromosomes, etc. The Bloom filters include a collection of hash functions, a bit array, and associated logic for applying reads to the filter. Each filter, and there may be multiple of these used in a particular application, is used to determine whether an applied read is present in a reference sequence. Each Bloom filter is associated with a single reference sequence such as the sequence of a particular chromosome. In one example, chromosomal abundance is determined by aligning reads from a sequencer to multiple chromosomes, each having an associated Bloom filter or other set membership tester.

Set membership testers for aligning nucleic acid samples

A data de-duplication system is used with network attached storage and serves to reduce data duplication and file storage costs. Techniques utilizing both symlinks and hardlinks ensure efficient deletion file/data cleanup and avoid data loss in the event of crashes.

Representing and storing an optimized file system using a system of symlinks, hardlinks and file archives

A unique identifier is assigned to a network node and is used to obtain an 'asset model' corresponding to the node and to determine whether the node is a member of a particular category. An asset model is a set of information about a node (e.g., the node's role within the enterprise, software installed on the node, and known vulnerabilities/weaknesses of the node). An identifier lookup module determines a node's identifier based on characteristics of the node (such as IP address, host name, network zone, and/or MAC address), which are used as keys into lookup data structures. A category lookup module determines whether a particular node is a member of (i.e., within) a particular category using a transitive closure to model the categories (properties) that can be attached to an asset model. A transitive closure for a particular asset category is stored as a bitmap, similar to bitmap indexing.

Real-time identification of an asset model and categorization of an asset to assist in computer network security

A technique for accessing a shared resource of a computerized system involves running a first portion of a first thread within the computerized system, the first portion (i) requesting a lock on the shared resource and (ii) directing the computerized system to make operations of a second thread visible in a correct order. The technique further involves making operations of the second thread visible in the correct order in response to the first portion of the first thread running within the computerized system, and running a second portion of the first thread within the computerized system to determine whether the first thread has obtained the lock on the shared resource. Such a technique alleviates the need for using a MEMBAR instruction in the second thread.

Techniques for accessing a shared resource using an improved synchronization mechanism

Growing community of inventors

Sunnyvale, CA, United States of America

Hui Huang