Abstract: Compositions and methods are provided for genome modification of a target sequence in the genome of a plant or plant cell, without incorporating a selectable transgene marker. The methods and compositions employ a guide polynucleotide/Cas endonuclease system to provide an effective system for modifying or altering target sites within the genome of a plant, plant cell or seed, without incorporating a selectable transgene marker. Once a genomic target site is identified, a variety of methods can be employed to further modify the target sites such that they contain a variety of polynucleotides of interest. Breeding methods and methods for selecting plants utilizing a guide polynucleotide/Cas endonuclease system are also disclosed. Compositions and methods are also provided for editing a nucleotide sequence in the genome of a cell, without incorporating a selectable transgene marker.

Abstract: A distributed computing environment is provided with a system and method for supporting rare copy-on-write data access. The system operates a data structure in a read only pattern suitable for serving a plurality of read requests with reduced overhead. The system, upon receiving a write request, creates a copy of data to execute the write request. The system defers writing the mutated data back to the read-only data structure. The system thus allows for multiple mutations to be made to the copy of the data using a read/write access pattern. After a number of read-only requests are received, the mutated data is written back to the read-only data structure. A monitor counts read and write requests in order to reduce overall read/write overhead and enhance performance of the distributed data grid.

Abstract: A distributed computing environment is provided with a system and method for supporting rare copy-on-write data access. The system operates a data structure in a read only pattern suitable for serving a plurality of read requests with reduced overhead. The system, upon receiving a write request, creates a copy of data to execute the write request. The system defers writing the mutated data back to the read-only data structure. The system thus allows for multiple mutations to be made to the copy of the data using a read/write access pattern. After a number of read-only requests are received, the mutated data is written back to the read-only data structure. A monitor counts read and write requests in order to reduce overall read/write overhead and enhance performance of the distributed data grid.

Abstract: A distributed computing environment is provided with a system and method for supporting rare copy-on-write data access. The system operates a data structure in a read only pattern suitable for serving a plurality of read requests with reduced overhead. The system, upon receiving a write request, creates a copy of data to execute the write request. The system defers writing the mutated data back to the read-only data structure. The system thus allows for multiple mutations to be made to the copy of the data using a read/write access pattern. After a number of read-only requests are received, the mutated data is written back to the read-only data structure. A monitor counts read and write requests in order to reduce overall read/write overhead and enhance performance of the distributed data grid.

Abstract: A system and method for providing store and forward messaging on a partitioned cache provided by a distributed data grid. The store and forward message system implements publish and subscribe semantics in a way that distributed messages over the partitions of the distributed cache, reduces contention and makes efficient use of processor and network resources.

Abstract: A system and method for supporting an association-aware executor service in a distributed computing environment comprising. The system can provide an executor service associated with a thread pool, the thread pool containing a plurality of threads. The system can receive, at the executor service, a plurality of work requests, each work request being associated with a key of a plurality of keys. The system can define groups of work requests, each group of work requests comprising one or more work requests having a same key. The system can queue, on the plurality of threads in the thread pool, the groups of work requests, each group of work requests being queued on a different thread. All work requests in a particular group are executed on the same thread.

Abstract: A system and method can support recovery of persisted data from persistent storage of a distributed data grid, and provide persistent store versioning and integrity. A coordinator in the distributed data grid can receive a plurality of identifiers from one or more members of the distributed data grid, wherein each said identifier is associated with a persisted partition in a persistent storage for the distributed data grid. Then, the coordinator can select an identifier for each partition, wherein each selected identifier is associated with a most recent valid version of a partition. Furthermore, the coordinator can determine an active member in the distributed data grid that is responsible for recovering said partition from a persisted partition associated with the selected identifier.

Abstract: A system and method for supporting universal timeout in a distributed computing environment. The universal timeout feature can enforce a defined timeout for a block (or group of blocks) or code executing on a thread regardless of the number of network hops required to effectuate the code. The universal timeout feature allows a thread to express a timeout which is respected across the platform thereby improving timeout functionality compared to prior timeout implementations which pass a timeout between functions. Universal timeout may be implemented using a try-with-resources paradigm where the timeout period is treated as a resource.

Abstract: A system and method can support persistence in a distributed data grid. A plurality of members in the distributed data grid can persist a plurality of partitions associated with one or more cache services in persistent storage. Furthermore, a coordinator, which may be a member in the distributed data grid, can synchronize a view of partition ownership among the plurality of members in the distributed data grid, and form a distributed consensus on which partition can be recovered from which member in the distributed data grid.

Abstract: A system and method for providing a message bus component or version thereof (referred to herein as an implementation), and a messaging application program interface, for use in an enterprise data center, middleware machine system, or similar environment that includes a plurality of processor nodes together with a high-performance communication fabric (or communication mechanism) such as InfiniBand. In accordance with an embodiment, the messaging application program interface enables features such as asynchronous messaging, low latency, and high data throughput, and supports the use of in-memory data grid, application server, and other middleware components.

Abstract: A system and method can support recovery of persisted data from persistent storage of a distributed data grid, and provide persistent store versioning and integrity. A coordinator in the distributed data grid can receive a plurality of identifiers from one or more members of the distributed data grid, wherein each said identifier is associated with a persisted partition in a persistent storage for the distributed data grid. Then, the coordinator can select an identifier for each partition, wherein each selected identifier is associated with a most recent valid version of a partition. Furthermore, the coordinator can determine an active member in the distributed data grid that is responsible for recovering said partition from a persisted partition associated with the selected identifier.

Abstract: A system and method for providing store and forward messaging on a partitioned cache provided by a distributed data grid. The store and forward message system implements publish and subscribe semantics in a way that distributed messages over the partitions of the distributed cache, reduces contention and makes efficient use of processor and network resources.

Abstract: A system and method can support persistence in a distributed data grid, such as persistent store versioning and integrity. A resolver in the distributed data grid can receive a plurality of identifiers from one or more members of the distributed data grid, wherein each said identifier is associated with a persisted partition in a persistent storage for the distributed data grid. Then, the resolver can select an identifier for each partition, wherein each selected identifier is associated with a most recent valid version of a partition. Furthermore, the resolver can determine a member in the distributed data grid that is responsible for recovering said partition from a persisted partition associated with the selected identifier.

Abstract: A system and method which supports a low contention queue in a multithreaded processing environment such as a distributed data grid. The queue is optimized to reduce memory contention and queue processing overhead, and is lock-free. The queue includes a doubly-linked list of nodes, wherein each node is associated with a value, a reference to a next node and a reference to a previous node. Furthermore, the queue allows one or more consumer threads to access the queue via a reference to a last removed node from the doubly linked list, and allows one or more producer threads to insert a new node via a reference to a tail node in the doubly-linked list. The low queue efficiently serves large number of threads with reduced contention, overhead, and latency, thereby improving performance in a multithreaded processing environment such as a distributed data grid.

Abstract: A system and method is described for use with a data grid cluster, for supporting service level quorum in the data grid cluster. The data grid cluster includes a plurality of cluster nodes that support performing at least one service action. A quorum policy, defined in a cache configuration file associated with the data grid cluster, can specify a minimum number of service members that are required in the data grid cluster for performing the service action. The data grid cluster uses the quorum policy to determine whether the service action is allowed to be performed, based on a present state of the plurality of cluster nodes in the data grid cluster.

Abstract: A system and method for waiting-thread notification offloading supports thread notification offloading in a multi-threaded messaging system such as a distributed data grid. Pending notifiers are maintained in a pending notifier collection. A service thread adds pending notifiers to the collection instead of signaling the notifiers on the service thread. An active thread associated with the service thread determines that it is ready to enter a wait state. Before entering the wait state or instead of entering the wait state, the active thread retrieves pending notifiers from the pending notifier collection, signals the retrieved pending notifiers, and wakes the waiting threads associated with the pending notifiers, thereby offloading the notifier signaling overhead from the service thread to the active thread.

Abstract: A system and method can support socket programming in a server environment, such as a distributed data grid. The server environment can include a selection service that operates to register a plurality of sockets, wherein each said socket is associated with a handler in a plurality of handlers. Furthermore, the selection service can listen for one or more incoming connection requests on the plurality of sockets, and invoke a pluggable callback provided by a said handler associated with a registered socket in the plurality of sockets, when said registered socket receives an incoming connection request.

Abstract: A system and method for cooperative notification offloading supports thread notification offloading in a multi-threaded messaging system such as a distributed data grid. Pending notifiers are maintained in a collection of pending notifiers. A signaling thread processes a first notifier in the collection of pending notifiers to wake a first thread. The first awoken thread processes additional notifiers in the collection of pending notifiers to wake additional threads. The additional awoken threads can process additional notifiers in a cycle until all pending notifiers in the collection are processed. Such cooperative notification offloading of notifier processing from the signaling thread improves performance of the signaling thread with respect to other tasks thereby improving performance of the signaling thread and the distributed data grid.

Abstract: Systems and methods can support flow control in a distributed data grid. The distributed data grid includes a plurality of server nodes that are interconnected with one or more communication channels. The distributed data grid can provide a flow control mechanism, which controls the execution of the tasks in an underlying layer in the distributed data grid. Then, the system allows the client to interact with the flow control mechanism in the distributed data grid, and use the flow control mechanism to configure and execute one or more tasks that are received from the client.

Abstract: A system and method can support socket programming in a server environment, such as a distributed data grid. The server environment can include a selection service that operates to register a plurality of sockets, wherein each said socket is associated with a handler in a plurality of handlers. Furhtermore, the selection service can listen for one or more incoming connection requests on the plurality of sockets, and invoke a pluggable callback provided by a said handler associated with a registered socket in the plurality of sockets, when said registered socket receives an incoming connection request.