Sun Microsystems, Inc.

Ginkgo Bioworks, Inc.

Bolt Beranek and Newman Inc.

Randall David Rettberg

Whay Sing Lee

Nisha D Talagala

Chia Y Wu

Fay Chong, Jr

Mizanur Mohammed Rahman

Kumar Ramaswamy

Cher-Wen Lin

Thomas F Knight, Jr

David L Satterfield

Daniel R Cassiday

Reshma P Shetty

Thomas J Moser

Philip P Carvey

David G Robinson

John H Howard

Lance A Glasser

William R Crowther

Marc Thadeus Roskow

Robert A Doolittle

Systems, methods, libraries, kits, and computer software tools are provided for designing and producing engineered cells. Such engineered cells can be used for cell state quantification, such as genome, transcriptome and/or proteome quantification. In one aspect, an engineered cell having a plurality of artificially designed oligonucleotides introduced into the genome of the cell is provided. The oligonucleotides are each located in proximity of a gene of interest encoding a protein of interest, and are different from one another. The oligonucleotides can each encode a unique peptide tag for each protein of interest, wherein each peptide tag has a unique quantitatively measurable value such as mass-to-charge ratio which can be quantified by a mass spectrometer. The engineered cell is capable of expressing a plurality of proteins of interest each fused to its corresponding unique peptide tag, wherein each peptide tag is capable of being released therefrom.

Methods and systems for cell state quantification

A storage array interconnection fabric may be configured using multiple independent paths. A storage system including a plurality of communication paths is configured for connecting each node of a plurality of nodes forming an interconnection fabric. Each of the communications paths is an independent communications path. In addition, a first portion of the plurality of nodes is configured to communicate with a plurality of mass storage devices such as disk drives. A second portion of the plurality of nodes may be configured to communicate with a host.

High performance storage array interconnection fabric using multiple independent paths

Systems and methods for routing messages in an interconnection fabric are provided. The fabric includes a plurality of nodes, each node having, for example, four ports coupled to adjacent nodes in the fabric. A source node initiating a message in the fabric can transmit the message out of one of its four ports. Between a source node and a destination node, there are at least four independent paths which may be taken, depending on the output port from the source node. However, the precise path is not expressly delineated in the message. Instead, the message contains the address of the destination node, the address of the originating node, and a target region for the message. Each intermediate node is configured to receive a message via one of its four ports, and then select an appropriate output port based on the location of the port which received the message combined with the address and target information contained in the message. By providing a system by which four independent paths can be taken by a message, at least three intermediate nodes can fail in the fabric before the message is prevented from reaching the destination node.

Message routing in a torus interconnect

A storage system comprises a storage array controller and a storage array, which includes multiple storage devices and disk drive controllers. The storage array controller issues scrubbing operation commands to one or more of the disk drive controllers. In response, each disk drive controller that receives a scrubbing operation command reads data from within a data range from at least one of the disk drives, calculates a new checksum for the data, and compares the new checksum to a preexisting checksum for the data. If the new checksum doesn't equal the preexisting checksum, the data within the data range is determined to be erroneous.

Storage array employing scrubbing operations using multiple levels of checksums

A storage system comprises a storage array controller and a storage array, which includes multiple disk drives and disk drive controllers. The storage array controller issues scrubbing operation commands to one or more of the disk drive controllers. In response, each disk drive controller that receives a scrubbing operation command reads data from within a data range from at least one of the disk drives, calculates a new checksum for the data, and compares the new checksum to a preexisting checksum for the data. If the new checksum doesn't equal the preexisting checksum, the data within the data range is determined to be erroneous.

Storage array employing scrubbing operations at the disk-controller level

Embodiments of a routing system are disclosed, including a method for routing communications in a storage system. The storage system may include multiple nodes interconnected by an interconnection fabric that provides multiple independent paths between a source node and a destination node. Some nodes may be connected to one or more disk drives. The method may include receiving a communication to be sent from a source node to a destination node, selecting a communication path from the multiple independent paths, and sending the communication on the selected communication path. This process may be repeated so that multiple communications may be sent. Each communication path may be selected according to a preference assigned to it, so that a more preferred path is selected more often than a less preferred path.

Routing scheme using preferred paths in a multi-path interconnection fabric in a storage network

A single field replaceable storage or computer system may include a processor coupled to a peripheral bus by a bridge device. The field replaceable unit (FRU) may also include system memory coupled to the processor and a network interface coupled to the peripheral bus. One or more drive controllers may also be included coupled to the peripheral bus. Additionally, the single field replaceable unit includes an array of disk drives coupled to the one or more drive controllers. The array of disk drives may be configured as one or more RAID logical volumes and exported or presented to client machines as one or more file systems through the network interface. The processor, system memory, network interface, drive controllers, and array of disk drives are all packaged together as a single field replaceable unit. The processor, system memory, network interface, drive controllers, and array of disk drives may be configured not to be individually field serviceable or replaceable. If the unit fails and needs servicing or replacement, the unit may be replaced as a whole.

Field replaceable storage array

An apparatus includes a computing node and a metadata server. The computing node may transmit a request to open a file to the metadata server, which may provide a corresponding file identifier to the computing node. The computing node may use the file identifier to directly access the storage storing the file. In one embodiment, the storage may be an object-based storage. The storage may receive the file identifier with an access command and may perform the mapping from file identifier to storage blocks internally. Thus, accesses to the storage may be performed on an arbitrary boundary within the file. In other words, the entire block including the data needed by the computing node may not be transferred to the computing node. Instead, the storage may select the data requested from the file (e.g. via an offset and a number of bytes or some similar mechanism) and return that data to the computing node.

Direct access from client to storage device

A system and method for superimposing a sequence number of a packet into the CRC segment of the packet thereby allowing more bandwidth in the payload portion of the packet for carrying data is described. Also described is a method of acquiring additional information on the type of error in a packet, e.g., data transmission errors or sequence errors, from analyzing a CRC error. For example, a reported CRC error can be the result of the receipt of a packet with a sequence number the receiver is not expecting (which is a normal occurrence on transmission links due to transmitters resending packets that a receiver has already accepted) or can result from a real error in the transmission of a packet. A first error code check (CRC) value is calculated for the payload segment of a data packet. A second CRC value is calculated for the sequence number of the data packet. The first CRC value and the second CRC value are combined thereby creating a third CRC value. The third CRC value is then combined with the payload segment of the data packet thereby creating a data packet that can be transmitted across the link.

Method for superimposing a sequence number in an error detection code in a data network

Embodiments of a routing system are disclosed, including a method for routing communications in a storage system. The storage system may include multiple nodes interconnected by an interconnection fabric that provides multiple independent paths between a source node and a destination node. Some nodes may be connected to one or more disk drives. The method may include receiving a communication to be sent from a source node to a destination node, selecting a communication path from the multiple independent paths, and sending the communication on the selected communication path. This process may be repeated so that multiple communications may be sent. Each communication path may be selected according to a preference assigned to it, so that a more preferred path is selected more often than a less preferred path. The preferences may be updated to reflect changed conditions in the interconnection fabric.

Fault-tolerant, self-healing routing scheme for a multi-path interconnection fabric in a storage network

Embodiments of a routing system are disclosed, including a method for routing a plurality of communications in a storage system. The storage system may include a plurality of nodes interconnected by an interconnection fabric that provides multiple independent paths between each source node and each destination node. Some nodes may be connected to one or more disk drives. The method may include receiving a communication to be sent from a source node to a destination node, selecting a communication path from the multiple independent paths between the source and destination nodes, and sending the communication on the selected communication path. This process may be repeated so that multiple communications may be sent. Each communication path is systematically selected at least occasionally to send at least one of the communications to prevent any path from having undetected problems.

Fault-tolerant routing scheme for a multi-path interconnection fabric in a storage network

A data storage subsystem including a storage disk array employing dynamic data striping. A data storage subsystem includes a plurality of storage devices configured in an array and a storage controller coupled to the storage devices. The storage controller is configured to store a first stripe of data as a plurality of data stripe units across the plurality of storage devices. The plurality of data stripe units includes a plurality of data blocks and a parity block which is calculated for the plurality of data blocks. The storage controller is further configured to store a second stripe of data as a plurality of data stripe units across the storage devices. The second plurality of data stripe units includes another plurality of data blocks, which is different in number than the first plurality of data blocks, and a second parity block calculated for the second plurality of data blocks. Furthermore, the second plurality of data blocks may be a modified subset of the first plurality of data blocks. The storage controller is also configured to store the second plurality of data blocks and the second parity block to new locations.

Data storage subsystem including a storage disk array employing dynamic data striping

A storage array interconnection fabric may be configured using a torus topology. A storage system including a path-redundant torus interconnection fabric is coupled to a plurality of nodes. The torus interconnection fabric may be configured to connect the plurality of nodes in an array including N rows and M columns, where N and M are positive integers. The array may be configured such that a first node in a first row of the N rows is connected to a second node in the first row and a first node in a first column of the M columns is connected to a second node in the first column. Also an ending node in the first row is connected to the first node in the first row and an ending node in the first column is connected to the first node in the first column. In addition, a first portion of the plurality of nodes is configured to communicate with a plurality of storage devices such as disk drives.

Storage array interconnection fabric using a torus topology

System and method for rapidly calculating CRC values for messages including encoded bits is described. Tabularized CRC values are used in combination with a logical grid to quickly determine an appropriate CRC value of a message. This determination can take into account encoded inversion bits in the message. A collection of pre-calculated CRC values are arranged in a single-column table and then implemented with selected bits of a message by superimposing the bits in each CRC value onto a logical grid. Vertical lines of the grid are associated with 30 exclusive OR (XOR) gates and horizontal lines are associated with bits in an 88-bit message (or the 30 bits of a CRC value or with 8 bits of a sequence number). Through this grid, the inputs to the XOR gates are determined, thereby facilitating rapid calculations of CRC values due to the high processing speeds possible in XOR gates.

Growing community of inventors

Danville, CA, United States of America

Randall David Rettberg