Abstract: An example method includes reacting a first solution and a different, second solution on a flow cell by flowing the first solution over amplification sites on the flow cell and subsequently flowing the second solution over the amplification sites. The first solution includes target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates and replication enzymes. The target nucleic acids in the first solution transport to and bind to the amplification sites at a transport rate. The first reagent mixture amplifies the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from corresponding target nucleic acids. The amplicons are produced at an amplification rate that exceeds the transport rate. The second solution includes a second reagent mixture and lacks the target nucleic acids. The second solution is to increase a number of the amplicons at the amplification sites.

Abstract: The present invention relates to improvements in methods of high throughput nucleic acid sequencing, and in particular to improvements to methods of carrying out extension reactions during pairwise sequencing. The present invention relates to a method for carrying out a strand resynthesis extension reaction during pairwise sequencing, wherein said strand resynthesis extension reaction is carried out between a first sequencing read and a second sequencing read, and wherein said strand resynthesis extension reaction extends one or more immobilised primers to copy a first template strand to generate a second immobilised template strand; characterised in that the strand resynthesis extension reaction is carried out using a non-thermostable strand displacement polymerase at a temperature of less than 55° C., preferably at 38° C.

Abstract: A method of preparing templates for high throughput nucleic acid sequencing, comprising: a) providing a solid support, wherein said solid support comprises a plurality of nucleic acid primers immobilised adaptor nucleic acid sequences which hybridise to one or more of the nucleic acid primers, and the library preparation having a nucleic acid concentration of 400 pM or less; c) allowing single stranded fragments of template nucleic acid to bind to said nucleic acid primers, thereby immobilising said single stranded fragments on said solid support; and d) repeating steps b) and c) at least three further times, i.e. multiple loadings or rounds of template hybridization to improve occupation rates, e.g., of nanowells on a flow cell.

Abstract: An example method includes reacting a first solution and a different, second solution on a flow cell by flowing the first solution over amplification sites on the flow cell and subsequently flowing the second solution over the amplification sites. The first solution includes target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates and replication enzymes. The target nucleic acids in the first solution transport to and bind to the amplification sites at a transport rate. The first reagent mixture amplifies the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from corresponding target nucleic acids. The amplicons are produced at an amplification rate that exceeds the transport rate. The second solution includes a second reagent mixture and lacks the target nucleic acids. The second solution is to increase a number of the amplicons at the amplification sites.

Abstract: An example method includes reacting a first solution and a different, second solution on a flow cell by flowing the first solution over amplification sites on the flow cell and subsequently flowing the second solution over the amplification sites. The first solution includes target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates and replication enzymes. The target nucleic acids in the first solution transport to and bind to the amplification sites at a transport rate. The first reagent mixture amplifies the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from corresponding target nucleic acids. The amplicons are produced at an amplification rate that exceeds the transport rate. The second solution includes a second reagent mixture and lacks the target nucleic acids. The second solution is to increase a number of the amplicons at the amplification sites.

Abstract: An example method includes reacting a first solution and a different, second solution on a flow cell by flowing the first solution over amplification sites on the flow cell and subsequently flowing the second solution over the amplification sites. The first solution includes target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates and replication enzymes. The target nucleic acids in the first solution transport to and bind to the amplification sites at a transport rate. The first reagent mixture amplifies the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from corresponding target nucleic acids. The amplicons are produced at an amplification rate that exceeds the transport rate. The second solution includes a second reagent mixture and lacks the target nucleic acids. The second solution is to increase a number of the amplicons at the amplification sites.

Abstract: Methods, systems, and apparatus, including computer program products, for searching for and presenting backups. A first search result including a first version of an item is presented. The first version is associated with a first date range having a first start date and a first end date. User input requesting that an archive including one or more versions of the item be searched is received. A second search result including a second version of the item is presented. The second version is different from the first version. The second version is associated with a second date range having a second start date and a second end date. The second date range does not overlap with the first date range.

Abstract: Systems and methods are provided for storing and restoring digital data. In some implementations, a method is provided. The method includes initiating a backup operation of data including a plurality of items, interrupting the backup operation, where interrupting occurs after a portion of the data has been completed, receiving an input to resume the backup operation, identifying a previously completed portion of the backup data, and performing a backup of a remaining uncompleted portion of the backup data. Other embodiments of this aspect include corresponding systems, apparatus, computer program products, and computer readable media.

Abstract: Systems and methods are provided for storing and restoring digital data. In some implementations, a method is provided. The method includes initiating a backup operation of data including a plurality of items, interrupting the backup operation, where interrupting occurs after a portion of the data has been completed, receiving an input to resume the backup operation, identifying a previously completed portion of the backup data, and performing a backup of a remaining uncompleted portion of the backup data. Other embodiments of this aspect include corresponding systems, apparatus, computer program products, and computer readable media.

Abstract: Systems and methods are provided for storing and restoring digital data. In some implementations, a method is provided. The method includes initiating a backup operation of data including a plurality of items, interrupting the backup operation, where interrupting occurs after a portion of the data has been completed, receiving an input to resume the backup operation, identifying a previously completed portion of the backup data, and performing a backup of a remaining uncompleted portion of the backup data. Other embodiments of this aspect include corresponding systems, apparatus, computer program products, and computer readable media.

Abstract: Methods, systems, and apparatus, including computer program products, for searching for and presenting backups. A first search result including a first version of an item is presented. The first version is associated with a first date range having a first start date and a first end date. User input requesting that an archive including one or more versions of the item be searched is received. A second search result including a second version of the item is presented. The second version is different from the first version. The second version is associated with a second date range having a second start date and a second end date. The second date range does not overlap with the first date range.

Abstract: Systems and methods are provided for performing backup operations while a user is using a device. In one implementation, a method is provided. A backup operation of data including a plurality of related items is initiated. Modifications to one or more items of the plurality of related items are monitored for during the backup operation. The backup operation is completed. If a modification occurred to one or more items, a second backup operation is performed for the modified items.

Abstract: Systems and methods are provided for storing and restoring digital data. In some implementations, a method is provided. The method includes displaying a current view, initiating a history view, the history view including two or more visual representations of corresponding earlier versions of the current view, identifying a selection of an item in a visual representation, receiving an input to delete the selected item, and deleting each instance of the selected item in the history view. Other embodiments of this aspect include corresponding systems, apparatus, computer program products, and computer readable media.

Abstract: Systems and methods are provided for storing and restoring digital data. In some implementations, a method is provided. The method includes initiating a backup operation of data including a plurality of items, interrupting the backup operation, where interrupting occurs after a portion of the data has been completed, receiving an input to resume the backup operation, identifying a previously completed portion of the backup data, and performing a backup of a remaining uncompleted portion of the backup data. Other embodiments of this aspect include corresponding systems, apparatus, computer program products, and computer readable media.

Abstract: Systems and methods are provided for event notification. In one implementation, a method is provided. A determination is made as to whether a threshold associated with pending event notifications has been exceeded by an incoming event notification. A plurality of pending event notifications that can be combined are identified. Two or more event notifications are combined.

Abstract: Systems and methods are provided for performing backup operations while a user is using a device. In one implementation, a method is provided. A backup operation of data including a plurality of related items is initiated. Modifications to one or more items of the plurality of related items are monitored for during the backup operation. The backup operation is completed. If a modification occurred to one or more items, a second backup operation is performed for the modified items.

Abstract: Systems and methods are provided for storing and restoring digital data. In some implementations, a method is provided. The method includes initiating a backup operation of data including a plurality of items, interrupting the backup operation, where interrupting occurs after a portion of the data has been completed, receiving an input to resume the backup operation, identifying a previously completed portion of the backup data, and performing a backup of a remaining uncompleted portion of the backup data. Other embodiments of this aspect include corresponding systems, apparatus, computer program products, and computer readable media.

Abstract: Adaptive techniques for handling notifications and updating a directory of a file system in a graphical user interface of a computing environment. Adaptive techniques include determining that something has been potentially changed in the node. A time of the notification is obtained, and a preferred time value or trigger time for responding to the notification is calculated. The preferred time value may be calculated by adding an adjustment to a recorded time of the last synchronization performed on the directory. The adjustment may be calculated by weighting duration of synchronizations performed on the directory. Adaptive techniques may then compare the time value to the trigger time. If the time value is less than the trigger time, the display and directory are synchronized. Otherwise, a timer may be set to the trigger time, and synchronization of the display and directory may be delayed until the trigger time.

Abstract: Adaptive techniques for handling notifications and updating a directory of a file system in a graphical user interface of a computing environment are disclosed. The adaptive techniques include receiving a notification that at least something has been potentially changed in the node. A current time value of the notification is obtained, and a preferred time value or trigger time for responding to the notification is calculated. In a preferred embodiment, the preferred time value is calculated by adding an adjustment or incremental value to a recorded time of the last synchronization performed on the directory. The adjustment or incremental value is preferably calculated by weighting a duration of one or more synchronizations performed on the directory. The adaptive techniques then compare the current time value to the trigger time. If the current time is greater than the trigger time, the Finder and the directory are synchronized.

Abstract: Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for presenting data. In one aspect, a method includes receiving a request for data; submitting the request while maintaining a currently displayed user interface; determining whether a specified amount of the data has been received within a threshold delay period; if the data has been received within the threshold delay period, displaying a new user interface including representations of a portion of the received data; and if the data has not been received within the threshold delay period, displaying a placeholder user interface.