Abstract: A method includes receiving, by a processing device, a plurality of genome files. Each genome file corresponds to a different sample and defining a genetic sequence. The method also includes generating, by the processing device, a two-dimensional alignment file based on the genome files and a reference sequence. A first dimension of the alignment file corresponds to individual genetic sequences and each of the genetic sequences is aligned with respect to the reference sequence along a second dimension of the alignment file. The method includes separating, by the processing device, the alignment file into a plurality of groups and storing the groups in a non-transitory genome data store. Each group contains segments of the genetic sequences of two or more of the genomic files.

Abstract: A method includes receiving, by a processing device, a plurality of genome files. Each genome file corresponds to a different sample and defining a genetic sequence. The method also includes generating, by the processing device, a two-dimensional alignment file based on the genome files and a reference sequence. A first dimension of the alignment file corresponds to individual genetic sequences and each of the genetic sequences is aligned with respect to the reference sequence along a second dimension of the alignment file. The method includes separating, by the processing device, the alignment file into a plurality of groups and storing the groups in a non-transitory genome data store. Each group contains segments of the genetic sequences of two or more of the genomic files.

Abstract: A system including a collection of local data processing devices and a collection of remote data processing devices. At least one local data processing device executes instructions configuring the at least one local data processing device to implement a resource manager, a virtual machine, and a virtual machine manager. The resource manager associates application threads of a software application executing on a data processing device with local processors. The virtual machine includes a plurality of virtual processors, and each virtual processor emulates a data processing device. The virtual machine associates local processors with virtual processors. Finally, the virtual machine manager associates at least one virtual processor with a local data processing device and at least one virtual processor with a remote data processing device.

Abstract: Optimization techniques for selecting indicator polynucleotides for an experiment and for determining expression levels resulting from the experiment. The optimization technique corrects for variations in polynucleotide melting temperatures during analysis of the experimental results. The optimization technique selects set of indicator polynucleotides for the experiment. The optimization technique then performs the experiment with the indicator polynucleotides and a sample and identifies the relative amounts of the indicated polynucleotides. The optimization technique then adjusts the relative amounts of the indicated polynucleotides based on melting temperatures associated with the indicator polynucleotides.

Abstract: A method and system for identifying mRNA present in a sample. A splice variant technique selects a set of possible exon-exon junctions based on exons of expected mRNA transcripts. The splice variant technique then selects indicator polynucleotides for the exon-exon junctions and detects the expression level of the indicator polynucleotides in the sample. The splice variant technique then may use a mathematical algorithm to identify possible splice variants in the sample from the observed expression levels.

Abstract: Methods of selecting indicator polynucleotide controls for use, for example, in determining amounts of indicated polynucleotides in a sample are described. Devices that include indicator polynucleotide controls and data representations relevant to them are also described. A storage medium comprising data obtained from a study using a nucleotide array that includes one or more of the indicator polynucleotide controls is also described.

Abstract: Optimization techniques for selecting indicator polynucleotides for an experiment and for determining expression levels resulting from the experiment. The optimization technique corrects for variations in polynucleotide melting temperatures during analysis of the experimental results. The optimization technique selects set of indicator polynucleotides for the experiment. The optimization technique then performs the experiment with the indicator polynucleotides and a sample and identifies the relative amounts of the indicated polynucleotides. The optimization technique then adjusts the relative amounts of the indicated polynucleotides based on melting temperatures associated with the indicator polynucleotides.

Abstract: A method and system for identifying mRNA present in a sample. A splice variant technique selects a set of possible exon-exon junctions based on exons of expected mRNA transcripts. The splice variant technique then selects indicator polynucleotides for the exon-exon junctions and detects the expression level of the indicator polynucleotides in the sample. The splice variant technique then may use a mathematical algorithm to identify possible splice variants in the sample from the observed expression levels.

Abstract: A gene product representation technique combines gene product expression data with a genome browser or splice graph view of the gene product sequences. The representation technique indicates the expression level of a gene product, or region of a gene product, in the view in a graphical way. It may varies the color saturation of a portion of the gene product representation according to the expression level. The gene product representation may consist of a geometric shape, a text string, or a symbol. It may consist of multiple regions whose expression levels have been measured independently.

Abstract: Optimization techniques for selecting indicator polynucleotides for an experiment and for determining expression levels resulting from the experiment. The optimization technique corrects for variations in polynucleotide melting temperatures during analysis of the experimental results. The optimization technique selects set of indicator polynucleotides for the experiment. The optimization technique then performs the experiment with the indicator polynucleotides and a sample and identifies the relative amounts of the indicated polynucleotides. The optimization technique then adjusts the relative amounts of the indicated polynucleotides based on melting temperatures associated with the indicator polynucleotides.

Abstract: A method and system for identifying mRNA present in a sample. A splice variant technique selects a set of possible exon-exon junctions based on exons of expected mRNA transcripts. The splice variant technique then selects indicator polynucleotides for the exon-exon junctions and detects the expression level of the indicator polynucleotides in the sample. The splice variant technique then may use a mathematical algorithm to identify possible splice variants in the sample from the observed expression levels.