Abstract: After installation, a device may be asleep. A light signal device may send a message to the sleeping device to wake it up. This wake-up message may comprise the light signal device sending programmed light signals, the programmed light signals in modified morse code. An authentication part may also be included in the message. The light signal device may request an authentication message from the sleeping device.

Abstract: Portable biosurveillance kits for sequencing and sample identification are provided, and techniques for configuring said kits are provided. A system for configuring a kit may receive data representing a first and second set of nucleic acid sequences, and may generate and store first and second indexes representing the respective sets. The system may then use the indexes to identify conserved-signature sequences that satisfy abundance criteria with respect to the first set and sparsity criteria with respect to the second set. The identified conserved-signature sequences may be stored on (or represented in storage on) a portable sequencing and sample-identification kit, which may compare the conserved-signature sequence to a sample sequence in order to identify the sample sequence.

Abstract: After installation, a device may be asleep. A light signal device may send a message to the sleeping device to wake it up. This wake-up message may comprise the light signal device sending programmed light signals, the programmed light signals in modified morse code. An authentication part may also be included in the message. The light signal device may request an authentication message from the sleeping device.

Abstract: After installation, a device may be not yet powered. It may be awakened by receiving a flash of light of sufficient frequency and amplitude. After waking, the device decodes the message to determine its next action, and, upon request sends an authentication message. This enables a single user action to wake the device up and set it up with networking credentials. The same process may be used to wake the device outside of a normal sleep-wake cycle.

Abstract: In some embodiments, techniques for identifying one or more species in an undifferentiated environmental sample comprising a plurality of nucleic acid sequences are provided. One or more indices that represent a plurality of reference nucleic acid sequences may be provided, and data may be received comprising digital representations of respective nucleic acid sequences. The respective nucleic acid sequences may be aligned, if possible, using the indices. A respective alignment ration may be calculated for each one of the reference nucleic acid sequences, based on the number of nucleic acid sequences aligned to the respective reference nucleic acid sequence and the total number of nucleic acid sequences in the received data.

Abstract: In some embodiments, techniques for identifying one or more species in an undifferentiated environmental sample comprising a plurality of nucleic acid sequences are provided. One or more indices that represent a plurality of reference nucleic acid sequences may be provided, and data may be received comprising digital representations of respective nucleic acid sequences. The respective nucleic acid sequences may be aligned, if possible, using the indices. A respective alignment ration may be calculated for each one of the reference nucleic acid sequences, based on the number of nucleic acid sequences aligned to the respective reference nucleic acid sequence and the total number of nucleic acid sequences in the received data.

Abstract: A portable kit for nucleic acid sequencing is disclosed, the kit including a DNA extraction system configured to perform a DNA extraction protocol, a DNA sequencing preparation system configured to perform a DNA sequencing preparation protocol, a sequencer system, and a portable enclosure configured to house the DNA extraction system, the sequencer preparation system, and the sequencer system.

Abstract: Techniques for determining whether a nucleic acid sequence is genetically engineered are provided. In some embodiments, a ratio is calculated based on a number of input reads that align with reference data, and the ratio is inputted into a classifier to determine whether the input reads represent an engineered sequence. In some embodiments, first output data is generated based on unassembled read-based comparison of nucleic acid data, while second output data is generated based on assembly-based comparison of the nucleic acid data; the first and second output data are inputted into a classifier to determine whether the input data represents an engineered sequence. In some embodiments, nucleic acid data is compared to three reference datasets representing (i) engineered sequences, (ii) evolutionary variations of an organism, and (iii) evolutionary variations of other organisms; a determination as to whether the input data represents an engineered sequence is based on the three comparisons.

Abstract: Systems and methods for performing genomic information compression, transmission, and decompression are provided. A system for compression, transmission, and decompression of genomic information includes a first computer associated with a first index and a second computer associated with a second index, each index containing reference permutations of nucleic acid sequence portions, each permutation associated with a reference number. The first computer uses input genomic information and the first index to produce a compressed representation of the genomic information, and transmits the compressed representation to the second computer. The second computer uses the compressed representation and the second index to assemble a data representation of the genomic information. The compressed representation comprises references to permutations, indications of locations of each permutation in the input information, indications of variations to permutations, and/or indications of sequence length.

Abstract: In some embodiments, techniques for identifying one or more species in an undifferentiated environmental sample comprising a plurality of nucleic acid sequences are provided. One or more indices that represent a plurality of reference nucleic acid sequences may be provided, and data may be received comprising digital representations of respective nucleic acid sequences. The respective nucleic acid sequences may be aligned, if possible, using the indices. A respective alignment ration may be calculated for each one of the reference nucleic acid sequences, based on the number of nucleic acid sequences aligned to the respective reference nucleic acid sequence and the total number of nucleic acid sequences in the received data.

Abstract: In one embodiment, a system comprising a processor and a memory storing instructions executable by the processor creates an index for a nucleic acid sequence. The index comprises a plurality of elements. Each element corresponds to a permutation of a nucleic acid sequence. Data representing a nucleic acid sequence is received. A subsequence of the nucleic acid sequence is identified in the data at a first position of the nucleic acid sequence. A hash of the subsequence is computed to determine a corresponding element of the index. Position data reflecting the first position is stored in the corresponding element of the index.

Abstract: Systems and methods for identifying pathogens in food using whole genome sequencing are provided. In some embodiments, gene sequence data derived from food pathogen samples are subject to bioinformatics processing in order to align the sequences and detect single-nucleotide polymorphisms (SNP's). In some embodiments, a SNP matrix is generated and a phylogenic tree is created, and it is determined whether the strain of pathogens detected in one food pathogen sample is the same strain of pathogen present in other previously-encountered food pathogen samples. If a match between samples is determined, then metadata associated with the matching samples is leveraged to trace the spread of the strain through a supply chain in space and time, and parties associated with the matching samples may be notified.

Abstract: Systems and methods for performing genomic information compression, transmission, and decompression are provided. A system for compression, transmission, and decompression of genomic information includes a first computer associated with a first index and a second computer associated with a second index, each index containing reference permutations of nucleic acid sequence portions, each permutation associated with a reference number. The first computer uses input genomic information and the first index to produce a compressed representation of the genomic information, and transmits the compressed representation to the second computer. The second computer uses the compressed representation and the second index to assemble a data representation of the genomic information. The compressed representation comprises references to permutations, indications of locations of each permutation in the input information, indications of variations to permutations, and/or indications of sequence length.

Abstract: In one embodiment, a system comprising a processor and a memory storing instructions executable by the processor creates an index for a nucleic acid sequence. The index comprises a plurality of elements. Each element corresponds to a permutation of a nucleic acid sequence. Data representing a nucleic acid sequence is received. A subsequence of the nucleic acid sequence is identified in the data at a first position of the nucleic acid sequence. A hash of the subsequence is computed to determine a corresponding element of the index. Position data reflecting the first position is stored in the corresponding element of the index.