The generation of a factory order to control production of nucleotide sequences by a gene manufacturing system includes receiving an expression indicating an operation on sequence operands, each representing at least one nucleotide sequence part, evaluating the expression to a sequence specification, wherein the sequence specification comprises a data structure including one or more first-level operations and one or more second-level operations, and generating the factory order based upon execution of the one or more first-level operations and the one or more second-level operations. In a recursive manner, the one or more first-level operations operate on at least one first-level sequence operand, the value of which is resolved by execution of one or more of the second-level operations. The factory order may then be provided to the gene manufacturing system to assemble the sequence parts into nucleotide sequences represented by the sequence specification.

The present disclosure provides a novel approach for shifting or distributing various information (e.g., protocols, analysis methods, sample preparation data, sequencing data, etc.) to a cloud-based network. For example, the techniques relate to a cloud computing environment configured to receive this information from one or more individual sample preparation devices, sequencing devices, and/or computing systems. In turn, the cloud computing environment may generate information for use in the cloud computing environment and/or to provide the generated information to the devices to guide a genomic analysis workflow. Further, the cloud computing environment may be used to facilitate the sharing of sample preparation protocols for use with generic sample preparation cartridges and/or monitoring the popularity of the sample preparation protocols.

A method for at least one of characterizing, diagnosing, and treating an autoimmune disorder in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the autoimmune condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the autoimmune condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.

Various methods and systems for processing at least some of genome sequences and at least some of associated information, for an individual, may be described and disclosed herein. A purpose of such processing may be to prevent, minimize, and/or mitigate against (1) identification of the individual from such genome sequence information and/or from associated information; and/or (2) using such genome sequence information and/or associated information as a basis for discriminating against the individual. In some embodiments, such processing may comprise one or more of: segmenting genome sequences for at least a purpose of anonymizing genome information; using anchor segments for a purpose of minimizing storage space in storing of genetic sequence information; generating at least one linkage record; generating at least one anonymized linkage record; processing a request for genetic study results; processing genetic study results received; and/or generating personalized information of interest pertaining to the individual.

Embodiments of a method and system for microbial pharmacogenomics can include: a sample handling system operable to collect containers including biological samples from a set of users, the handling system including a sequencing system operable to determine microorganism sequences from the biological samples; a microbiome characterization system operable to: determine microbiome pharmacogenomics data based on the microorganism sequences, collect supplementary data associated with the antibiotics-associated condition for the set of users, and transform the supplementary data and features extracted from the microbiome pharmacogenomics data into a characterization model associated with the antibiotics-associated condition; and a treatment system operable to promote a treatment to the user for the antibiotics-associated condition based on characterizing user biological material with the characterization model in relation to the antibiotics-associated condition.

A method of analyzing hydrocarbon-related data is disclosed. Data representative of a hydrocarbon entity is presented. A physiological response of a viewer of the data is sensed. The physiological response is associated with the data. The data and a representation of the associated physiological response is outputted.

Methods and systems for biochemical data analysis are provided. A dataset can be received and a selection of a compare field can be used for creation of sub-groups of data to run statistical analysis on. The sub-groups of the dataset can be created based on the selection of the compare field. Statistical information about each sub-group of data can be calculated and displayed on a user display. Other information can be provided for further dataset refinements. A user may supply a control group selection, and such a selection may then result in an indication on the display of which population represents the control group. A user may supply information for further dataset filtering. Such information may be used to filter data, prior to creating the sub-groups for statistical analysis.

A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit that may be connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits may be arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the bioinformatics analysis on the reads of genomic data. Each subset of the hardwired digital logic circuits may be formed in a wired configuration to perform the one or more steps in the bioinformatics analysis.

A method and system for determining interaction sites between biosequences is described herein. A dataset of contact data for a plurality of biomolecule pairs is obtained to account their frequency of occurrence. Statistical weights are determined for each frequency of occurrence. Each vector of a statistical residual vector space (SRV) is decomposed through principal component decomposition. The vectors of the SRV are re-projected back to a new SRV with a new set of coordinates. A feature vector is generated and inputted into a predictor for outputting a likelihood of an interaction site.

A method of making a synthetic foldable having a tertiary structure emulating the tertiary structure of a reference foldable protein is described. The method includes determining a folding nucleus peptide sequence associated with folding the reference foldable protein. The synthetic foldable protein is synthesized by including the determined folding nucleus peptide sequence and at least one repeat thereof in the peptide sequence of the synthetic foldable protein.