Disclosed herein is Arrowland, a web-based software tool for inputting, managing and viewing multiomics data, such as transcriptomics, proteomics, metabolomics and fluxomics data in an interactive, intuitive and multiscale system.

Systems and methods for diagnosing prostate cancer. Image sets (e.g., MRI collected at one or more b-values) and biological values (e.g., prostate specific antigen (PSA)) have features extracted and integrated to produce a diagnosis of prostate cancer. The image sets are analyzed primarily in three steps: (1) segmentation, (2) feature extraction, smoothing, and normalization, and (3) classification. The biological values are analyzed primarily in two steps: (1) feature extraction and (2) classification. Each analysis results in diagnostic probabilities, which are then combined to pass through an additional classification stage. The end result is a more accurate diagnosis of prostate cancer.

Systems and methods for diagnosing prostate cancer. Image sets (e.g., MRI collected at one or more b-values) and biological values (e.g., prostate specific antigen (PSA)) have features extracted and integrated to produce a diagnosis of prostate cancer. The image sets are analyzed primarily in three steps: (1) segmentation, (2) feature extraction, smoothing, and normalization, and (3) classification. The biological values are analyzed primarily in two steps: (1) feature extraction and (2) classification. Each analysis results in diagnostic probabilities, which are then combined to pass through an additional classification stage. The end result is a more accurate diagnosis of prostate cancer.

In one aspect, a method is disclosed for presenting, on a computing device, a graphical user interface (GUI) of a therapeutic tool. The method includes presenting, in a first screen of the GUI, a design space for a protein for an application, where the design space includes a set of sequences, where each sequence contains a respective set of activities pertaining to the application. The method also includes receiving, via a graphical element in the first screen, a selection of one or more query parameters of the design space, and presenting, in a second screen of the GUI, a solution space that includes a subset of the set of sequences, where each sequence contains the respective set of activities, where the subset of the set of sequences is selected based on the one or more query parameters.

In one aspect, a method is disclosed for presenting, on a computing device, a graphical user interface (GUI) of a therapeutic tool. The method includes presenting, in a first screen of the GUI, a design space for a protein for an application, where the design space includes a set of sequences, where each sequence contains a respective set of activities pertaining to the application. The method also includes receiving, via a graphical element in the first screen, a selection of one or more query parameters of the design space, and presenting, in a second screen of the GUI, a solution space that includes a subset of the set of sequences, where each sequence contains the respective set of activities, where the subset of the set of sequences is selected based on the one or more query parameters.

A system for selecting an immunogenic peptide composition comprising a processor and a memory storing processor-executable instructions that, when executed by the processor, cause the processor to create a first peptide set by selecting a plurality of base peptides, wherein at least one peptide of the plurality of base peptides is associated with a disease, create a second peptide set by adding to the first peptide set a modified peptide, wherein the modified peptide comprises a substitution of at least one residue of a base peptide selected from the plurality of base peptides, and create a third peptide set by selecting a subset of the second peptide set, wherein the selected subset of the second peptide set has a predicted vaccine performance, wherein the predicted vaccine performance has a population coverage above a predetermined threshold, and wherein the subset comprises at least one peptide of the second peptide set.

A system for selecting an immunogenic peptide composition comprising a processor and a memory storing processor-executable instructions that, when executed by the processor, cause the processor to create a first peptide set by selecting a plurality of base peptides, wherein at least one peptide of the plurality of base peptides is associated with a disease, create a second peptide set by adding to the first peptide set a modified peptide, wherein the modified peptide comprises a substitution of at least one residue of a base peptide selected from the plurality of base peptides, and create a third peptide set by selecting a subset of the second peptide set, wherein the selected subset of the second peptide set has a predicted vaccine performance, wherein the predicted vaccine performance has a population coverage above a predetermined threshold, and wherein the subset comprises at least one peptide of the second peptide set.

This disclosure describes example techniques and systems for identifying the presence and/or composition of nucleic acids in the blood of a host organism of a model species harboring tissue of a donor organism of another species. For example, the technique may involve identifying the presence and composition of nucleic acids in the blood of a mouse harboring tissue of a human or another companion animal. These cell-free nucleic acids that are identified can be used as biomarkers to determine the presence of a disease, its biological behavior, its rate of progression, and/or the response of the disease to one or more unique therapies. In other examples, the cell-free nucleic acids may be used as biomarkers to determine a response of the host species to the tissue of the donor organism or a response of tissue derived from the second organism to transplantation within the first organism of the first species.

This disclosure describes example techniques and systems for identifying the presence and/or composition of nucleic acids in the blood of a host organism of a model species harboring tissue of a donor organism of another species. For example, the technique may involve identifying the presence and composition of nucleic acids in the blood of a mouse harboring tissue of a human or another companion animal. These cell-free nucleic acids that are identified can be used as biomarkers to determine the presence of a disease, its biological behavior, its rate of progression, and/or the response of the disease to one or more unique therapies. In other examples, the cell-free nucleic acids may be used as biomarkers to determine a response of the host species to the tissue of the donor organism or a response of tissue derived from the second organism to transplantation within the first organism of the first species.

The invention is directed to methods for selecting a treatment option for an activated B cell-like diffuse large B cell lymphoma (ABC DLBCL) subject, a germinal center B cell-like diffuse large B cell lymphoma (GCB DLBCL) subject, a primary mediastinal B cell lymphoma (PMBL) subject, a Burkitt lymphoma (BL) subject, or a mantle cell lymphoma (MCL) subject by analyzing digital gene expression data obtained from the subject, e.g., from a biopsy sample.