Methods and systems for determining amino acid sequence of a polypeptide or protein from mass spectrometry data is provided, using a weighted de Bruijn graph. Extracted and purified protein is cleaved into a mixture of peptide and then analyzed using mass spectrometry. A list of peptide sequences is derived from mass spectrometry fragment data by de novo sequencing, and amino acid confidence scores are determined from peak fragment ion intensity. A weighted de Bruijn graph is constructed for the list of peptide sequences having node weights defined by k−1 mer confidence scores. At least one contig is assembled from the de Bruijn graph by identifying node weights having the highest k-1 mer confidence scores.

According to one aspect, systems and processes for assaying a plurality of nucleic acid samples are provided. In an exemplary process, a matrix is generated including pools and samples using a pooling scheme with decoding capability equal to a number D. Matrix organization includes assigning one pool in a set of pools per row by one sample in a set of samples per column. Sample assignment creates a known pattern of pools, wherein each sample in the set of pools is assigned a total number of D+1 times and any two pools have at most one sample in common. Samples are pooled based on a pooling scheme, where pooled samples are assayed. Positive pools are determined and one or more positive samples are identified. The matrix is displayed as a visual pattern representing the known pattern of pools, the identified positive samples, and the determined positive pools.

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.

The present invention provides for a simultaneous graphical representation, a risk of bleeding and a risk of thrombosis providing a visualized bridge therapy process. Furthermore, the present invention provides for a computer-based prediction of the haemostatic situation of the examined blood circulation by using a combination of a biochemical model and a pharmacokinetic model for calculation or another mathematical representation of the blood circulation.

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.

Methods and systems for visualizing gene expression data in a way that permits the comparison of different patient groups to facilitate medical applications, including cancer diagnostics and treatment planning, particularly breast cancer. The method organises gene expression data for at least one patient into a plurality of windows of a specified size, calculates an average RSEM score for all of the genes in each window and presents the average RSEM scores in a two-dimensional array, wherein one axis organises the windows by patient and the other axis organises the windows by sequence.

Methods and systems for generating and analyzing genetic variant-phenotype association results are disclosed.

Systems and methods for targeted therapy based on single-cell stimulus perturbation response. In one embodiment, a method for optimizing stimulus combinations for therapy includes receiving a cell sample, treating the cell sample with a plurality of stimuli by treating a different portion of the cell sample with one of the plurality of stimuli for each of the plurality of stimuli, labeling the cell sample with a plurality of metal-conjugated probes, analyzing the cell sample using a mass spectrometer, obtaining mass spectrometry data from the mass spectrometer, identifying subpopulations within the cell sample using the mass spectrometry data, computing stimulus effects, generating a nested-effects model using the mass spectrometry data, and scoring stimuli combinations using the computing device, wherein the stimulus combinations are combinations made from the plurality of stimuli.

The invention relates to a computer system, a computer-implemented method, a computer program product and a user interface for controlling, detecting, regulating, and/or analyzing biological, biochemical, chemical and/or physical processes, comprising at least two units which are designed to receive a substance or material in order to carry out at least one biological, biochemical, chemical, and/or physical process on said substance. Each unit has at least one sensor which is designed to detect measurement data relating to the process. Additionally, the computer system comprises at least one display unit via which the measurement data of the two units is displayed in respective temporal correlations which allows information to be obtained on a relationship inherent in the displayed measurement data.

The present invention describes a biomolecule based storage system for converting, storing the data in DNA coded form and retrieving data using pointer file approach. User input data is converted into 4base DNA sequence, called Nibble, which is further mapped onto the DNA sequence of an organism. The first position of each converted nibble is then obtained and stored in a pointer file. By mapping the positions of pointer file onto the DNA sequence of the organism, the data can be retrieved.