Described are platforms, systems, media, and methods for providing a biologic information visual synthesis application, the biologic information including one or more of: genome data, microbiome data, and metabolome data.

A computer-controlled micro-instrumentation biochemical reaction environment system includes an electrically-controllable microfludic routing system, at least one microreaction chamber, at least one micro-instrumentation device, and at least one electronic microprocessor. The microreaction chamber supports at least one chemical reaction associated with a biological signaling pathway. The micro-instrumentation device measures at least one physical quantity associated with the signaling pathway. The microprocessor transmits electrical control signals, receives electrical measurement signals, and executes at least one software algorithm. The microreaction chamber is connected to the microfludic routing system to receive and transmit at least a fluid or gas, and the electronic microprocessor receives electrical measurement signals from the micro-instrumentation device via a first electric interface and transmits electrical control signals to electrically-controllable microfludic routing system via a second electrical interface.

A method of modeling a background signal when sequencing a polynucleotide strand using sequencing-by-synthesis includes: flowing a series of nucleotide flows onto a reactor array having multiple reaction confinement regions, one or more copies of the polynucleotide strand being located in a loaded reaction confinement region of the reactor array, the loaded reaction confinement region being located in a vicinity of one or more neighboring reaction confinement regions that may or may not be loaded; receiving output signals from the reactor array; and modeling a background signal for the loaded reaction confinement region using the received output signals and a model adapted to account at least for an exchange of ions between the one or more neighboring reaction confinement regions and a headspace adjacent the loaded reaction confinement region and the one or more neighboring reaction confinement regions.

An embodiment of the invention receives input including a list of drugs, drug characteristics of each drug, and known drug-disease associations including a disease and a drug having a threshold efficacy for treating the disease. For each drug in the list of drugs, a processor predicts whether the drug meets a threshold efficacy for treating a first disease based on the drug characteristics and the drug-disease associations. For each drug in the list of drugs, the processor predicts whether the drug meets a threshold efficacy for treating a second disease based on the drug characteristics and the predicting of whether the drug meets the threshold efficacy for treating the first disease. Output is generated output based on the predictions, the output including an identified drug-disease association, an identified disease-disease association, an identified chemical fingerprint for the first disease, and an identified chemical fingerprint for the second disease.

The present invention describes a two-step computational procedure that both identifies the optimum overall stoichiometry of conversion, along with alternate co-reactant (or co-product) combinations, of a feedstock substrate to a biochemical product, and selects for (non-)native reactions accessed from a universal database to identify at least one stoichiometry-balanced minimal metabolic network, in terms of number of reactions or sum of the flux in the network, that maximize carbon or energy efficiency while satisfying thermodynamic feasibility requirements. A representation of the overall stoichiometry of conversion and the minimal metabolic network as designed can be stored.

Methods, apparatus, systems, computer programs and computing devices related to biologically assembling and/or synthesizing peptides and/or proteins are disclosed.

A method of processing a signal may include receiving an input signal including a motion artifact, determining a filter parameter based on a frequency component of a motion-based signal analogous to the motion artifact, and filtering the input signal using a filter having the determined filter parameter.

Methods for recognizing a virtual tooth surface, defining a virtual tooth coordinate system, and simulating a collision between virtual teeth are provided. Methods include receiving input data specifying a point on the rendered surface model associated with a tooth, deriving a perimeter on the surface model of the tooth based on the input data, and analyzing the surface model along a plurality of paths outwardly extending from points on the perimeter along the three-dimensional surface to produce gingival margin data. Methods also include receiving point input data that defines a point on the virtual tooth, receiving axis input data that defines first and second axes associated with the virtual tooth, computing a substantially normal vector for a portion of the tooth surface surrounding the point, and computing a coordinate system based on the axis input and the computed vector. Methods also include receiving permissible movement input data directed to permissible movement of a first virtual tooth, simulating, in three dimensional space, bringing the first virtual tooth into contact with a second virtual tooth while constraining movement of the first virtual tooth based on the permissible movement input data, and displaying data resulting from the simulation.

Disclosed herein are systems and methods for efficient 3D structure estimation from images of a transmissive object, including cryo-EM images. The method generally comprises, receiving a set of 2D images of a target specimen from an electron microscope, carrying out a reconstruction technique to determine a likely molecular structure, and outputting the estimated 3D structure of the specimen. The described reconstruction technique comprises: establishing a probabilistic model of the target structure; optimizing using stochastic optimization to determine which structure is most likely; and, optionally utilizing importance sampling to minimize computational burden.

Specification of a point of interest is received. After then, a distance of movement on a path from an initial viewpoint is obtained based on an operation amount obtained at an operation unit, such as a mouse. View line vectors are set by sequentially changing the view line vectors from an initial view line vector with its start point located at the initial viewpoint to a shortest view line vector connecting a point of interest and a viewpoint at a shortest distance by moving, along the path, a viewpoint of a virtual endoscope on the path from the initial viewpoint closer to the point of interest and by changing the direction of a view line of the virtual endoscope closer to a direction toward the point of interest. Virtual endoscopic images are sequentially generated based on the set view line vectors, and the generated virtual endoscopic images are sequentially displayed.