Systems and methods are disclosed for correcting for artificial deformations in anatomical modeling. One method includes obtaining an anatomic model; obtaining information indicating a presence of an artificial deformation of the anatomic model; identifying a portion of the anatomic model associated with the artificial deformation; estimating a non-deformed local area corresponding to the portion of the anatomic model; and modifying the portion of the anatomic model associated with the artificial deformation, based on the estimated non-deformed local area.

The present invention relates to a method for identifying a relationship between biological elements, said elements optionally having a measurable activity, the method comprising the following steps: defining candidate graphs, each candidate graph being a graph associated with one of the thresholding values from the plurality of thresholding values, for each thresholding value, obtaining a distribution associated by optimization of the distribution into classes of the apices of the graph associated with the relevant thresholding value, the optimization starting with an initial distribution in which with each core is associated a class for obtaining a final distribution in which each apex of a class shares more links with the other apices of the same class than with the apices of another class, selecting an optimum graph from among the plurality of candidate graphs according to at least one criterion.

The present invention provides methods for rapidly and efficiently searching biologically-related data space. More specifically, the present invention provides methods for identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The present invention also provides methods for modeling sequence-activity relationships, including but not limited to stepwise addition or subtraction techniques, Bayesian regression, ensemble regression and other methods. The present invention further provides digital systems and software for performing the methods provided herein.

In one embodiment, the invention provides a system including at least one computing device for enhancing the recovery of heavy oil in an underground, near-surface crude oil extraction environment by performing a method comprising sampling and identifying microbial species (bacteria and/or fungi) that reside in the underground, near-surface crude oil extraction environment; collecting rock and fluid property data from the underground, near-surface crude oil extraction environment; collecting nutrient data from the underground, near-surface crude oil extraction environment; identifying a preferred microbial species from the underground, near-surface crude oil extraction environment that can transform the heavy oil into a lighter oil; identifying a nutrient from the underground, near-surface crude oil extraction environment that promotes a proliferation of the preferred microbial species; and introducing the nutrient into the underground, near-surface crude oil extraction environment.

Systems and methods are proposed for synthetic biology design and host cell simulation. In one form, a synthetic biology design system is proposed, comprising a model conversion component configured to: receive genetic circuit data indicative of a user-specified genetic circuit design; identify, from the genetic circuit data, constituent parts of the genetic circuit design, and the connections between the constituent parts; obtain mathematical models corresponding to the constituent parts; and combine the obtained mathematical models into a composite model configured to generate genetic circuit output data based on input data indicative of one or more of: free RNA polymerase concentration, free ribosome concentration and rRNA concentration. The system further comprises a host cell simulation component configured to receive, as input, the genetic circuit output data from the composite model, and based on the genetic circuit output data, generate host cell output data representing a physiological state of the host.

A computing system automatically analyzes various drug or other compound targets using biologic activity data for cellular proteins, and develops a target/anti-target matrix identifying pharmacologically responsive targets intended for drug engagement, and pharmacologically responsive anti-targets intended for avoidance of drug engagement. The system separates compounds into subsets based on biological threshold data and groups proteins through pharmacological similarity. The system ranks protein groupings in generating the matrix and uses the rankings to recommend compounds and compound groupings for testing to treat a pathology. The system compares new compounds against the matrix to recommend new compounds for testing.

The invention provides a model of a reaction network integrated with regulatory controls related to the reactions. A method is provided for determining a systemic property of a reaction network using a model of the invention. Also provided is a method for modeling changes that occur in a reaction network at various time points due to regulatory events.

A method for determining the presence of a biological entity. The method may include entering into a digital computer, at least a plurality of first input values associated with a first genetic element, a plurality of second input values associated with a second genetic element, and a plurality of third input values associated with a third genetic element associated with a plurality of samples. The method also includes determining a threshold value associated with the third genetic element, separating the samples using the threshold value into a first set of samples and a second set of samples, clustering the first set of samples in a feature space defined by the first genetic element and the second genetic element, defining a first boundary space using the first set of samples, and defining a second boundary space using the second set of samples.

Embodiments describe computer systems and computer programs for implementing BioCAD methods comprising one or more data models and one or more BioCAD tools, wherein the BioCAD tools enable users to design or refactor a biomolecule or to conduct a biological experiment in silico by user input of one or more components selected by the user from a database populated with information on components and scientific data of existing biomolecules and experiments. Data models of the programs are operable to manage development of the new biomolecule or experiment based on information in the databases. Computer programs also provide an output with information that enables the users to determine in silico if the newly designed or refactored molecule or biological experiment is satisfactory or not for its intended purpose in vitro and also provides the user the capability to re-design the biomolecule or experiment till it is satisfactory.

Ablated object region determining apparatuses and methods for determining an ablated object region for ablating an object of interest are provided. A user can set an orientation and position of an ablation element with respect to a geometrical representation of the object of interest, at least one energy influencing element and a spatial relationship between the object of interest and the at least one energy influencing element. A model ablation region retrieving unit retrieves a model ablation region depending on the respective set orientation and position of the ablation element from a model ablation region storing unit. An ablated object region determining unit determines at least one of a) an ablated object region of the object of interest being located within the retrieved model ablation region and b) a non-ablated object region of the object of interest being located outside the retrieved model ablation region.