More Than an Academic Question: Defining Student Ownership of Intellectual Property Rights

Intellectual property is increasingly important due to technology’s rapid development. The importance of intellectual property is also reflected within universities as traditional centers of research and expression, where students and faculty are encouraged to develop inventions and creative works throughout the educational experience. The commercialization potential of the intellectual property that emerges from these efforts has led many universities to adopt policies to determine ownership of intellectual property rights. Many of these policies take different approaches to ownership, and most students are unaware of their rights and are unlikely to consider whether the university has a claim to ownership. The purpose of this Article is to outline how intellectual property rights arise in the academic environment and to analyze how university policies determine ownership rights for students and the university. This Article concludes by urging universities and students to acknowledge the existence of these issues, adopt policies to address ownership rights, and make these policies known to members of the university community

Conditions for duality between fluxes and concentrations in biochemical networks

Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective equivalent to the other? Mathematical duality translates concepts, theorems or mathematical structures into other concepts, theorems or structures, in a one-to-one manner. We present a novel stoichiometric condition that is necessary and sufficient for duality between unidirectional fluxes and concentrations. Our numerical experiments, with computational models derived from a range of genome-scale biochemical networks, suggest that this flux-concentration duality is a pervasive property of biochemical networks. We also provide a combinatorial characterisation that is sufficient to ensure flux-concentration duality. That is, for every two disjoint sets of molecular species, there is at least one reaction complex that involves species from only one of the two sets. When unidirectional fluxes and molecular species concentrations are dual vectors, this implies that the behaviour of the corresponding biochemical network can be described entirely in terms of either concentrations or unidirectional fluxes

PLSS: A Projected Linear Systems Solver

We propose iterative projection methods for solving square or rectangular consistent linear systems $Ax = b$. Projection methods use sketching matrices (possibly randomized) to generate a sequence of small projected subproblems, but even the smaller systems can be costly. We develop a process that appends one column each iteration to the sketching matrix and that converges in a finite number of iterations independent of whether the sketch is random or deterministic. In general, our process generates orthogonal updates to the approximate solution $x_k$. By choosing the sketch to be the set of all previous residuals, we obtain a simple recursive update and convergence in at most rank($A$) iterations (in exact arithmetic). By choosing a sequence of identity columns for the sketch, we develop a generalization of the Kaczmarz method. In experiments on large sparse systems, our method (PLSS) with residual sketches is competitive with LSQR, and our method with residual and identity sketches compares favorably to state-of-the-art randomized methods

solveME: fast and reliable solution of nonlinear ME models.

BackgroundGenome-scale models of metabolism and macromolecular expression (ME) significantly expand the scope and predictive capabilities of constraint-based modeling. ME models present considerable computational challenges: they are much (>30 times) larger than corresponding metabolic reconstructions (M models), are multiscale, and growth maximization is a nonlinear programming (NLP) problem, mainly due to macromolecule dilution constraints.ResultsHere, we address these computational challenges. We develop a fast and numerically reliable solution method for growth maximization in ME models using a quad-precision NLP solver (Quad MINOS). Our method was up to 45 % faster than binary search for six significant digits in growth rate. We also develop a fast, quad-precision flux variability analysis that is accelerated (up to 60× speedup) via solver warm-starts. Finally, we employ the tools developed to investigate growth-coupled succinate overproduction, accounting for proteome constraints.ConclusionsJust as genome-scale metabolic reconstructions have become an invaluable tool for computational and systems biologists, we anticipate that these fast and numerically reliable ME solution methods will accelerate the wide-spread adoption of ME models for researchers in these fields