Minimizing Breaks by Maximizing Cuts

Jean Charles Régin and Michael Trick have proposed to solve the schedule generation problem for sports leagues in two phases in which the first generates a tournament schedule and the second fixes the home-away pattern so as to minimize the number of breaks. While constraint programming techniques appear to be the methods of choice for the first phase, we propose to solve the break minimization problem in sports scheduling by transforming it into a maximum cut problem in an undirected graph and applying a branch-and-cut algorithm. Our approach outperforms previous approaches with constraint programming and integer programming techniques

Minimizing Breaks by Maximizing Cuts

Jean Charles Régin and Michael Trick have proposed to solve the schedule generation problem for sports leagues in two phases in which the first generates a tournament schedule and the second fixes the home-away pattern so as to minimize the number of breaks. While constraint programming techniques appear to be the methods of choice for the first phase, we propose to solve the break minimization problem in sports scheduling by transforming it into a maximum cut problem in an undirected graph and applying a branch-and-cut algorithm. Our approach outperforms previous approaches with constraint programming and integer programming techniques

SCIL - Symbolic Constraints in Integer Linear Programming

We describe SCIL. SCIL introduces symbolic constraints into branch-and-cut-and-price algorithms for integer linear programs. Symbolic constraints are known from constraint programming and contribute significantly to the expressive power, ease of use, and efficiency of constraint programs

Tuning transcription factor availability through acetylation-mediated genomic redistribution

It is widely assumed that decreasing transcription factor DNA-binding affinity reduces transcription initiation by diminishing occupancy of sequence-specific regulatory elements. However, in vivo transcription factors find their binding sites while confronted with a large excess of low-affinity degenerate motifs. Here, using the melanoma lineage survival oncogene MITF as a model, we show that low-affinity binding sites act as a competitive reservoir in vivo from which transcription factors are released by mitogen-activated protein kinase (MAPK)-stimulated acetylation to promote increased occupancy of their regulatory elements. Consequently, a low-DNA-binding-affinity acetylation-mimetic MITF mutation supports melanocyte development and drives tumorigenesis, whereas a high-affinity non-acetylatable mutant does not. The results reveal a paradoxical acetylation-mediated molecular clutch that tunes transcription factor availability via genome-wide redistribution and couples BRAF to tumorigenesis. Our results further suggest that p300/CREB-binding protein-mediated transcription factor acetylation may represent a common mechanism to control transcription factor availability

SBML Level 3: an extensible format for the exchange and reuse of biological models

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution

Rotation Planning for the Continental Service of a European Airline

We consider a version of the aircraft rotation problem where the objective is to minimize delay risks. Given a set of flights to be flown by a subfleet the rotation problem is to find a specific route for each aircraft of the subfleet such that each flight is flown by exactly one aircraft. Additionally, the sequence of flights defining a route must satisfy certain requirements mainly to avoid delays. We present a mathematical model for the problem of minimizing the delay risk according to special requirements of a major airline. An efficient Lagrangian heuristic is proposed that uses subgradient optimization and linear assignments as subproblems. Computational results on real data are given and compared to actual aircraft rotations of that airline

SCIL - Symbolic Constraints in Integer Linear Programming

We describe a new software system SCIL that introduces symbolic constraints into branch-and-cut-and-price algorithms for integer linear programs. Symbolic constraints are known from constraint programming and contribute signi cantly to the expressive power, ease of use, and eciency of constraint programming systems

SCIL - Symbolic Constraints in Integer Linear Programming.

We describe a new software system SCIL that introduces symbolic constraints into branch-and-cut-and-price algorithms for integer linear programs. Symbolic constraints are known from constraint programming and contribute significantly to the expressive power, ease of use, and efficiency of constraint programming systems