In this paper we address particular aspects of integration of formal methods in large-scale industrial projects, namely collaborative aspects. We review recent works addressing such aspects, identify some current trends and discuss directions for further research.

This paper presents the use of recursive least squares for online estimation of the self interference channel for an In Band Full Duplex communications link without the use of half duplex pilot signals. By using a long effective filter length it is possible to overcome the extra interference of the receieved signal, and it proves to be an effective way to estimate the channel in all scenarios, but it provides the greatest efficiency gain over current methods with a short channel coherence time. Recursive least squares estimation provides a way to take advantage of the constant knowledge of the transmitted signal to track the channel while consuming relatively few computational resources. Introducing online RLS estimation for In-Band Full Duplex communication provides a way to take advantage of the self interference cancellation gains from digital cancellation without introducing additional protocol overhead to the transmissions.

A consensus sequence of the euchromatic portion of human genome has been generated by the whole genome shot-gun sequencing method that was developed while sequencing the genomes of Haemophilus influenzae and Drosophila melanogaster. The 2.9 billion bp sequence, was generated over nine months from 27,271,853 high quality sequence reads (≁5X coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals: three females and two males of African-American, Asian-Chinese, Hispanic and Caucasian ethnicity. The coverage of the genome in cloned DNA represented by paired end-sequences exceeds 37X. Two assembly methods, a whole genome assembly and a regional hybrid assembly were utilized, combining BAC data from GenBank with Celera data. Over 90 assemblies of 500,000 bp or greater and 2510 million bp or larger. Analysis of the genome sequence reveals - 26,178 protein-encoding genes for which there is strong corroborating evidence and an additional 12,000 computationally derived genes with mouse homologues or other weak supporting evidence. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, tissue-specific developmental regulation, and in the hemostasis and immune systems. DNA sequence comparisons among the five individuals provided locations of 2.6 million single nucleotide polymorphisms (SNPs). The haploid genomes of a randomly drawn pair of humans differ at a rate of one per 1,250 bp on average but there is marked heterogeneity in the level of polymorphism across the genome. Only 0.75% of the SNPs led to possibly dysfunctional proteins.

Multigrid is a popular solution method for the system of linear algebraic equations that arise from PDEs discretized with the finite element method.The application of multigrid to unstructured grid problems, however, is not well developed.We discuss a method, that uses many of the same techniques as the finite element method itself, to apply standard multigrid algorithms to unstructured finite element problems.We use maximal independent sets (MISs) as a mechanism to automatically coarsen unstructured grids; the inherent flexibility in the selection of an MIS allows for the use of heuristics to improve their effectiveness for a multigrid solver.We present parallel algorithms, based on geometric heuristics, to optimize the quality of MISs and the meshes constructed from them, for use in multigrid solvers for 3D unstructured problems.We conduct scalability studies that demonstrate the effectiveness of our methods on a problem in large deformation elasticity and plasticity of up to 40 million degrees of freedom on 960 processor IBM PowerPC 4-way SMP cluster with about 60% parallel efficiency.