Theory and Techniques for Synthesizing a Family of Graph Algorithms

Although Breadth-First Search (BFS) has several advantages over Depth-First Search (DFS) its prohibitive space requirements have meant that algorithm designers often pass it over in favor of DFS. To address this shortcoming, we introduce a theory of Efficient BFS (EBFS) along with a simple recursive program schema for carrying out the search. The theory is based on dominance relations, a long standing technique from the field of search algorithms. We show how the theory can be used to systematically derive solutions to two graph algorithms, namely the Single Source Shortest Path problem and the Minimum Spanning Tree problem. The solutions are found by making small systematic changes to the derivation, revealing the connections between the two problems which are often obscured in textbook presentations of them.Comment: In Proceedings SYNT 2012, arXiv:1207.055

Synthesis of Greedy Algorithms Using Dominance Relations

Greedy algorithms exploit problem structure and constraints to achieve linear-time performance. Yet there is still no completely satisfactory way of constructing greedy algorithms. For example, the Greedy Algorithm of Edmonds depends upon translating a problem into an algebraic structure called a matroid, but the existence of such a translation can be as hard to determine as the existence of a greedy algorithm itself. An alternative characterization of greedy algorithms is in terms of dominance relations, a well-known algorithmic technique used to prune search spaces. We demonstrate a process by which dominance relations can be methodically derived for a number of greedy algorithms, including activity selection, and prefix-free codes. By incorporating our approach into an existing framework for algorithm synthesis, we demonstrate that it could be the basis for an effective engineering method for greedy algorithms. We also compare our approach with other characterizations of greedy algorithms

Tactical Synthesis Of Efficient Global Search Algorithms

Algorithm synthesis transforms a formal specification into an efficient algorithm to solve a problem. Algorithm synthesis in Specware combines the formal specification of a problem with a high-level algorithm strategy. To derive an efficient algorithm, a developer must define operators that refine the algorithm by combining the generic operators in the algorithm with the details of the problem specification. This derivation requires skill and a deep understanding of the problem and the algorithmic strategy. In this paper we introduce two tactics to ease this process. The tactics serve a similar purpose to tactics used for determining indefinite integrals in calculus, that is suggesting possible ways to attack the problem

CSGM Designer: a platform for designing cross-species intron-spanning genic markers linked with genome information of legumes.

BackgroundGenetic markers are tools that can facilitate molecular breeding, even in species lacking genomic resources. An important class of genetic markers is those based on orthologous genes, because they can guide hypotheses about conserved gene function, a situation that is well documented for a number of agronomic traits. For under-studied species a key bottleneck in gene-based marker development is the need to develop molecular tools (e.g., oligonucleotide primers) that reliably access genes with orthology to the genomes of well-characterized reference species.ResultsHere we report an efficient platform for the design of cross-species gene-derived markers in legumes. The automated platform, named CSGM Designer (URL: http://tgil.donga.ac.kr/CSGMdesigner), facilitates rapid and systematic design of cross-species genic markers. The underlying database is composed of genome data from five legume species whose genomes are substantially characterized. Use of CSGM is enhanced by graphical displays of query results, which we describe as "circular viewer" and "search-within-results" functions. CSGM provides a virtual PCR representation (eHT-PCR) that predicts the specificity of each primer pair simultaneously in multiple genomes. CSGM Designer output was experimentally validated for the amplification of orthologous genes using 16 genotypes representing 12 crop and model legume species, distributed among the galegoid and phaseoloid clades. Successful cross-species amplification was obtained for 85.3% of PCR primer combinations.ConclusionCSGM Designer spans the divide between well-characterized crop and model legume species and their less well-characterized relatives. The outcome is PCR primers that target highly conserved genes for polymorphism discovery, enabling functional inferences and ultimately facilitating trait-associated molecular breeding

Megawatt solar power systems for lunar surface operations

The work presented here shows that a solar power system can provide power on the order of one megawatt to a lunar base with a fairly high specific power. The main drawback to using solar power is still the high mass, and therefore, cost of supplying energy storage through the solar night. The use of cryogenic reactant storage in a fuel cell system, however, greatly reduces the total system mass over conventional energy storage schemes

Genetic mapping of legume orthologs reveals high conservation of synteny between lentil species and the sequenced genomes of Medicago and chickpea.

Lentil (Lens culinaris Medik.) is a global food crop with increasing importance for food security in south Asia and other regions. Lens ervoides, a wild relative of cultivated lentil, is an important source of agronomic trait variation. Lens is a member of the galegoid clade of the Papilionoideae family, which includes other important dietary legumes such as chickpea (Cicer arietinum) and pea (Pisum sativum), and the sequenced model legume Medicago truncatula. Understanding the genetic structure of Lens spp. in relation to more fully sequenced legumes would allow leveraging of genomic resources. A set of 1107 TOG-based amplicons were identified in L. ervoides and a subset thereof used to design SNP markers for mapping. A map of L. ervoides consisting of 377 SNP markers spread across seven linkage groups was developed using a GoldenGate genotyping array and single SNP marker assays. Comparison with maps of M. truncatula and L. culinaris documented considerable shared synteny and led to the identification of a few major translocations and a major inversion that distinguish Lens from M. truncatula, as well as a translocation that distinguishes L. culinaris from L. ervoides. The identification of chromosome-level differences among Lens spp. will aid in the understanding of introgression of genes from L. ervoides into cultivated L. culinaris, furthering genetic research and breeding applications in lentil

Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures

<p>Abstract</p> <p>Background</p> <p><it>Vitis vinifera </it>(<it>V. vinifera</it>) is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS) and combined it with available Expressed Sequence Tag (EST) data. These tag-based technologies, which do not require <it>a priori </it>knowledge of genomic sequence, are well-suited for transcriptional profiling. The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry.</p> <p>Results</p> <p>The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS). A total of 2,635,293 17-base and 2,259,286 20-base signatures were obtained, representing at least 30,737 and 26,878 distinct sequences. The average normalized abundance per signature was ~49 TPM (Transcripts Per Million). Comparisons of the MPSS signatures with available <it>Vitis </it>species' ESTs and a unigene set demonstrated that 6,430 distinct contigs and 2,190 singletons have a perfect match to at least one MPSS signature. Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the <it>V. vinifera </it>transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from <it>Vitis vinifera</it>.</p> <p>Conclusion</p> <p>The MPSS data presented here not only achieved a higher level of saturation than previous EST based analyses, but in doing so, expand the known set of transcripts of grape berries during the unique stage in development that immediately precedes the onset of ripening. The MPSS dataset also revealed evidence of antisense expression not previously reported in grapes but comparable to that reported in other plant species. Finally, we developed a novel web-based, public resource for utilization of the grape MPSS data <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>.</p

Genomic and phenotypic analysis of Vavilov's historic landraces reveals the impact of environment and genomic islands of agronomic traits.

The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR's 147 chickpea accessions from Turkey and Ethiopia, representing chickpea's center of origin and a major location of secondary diversity. Genotyping by sequencing identified 14,059 segregating polymorphisms and genome-wide association studies revealed 28 GWAS hits in potential candidate genes likely to affect traits of agricultural importance. The proportion of polymorphisms shared among accessions is a strong predictor of phenotypic resemblance, and of environmental similarity between historical sampling sites. We found that 20 out of 28 polymorphisms, associated with multiple traits, including days to maturity, plant phenology, and yield-related traits such as pod number, localized to chromosome 4. We hypothesize that selection and introgression via inadvertent hybridization between more and less advanced morphotypes might have resulted in agricultural improvement genes being aggregated to genomic 'agro islands', and in genotype-to-phenotype relationships resembling widespread pleiotropy

Inferred summer precipitation for southern Ontario back to AD 610, as reconstructed from ring widths of Thuja occidentalis

We present a network of seven ring-width chronologies of eastern white-cedar (Thuja occidentalis L.) from the Niagara Escarpment in southern Ontario, Canada. Using principal component regression, a 350-year June-July precipitation reconstruction (SOR) is developed for the region. Prior to the 20th century, the SOR series shows reasonable coherence, particularly at the decadal scale, with an independent tree-ring-based reconstruction of the Palmer drought severity index (PDSI) for roughly the same region. A weakening of the tree-growth – climate relationship in recent decades results in a regression model explaining 21% of the variance in the original climate series when the recent data are used for calibration. We therefore compromise with a model, calibrated for the period 1900–1960, which explains 33% of the variance. The model, while not terribly strong, does pass verification tests, indicating some degree of predictive skill. The longest chronology in our network, the 2787-year Flowerpot Island (FLOW) chronology, also exhibits common variability with the PDSI reconstruction, particularly on decadal and longer time scales and was used to infer hydroclimatic conditions back to AD 610. The combined information of the SOR, PDSI, and FLOW series suggests that dry conditions existed for the periods 1700–1725, 1750–1800, and 1840–1900, and wet conditions for the periods 1675–1700, 1730–1750, and 1810–1840. Over longer time scales, the FLOW chronology shows that summer precipitation was particularly variable during the 7th, 9th, 13th, and 16th centuries