Strains of the Mycobacterium tuberculosis complex (MTBC) can be classified into coherent lineages of similar traits based on their genotype. We present a tensor clustering framework to group MTBC strains into sublineages of the known major lineages based on two biomarkers: spacer oligonucleotide type (spoligotype) and mycobacterial interspersed repetitive units (MIRU). We represent genotype information of MTBC strains in a high-dimensional array in order to include information about spoligotype, MIRU, and their coexistence using multiple-biomarker tensors. We use multiway models to transform this multidimensional data about the MTBC strains into two-dimensional arrays and use the resulting score vectors in a stable partitive clustering algorithm to classify MTBC strains into sublineages. We validate clusterings using cluster stability and accuracy measures, and find stabilities of each cluster. Based on validated clustering results, we present a sublineage structure of MTBC strains and compare it to the sublineage structures of SpolDB4 and MIRU-VNTRplus.

We present a breadth-first, lecture-and lab-based approach to introducing Computer Science that uses functional programming.Functional programming provides a lowoverhead introduction to programming (no types, few constructs, and little syntax), enabling students to write, in their first semester, programs sophisticated enough to exemplify important concepts of Computer Science.It also encourages good programming style (modular design and testing, e.g.) and serves as an introduction to an important problem-solving paradigm.The course gives the students a broad overview of Computer Science and helps them gauge their interest in the field.

Relational database systems and most object-oriented database systems provide support for queries. Usually these queries represent retrievals over sets or multisets. Many new applications for databases, such as multimedia systems and digital libraries, need support for queries on complex bulk types such as lists and trees. In this paper we describe an object-oriented query algebra called AQUA (= A Query Algebra) for lists and trees. The operators in the algebra preserve the ordering between the elements of a list or tree, even when the result list or tree contains an arbitrary set of nodes from the original tree. We also present predicate languages for lists and trees which allow order-sensitive queries because they use pattern matching to examine groups of list or tree nodes rather than individual nodes. The ability to decompose predicate patterns enables optimizations that make use of indices.>

Algebraic query processing and optimization for relational databases is a proven and reasonably well-understood technology.Recently the algebraic approach has been extended to more advanced data models (nested relations, complex objects, object-oriented systems).Here we continue this evolution by presenting novel algebraic operators and transformations supporting grouping, arrays, references, and multisets.We also propose a new approach to processing and optimizing overridden methods in the presence of multiple inheritance.The utility of Lxsth the algebraic operators and the transformation rules is demonstrated with examples.Object identity is incorporated into the algebraic domains, giving an original, intuitive set-theoretic semantics for the domains of object identifiers in the presence of multiple inheritance.We prove that the algebra is eqtripollent to the QUEL-like user-level query language and discuss some other expressiveness issues.

In this paper, we present the design of the EXTRA data model and the EXCESS query language for the EXODUS extensible database system. The EXTRA data model includes support for complex objects with shared subobjects, a novel mix of object- and value-oriented semantics for data, support for persistent objects of any type in the EXTRA type lattice, and user-defined abstract data types (ADTs). The EXCESS query language provides facilities for querying and updating complex object structures, and it can be extended through the addition of ADT functions and operators, procedures and functions for manipulating EXTRA schema types, and generic set functions EXTRA and EXCESS are intended to serve as a test vehicle for tools developed under the EXODUS extensible database system project.