A two-base encoded DNA sequence alignment problem in computational biology

The recent introduction of instruments capable of producing millions of DNA sequence reads in a single run is rapidly changing the landscape of genetics. The primary objective of the "sequence alignment" problem is to search for a new algorithm that facilitates the use of two-base encoded data for large-scale re-sequencing projects. This algorithm should be able to perform local sequence alignment as well as error detection and correction in a reliable and systematic manner, enabling the direct comparison of encoded DNA sequence reads to a candidate reference DNA sequence. We will first briefly review two well-known sequence alignment approaches and provide a rudimentary improvement for implementation on parallel systems. Then, we carefully examin a unique sequencing technique known as the SOLiDTM System that can be implemented, and follow by the results from the global and local sequence alignment. In this report, the team presents an explanation of the algorithms for color space sequence data from the high-throughput re-sequencing technology and a theoretical parallel approach to the dynamic programming method for global and local alignment. The combination of the di-base approach and dynamic programming provides a possible viewpoint for large-scale re-sequencing projects. We anticipate the use of distributed computing to be the next-generation engine for large-scale problems like such

Behavioural Types

Behavioural type systems in programming languages support the specification and verification of properties of programs beyond the traditional use of type systems to describe data processing. A major example of such a property is correctness of communication in concurrent and distributed systems, motivated by the importance of structured communication in modern software. Behavioural Types: from Theory to Tools presents programming languages and software tools produced by members of COST Action IC1201: Behavioural Types for Reliable Large-Scale Software Systems, a European research network that was funded from October 2012 to October 2016. As a survey of the most recent developments in the application of behavioural type systems, it is a valuable reference for researchers in the field, as well as an introduction to the area for graduate students and software developers

Behavioural Types

Behavioural type systems in programming languages support the specification and verification of properties of programs beyond the traditional use of type systems to describe data processing. A major example of such a property is correctness of communication in concurrent and distributed systems, motivated by the importance of structured communication in modern software. Behavioural Types: from Theory to Tools presents programming languages and software tools produced by members of COST Action IC1201: Behavioural Types for Reliable Large-Scale Software Systems, a European research network that was funded from October 2012 to October 2016. As a survey of the most recent developments in the application of behavioural type systems, it is a valuable reference for researchers in the field, as well as an introduction to the area for graduate students and software developers

Kompics: a message-passing component model for building distributed systems

The Kompics component model and programming framework was designedto simplify the development of increasingly complex distributed systems. Systems built with Kompics leverage multi-core machines out of the box and they can be dynamically reconfigured to support hot software upgrades. A simulation framework enables deterministic debugging and reproducible performance evaluation of unmodified Kompics distributed systems. We describe the component model and show how to program and compose event-based distributed systems. We present the architectural patterns and abstractions that Kompics facilitates and we highlight a case study of a complex distributed middleware that we have built with Kompics. We show how our approach enables systematic development and evaluation of large-scale and dynamic distributed systems

RELEASE: A High-level Paradigm for Reliable Large-scale Server Software

Erlang is a functional language with a much-emulated model for building reliable distributed systems. This paper outlines the RELEASE project, and describes the progress in the rst six months. The project aim is to scale the Erlang's radical concurrency-oriented programming paradigm to build reliable general-purpose software, such as server-based systems, on massively parallel machines. Currently Erlang has inherently scalable computation and reliability models, but in practice scalability is constrained by aspects of the language and virtual machine. We are working at three levels to address these challenges: evolving the Erlang virtual machine so that it can work effectively on large scale multicore systems; evolving the language to Scalable Distributed (SD) Erlang; developing a scalable Erlang infrastructure to integrate multiple, heterogeneous clusters. We are also developing state of the art tools that allow programmers to understand the behaviour of massively parallel SD Erlang programs. We will demonstrate the e ectiveness of the RELEASE approach using demonstrators and two large case studies on a Blue Gene

A Peer-to-Peer Middleware Framework for Resilient Persistent Programming

The persistent programming systems of the 1980s offered a programming model that integrated computation and long-term storage. In these systems, reliable applications could be engineered without requiring the programmer to write translation code to manage the transfer of data to and from non-volatile storage. More importantly, it simplified the programmer's conceptual model of an application, and avoided the many coherency problems that result from multiple cached copies of the same information. Although technically innovative, persistent languages were not widely adopted, perhaps due in part to their closed-world model. Each persistent store was located on a single host, and there were no flexible mechanisms for communication or transfer of data between separate stores. Here we re-open the work on persistence and combine it with modern peer-to-peer techniques in order to provide support for orthogonal persistence in resilient and potentially long-running distributed applications. Our vision is of an infrastructure within which an application can be developed and distributed with minimal modification, whereupon the application becomes resilient to certain failure modes. If a node, or the connection to it, fails during execution of the application, the objects are re-instantiated from distributed replicas, without their reference holders being aware of the failure. Furthermore, we believe that this can be achieved within a spectrum of application programmer intervention, ranging from minimal to totally prescriptive, as desired. The same mechanisms encompass an orthogonally persistent programming model. We outline our approach to implementing this vision, and describe current progress.Comment: Submitted to EuroSys 200

Systematic composition of distributed objects: Processes and sessions

We consider a system with the infrastructure for the creation and interconnection of large numbers of distributed persistent objects. This system is exemplified by the Internet: potentially, every appliance and document on the Internet has both persistent state and the ability to interact with large numbers of other appliances and documents on the Internet. This paper elucidates the characteristics of such a system, and proposes the compositional requirements of its corresponding infrastructure. We explore the problems of specifying, composing, reasoning about and implementing applications in such a system. A specific concern of our research is developing the infrastructure to support structuring distributed applications by using sequential, choice and parallel composition, in the anarchic environment where application compositions may be unforeseeable and interactions may be unknown prior to actually occurring. The structuring concepts discussed are relevant to a wide range of distributed applications; our implementation is illustrated with collaborative Java processes interacting over the Internet, but the methodology provided can be applied independent of specific platforms

A Historical Perspective on Runtime Assertion Checking in Software Development

This report presents initial results in the area of software testing and analysis produced as part of the Software Engineering Impact Project. The report describes the historical development of runtime assertion checking, including a description of the origins of and significant features associated with assertion checking mechanisms, and initial findings about current industrial use. A future report will provide a more comprehensive assessment of development practice, for which we invite readers of this report to contribute information