DNA Computing and Implementations

DNA Computing aims to harness the molecules at the Nano level for computational purpose. DNA Computing features high data density and massive storage capability therefore, its approach can be used to solve various combinatorial Problems like solving Non Deterministic Problems (i.e. NP- Complete and NP-Hard). This Molecular Level Computational involve input and output both in the molecule form. Since DNA has already been explored as an exquisite material and is a fundamental block for manufacturing large scale Nano mechanical devices. DNA Computing is an approach towards the Biomolecular Computation where the aim is not only to process the information but also to transfer it to other molecular structures for utilization. DNA Computing is slower when an individual DNA Computes in compare to silica based chips. Its Efficiently and throughput increases as the number of DNA increase. DNA provides the possibility of massive parallelism. Starting with the Introduction about the DNA Structure, followed up by DNA Computers, this paper will discuss some recent advancements and challenges of DNA Computing. We will also discuss the possible future scope and implementation as well how the Artificial Intelligence approach can be used with DNA Based Computers to achieve a better and efficient Machine Learning

Automating Fault Tolerance in High-Performance Computational Biological Jobs Using Multi-Agent Approaches

Background: Large-scale biological jobs on high-performance computing systems require manual intervention if one or more computing cores on which they execute fail. This places not only a cost on the maintenance of the job, but also a cost on the time taken for reinstating the job and the risk of losing data and execution accomplished by the job before it failed. Approaches which can proactively detect computing core failures and take action to relocate the computing core's job onto reliable cores can make a significant step towards automating fault tolerance. Method: This paper describes an experimental investigation into the use of multi-agent approaches for fault tolerance. Two approaches are studied, the first at the job level and the second at the core level. The approaches are investigated for single core failure scenarios that can occur in the execution of parallel reduction algorithms on computer clusters. A third approach is proposed that incorporates multi-agent technology both at the job and core level. Experiments are pursued in the context of genome searching, a popular computational biology application. Result: The key conclusion is that the approaches proposed are feasible for automating fault tolerance in high-performance computing systems with minimal human intervention. In a typical experiment in which the fault tolerance is studied, centralised and decentralised checkpointing approaches on an average add 90% to the actual time for executing the job. On the other hand, in the same experiment the multi-agent approaches add only 10% to the overall execution time.Comment: Computers in Biology and Medicin

2006 Major Sponsored Program and Faculty Awards for Research & Creative Activity

Awards of $3 million or more Awards of$1 million to $2,999,999 Awards of$200,000 to $999,999 Career and K Awards Arts and Humanities Awards of$50,000 or more Arts and Humanities Awards of $5,000 to$49,999 Patents Issued Intellectual Property Licences Creative Works in Fine and Performing Arts Books Recognitions and Honors Glossary of Federal Agency Abbreviations This is the fifth annual “Major Sponsored Program and Faculty Awards for Research and Creative Activity” report. This booklet highlights the successes of University of Nebraska–Lincoln faculty during 2006. The funding sources, projects and investigators on major grants and sponsored program awards received during the year are listed, as well as patents issued; published books and scholarship; fellowships and other recognitions; intellectual property licenses; and performances and exhibitions in the fine and performing arts. This impressive list grows each year and I am pleased to present evidence of our faculties’ accomplishments. During FY2005-06, we achieved a funding milestone — UNL faculty attracted $104.6 million in external funding to the institution. This is the first time we exceeded$100 million and this in fact tripled the comparable figure achieved ten years ago. How have we reached this success? We have worked to closely integrate our research priorities with our established programs of excellence building on each success. We zealously foster interdisciplinary research and collaborations with public and private partnerships, thus expanding our economic development efforts by working with business and industry. And we celebrate our achievements and recognize that excellence attracts excellence. This booklet reports only the largest dollar amounts as reported through our Office of Sponsored Programs. However, the majority of our research and creative activity is conducted by single investigators and scholars who are pioneering new frontiers across all fields. Many faculty obtain funding at levels below the significantly high thresholds set for inclusion in this report. This in no way diminishes their scholarly contributions and we are proud of all faculty achievement

Major Sponsored Programs and Faculty Awards for Research and Creative Activity 2007

This is the sixth annual “Major Sponsored Programs and Faculty Awards for Research and Creative Activity” report. This booklet highlights the successes of University of Nebraska–Lincoln faculty during 2007. It lists the funding sources, projects and investigators on major grants and sponsored program awards received during the year, as well as patents issued; published books and scholarship; fellowships and other recognitions; intellectual property licenses; and performances and exhibitions in the fine and performing arts. This impressive list grows each year and I am pleased to present evidence of our faculty’s accomplishments. Researchers at the University of Nebraska–Lincoln have pushed the frontiers in their disciplines in the past year, setting new drilling records in Antarctica, winning the nation’s highest honor for technology and building an ultra-fast, high-intensity laser that has the highest combination of peak power and repetition rate of any U.S. laser. Our sponsored funding continues to grow, with awards of $171.9 million last year alone. How have we reached this success? We have worked to integrate our research priorities with our established programs of excellence, building on each success. We zealously foster interdisciplinary research and collaborations with public and private partnerships, thus expanding our economic development efforts by working with business and industry. And we celebrate our achievements and recognize that excellence attracts excellence. These accomplishments exemplify how UNL’s emphasis on innovation, interdisciplinarity and international collaborations is propelling our research into new arenas, producing new products and technologies for the marketplace and offering our students intensive research experiences

“Major Sponsored Program and Faculty Awards for Research and Creative Activity for 2005

I am pleased to present the fourth annual “Major Sponsored Program and Faculty Awards for Research and Creative Activity” report. This booklet highlights the successes of University of Nebraska–Lincoln faculty during 2005. The funding sources, projects and investigators on major sponsored program awards received during the year are listed, as well as patents issued, published books and scholarship, fellowships and other recognitions. New this year are intellectual property licenses and performances and exhibitions in the fine and performing arts. The list is impressive and continues to grow each year—further evidence the University of Nebraska–Lincoln is on the move! We work to closely integrate our research priorities with our established programs of excellence. We are dedicated to fostering interdisciplinary research and collaborations with public and private partnerships, expanding our economic development efforts by working with business and industry

Modeling Biochemical Processes as Designed Systems

Being in the post-genomic era, there is a need for new methodologies from an interdisciplinary perspective, which can complement current genomics research. Bioinformatics and systems biology are rapidly growing research areas that are meeting this need. Operating with the assumption that there is design with a purpose, creationists provide a unique perspective for discovering order in the complexity of genes, regulatory networks, and biochemical reactions. Since the genome acts as an information storage system, it seems reasonable to apply design concepts, originating from computer and network programming, to make sense of genomic information. One such concept is that of design patterns, which has been formalized by programmers and analysts working with object-oriented programming (OOP). Several patterns are introduced and related to biochemical systems in the cell. A more detailed analysis of the observer pattern is made in the context of galactose metabolism in Saccharomyces cerevisiae. Since design patterns embody good OOP practice and do not specify a specific implementation, it is possible to explore a variety of implementations that can achieve regulation of galactose metabolism. This methodology can complement current research approaches by clarifying what is meant by system homology at the biochemical level

Modeling Biochemical Processes as Designed Systems

Being in the post-genomic era, there is a need for new methodologies from an interdisciplinary perspective, which can complement current genomics research. Bioinformatics and systems biology are rapidly growing research areas that are meeting this need. Operating with the assumption that there is design with a purpose, creationists provide a unique perspective for discovering order in the complexity of genes, regulatory networks, and biochemical reactions. Since the genome acts as an information storage system, it seems reasonable to apply design concepts, originating from computer and network programming, to make sense of genomic information. One such concept is that of design patterns, which has been formalized by programmers and analysts working with object-oriented programming (OOP). Several patterns are introduced and related to biochemical systems in the cell. A more detailed analysis of the observer pattern is made in the context of galactose metabolism in Saccharomyces cerevisiae. Since design patterns embody good OOP practice and do not specify a specific implementation, it is possible to explore a variety of implementations that can achieve regulation of galactose metabolism. This methodology can complement current research approaches by clarifying what is meant by system homology at the biochemical level

Modeling Biochemical Processes as Designed Systems

Being in the post-genomic era, there is a need for new methodologies from an interdisciplinary perspective, which can complement current genomics research. Bioinformatics and systems biology are rapidly growing research areas that are meeting this need. Operating with the assumption that there is design with a purpose, creationists provide a unique perspective for discovering order in the complexity of genes, regulatory networks, and biochemical reactions. Since the genome acts as an information storage system, it seems reasonable to apply design concepts, originating from computer and network programming, to make sense of genomic information. One such concept is that of design patterns, which has been formalized by programmers and analysts working with object-oriented programming (OOP). Several patterns are introduced and related to biochemical systems in the cell. A more detailed analysis of the observer pattern is made in the context of galactose metabolism in Saccharomyces cerevisiae. Since design patterns embody good OOP practice and do not specify a specific implementation, it is possible to explore a variety of implementations that can achieve regulation of galactose metabolism. This methodology can complement current research approaches by clarifying what is meant by system homology at the biochemical level

CERN openlab Whitepaper on Future IT Challenges in Scientific Research

This whitepaper describes the major IT challenges in scientific research at CERN and several other European and international research laboratories and projects. Each challenge is exemplified through a set of concrete use cases drawn from the requirements of large-scale scientific programs. The paper is based on contributions from many researchers and IT experts of the participating laboratories and also input from the existing CERN openlab industrial sponsors. The views expressed in this document are those of the individual contributors and do not necessarily reflect the view of their organisations and/or affiliates