Abstract
This paper describes a recent initiative of the The National Center for Biotechnology Information, which is a national resource for molecular biology information. The project is known as Western Washington University Periodic Search Agent for Protein Database Information or WWU Search Agent. This web-based search engine browses and does periodic searches of the protein databases of the National Center for Biotechnology Information (NCBI) using the Basic Local Alignment Search Tool or BLAST. The writer describes the benefits of this project, which include its interfacing with the NCBI BLAST and the continuous updates and enhancements done by NCBI on the system.

Includes Charts:

Chart - Content of Protein Sequence Databases
Fig. 1 - General Subsequence and Database Input Area
Figure 2 - Options for Advanced BLASTing Input Area
Figure 3 - Format input area for report outputs

From the Paper
"The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. The summary of the Content of Protein Sequence Databases with the sequences they contain are as follows: (NCBI, 2006)"

Tags:Bioinformatics, Search, Engine, bioinformatics, protein, database

Abstract
This paper discusses how the introduction of new materials in recent decades has provided urban designers and architects with the opportunity to transform the relationship that has historically existed between people and their environments through innovations in construction and the materials from which these buildings are constructed. This paper provides an overview of some of the historical issues, such as the history of plastics, ceramics, semiconductors and reviews questions about the design issues that emerge from the nature of the materials themselves. This is followed by a summary of the research and salient findings in the conclusion.

Outline:
Introduction
Review and Discussion
Background and Overview
Historical Issues and Influences
Emergent Technological and Design Issues
Conclusion

From the Paper
"Citing the example of Japan finding itself in need of coal during the 1930s, Bell reports that the Japanese simply acquired more material by invading Manchuria and appropriating their resources. This author also observed early on that the materials revolution would have a profound effect on how architects and designers selected the materials needed for any given applications, and suggested that new technologies would emerge that would allow for completely customizable materials for any given purpose. This, in fact, is what has taken place in recent years. Indeed, innovations in materials science as well as manufacturing applications that have introduced new composites and the potential for increasingly tiny applications of these substances at the molecular level through nanotechnology promise even more science-fiction-into-science fact realities. "

Tags:alchemists, scientists, bioinformatics, engineering, biomaterials, innovations

Abstract
The paper introduces the concept of Nanotechnology, and considers the usage of both proteins and nucleic acids as molecular components of Nanomachines. Their pros and cons (including strength, speed, comparison to macro-scale materials) are considered in detail, and a conclusion is drawn based on these observations.

From the Paper
"Our modern technology builds on an ancient tradition. Thirty thousand years ago, chipping flint was the high technology of the day. Our ancestors grasped stones containing trillions of trillions of atoms and removed chips containing billions of trillions of atoms to make their axe heads; they made fine work with skills difficult to imitate today. They also made patterns on cave walls in France with sprayed paint, using their hands as stencils. Later they made pots by baking clay, then bronze by cooking rocks. They shaped bronze by pounding it. They made iron, then steel, and shaped it by heating, pounding, and removing chips. We now cook up pure ceramics and stronger steels, but we still shape them by pounding, chipping, and so forth. We cook up pure silicon, saw it into slices, and make patterns on its surface using tiny stencils and sprays of light. We call the products "chips" and we consider them exquisitely small, at least in comparison to axheads."

Tags:acid, assembler, bioinformatics, biotechnology, folding, nanomachine, nanotechnology, nucleic, protein

Abstract
This paper discusses how, since the publication of the human genome sequence in 2001, biologists have developed and applied a range of novel technologies in an attempt to extract the valuable biological information encoded within the genome sequence. In particular, it examines they way in which we have set about decoding the human genome to date and provides an insight into some of the progressive new technologies currently under development.

Outline
Objectives and Achievements of the HGP
Computational Biology and Genome Annotation
Comparative Genomics
Functional Genomics
Genetic Perturbations
The Transcriptome
The Proteome
The Interactome
Conclusion: The Rise of Systems Biology

From the Paper
"The objectives of the HGP can be considered as four overlapping goals: 1. The construction of high resolution genetic and physical maps. 2. A high quality, complete genomic sequence. 3. Identification of sequence variation within the human genome. 4. A complete list characterising each and every gene. Both working drafts have achieved almost complete sequencing of the euchromatic DNA in the human genome14. The highly repetitive nature of heterochromatic DNA renders its sequencing difficult and it is unlikely to be well represented even in the final sequence, anticipated by April 2003. To date, the public consortium (IHGSC) report that 75% of the human genome sequence is in "finished" state. That is, a continuous sequence with gaps no larger than 150kb and an expected error rate of less than 1 in 10,000 nucleotides. The public consortium's effort also resulted in a high resolution physical map of the genome, constructed to facilitate accurate assembly of sequenced fragments16. However, the genome sequence itself represents a physical map of the highest possible resolution."

Tags:bioinformatics, organisms, proteomics, transcriptome