SciApps

Lush is an object-oriented programming language designed for researchers, experimenters, and engineers interested in large-scale numerical and graphic applications. Lush is designed to be used in situations where one would want to combine the flexibility

Microsoft Releases 'Trident' Software to Help Scientists Organize Research\n\nA new data-management tool unveiled today by Microsoft Research at its annual Faculty Summit will be available to colleges and universities free.

Applications & Developer Tools

A free online tutorial, Introduction to Performance Tools, has been released in CI-Tutor. This tutorial provides an introduction to a number of commonly-used performance tools on the TeraGrid's high-performance computing resources. The highlighted tools include two Linux utilities: strace, which traces system calls and signals during program execution; and gprof, which can be used to track how functions are using system resources. More complex toolsets include NCSA's PerfSuite, a collection of tools and supporting libraries that provides a higher-level view of application performance, and TAU (Tuning and Analysis Utilities), a suite of tools for performance instrumentation, analysis, and visualization of large-scale parallel computer systems and applications. The course is organized as individual lessons that provide a general overview of each tool, demonstrate how the tool might be run on a TeraGrid computing resource, provide examples of subsequent data analysis, and conclude with self-assessment and pointers to more comprehensive resources regarding each tool. CI-Tutor offers a number of courses covering topics in high-performance computing, such as multi-core performance, performance tuning, large-scale parallel simulation, scientific visualization, and debugging. The courses are available to everyone and can be accessed by registering and creating a login. To see the courses offered, go to the course catalog at http://www.citutor.org/browse.php. To login and take a course, go to the CI-Tutor homepage at http://www.citutor.org/. CI-Tutor is hosted by the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign. The effort is supported in part by the National Science Foundation Office of Cyberinfrastructure through the TeraGrid and Blue Waters projects."

"Genome sequence assembly primer Our genetic heritage, as well as that of all living organisms, is encoded in a set of DNA molecules called chromosomes. Each such molecule can be represented as a string of just four letters: A, C, T, G; representing the four basic molecules (called nucleotides or bases) that compose the DNA. In most organisms DNA is structured as two molecules twisted around each other into a double-helix and held together by bonds between complementary nucleotides A-T and C-G. The two molecules (also called strands) have a natural orientation defined by their chemical structure and are twisted together in opposite orientations. Both strands, thus, contain the same information and the sequence of one strand can be obtained from the sequence of the other strand by reverse complementation, namely by reversing it's sequence and then replacing each nucleotide with its complement (replacing each A with a T, each G with a C and so on). This characteristic of DNA is essential to life as it allows the replication of the DNA molecule -- an important element of our ability to pass genetic information to our offspring. "

"Summary The primary data produced by genome sequencing projects are often highly fragmented and sparsely annotated. This is especially true for the Human Genome Project as a result of its policy of releasing sequence data to the public sequence databases every day (1, 2). So that individual researchers do not have to piece together extended segments of a genome and then relate the sequence to genetic maps and known genes, NCBI provides annotated assemblies of public genome sequence data. NCBI assimilates data of various types, from numerous sources, to provide an integrated view of a genome, making it easier for researchers to spot informative relationships that might not have been apparent from looking at the primary data. The annotated genomes can be explored using Map Viewer (Chapter 20) to display different types of data side-by-side and to follow links between related pieces of data. This chapter describes the series of steps, the "pipeline", that produces NCBI's annotated genome assembly from data deposited in the public sequence databases. A variant of the annotation process developed for the human genome is used to annotate the mouse genome, and similar procedures will be applied to other genomes (Box 1). NCBI constantly strives to improve the accuracy of its human genome assembly and annotation, to make the data displays more informative, and to enhance the utility of our access tools. Each run through the assembly and annotation procedure, together with feedback from outside groups and individual users, is used to improve the process, refine the parameters for individual steps, and add new features. Consequently, the details of the assembly and annotation process change from one run to the next. This chapter, therefore, describes the overall human genome assembly and annotation process and provides short descriptions of the key steps, but it does not detail specific procedures or parameters. However, sufficient detail is provided to enable users of

iPad is a powerful, simple, flexible and free Electronic Laboratory Notebook for all those who take and use experimental research notes: researchers, technicians, group leaders, and R&D directors. It improves the management of research-related information

elcome to the Directory of Open Access Journals. This service covers free, full text, quality controlled scientific and scholarly journals. We aim to cover all subjects and languages. There are now 3371 journals in the directory. Currently 1151 journals a

Virtual research environments (VREs), as one hopes the name suggests, comprise digital infrastructure and services which enable research to take place. The idea of a VRE, which in this context includes cyberinfrastructure and e-infrastructure, arises from and remains intrinsically linked with, the development of e-science. The VRE helps to broaden the popular definition of e-science from grid-based distributed computing for scientists with huge amounts of data to the development of online tools, content, and middleware within a coherent framework for all disciplines and all types of research. This article highlights some of the issues relating to the development and deployment of VREs and introduces three VRE projects in which Oxford University is leading or playing a significant role.

Distributed data processing with Hadoop, Part 1: Getting started\nInstall and configure a simple cluster\nM. Tim Jones, Independent author\nSummary:  This article-the first in a series on Hadoop-explores the Hadoop framework, including its fundamental elements, such as the Hadoop file system (HDFS), and node types that are commonly used. Learn how to install and configure a single-node Hadoop cluster, and delve into the MapReduce application. Finally, discover ways to monitor and manage Hadoop using its core Web interfaces.

Rasmol Home Page Molecular

Semantic Web between various scientific journal articles

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry,

News for Octave Version 3

ORNL\nElectronic Notebook Project

Programs for Protein, DNA, and RNA structure determination by NMR\n\nSeveral groups at UC San Francisco have developped software useful for studying biomolecules with NMR. Software has been developped by

Open Notebook Science involves a variety of internet-based techniques for sharing of scientific information, from the use of wikis for experiments, to the Chemspider database, where chemists share molecules in a fashion that is socially (but not technical

ChemSpider is a free access service providing a structure centric community for chemists. Providing access to millions of chemical structures and integration to a multitude of other online services ChemSpider is the richest single source of structure-base

SciPy (pronounced "Sigh Pie") is open-source software for mathematics, science, and engineering. It is also the name of a very popular conference on scientific programming with Python. The SciPy library depends on NumPy, which provides convenient and fast

GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.