The Leading Source for Global News and Information Covering the Ecosystem of High Productivity Computing
February 29, 2008
SDSC Intros Next Generation Biology Workbench, Version 1.0
1 | 2 All »
Free Web resource, code-named 'Swami,' used by scientists and students
Feb. 27 -- The San Diego Supercomputer Center (SDSC) at UC San Diego has announced the release of the Next Generation Biology Workbench, version 1.0. The popular system, code-named Swami, is a free Web resource accessed thousands of times per week by scientists and students in bioinformatics, genomics, proteomics, and phylogenetics communities worldwide.
Swami links major molecular biology databases with analysis programs through an easy-to-use Web interface. Searching is integrated with a wide variety of analysis and modeling tools, and is designed to eliminate file format compatibility problems. Swami, which runs on powerful computational resources at SDSC, also offers speed, letting researchers complete within hours complex tasks that once took days, weeks, or even months.
"Swami is designed to put powerful biological analysis tools within easy reach of biology educators, students, and researchers, without the cost of having to install and manage a complex infrastructure," said Mark Miller, Swami project leader at SDSC. "Our goal is to provide services to biologists at institutions of all scales, so the biology research community isn't fragmented into cyber haves and cyber have-nots."
Funded by the National Institutes of Health (NIH), Swami is based on the original Biology Workbench introduced more than 10 years ago by UCSD bioinformatics pioneer Shankar Subramaniam when he was at the National Center for Supercomputing Applications (NCSA).
The Next Generation Biology Workbench has been re-engineered so that new tools and data types can be added easily. This will help the toolkit grow according to the evolving needs of the community, and make it possible for other developers to contribute tools to the Workbench. The re-engineered workbench also simplifies adding new databases, and makes it possible to easily move the application to other computational resources.
Swami v1.0 features include:
- Most original Biology Workbench tools, with greater data handling flexibility in the new Swami environment.
- The Sirius protein structure viewer, a full-featured structure and modeling tool that permits creation, display, and overlay of complex model structures.
- Tools from the Phylip Phylogeny Inference Package.
Additional features that the development team plans to release in 2008 include an interactive phylogenetic tree viewer, the ability to share data with colleagues within the workbench, and tools for DNA sequence assembly.
A focus of the development team has been to make this advanced tool available to users with all levels of training, from beginning students to advanced researchers, and to make Swami available independent of where users are located and with minimal barriers to entry.
The project team has embraced best practices in software development, focusing on reliable and well-understood technologies that ensure a dependable production resource.
Page: 1 of 21 | 2 All »
Article Tools
Share Options
(Digg, Technorati, more)
Subscribe
Sponsored Links
New Paper: Parallel Computing Without Parallel Programming
Learn how domain experts can run VHLL programs like MATLAB® on a variety of high-performance platforms without low-level reprogramming and how to work with the largest datasets and complex algorithms without sacrificing ease of use or reducing productivity.
RSS Feeds
Feeds by Topic
- Applications
- Developer Tools
- Interconnects
- Middleware
- Networks
- Processors
- Storage
- Systems
- Visualization
Feeds by Industry
Feeds by Content Type
Feature Articles
Spider Up and Spinning Connections to All Computing Platforms at ORNL
Spider, the world's biggest Lustre-based, centerwide file system, has been fully tested to support Oak Ridge National Laboratory's new petascale Cray XT4/XT5 Jaguar supercomputer and is now offering early access to scientists.
Read More...
Wolfram Alpha: A Web-Based Application That Embraced Supercomputers
Wolfram Alpha, the Web-based computational engine introduced in May, is not a traditional supercomputing application, but relies on supercomputers to satisfy its unique requirements.
Read More...
TeraGrid '09: Student Participation Soars
There was a new energy at this year's TeraGrid '09 conference thanks to an outstanding turnout for the student program. Thanks to support from the National Science Foundation, more than 100 high school, undergraduate and graduate students were able to participate in the conference.
Read More...
Top Headlines
3D Seismic Data: Taking a Smarter Approach to Interpretation
Jul 09 | Engineer Live | The demand for computational tools to underpin the 3D seismic interpretation process has never been more apparent. Read more...
Engineering Unemployment Soared in 2Q to 8.6%
Jul 08 | EE Times | Unemployment for U.S. engineers has reached record levels, according to government figures. Read more...
Gartner Adjusts 2009 IT Spend Downward Again
Jul 08 | Network World | Global spending for 2009 projected to drop 6 percent, for a total of $3.2 trillion. Read more...
Concurrent and Parallel Are Not The Same
Jul 08 | Linux Magazine | Portability or efficiency? Neither is guaranteed when writing explicit parallel code. Read more...
800 TFLOP Real-Time Ray Tracing GPU Unveiled, Not for Gamers
Jul 07 | Ars Technica | Japanese company builds custom ASIC to accelerate real-time ray traced rendering for the auto industry. Read more...
Featured Whitepapers
Parallel Computing Without Parallel Programming
Jul 10 | | Engineers, scientists, and other domain experts depend on the productivity enabled by very high-level language (VHLL) tools like MATLAB® and Python. However, as datasets grow larger and programs get more sophisticated, ordinary desktop computers can no longer keep up. The paper explores how to run VHLL programs on high-performance platforms without low-level reprogramming. Work with large datasets and complex algorithms without sacrificing ease of use or reducing productivity.
Building High Performance Computing in a Green and Modular Solution Building Block
Apr 14 | | Many HPC IT departments are feeling the rising pressure to deliver more capacity computing and performance while trying to reduce the total cost of ownership. This white paper discusses how an environmentally-friendly and open-standards HPC building block based computing system using flexible interconnect options helps address capacity computing needs.
Multimedia
Webcast: Dell Expands HPC Access and Adoption with Intel Cluster Ready Program
Source: Addison Snell, GM/VP, Tabor Research; sponsored by Dell
Many organizations that could benefit from the use of HPC clusters find that it is complicated to get the systems up and running because of limited IT resources or the complexities of the clusters themselves. Learn how the Intel Cluster Ready program, for which Dell was an original partner, seeks to address this challenge for entry level and mid-range HPC users.
Video White Paper: Architecting a Better Network Storage Solution
BlueArc's Titan architecture represents an evolutionary step in file servers by creating a hardware-based file system that can scale bandwidth, IOPS, and overall data capacity well beyond conventional software-based devices. With its ability to virtualize a massive storage pool of up to four usable petabytes of tiered storage, Titan can scale with growing data requirements, offering a competitive advantage for businesses, researchers, or other enterprises seeking to better manage data growth while still ensuring optimal performance.
Webcast: HPC Development Solutions: Sun Studio & Sun HPC ClusterTools
Sun Studio Compilers and Tools and Sun HPC ClusterTools allow you to create high performance parallel applications for OpenSolaris, Solaris and Linux. Sun Studio Express 11/08 includes MPI performance analysis capabilities and full OpenMP 3.0 compiler support. Learn about all this and the latest in Sun HPC ClusterTools 8.1.
Newsletters
Stay informed! Subscribe to HPCwire email Newsletters.
HPC Job Bank
-
HPC Systems Administrator
McGill University -
High Performance Computing Systems Administrator
Idaho National Laboratory -
Solution Engineer- HPC
Dell Inc -
Parallel Programmer
Cardiff University -
Principal Software Research Engineer
Indiana University -
Post Doctoral Researcher - Exascale Stream Computing
IBM - Visit the HPCwire Job Bank
Featured Events
-
July 13-16, 2009
WORLDCOMP'09
Las Vegas , NV
USA
-
August 24-28, 2009
Data Mining: Levels I, II, & III
Denver , CO
USA