Category Archives: Computing

AbokiaBLAST 2.0 Released

AbokiaBLAST 2.0

AbokiaBLAST is a parallel implementation of NCBI BLAST created by the inventors of the open-source mpiBLAST project. AbokiaBLAST inherits the super-scalable architecture from mpiBLAST but is re-factored and re-engineered to offer production quality. With intelligent task parallelization and I/O optimization, AbokiaBLAST enables users to massively accelerate large-scale BLAST search on clusters or supercomputers with a single command.

Why Use AbokiaBLAST?

  • Performance. AbokiaBLAST is up to 10 times faster than the open-source mpiBLAST. Its parallel engine scales efficiently across tens of thousands of compute cores.

  • Accuracy. The results of AbokiaBLAST match the new NCBI BLAST engine, i.e., 2.2.25.

  • Auto-Configuration. AbokiaBLAST greatly improves usability by automating the system configuration for optimal performance.

  • Timely Upgrades. The BLAST search engine is regularly upgraded to support the latest version of NCBI BLAST.

  • Service and Support. AbokiaBLAST offers rapid response and support from an experienced team of bioinfomaticists and computer scientists.

For further information, please contact info@abokia.com.

SDSC Computational Science

With the dramatic increase in humankind’s ability to change the physical environment of the world around us, the environmental sciences have become one of the most prolific scientific research areas. Already strong at UCSD — with major research efforts at SIO, the Division of Physical Sciences, Cal-(IT)2, and elsewhere — the area is also becoming increasingly critical to the State of California.

In response to these expanding opportunities, the Computational Sciences program area, led by Kim Baldridge, will develop a strong Environmental Informatics group. “As in biosciences, SDSC and UCSD are well positioned to build and support a large-scale program in environmental sciences that spans scales from the molecular level to entire populations, accurately modeling the impact of population on the environment,” Baldridge said. “SDSC and the campus will work together to build a program that advances the capacity to monitor, guide, understand, and explain environmental complexity.”

SDSC will provide the computational and data-management components of this program. The ability to integrate large-scale information from different disciplines and multiple spatial and temporal scales provides the foundation for a distinctive and substantive contribution to environmental sciences. SDSC will apply its expertise in partnerships that couple wireless and sensing technologies to large-scale computational and data management capabilities. These “sensors-to-supercomputers” capabilities will be critical for partners such as NPACI, LTER, SIO, Cal-(IT)2, the Partnership for Biodiversity Informatics, and the Division of Physical Sciences.

In addition, this program area will nurture and maintain SDSC’s leadership in other critical strategic capabilities, including chemistry, parallel applications and performance modeling, and design visualization.