Active Motif and the Center for Biotechnology (Cebitec) Form Partnership to Jointly Develop Computational Tools for TimeLogic Corporation's FPGA-Based Hardware Accelerated Bioinformatics Platform

Published: Nov 14, 2011

Bielefeld, Germany and Carlsbad, CA—November 15, 2011. The Center for Biotechnology (CeBiTec) at Bielefeld University has agreed to work with Active Motif to develop accelerated sequence comparison algorithms for the TimeLogic Field Programmable Gate Array (FPGA) based DeCypher® high performance biocomputing platform. TimeLogic’s DeCypher systems greatly increase the speed of DNA and protein sequence comparison by combining FPGA based PCIe accelerator cards with high-performance servers to accelerate optimized implementations of BLAST, Smith-Waterman, HMMER and gene modeling algorithms.

According to Michael Murray, Manager of Sales & Marketing for TimeLogic products at Active Motif, “We feel very fortunate to be able to work with CeBiTec as they have tremendous expertise in large scale computing and high-performance bioinformatics. Our recently announced new hardware platform will run Tera-BLAST, our accelerated BLAST implementation, over 400 times faster than running BLAST in software.” Ted DeFrank, President of Active Motif added, “Recent advances in next-gen DNA sequencing technology have created great opportunities for our TimeLogic division and, as a result, Active Motif is investing heavily in this portion of our business. In addition to a major hardware revision, TimeLogic has several additional projects ongoing and we recognize that working with CeBiTec affords us a great opportunity to further strengthen our position as the leader in the field of FPGA-accelerated Biocomputing solutions.”

Dr. Alexander Goesmann, Executive Director of the Bioinformatics Resource Facility (BRF) at CeBiTec added, “We are really delighted about the latest TimeLogic developments and we are looking forward to collaborating on projects that are highly relevant for us. We have already deployed the TimeLogic system and integrated Tera-BLAST into our genome annotation system, GenDB, which has relieved the enormous pressure on our sizeable compute cluster. We are also working on a new platform for metagenomics that will rely heavily on the TimeLogic system.” Goesmann continued, “Our highly experienced team is excited to provide input, validation, and benchmarking for TimeLogic’s new accelerated Next Gen mapping tool and new and faster accelerated BLAST implementation. We also look forward to strengthening our relationship with Active Motif and TimeLogic as participants in future research projects”

About CeBiTec

The CeBiTec is a central academic institution at Bielefeld University, Germany dedicated to interdisciplinary research in life sciences. It is a place to encourage and support the creation of innovative projects that cross discipline boundaries. For this purpose it consolidates research activities in the fields of biotechnology, molecular biology, genome research, systems biology, biochemistry, nano- and biophysics, as well as bioinformatics and computer science. With respect to the scientific alliance of genome research and computer science, CeBiTec strives to provide both bioinformatics support to ongoing research projects in genomics, as well as fundamental algorithms and tools applicable in the worldwide bioinformatics community.

The Technology Platform Bioinformatics provides general hardware and software support for 400 researchers of the CeBiTec and more than 1500 cooperation partners worldwide within genome and post-genome projects.

About Bielefeld University

Bielefeld University was founded in 1969 with an explicit research assignment and a mission to provide high-quality research-oriented teaching. Today it encompasses 13 faculties covering a broad spectrum of disciplines in the humanities, natural sciences, social sciences, and technology. With about 17,500 students in 80 degree courses (in German) and 2,600 staff (including approx. 1,480 academic staff) it is one of Germany's medium-sized universities.

Since its foundation the University has been guided by the paradigm of interdisciplinarity, as today's complex problems can no longer be adequately tackled through mono-disciplinary approaches alone. Here interdisciplinarity stands for a spectrum of multiperspectival approaches of different kinds and intensities. As the architectural expression of its interdisciplinarity, the University unites - uniquely in Germany - almost all its departments in a single building. This striking structure brings people working in different disciplines together in close proximity. The culture of communication fostered between students and teaching staff as well as between researchers, management, and administration is characterized by great openness towards new and unconventional ideas. Thus, it is not surprising that Bielefeld University has been one of the first places world-wide to establish the emerging discipline of bioinformatics both in research and education.

About TimeLogic

TimeLogic, a division of Active Motif, Inc, is the world leader in hardware accelerated bioinformatics search tools which accelerate genome annotation by combining optimized bioinformatics applications with powerful FPGA-based PCIe accelerator cards. This blend of specialized hardware and optimized software provides a perfect combination of performance, accuracy and value. Furthermore, these systems are simple to maintain and scale easily. Utilizing a TimeLogic system reduces pressure on over-used CPU-clusters by off-loading BLAST, Smith-Waterman (SW) and Hidden Markov Model (HMM) tasks to a highly time and energy efficient solution. From the earliest genome sequencing projects in the 1990’s to the largest metagenomics projects undertaken to date, TimeLogic has provided the enabling technology to make this research possible. Active Motif/TimeLogic operates globally through its corporate headquarters in Carlsbad, California, European headquarters in Rixensart, Belgium and Japanese headquarters in Tokyo, Japan. Active Motif/TimeLogic applies a multi-disciplinary approach to create new and modify existing technologies to meet the current and future needs of life science researchers.

Find out more by visiting us at or contact Michael Murray at

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