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Bioinfomatics Acceleration

Time that matters. We speed up your life science research with our computer technologies.

Our Services

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Custom Application Development

Fixstars’ software engineering team has deep and broad knowledge of bioinformatics and excellent skills to design and implement tailor-made applications to meet your requirements. We offer one-stop service ranging from hardware consultation to application development. You can enjoy better bioinformatics application performance on x86, ARM, POWER, GPU, and FPGA with our support. We will quickly respond to your needs and to help you move your projects forward.

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Optimization

Time that matters. You can accelerate your research with our optimization services. Fixstars’ engineers have superior skills and techniques in software optimization exploiting hardware acceleration features such as SIMD, multi-cores, and accelerators (GPU, FPGA) to dramatically boost your application performance.

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IT System Installation

Our engineering team will support installation of computing clusters for your bio research. We offer consultation services where Fixstars with our hardware partner finds out the best computing cluster system suitable for your workload. After-installation technical support with our talented engineers is also available.

Case Studies

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GPU Acceleration for NoRMCorre

NoRMCorre is an algorithm widely used in neuro science, especially calcium imagining, however, it is one of the time-consuming pipelines in neuro analysis. Thus we ported and optimized NoRMCorre to GPU. Our GPU version achieved 2x performance compared to the original CPU version of NoRMCorre in a rigid mode data set.

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Cluster System Installation Support

Fixstars successfully delivered and installed GPU clusters to a research institute, CSHL (see our new release here). In the early phase of this project, we profiled and analyzed their time-consuming software, and concluded that they should be able to achieve at least 4-fold acceleration using the new GPU clusters.

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In Situ Sequencing Acceleration

In situ sequencing is a new method to profile sequence of bases and their locations in a cell. Data processing, especially, image processing to perform in-situ sequencing was a time-consumed task and it took 6 months to analyze 10TB data. We optimized this process and it should achieve 35x speed-up (6 months → 5 days) with GPU clusters and high speed data storage.

Related hardware

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ExM Workstation

  • 1x Intel Xeon W-2133, 6 Core
  • 2x NVIDIA GeForce RTX 2080 Ti
  • 8x 16GB Memory
  • 1x M.2 1TB SSD (For OS)
  • 2x SATA 4TB HDD (For Data)
  • ExM Studio Pre-install
  • ExM Studio Technical Support
  • Starting form $8,500
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ExM Server

  • 2x Intel Xeon Gold 6130, 16 Core
  • 1x NVIDIA Tesla P100 12GB HBM2
  • 12x 16 GB Memory
  • 1x M.2 512GB SSD (For OS)
  • 2x SATA 4TB HDD (For Data)
  • ExM Studio Pre-install
  • ExM Studio Technical Support
  • Starting form $23,000
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