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We are part of BioPIM, a project funded by the European Union’s Horizon Europe programme for research and innovation for the period 2022-2026.

The vision of BioPIM is the realization of cheap, ultra-fast and ultra-low energy mobile genomics that eliminates the current dependence of sequence analysis on large and power-hungry computing clusters/data-centers.

BioPIM is led by Can Alkan at Bilkent University, with Onur Mutlu, Juan Gómez Luna  and Mohammed Alser leading the research activities in our group at ETH Zurich, together with the project partners from IBM, Institut Pasteur, UPMEM, CNRS, and TECHNION.

BioPIM aims to leverage the emerging processing-in-memory (PIM) technologies to enable powerful edge computing. We will focus on co-designing algorithms and data structures commonly used in bioinformatics together with several types of PIM architectures to obtain the highest benefit in cost, energy, and time savings. BioPIM will also impact other fields that employ similar algorithms. Our designs and algorithms will not be limited to cheap hardware, and they will impact computation efficiency on all forms of computing environments including cloud platforms.

The targeted breakthrough of BioPIM is to invent and leverage in-memory computing architectures to fundamentally improve the performance and energy efficiency of various important bioinformatics algorithms to make mobile genomics a reality, focusing on

  • in-memory alignment and search,
  • in-memory global and local genome assembly,
  • in-memory pangenome analysis, and
  • in-memory variation calling and base calling.

Read the latest updates and project contributions on the BioPIM website.

ETH Team Lead: Onur Mutlu with Juan Gómez Luna, Mohammed Alser
ETH Team members: Joël Lindegger, Nika Mansouri Ghiasi, Can Firtina, Banu Cavlak


Recent SAFARI Research Group Contributions:

Workshops, Courses and Tutorials: 

We organized the first BIO-Arch: Workshop on Hardware Acceleration of Bioinformatics Workloads held with RECOMB 2023 in Istanbul in April 2023.  The workshop brought together researchers in bioinformatics, computational biology, and computer architecture communities to discuss the latest work on accelerating bioinformatics analysis (e.g., genome analysis) with efficient system designs that include hardware acceleration and software systems tailored for new hardware technologies.  The workshop was followed by a Panel on Hardware Acceleration of Bioinformatics Workloads.
BIO-Arch website  | BIO-Arch program | BIO-Arch talk recordings on YouTube

We held tutorials on Real-world Processing-in-Memory Systems at HPCA 2023 & ASPLOS 2023 in Feb and March 2023 with invited speakers from academia and industry, organized by Juan Gomez Luna, Onur Mutlu, and Ataberk Olgun.  You can find the programs and talk recordings here: HPCA 2023 Tutorial Website | YouTube recordings ASPLOS 2023 Tutorial Website | YouTube recordings

We have several courses related to BioPIM.  You can find all our recent courses, with online lectures and course materials here: spring 2023 courses.  Below, are our recent BioPIM related courses:

Upcoming: 

We’ll be giving another Real-World PIM tutorial at ISCA 2023 in June: ISCA 2023 Tutorial: Real-world Processing-in-Memory Systems for Modern Workloads, Sunday, June 18 (held during ISCA 2023, June 17 – 21, 2023 in Orlando, Florida).


Publications: 

Can Firtina, Nika Mansouri Ghiasi, Joel Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, and Onur Mutlu, “RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes”, Proceedings of the 31st Annual Conference on Intelligent Systems for Molecular Biology and the 22nd European Conference on Computational Biology (ISMB/ECCB), Lyon, France, July 2023. [RawHash Source Code] [Poster presented at RECOMB 2023 (PDF)]

Onur Mutlu and Can Firtina, “Accelerating Genome Analysis via Algorithm-Architecture Co-Design”, Invited Paper in Proceedings of the 60th Design Automation Conference (DAC), Orlando, FL, USA, July 2023.

Juan Gómez Luna, Yuxin Guo, Sylvan Brocard, Julien Legriel, Remy Cimadomo, Geraldo F. Oliveira, Gagandeep Singh, and Onur Mutlu, “Evaluating Machine Learning Workloads on Memory-Centric Computing Systems”, Proceedings of the 2023 IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS), Raleigh, North Carolina, USA, April 2023. [Extended arXiv version] [Slides (pptx) (pdf)] [PIM-ML Source Code] [Talk Video (15 minutes)]
Best paper session.

Maurus Item, Juan Gómez Luna, Yuxin Guo, Geraldo F. Oliveira, Mohammad Sadrosadati, and Onur Mutlu, “TransPimLib: Efficient Transcendental Functions for Processing-in-Memory Systems”, Proceedings of the 2023 IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS), Raleigh, North Carolina, USA, April 2023. [arXiv version] [Slides (pptx) (pdf)] [TransPimLib Source Code] [Talk Video (17 minutes)] 

M. Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joel Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan, and Onur Mutlu, “TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering”, Proceedings of the 21st Asia Pacific Bioinformatics Conference (APBC), Changsha, China, April 2023. [TargetCall Source Code] [arXiv version] [Talk Video at BIO-Arch 2023 Workshop] [Poster presented at RECOMB 2023 (PDF)]

Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri Ghiasi, and Onur Mutlu, “Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs”, Bioinformatics, [published online on] 24 March 2023. [Online link at Bioinformatics Journal] [arXiv version] [Scrooge Source Code] [Poster presented at RECOMB 2023 (PDF)] [Talk Recording BIO-Arch Workshop]

Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez Luna, Onur Mutlu, and Izzat El Hajj, “A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems”, Bioinformatics, [published online on] 27 March 2023. [Online link at Bioinformatics Journal] [arXiv version] [AiM Source Code]

Can Firtina, Jisung Park, Mohammed Alser, Jeremie S Kim, Damla Senol Cali, Taha Shahroodi, Nika Mansouri Ghiasi, Gagandeep Singh, Konstantinos Kanellopoulos, Can Alkan, Onur Mutlu, “BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis”, NAR Genomics and Bioinformatics, March 2023. [arXiv version] [Journal Article] [BLEND Source Code] [Slides (pdf)(pptx)] [Talk Video RECOMB 2023]


Additional resources:

EU Horizon Project BioPIM kick-off, 8 June 2022, online
Presentations: 

Mohammed Alser, “Processing-in-Memory Algorithm/Architecture Co-Design for Genome Analysis”, BioPIM Kick-off Meeting, 8 June 2022 [Slides (pptx) (pdf)]

Nika Mansouri Ghiasi, “GenStore: A High-Performance In-Storage Processing System for Genome Sequence Analysis”, BioPIM Kick-off Meeting, 8 June 2022 [Slides (pptx) (pdf)]

Damla Senol Cali, “Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design”, BioPIM Kick-off Meeting, 8 June 2022 [Slides (pptx) (pdf)]


Related papers and links: 

Mohammed Alser, Joel Lindegger, Can Firtina, Nour Almadhoun Alserr, Haiyu Mao, Gagandeep Singh, Juan Gomez-Luna, and Onur Mutlu, “From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures”, Invited Article in Computational and Structural Biotechnology Journal (CSBJ), August 2022.
[arXiv version with all Supplementary Materials] [Source Code]

Nika Mansouri Ghiasi, Jisung Park, Harun Mustafa, Jeremie Kim, Ataberk Olgun, Arvid Gollwitzer, Damla Senol Cali, Can Firtina, Haiyu Mao, Nour Almadhoun Alserr, Rachata Ausavarungnirun, Nandita Vijaykumar, Mohammed Alser, Onur Mutlu, “GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis,” 2022 IEEE Computer Society Annual Symposium on VLSI (ISVLSI), July 2022.
[Conference Paper] [Slides (pptx) (pdf)] [GenStore Source Code] [ISVLSI’22 Talk Recording]

Damla Senol Cali, Konstantinos Kanellopoulos, Joel Lindegger, Zulal Bingol, Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie Kim, Nika MansouriGhiasi, Gagandeep Singh, Juan Gomez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, and Onur Mutlu, “SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping”, Proceedings of the 49th International Symposium on Computer Architecture (ISCA), New York, June 2022.
[Slides (pptx) (pdf)] [arXiv version] [SeGraM Source Code and Datasets] [Talk Video (22 minutes)]

Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alex Zelikovsky, Can Alkan, Onur Mutlu, and Serghei Mangul, “Technology Dictates Algorithms: Recent Developments in Read Alignment”
Genome Biology, 26 August 2021.
[Source Code and All Data] [Online link at Genome Biology] [Full arXiv version]

Damla Senol Cali, Gurpreet S. Kalsi, Zulal Bingol, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gomez-Luna, Amirali Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, and Onur Mutlu, “GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis”,  Proceedings of the 53rd International Symposium on Microarchitecture (MICRO), Virtual, October 2020.
[Slides (pptx) (pdf)] [Short Talk Slides (pptx) (pdf)] [Lightning Talk Slides (pptx) (pdf)] [ARM Research Summit Talk Slides (pptx) (pdf)] [ARM Research Summit Short Talk Slides (pptx) (pdf)] [Lecture Slides (pptx) (pdf)] [MICRO 2020 Talk Video (18 minutes)] [MICRO 2020 Short Talk Video (6 minutes)] [MICRO 2020 Lighting Talk Video (1.5 minutes)] [ARM Research Summit Talk Video (21 minutes)] [ARM Research Summit Short Talk Video (15 minutes)] [ARM Research Summit Short Talk Video and Q&A (31 minutes)] [Lecture Video (37 minutes)] [GenASM Source Code]

 

We gratefully acknowledge the Swiss State Secretariat for Education, Research and Innovation, SERI, for proving our Horizon Europe funding as a non-associated third country participant in Horizon Europe.  We also thank the ETH EU GrantsAccess office for all their support in facilitating this project.