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 goal 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 commonly based on FGPA or GPUs.

BioPIM Partners: 

BioPIM is led by Can Alkan at Bilkent University, with Juan Gómez Luna  and Mohammed Alser leading the research activities at ETH Zurich.  The project has five academic and two company partners from Turkey, Switzerland, France, and Israel, bringing together complementary expertise within the disciplines of computer science, computer engineering, electrical engineering and genomics allowing an interdisciplinary approach for achieving BioPIM’s goals:

Objective 1, focuses on optimizing algorithms and data structures for PIM will take guidance from Bilkent, Pasteur, and CNRS. We will use several software tools to profile computational behavior, some of which were developed in our group, in collaboration with IBM Research Zürich.
Objective 2, involves hardware/software co-development requires expertise by all participants, where algorithmic aspects will be guided by Bilkent, Pasteur, and CNRS, and hardware development will be guided by ETH, TECHNION, Bar-Ilan, IBM, and UPMEM.
Objective 3, focuses on PIM architecture prototyping and API design requires expertise in simulation infrastructures that ETH, IBM, and UPMEM have, and API development that Pasteur will lead with the participation of Bilkent, ETH, IBM, Bar-Ilan, and TECHNION.

Read more on the BioPIM website, and follow the BioPIM project on Twitter!

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


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]