@ProjectBioPIM

Funded by the @HorizonEU @EUeic to co-design algorithms and PIM technologies to accelerate bioinformatics applications and reduce energy requirements.

biopim.eu/
Joined November 2021
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We look forward to welcoming you to Ankara for two days of engaging talks and discussions!
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The program will also feature short presentations highlighting ongoing developments across the field. We will update the schedule accordingly. Event Details & Schedule (tentative, subject to change): biopim.eu/events/workshop Free Registration Form: forms.gle/YHYkxNvGa1oxKXCW7
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BioPIM Partner Speakers: Can Alkan (Bilkent University) Yoshihiro Shibuya (Institut Pasteur) Irem Boybat (IBM) Orhun Görkem (IBM) Dominique Lavenier (CNRS) Onur Mutlu (ETH Zürich)
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Invited Speakers: Victoria Popic (Broad Institute) Santiago Marco-Sola (Barcelona Supercomputing Center - BSC) Iman Hajirasouliha (Weill Cornell Medicine) Geraldo Francisco de Oliveira Junior (Huawei) Christina Giannoula (Max Planck Institute)
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We are thrilled to bring together leading voices from both our BioPIM consortium partners and world-renowned invited researchers:
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Event Details Dates: October 6–7, 2026 Location: Bilkent University, Ankara, Turkey Day 1 (Oct 6): Mithat Çoruh Auditorium (EB Building) Day 2 (Oct 7): EE-01
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The workshop is free to attend and open to the public. We warmly welcome undergraduate and graduate students, researchers, and industry professionals to join us!
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Join us at @BilkentUniv in Ankara, Turkey, on October 6–7, 2026, for a two-day workshop exploring the forefront of Processing-in-Memory (PIM) architectures and hardware acceleration for computational genomics and data-centric computing.
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BioPIM Project retweeted
Bilkent CompGen@BilkentCompGenAug 24
Our new paper, "De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping," is now published in Briefings in Bioinformatics. doi.org/10.1093/bib/bbag440

De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools...

Abstract. De Bruijn graphs are widely used in pangenome representation due to their numerous advantages and extensions, such as colored and compacted varia

academic.oup.com
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📖 Read the final version on IEEE Xplore: ieeexplore.ieee.org/document… 🔓 Or access the open-source preprint on arXiv: arxiv.org/abs/2506.00597 #Bioinformatics #PIM #Genomics #ComputerArch #BioPIM #Sustainability

Processing-in-Memory for Genomics Workloads

Low-cost, high-throughput DNA and RNA sequencing data are the backbone of the life sciences. Genome sequencing is now becoming a part of predictive, preventive, personalized, and participatory...

ieeexplore.ieee.org
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Our focus? Hardware-software co-design. We are optimizing: genomic data analysis algorithms using specialized data structures and multiple PIM architectures. The goal: Unprecedented cost, energy, and time savings for life sciences.
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The "Memory Wall" is real. High-throughput sequencing drives P4 medicine, but moving that data to the CPU wastes time and energy. The BioPIM Project is changing the game by leveraging Processing-in-Memory (PIM) to bring computation to the data.
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We’re excited to share our new position paper from the BioPIM Consortium: "Processing-in-memory for genomics workloads", published online in IEEE Micro, and will be a part of the upcoming Special Issue on Data-Centric Computing. Thread below 🧵👇
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We've updated our PIM Primer! We've expanded the overview to cover the extensive PIM work over the past few years. 💥A Modern Primer on Processing in Memory: arxiv.org/abs/2012.03112 @_onurmutlu_ @SaugataGhose @el1goluj R. Ausavarungnirun @MohammadSadr89 @geraldofojunior
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We're excited to share our recent @sigarch blog post highlighting our real-world PIM tutorials! Processing-in-Memory Tutorials: Experiences from Past Two Years and Thoughts Looking Forward: sigarch.org/processing-in-me… @geraldofojunior @el1goluj @_onurmutlu_ @ProjectBioPIM
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We were excited to celebrate two PhD defenses in November! We'd like to wish a very warm congratulations to @FirtinaC & @breitware on the successful completion of their PhDs. Read more on Can's thesis: safari.ethz.ch/can-firtina-s… canfirtina.com/ @_onurmutlu_ @ProjectBioPIM
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We're excited to be at #ICECS2024 this week in Nancy, France. @_onurmutlu_ will give a keynote tomorrow, Tuesday, Nov 19 at 9AM on Memory-Centric Computing, don't miss it! Talk details: ieee-icecs2024.org/keynote-s… @icecs2024 @ieeecassociety @IEEEorg
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Leaving Hinxton with an award in the bag!
Bilkent CompGen@BilkentCompGen15 Nov 2024
And the Best Poster Award goes to @zulal_b!! #genomeinformatics24
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Last day of #genomeinformatics24! We have presented our work in @ProjectBioPIM with talks from @calkan_cs and @camiladuitama1 and a poster by @zulal_b, increasing the awareness of hardware acceleration in the community.
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We are at the Genome Informatics 2024 meeting with two talks and a poster. @calkan_cs @zulal_b @camiladuitama1 @RayanChikhi in attendance.
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