BioPIM Project

The BioPIM Project aims to leverage the emerging processing-in-memory (PIM) technologies to accelerate #bioinformatics applications while reducing energy requirements and enabling powerful edge computing in mobile devices.

📖 Read the final version on IEEE Xplore: ieeexplore.ieee.org/document/11389… 🔓 Or access the open-source preprint on arXiv: arxiv.org/abs/2506.00597 #Bioinformatics #PIM #Genomics #ComputerArch #BioPIM #Sustainability

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.

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 🧵👇

Our consortium-wide position paper is now available as a preprint @arxiv arxiv.org/abs/2506.00597 @SAFARI_ETH_CMU @UPMEM @IBMResearch @RayanChikhi @institutpasteur @BarIlanU @CNRS

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

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-… @geraldofojunior @el1goluj @_onurmutlu_ @ProjectBioPIM

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-su… canfirtina.com @_onurmutlu_ @ProjectBioPIM

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-speake… @icecs2024 @ieeecassociety @IEEEorg

Leaving Hinxton with an award in the bag!

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.

We are at the Genome Informatics 2024 meeting with two talks and a poster. @calkan_cs @zulal_b @camiladuitama1 @RayanChikhi in attendance.

Online participation: Pinar Demirekler Burat (Bilkent), Gamze Kozanoglu (Bilkent), Ecem İlgün (Bilkent), Berkan Şahin (Bilkent), Akmuhammet Ashyralyyev (Bilkent), Erwan Drezen (Pasteur), Meven Mognol (UPMEM and CNRS), Leonid Yavits (Bar-Ilan), Zuher Jahshan (Bar-Ilan)

Elena Ferro (IBM), William Simon (IBM), Yoshihiro Shibuya (Pasteur), Abu Sebastian (IBM), Can Alkan (Bilkent), Orhun Görkem (IBM)

We held our third plenary meeting for the BioPIM Project in beautiful Zurich, marking the close of our second review period. Since our last meeting in May, we have published three additional papers, with several more submitted and available as preprints.