@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
  • Tweets110
  • Following79
  • Followers124
28Media
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
1
1
1
5
1,228
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
1
3
9
1,044
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
4
7
732
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
4
1
7
1,967
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
2
2
611
BioPIM Project retweeted
Ben Dicken
@BenjDicken18 Oct 2024
You asked for it, so here it is. Visualizing CPU cache speeds relative to RAM. Cache optimization is important too!
200
1,828
126
15,077
1,474,814
We're excited to share our joint work "AirLift" is now published in IEEE TCBB! ieeexplore.ieee.org/document… Paper on arXiv: arxiv.org/abs/1912.08735 Code: github.com/CMU-SAFARI/AirLif… @FirtinaC @damlasenolcali @mealser @NHajinazar @calkan_cs @_onurmutlu_ @ProjectBioPIM
4
6
954
We're glad to share our paper "RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization" is now published in Bioinformatics, August issue. Code: github.com/CMU-SAFARI/RawHas… academic.oup.com/bioinformat… @FirtinaC @lindegger_joel @_onurmutlu_ @ProjectBioPIM

GitHub - CMU-SAFARI/RawHash: RawHash can accurately and efficiently map raw nanopore signals to...

RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without basecalling. Described by Firtina et...

github.com
1
3
9
814
We're at the @UPMEM ABUMPIMP 2024 symposium in Madrid today. @geraldofojunior will present "Software Frameworks for Productive and Effective Processing-in-Memory Architectures" & discuss SimplePIM & DaPPA. Slides: safari.ethz.ch/wp-content/up… @_onurmutlu_ @el1goluj @ProjectBioPIM
2
8
779
We enjoyed #MICRO2023 last week! In case you missed our talks, posters, Real-World PIM tutorial or awards we've posted everything here: safari.ethz.ch/safari-contri… Looking forward to @MicroArchConf 2024! @_onurmutlu_ @agyaglikci @konkanello @el1goluj @ProjectBioPIM @MohammadSadr89
4
12
1,653
BioPIM Project retweeted
HiPEAC
@hipeac8 Nov 2023
📺 New video on #HiPEACTV! Reetuparna Das (@UMichECE) is your guide to the spectrum of #InMemory / #NearMemory computing. This #ACACES23 lecture covers the basics and rationale. 👉 bit.ly/ACACES23_Reetuparna_D…
1
1
3
363
We're excited to be at #MICRO2023! Join us for our talks tomorrow Day 3: Victima, Utopia @konkanello & Swordfish! S9C, Swordfish: arxiv.org/abs/2310.04366 T. Shahroodi w/ @GaganGdas @haiyu_mao @lindegger_joel @FirtinaC @_onurmutlu_ @tudelft @ProjectBioPIM @MicroArchConf @ETH_en
4
10
1,412
Join us for our talk on RawHash presented by @FirtinaC at #ISMBECCB2023 in July! RawHash is a hash-based mechanism to map raw nanopore signals to a reference genome in real-time. Premiere Tuesday August 15 3PM CEST: youtube.com/watch?v=ti0M6TvR… @_onurmutlu_ @ProjectBioPIM

RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals | ISMB-ECCB 2023

Talk of "RawHash: Enabling Fast and Accurate Real-Time Analysis of ...

youtube.com
3
1
9
3,097
RawHash authors: @FirtinaC @nika_mgh @lindegger_joel @GaganGdas M. @banu_cavlak @haiyu_mao @_onurmutlu_ Paper: academic.oup.com/bioinformat… Source code & datasets: github.com/CMU-SAFARI/RawHas… Slides (pdf): people.inf.ethz.ch/omutlu/pu… Slides (pptx): people.inf.ethz.ch/omutlu/pu… @ProjectBioPIM
SAFARI Research Group
@SAFARI_ETH_CMU13 Aug 2023
Join us for our talk on RawHash presented by @FirtinaC at #ISMBECCB2023 in July! RawHash is a hash-based mechanism to map raw nanopore signals to a reference genome in real-time. Premiere Tuesday August 15 3PM CEST: youtube.com/watch?v=ti0M6TvR… @_onurmutlu_ @ProjectBioPIM

RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals | ISMB-ECCB 2023

Talk of "RawHash: Enabling Fast and Accurate Real-Time Analysis of ...

youtube.com
1
6
9
1,947
Join us tomorrow for our talks presented at the AACBB workshop #ISCA2023! [2] BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis Premiere Monday July 17 2:45PM CEST: youtube.com/watch?v=EQPq9IB-… @FirtinaC @_onurmutlu_ @ProjectBioPIM
1
1
4
2,184
BLEND Paper: academic.oup.com/nargab/arti… Authors: @FirtinaC @jspark_phd @mealser J S Kim @damlasenolcali @ShahroodiTaha @nika_mgh @GaganGdas @konkanello @calkan_cs @_onurmutlu_ Source code: github.com/CMU-SAFARI/BLEND Slides (pdf): safari.ethz.ch/safari_public… @ProjectBioPIM

BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis

Abstract. Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching se

academic.oup.com
SAFARI Research Group
@SAFARI_ETH_CMU16 Jul 2023
Join us tomorrow for our talks presented at the AACBB workshop #ISCA2023! [2] BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis Premiere Monday July 17 2:45PM CEST: youtube.com/watch?v=EQPq9IB-… @FirtinaC @_onurmutlu_ @ProjectBioPIM
4
7
1,876
Join us Tuesday for more talks presented at the AACBB workshop #ISCA2023! [3] Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs, presenter: @_onurmutlu_ Premiere Tue July 18 2PM CEST: youtube.com/watch?v=uYWNeoq1… @lindegger_joel @ProjectBioPIM
1
1
2
692
Scrooge Paper: arxiv.org/abs/2208.09985 Authors: @lindegger_joel @damlasenolcali @mealser @el1goluj @nika_mgh @_onurmutlu_ Source code: github.com/CMU-SAFARI/Scroog… Slides (pdf): safari.ethz.ch/safari_public… Slides (pptx): safari.ethz.ch/safari_public… @ProjectBioPIM
SAFARI Research Group
@SAFARI_ETH_CMU16 Jul 2023
Join us Tuesday for more talks presented at the AACBB workshop #ISCA2023! [3] Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs, presenter: @_onurmutlu_ Premiere Tue July 18 2PM CEST: youtube.com/watch?v=uYWNeoq1… @lindegger_joel @ProjectBioPIM
1
2
417
TargetCall Paper: arxiv.org/pdf/2212.04953.pdf Authors: @banu_cavlak @GaganGdas @mealser @FirtinaC @lindegger_joel @MohammadSadr89 @nika_mgh @calkan_cs @_onurmutlu_ Slides (pdf): safari.ethz.ch/safari_public… Source code & datasets: github.com/CMU-SAFARI/Target… @ProjectBioPIM
SAFARI Research Group
@SAFARI_ETH_CMU16 Jul 2023
Join us Tuesday for more talks presented at the AACBB workshop #ISCA2023! [4] TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering, presenter: @banu_cavlak Premiere Tue July 18 2:45PM CEST: youtu.be/uujjclvOhIY @_onurmutlu_
2
4
814
Join us Tuesday for more talks presented at the AACBB workshop #ISCA2023! [5] A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, presenter: @el1goluj Premiere Tue July 18 3:30PM CEST: youtube.com/watch?v=fYWjB_Di… @ProjectBioPIM @_onurmutlu_
4
1
10
1,628
Load more