{"payload":{"pageCount":1,"repositories":[{"type":"Public","name":"AirLift","owner":"CMU-SAFARI","isFork":false,"description":"AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shared between the two reference genomes and enables remapping across all parts of the references. Described by Kim et al. (preliminary version at <a href=\"http://arxiv.org/abs/1912.08735\" rel=\"nofollow\">http://arxiv.org/abs/1912.08735</a>)","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":1,"issueCount":5,"starsCount":26,"forksCount":4,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-23T09:22:36.167Z"}},{"type":"Public","name":"RawHash","owner":"CMU-SAFARI","isFork":false,"description":"RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at <a href=\"https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440\" rel=\"nofollow\">https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440</a>)","topicNames":["bioinformatics","nanopore","seeding","segmentation","event-detection","genome-analysis","hash-tables","contamination","read-mapping","relative-abundances"],"topicsNotShown":8,"allTopics":["bioinformatics","nanopore","seeding","segmentation","event-detection","genome-analysis","hash-tables","contamination","read-mapping","relative-abundances","nanopore-sequencing","nanopore-analysis-pipeline","nanopore-reads","nanopore-data","nanopore-minion","raw-signal","rawhash","raw-nanopore-signal-analysis"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":1,"issueCount":2,"starsCount":39,"forksCount":4,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-24T17:09:45.691Z"}},{"type":"Public","name":"prim-benchmarks","owner":"CMU-SAFARI","isFork":false,"description":"PrIM (Processing-In-Memory benchmarks) is the first benchmark suite for a real-world processing-in-memory (PIM) architecture. PrIM is developed to evaluate, analyze, and characterize the first publicly-available real-world PIM architecture, the UPMEM PIM architecture. Described by Gómez-Luna et al. (<a href=\"https://arxiv.org/abs/2105.03814\" rel=\"nofollow\">https://arxiv.org/abs/2105.03814</a>).","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":2,"issueCount":3,"starsCount":124,"forksCount":45,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-29T13:51:46.737Z"}},{"type":"Public","name":"SimplePIM","owner":"CMU-SAFARI","isFork":false,"description":"SimplePIM is the first high-level programming framework for real-world processing-in-memory (PIM) architectures. Described in the PACT 2023 paper by Chen et al. (<a href=\"https://arxiv.org/pdf/2310.01893.pdf\" rel=\"nofollow\">https://arxiv.org/pdf/2310.01893.pdf</a>).","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":16,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-23T09:29:37.628Z"}},{"type":"Public","name":"Victima","owner":"CMU-SAFARI","isFork":false,"description":"Victima is a new software-transparent technique that greatly extends the address translation reach of modern processors by leveraging the underutilized resources of the cache hierarchy, as desribed in the MICRO 2023 paper by Kanellopoulos et al. (<a href=\"https://arxiv.org/pdf/2310.04158/\" rel=\"nofollow\">https://arxiv.org/pdf/2310.04158/</a>)","topicNames":["memory","virtual-memory"],"topicsNotShown":0,"allTopics":["memory","virtual-memory"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":22,"forksCount":10,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-13T22:39:21.488Z"}},{"type":"Public","name":"GateSeeder","owner":"CMU-SAFARI","isFork":false,"description":"GateSeeder is the first near-memory CPU-FPGA co-design for alleviating both the compute-bound and memory-bound bottlenecks in short and long-read mapping. GateSeeder outperforms Minimap2 by up to 40.3×, 4.8×, and 2.3× when mapping real ONT, HiFi, and Illumina reads, respectively.","topicNames":["bioinformatics","fpga","genomics","indexing","seeding","hbm","sequence-alignment","read-mapping","long-reads","minimap2"],"topicsNotShown":3,"allTopics":["bioinformatics","fpga","genomics","indexing","seeding","hbm","sequence-alignment","read-mapping","long-reads","minimap2","minimizers","short-reads","genome-on-diet"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":7,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-03T20:29:15.521Z"}},{"type":"Public","name":"Scrooge","owner":"CMU-SAFARI","isFork":false,"description":"Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improvements on top of GenASM, and high-performance CPU and GPU implementations. Described by Lindegger et al. at <a href=\"https://doi.org/10.48550/arXiv.2208.09985\" rel=\"nofollow\">https://doi.org/10.48550/arXiv.2208.09985</a>","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":2,"starsCount":36,"forksCount":4,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-23T03:23:26.345Z"}},{"type":"Public","name":"BLEND","owner":"CMU-SAFARI","isFork":false,"description":"BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB <a href=\"https://doi.org/10.1093/nargab/lqad004\" rel=\"nofollow\">https://doi.org/10.1093/nargab/lqad004</a>)","topicNames":["genome-analysis","genome-assembly","blend","read-mapping","de-novo-assembly","minimizers","strobemers","seed-matching","fuzzy-seeds","read-overlapping"],"topicsNotShown":2,"allTopics":["genome-analysis","genome-assembly","blend","read-mapping","de-novo-assembly","minimizers","strobemers","seed-matching","fuzzy-seeds","read-overlapping","spaced-seeds","bioinformatics"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":34,"forksCount":3,"license":"Other","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-10T14:10:43.390Z"}},{"type":"Public","name":"alignment-in-memory","owner":"CMU-SAFARI","isFork":false,"description":"AIM (Alignment-in-Memory), A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, <a href=\"https://doi.org/10.1093/bioinformatics/btad155\" rel=\"nofollow\">https://doi.org/10.1093/bioinformatics/btad155</a>","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-01T08:33:47.888Z"}},{"type":"Public","name":"pim-ml","owner":"CMU-SAFARI","isFork":false,"description":"PIM-ML is a benchmark for training machine learning algorithms on the UPMEM architecture, which is the first publicly-available real-world processing-in-memory (PIM) architecture. Described in the ISPASS 2023 paper by Gomez-Luna et al. (<a href=\"https://arxiv.org/pdf/2207.07886.pdf\" rel=\"nofollow\">https://arxiv.org/pdf/2207.07886.pdf</a>).","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":16,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-21T16:25:42.148Z"}},{"type":"Public","name":"transpimlib","owner":"CMU-SAFARI","isFork":false,"description":"TransPimLib is a library for transcendental (and other hard-to-calculate) functions in general-purpose PIM systems, TransPimLib provides CORDIC-based and LUT-based methods for trigonometric functions, hyperbolic functions, exponentiation, logarithm, square root, etc. Described in ISPASS'23 paper by Item et al. (<a href=\"https://arxiv.org/pdf/2304.01951.pdf\" rel=\"nofollow\">https://arxiv.org/pdf/2304.01951.pdf</a>)","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":8,"forksCount":2,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-21T15:21:35.945Z"}},{"type":"Public","name":"GenASM","owner":"CMU-SAFARI","isFork":false,"description":"Source code for the software implementations of the GenASM algorithms proposed in our MICRO 2020 paper: Senol Cali et. al., \"GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis\" at <a href=\"https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_micro20.pdf\" rel=\"nofollow\">https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analys…</a>","topicNames":["approximate-string-matching","read-mapping","hw-sw-co-design","read-alignment","pre-alignment-filtering","bitap-algorithm","genome-sequence-analysis"],"topicsNotShown":0,"allTopics":["approximate-string-matching","read-mapping","hw-sw-co-design","read-alignment","pre-alignment-filtering","bitap-algorithm","genome-sequence-analysis"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":30,"forksCount":7,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-19T20:03:50.410Z"}},{"type":"Public","name":"SeGraM","owner":"CMU-SAFARI","isFork":false,"description":"Source code for the software implementation of SeGraM proposed in our ISCA 2022 paper: Senol Cali et. al., \"SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping\" at <a href=\"https://people.inf.ethz.ch/omutlu/pub/SeGraM_genomic-sequence-mapping-universal-accelerator_isca22.pdf\" rel=\"nofollow\">https://people.inf.ethz.ch/omutlu/pub/SeGraM_genomic-sequence-mapping-universal-accelerator_isca22.pdf</a>","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":12,"forksCount":2,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-03T16:07:22.864Z"}},{"type":"Public","name":"SparseP","owner":"CMU-SAFARI","isFork":false,"description":"SparseP is the first open-source Sparse Matrix Vector Multiplication (SpMV) software package for real-world Processing-In-Memory (PIM) architectures. SparseP is developed to evaluate and characterize the first publicly-available real-world PIM architecture, the UPMEM PIM architecture. Described by C. Giannoula et al. [<a href=\"https://arxiv.org/abs/2201.05072\" rel=\"nofollow\">https://arxiv.org/abs/2201.…</a>","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":69,"forksCount":10,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-06-29T12:44:38.320Z"}},{"type":"Public","name":"GenStore","owner":"CMU-SAFARI","isFork":false,"description":"GenStore is the first in-storage processing system designed for genome sequence analysis that greatly reduces both data movement and computational overheads of genome sequence analysis by exploiting low-cost and accurate in-storage filters. Described in the ASPLOS 2022 paper by Mansouri Ghiasi et al. at <a href=\"https://people.inf.ethz.ch/omutlu/pub/GenStore_asplos22-arxiv.pdf\" rel=\"nofollow\">https://people.inf.ethz.ch/omutlu/pub/GenS…</a>","topicNames":["ftl","ssd","sequence-alignment","read-mapping","long-reads","hardware-accelerator","near-data-processing","pre-alignment-filtering","in-storage-processing","exact-matching"],"topicsNotShown":0,"allTopics":["ftl","ssd","sequence-alignment","read-mapping","long-reads","hardware-accelerator","near-data-processing","pre-alignment-filtering","in-storage-processing","exact-matching"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":12,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-04-06T12:36:08.565Z"}},{"type":"Public","name":"SMASH","owner":"CMU-SAFARI","isFork":false,"description":"SMASH is a hardware-software cooperative mechanism that enables highly-efficient indexing and storage of sparse matrices. The key idea of SMASH is to compress sparse matrices with a hierarchical bitmap compression format that can be accelerated from hardware. Described by Kanellopoulos et al. (MICRO '19) <a href=\"https://people.inf.ethz.ch/omutlu/pub/SMASH-sparse-matrix-software-hardware-acceleration_micro19.pdf\" rel=\"nofollow\">https://people.inf.ethz.ch/omutlu/pub/SMA…</a>","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":14,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-05-17T14:44:52.085Z"}},{"type":"Public","name":"Shifted-Hamming-Distance","owner":"CMU-SAFARI","isFork":false,"description":"Source code for the Shifted Hamming Distance (SHD) filtering mechanism for sequence alignment. Described in the Bioinformatics journal paper (2015) by Xin et al. at <a href=\"http://users.ece.cmu.edu/~omutlu/pub/shifted-hamming-distance_bioinformatics15_proofs.pdf\" rel=\"nofollow\">http://users.ece.cmu.edu/~omutlu/pub/shifted-hamming-distance_bioinformatics15_proofs.pdf</a>","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":1,"issueCount":1,"starsCount":28,"forksCount":7,"license":"GNU General Public License v2.0","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-03-29T06:57:58.019Z"}},{"type":"Public","name":"GRIM","owner":"CMU-SAFARI","isFork":false,"description":"Source code of the processing-in-memory simulator used in the GRIM-Filter paper published at BMC Genomics in 2018: \"GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping using Processing-in-Memory Technologies\" (preliminary version at <a href=\"https://arxiv.org/pdf/1711.01177.pdf\" rel=\"nofollow\">https://arxiv.org/pdf/1711.01177.pdf</a>)","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":1,"starsCount":11,"forksCount":5,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-02-05T10:43:30.318Z"}},{"type":"Public","name":"IMPICA","owner":"CMU-SAFARI","isFork":false,"description":"This is a processing-in-memory simulator which models 3D-stacked memory within gem5. Also includes the workloads used for IMPICA (In-Memory PoInter Chasing Accelerator), an ICCD 2016 paper by Hsieh et al. at <a href=\"https://users.ece.cmu.edu/~omutlu/pub/in-memory-pointer-chasing-accelerator_iccd16.pdf\" rel=\"nofollow\">https://users.ece.cmu.edu/~omutlu/pub/in-memory-pointer-chasing-accelerator_iccd16.pdf</a>","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":1,"starsCount":43,"forksCount":24,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-06-02T17:15:09.851Z"}},{"type":"Public","name":"Cache-Memory-Hog","owner":"CMU-SAFARI","isFork":false,"description":"Cache and main memory hog programs. These are programs with specific access patterns to evict the already existing cache blocks of various applications. These programs were designed to demonstrate that application performance is nearly linearly correlated with cache access rate (as shown in Section 3.1 of Subramanian et al. \"The Application Slow…","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":19,"forksCount":8,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-11-02T00:25:36.355Z"}},{"type":"Public","name":"rowhammer","owner":"CMU-SAFARI","isFork":false,"description":"Source code for testing the Row Hammer error mechanism in DRAM devices. Described in the ISCA 2014 paper by Kim et al. at <a href=\"http://users.ece.cmu.edu/~omutlu/pub/dram-row-hammer_isca14.pdf\" rel=\"nofollow\">http://users.ece.cmu.edu/~omutlu/pub/dram-row-hammer_isca14.pdf</a>.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":1,"issueCount":2,"starsCount":210,"forksCount":43,"license":"GNU General Public License v2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2015-09-02T07:44:28.805Z"}},{"type":"Public","name":"sirFAST","owner":"CMU-SAFARI","isFork":false,"description":"sirFAST is designed to map short reads generated with the Compelete Genomics (CG) platform to reference genome assemblies in a fast and memory-efficient manner. Described in the Methods 2014 paper by Lee et al., <a href=\"http://users.ece.cmu.edu/~omutlu/pub/complete-genomics-mapper_methods14_proofs.pdf\" rel=\"nofollow\">http://users.ece.cmu.edu/~omutlu/pub/complete-genomics-mapper_methods14_proofs.pdf</a>.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2015-03-02T19:06:51.241Z"}},{"type":"Public","name":"FastHASH","owner":"CMU-SAFARI","isFork":false,"description":"Source code for the mrFAST DNA read mapper with FastHASH filtering mechanism for sequence alignment. Described in the BMC Genomics journal paper (2013) by Xin et al. <a href=\"http://www.biomedcentral.com/1471-2164/14/S1/S13/\" rel=\"nofollow\">http://www.biomedcentral.com/1471-2164/14/S1/S13/</a>","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2015-03-01T23:16:56.612Z"}},{"type":"Public","name":"BDICompression","owner":"CMU-SAFARI","isFork":false,"description":"Source code for the Base-Delta-Immediate Compression Algorithm (described in the PACT 2012 paper by Pekhimenko et al. at <a href=\"http://users.ece.cmu.edu/~omutlu/pub/bdi-compression_pact12.pdf\" rel=\"nofollow\">http://users.ece.cmu.edu/~omutlu/pub/bdi-compression_pact12.pdf</a>)","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":1,"starsCount":24,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2015-03-01T19:37:12.428Z"}}],"repositoryCount":24,"userInfo":null,"searchable":true,"definitions":[],"typeFilters":[{"id":"all","text":"All"},{"id":"public","text":"Public"},{"id":"source","text":"Sources"},{"id":"fork","text":"Forks"},{"id":"archived","text":"Archived"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"Repositories"}