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genome_seq_mobile [2020/10/03 11:19] – external edit 127.0.0.1genome_seq_mobile [2021/03/09 13:21] (current) alserm
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 **The course is conducted in English.** **The course is conducted in English.**
  
-[[http://www.vvz.ethz.ch/lerneinheitPre.do?semkez=2020W&lerneinheitId=151822&lang=en|Course description page]] +[[http://www.vvz.ethz.ch/Vorlesungsverzeichnis/lerneinheit.view?lerneinheitId=152991&semkez=2021S&ansicht=KATALOGDATEN&lang=en|Course description page]] \\ 
 +[[https://moodle-app2.let.ethz.ch/course/view.php?id=14549|Moodle]] \\ 
  
 **Mentors**  **Mentors** 
 ^ ^ Name ^ E-mail ^ Office ^ ^ ^ Name ^ E-mail ^ Office ^
-| **Lead Supervisor** | [[https://inf.ethz.ch/utils/search.MjUxNjUx.html?pagetype=people&search=mohammed+alser&language=en&lang_filter=false|Mohammed Alser]]| <mohammed.alser@inf.ethz.ch> | CAB F 72 +| **Lead Supervisor** | [[https://mealser.github.io/|Mohammed Alser]]| <alserm@ethz.ch>ETZ 
-| **Supervisor** | [[https://inf.ethz.ch/utils/search.MjI4Njcy.html?pagetype=people&search=jeremie+kim&language=en&lang_filter=false|Jeremie Kim]]| <jeremie.kim@inf.ethz.ch>CAB E 78 +| **Supervisor** | [[https://inf.ethz.ch/utils/search.MjI4Njcy.html?pagetype=people&search=jeremie+kim&language=en&lang_filter=false|Jeremie Kim]]| <jeremie.kim@safari.ethz.ch>ETZ 
-| **Supervisor** | [[https://inf.ethz.ch/utils/search.MjQ2MzEx.html?pagetype=people&search=can+firtina&language=en&lang_filter=false|Can Firtina]]| <can.firtina@inf.ethz.ch>CAB F 74.2 +| **Supervisor** | [[https://inf.ethz.ch/utils/search.MjQ2MzEx.html?pagetype=people&search=can+firtina&language=en&lang_filter=false|Can Firtina]]| <can.firtina@safari.ethz.ch>ETZ 
-| **Supervisor** | [[https://inf.ethz.ch/utils/search.MjQxMjgy.html?pagetype=people&search=juan+gomez+luna&language=en&lang_filter=false|Juan Gómez Luna]]| <juan.gomez@inf.ethz.ch>CAB D 77 |+| **Supervisor** | [[https://inf.ethz.ch/utils/search.MjQxMjgy.html?pagetype=people&search=juan+gomez+luna&language=en&lang_filter=false|Juan Gómez Luna]]| <juan.gomez@safari.ethz.ch>ETZ | 
 +| **Supervisor** | [[https://damlasenolcali.github.io|Damla Senol Cali]] | <dsenol@andrew.cmu.edu> |  |
  
-==== 2020 Meetings/Schedule ====+==== 2021 Meetings/Schedule ====
  
 ^ Week ^ Date ^ Meeting ^ Learning Materials ^ Assignments ^ ^ Week ^ Date ^ Meeting ^ Learning Materials ^ Assignments ^
-| W1  |  29.09 \\ Tue.  |<hi #fff200> M1: P&S Mobile Genomics Course Presentation</hi> \\ {{pscourse-mobilegenomics.pdf|(PDF)}}  {{pscourse-mobilegenomics.pptx| (PPT)}} \\ {{youtube>link:rbgnJl2nnUQ| Video}} |[[genome_seq_mobile#learning_materials| Required Materials]]  \\ [[genome_seq_mobile#learning_materials| Recommended Materials]]| +| W1  |  9.03 \\ Tue.  |<hi #fff200> M1: P&S Mobile Genomics Course Presentation</hi> \\ {{pns-mobilegenomics-spring2021-9march2021.pdf|(PDF)}}  {{pns-mobilegenomics-spring2021-9march2021.pptx| (PPT)}} \\ {{youtube>link:rbgnJl2nnUQ| Video}} |[[genome_seq_mobile#learning_materials| Required Materials]]  \\ [[genome_seq_mobile#learning_materials| Recommended Materials]]| 
  
 ==== Learning Materials ==== ==== Learning Materials ====
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   * [[https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_micro20.pdf|GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis]], Proceedings of the [[http://www.microarch.org/micro53/| 53rd International Symposium on Microarchitecture (MICRO)]], Virtual, October 2020.   * [[https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_micro20.pdf|GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis]], Proceedings of the [[http://www.microarch.org/micro53/| 53rd International Symposium on Microarchitecture (MICRO)]], Virtual, October 2020.
     * [[https://www.youtube.com/watch?v=oKYqVo1UTdE|ARM Research Summit Talk Video (21 minutes)]]     * [[https://www.youtube.com/watch?v=oKYqVo1UTdE|ARM Research Summit Talk Video (21 minutes)]]
-    * [[https://www.youtube.com/watch?v=omqCTHlnMA0|ARM Research Summit Short Talk Video (15 minutes)]] +    * [[https://www.youtube.com/watch?v=srQVqPJFqjo|MICRO'20 Full Talk Video (18 minutes)]] 
-    * [[https://www.youtube.com/watch?v=y1S6gtGz2bo|ARM Research Summit Short Talk Video and Q&(31 minutes)]]+    * [[https://www.youtube.com/watch?v=nJs3RRnvk_k|MICRO'20 Lightning Talk Video (1.5 minutes)]]
     * ARM Research Summit Talk Slides [[https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_ARMSummit20-long-talk.pptx|PPTX]] [[https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_ARMSummit20-long-talk.pdf|PDF]]     * ARM Research Summit Talk Slides [[https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_ARMSummit20-long-talk.pptx|PPTX]] [[https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_ARMSummit20-long-talk.pdf|PDF]]
-    * ARM Research Summit Short Talk Slides [[https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_ARMSummit20-short-talk.pptx|PPTX]] [[https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_ARMSummit20-short-talk.pdf|PDF]]+    * MICRO'20 Full Talk Slides [[https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_micro20-talk.pptx|PPTX]] [[https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_micro20-talk.pdf|PDF]] 
 +    * MICRO'20 Lightning Talk Slides [[https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_micro20-lightning-talk.pptx|PPTX]] [[https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_micro20-lightning-talk.pdf|PDF]]
    
-  * [[https://arxiv.org/pdf/1711.01177.pdf|GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies]], [[http://www.biomedcentral.com/bmcgenomics/ |BMC Genomics]], 2018.  + 
-    * Proceedings of the [[http://apbc2018.bio.keio.ac.jp/|16th Asia Pacific Bioinformatics Conference]] (APBC), Yokohama, Japan, January 2018. +  * [[ https://people.inf.ethz.ch/omutlu/pub/SneakySnake_UniversalGenomePrealignmentFilter_bioinformatics20.pdf|SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs]], [[http://bioinformatics.oxfordjournals.org/|Bioinformatics]], 2020. 
-    * Slides [[https://people.inf.ethz.ch/omutlu/pub/GRIM-filter-DNA-pre-alignment-in-memory_apbc18-talk.pptx|PPTX]] [[https://people.inf.ethz.ch/omutlu/pub/GRIM-filter-DNA-pre-alignment-in-memory_apbc18-talk.pdf|PDF]]+    * [[https://github.com/CMU-SAFARI/SneakySnake|Source Code]] 
 +    * [[https://doi.org/10.1093/bioinformatics/btaa1015|Online link at Bioinformatics Journal]] 
 +    * [[https://www.youtube.com/watch?v=ygmQpdDTL7o&t=8625s | Talk Video]] 
 +    * Poster presentation at [[https://www.health2030genome.ch/swiss-genomics-forum/|the Swiss Genomics Forum 2019]], Geneva, 27 Sept 2019. 
 +    * [Poster ([[https://safari.ethz.ch/safari_public_wp/wp-content/uploads/2019/08/SneakySnake-HITSeq2019-poster.pptx|pptx]]) ([[https://safari.ethz.ch/safari_public_wp/wp-content/uploads/2019/08/SneakySnake-HITSeq2019-poster.pdf|pdf]])] 
 +    * Poster presentation at [[https://www.iscb.org/cms_addon/conferences/ismbeccb2019/posters.php?track=HitSeq%20COSI&session=A|ISMB/ECCB 2019]], Basel, Switzerland July 21 - July 25. 
 +    * [Poster ([[https://safari.ethz.ch/safari_public_wp/wp-content/uploads/2019/08/SneakySnake-HITSeq2019-poster.pptx|pptx]]) ([[https://safari.ethz.ch/safari_public_wp/wp-content/uploads/2019/08/SneakySnake-HITSeq2019-poster.pdf|pdf]])] 
 + 
 + 
 +  * [[https://arxiv.org/pdf/1711.01177.pdf |GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies]], [[http://www.biomedcentral.com/bmcgenomics/|BMC Genomics]], 2018.  
 +    * [Proceedings of [[http://apbc2018.bio.keio.ac.jp/|the 16th Asia Pacific Bioinformatics Conference (APBC)]], Yokohama, Japan, January 2018. 
 +    * [Slides ([[https://people.inf.ethz.ch/omutlu/pub/GRIM-filter-DNA-pre-alignment-in-memory_apbc18-talk.pptx|pptx]]) ([[https://people.inf.ethz.ch/omutlu/pub/GRIM-filter-DNA-pre-alignment-in-memory_apbc18-talk.pdf|pdf]])]
     * [[https://github.com/CMU-SAFARI/GRIM|Source Code]]     * [[https://github.com/CMU-SAFARI/GRIM|Source Code]]
-    * [[https://arxiv.org/pdf/1711.01177.pdf|arxiv.org Version (PDF)]]+    * [[https://arxiv.org/pdf/1711.01177.pdf|arxiv.org Version (pdf)]]
     * [[https://www.youtube.com/watch?v=j5-I84iNVd8|Talk Video at AACBB 2019]]     * [[https://www.youtube.com/watch?v=j5-I84iNVd8|Talk Video at AACBB 2019]]
-  +
-  * [[https://people.inf.ethz.ch/omutlu/pub/gatekeeper_FPGA-genome-prealignment-accelerator_bionformatics17.pdf|GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping]], [[http://bioinformatics.oxfordjournals.org/|Bioinformatics]], [published online, May 31], 2017. +
-    * [[https://github.com/BilkentCompGen/GateKeeper|Source Code]] +
-    * [[https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx342|Online link at Bioinformatics Journal]] +
-    * [[https://www.youtube.com/watch?v=DTfNzcYIgOI&feature=youtu.be&list=PLq0KGCI4fRSO46us6WvuF7zd42XPcRCBf&t=2643|Video]]+
  
 === More Learning Materials === === More Learning Materials ===
genome_seq_mobile.1601723959.txt.gz · Last modified: 2021/02/05 08:39 (external edit)