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genome_seq_mobile [2020/10/05 11:59]
127.0.0.1 external edit
genome_seq_mobile [2021/03/09 14:21] (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=13822&​lang=en|Moodle]] \\ +[[https://​moodle-app2.let.ethz.ch/​course/​view.php?​id=14549|Moodle]] \\ 
-[[https://​piazza.com/​class/​kfwcq4ni2v749k|Piazza]] ​+
  
 **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&​A ​(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.1601891944.txt.gz · Last modified: 2021/02/05 09:39 (external edit)