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<strong>MediaWiki has been installed.</strong>
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<strong>Welcome to the U-M Big Data Summer Institute 2019 Wiki!</strong>
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== Reading Material ==
  
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Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.
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=== Machine Learning Group ===
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====Research Lecture Slides ====
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*[https://drive.google.com/file/d/1HF9cD0cnBEShUVn2Lq9vQYpRxT2ZZ8DJ/view?usp=sharing Introduction]
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*[https://drive.google.com/file/d/1LdxCkiFDmWGHcBYsHUw_W54cM6RETp8T/view?usp=sharing Explore MIMIC]
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*[https://drive.google.com/file/d/15yChJcEgzHjrn_bhYF7wqaaLh5NMCkzA/view?usp=sharing Getting x and y]
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*[https://drive.google.com/file/d/17BCOb3-t5ZJ3eE0Yy9rjlOGn0cn36PUp/view?usp=sharing Some tips]
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*[https://drive.google.com/file/d/1T8PEwWfi7PA8uMnuA9_kF6BSz69A6VKM/view?usp=sharing Sample Pipeline]
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*[https://drive.google.com/file/d/1OBckV_yjuYrl36tOF1lAKiOcWJA8-q34/view?usp=sharing Training Pipleline]
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*[https://drive.google.com/file/d/1i1nel98HYV1mSpro5SaDoMdOqMH5i5Gr/view?usp=sharing CNN]
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*[https://drive.google.com/file/d/1y14n4kl9u4LBQ9M5AnP6knFZpfwgOUAW/view?usp=sharing LSTM]
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*[https://drive.google.com/file/d/1XF-P43lIhYXU0HnS0pyGrIvPzF4HiB0B/view?usp=sharing Structuring]
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*[https://drive.google.com/file/d/12HgspYuZAVVSU49c8AEs8FPqZyoF3c1E/view?usp=sharing Dataset and DataLoader]
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*[https://drive.google.com/file/d/1vnUj-Stf5arWNyLguCPuCm1OYRwZGGr1/view?usp=sharing pytorch models]
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*[https://drive.google.com/file/d/1-r9sC3GMH_qVL3SCsPBgkDh9upS3hfEM/view?usp=sharing Model Development]
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*[https://drive.google.com/file/d/1n2md6F3XQ85WOgMV_20G_DgFqmmBgU3k/view?usp=sharing Population]
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*[https://drive.google.com/file/d/1HEAWEbwP7R1o-UZ1NcrMp2C0Ub3ivAzK/view?usp=sharing Benchmark Features]
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*[https://drive.google.com/file/d/1QpFDYzmyQBvvT9tk4Nr7EYIbh8mMmMOr/view?usp=sharing Inclusion Exclusion]
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====Lecture Notes====
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*[https://drive.google.com/file/d/1ogusN8iQqfEfmarjKUqKtFZaSX-LZw3k/view?usp=sharing Recurrent Neural Networks]
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*[https://drive.google.com/file/d/11sJeWngMmTpX_PWcobdxX180_xEzOfV-/view?usp=sharing Convolutional Neural Networks]
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*[https://drive.google.com/file/d/17m8Y5DcmJCeHgB1spA_b27WYJvzyhLi4/view?usp=sharing Deep Learning]
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*[https://drive.google.com/open?id=19qcnGMIdoYZ9mvPwsU2kAvZcqArmd6oO BDSI Lecture]
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*[https://drive.google.com/open?id=1gZtk4LjLDcdUSBEsNZ1qTJ2UHRDL--JO Flux Guide]
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*[https://drive.google.com/open?id=1XDX7hkicATX0y7cVDb9PDCsPZo1gLdPi Python Guide]
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*[https://drive.google.com/open?id=1kueXa-kFk6DiKVqItTEL-sFT_xmHg9Fb Python Tutorial]
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====Readings====
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*[https://drive.google.com/file/d/1dvEdmapBY-jgdLOCZLdPwDgbybTWEni9/view?usp=sharing ARF Epidemiology]
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*[https://drive.google.com/file/d/1EzJxIVlXgkGGge20eHGC5HGtl-E7CPO_/view?usp=sharing CNN for Sentence Clarification]
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*[https://drive.google.com/file/d/1rdUGIYh7WkI4qbaJEQjaIXxaXtYYDvQN/view?usp=sharing Learning from Heterogenous Temporal Data]
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*[https://drive.google.com/file/d/12aIplGTH982iBvR7Kao6UBk2lY9Q3311/view?usp=sharing MIMC 3]
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*[https://drive.google.com/file/d/1jQVuZfnbrxzu79ujr_uKYQGvJVmkoJGy/view?usp=sharing MIMIC Benchmarks and Multitask RNN]
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*[https://drive.google.com/file/d/1uh5U_-3NIoUUM7aItA39iTGNkgwI01M7/view?usp=sharing RNNs for Multivariate Time Series]
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*[https://drive.google.com/file/d/1r1y4gez3o46mbqkaWP3umHJv6o6uvzf-/view?usp=sharing TREWScore for Septic Shock]
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*[https://drive.google.com/file/d/1EZnegIgxpmKNLorKwtkh8Veh5kIJu-lV/view?usp=sharing TREWScore Supplement]
  
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== Getting started ==
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=== Genomics Group ===
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* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
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* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
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===== Lectures =====
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* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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*[https://drive.google.com/open?id=19jBLxGLRKtJD-5Id-H3d0AK0Vu_dfGko BDSI Genomics Intro]
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* [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
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*[https://drive.google.com/file/d/1nZkKKbwgRWkfEeyEGzsueJ8Dh_Zjahpv/view?usp=sharing PopGen Intro]
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* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Combating_spam Learn how to combat spam on your wiki]
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===== Intro Exercises =====
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*[https://drive.google.com/open?id=1Wl1JensClieYfVNIcTWzJVxN_N7Tugte Single Cell Exercise]
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*[https://drive.google.com/open?id=18yGPNL0ZhxJR6Rya4K1IDnH1E8Yz6sjS Single Cell R Code]
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*[https://drive.google.com/file/d/1hFlCoxcw758XGfm_LrY6T9kuH6c0R6pJ/view?usp=sharing Intro Integrative]
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===== Papers =====
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====== Population Genetics ======
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*[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]
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*[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]
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*[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]
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*[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]
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======Single Cell RNA ======
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*[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]
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*[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]
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======Transcriptomics ======
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*[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]
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*[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]
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==== Online videos to better understand genetics and genomics ====
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===== ''Genetics'' =====
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* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
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* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
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* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
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* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]
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===== ''Useful 3D Animations'' =====
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* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
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* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
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* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
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* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
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* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
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* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]
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===== ''Gene Regulation and Epigenetics'' =====
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* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
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* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
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* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
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* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]
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===== ''Sequencing Technologies'' =====
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* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
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* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]
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=== Data Mining on Large Complex Datasets ===
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*
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====Papers====
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*
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== 2019 Presentations ==
 +
 
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=== <u>Week 1</u> ===
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==== Day 1: June 17 ====
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*
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==== Day 2: June 18 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 3: June 19 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 4: June 20 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 4: June 21 ====
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*
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=====Recorded Lectures=====
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*
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====Day 5: June 22 ====
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*
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=====Recorded Lectures=====
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*
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=== <u>Week 2</u> ===
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==== Day 6: June 25 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 7: June 26 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 8: June 27 ====
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*
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==== Day 9: June 28 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 10: June 29 ====
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*
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=====Recorded Lectures=====
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*
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=== <u>Week 3</u> ===
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==== Day 11: July 2 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 12: July 3 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 13: July 4 (NO CLASS) ====
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==== Day 14: July 5 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 15: July 6 ====
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*
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=====Recorded Lectures=====
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*
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=== <u>Week 4</u> ===
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==== Day 16: July 9 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 17: July 10 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 18: July 11 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 19: July 12 ====
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*
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==== Day 20: July 13 ====
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*
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=====Recorded Lectures=====
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*
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=== <u>Week 5</u> ===
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==== Day 21: July 16 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 22: July 17 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 23: July 18 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 24: July 19 ====
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*
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=====Recorded Lectures=====
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*
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==== Day 25: July 20 ====
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*
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=====Recorded Lectures=====
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*
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== Day 29: Symposium ==
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'''2019 Professor Lectures Presentations'''
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*
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'''2019 Student Poster Presentations'''
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*
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'''2018 Professor Lectures Presentations'''
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*[https://drive.google.com/file/d/19QJ9SmqsCP66urThKu5hlSxZdobyAd7z/view?usp=sharing 2018 Symposium Flyer]
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*[https://drive.google.com/file/d/1ukz_fd4kLGR2JaqjbAdFz6HuRmkD9BdM/view?usp=sharing Symposium Welcome Remarks]
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*[https://drive.google.com/file/d/1yUAUsxe_aElBdfZDItsdkBFKgJs9Ig8N/view?usp=sharing Calibration Concordance] - Chen
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*[https://drive.google.com/file/d/1U8Rt4mDPAmZuqv9RXhsPkMnL1VmoI3G0/view?usp=sharing Data Science and Predictive Health Analytics] - Dinov
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*[https://drive.google.com/file/d/118HtI_euaMBmCl7-bibqDYJPRlablmOY/view?usp=sharing Models of Human Choice] - Feinberg
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*[https://drive.google.com/file/d/1O3q32tp2J87Tmigz75ozVAonX-YYKwam/view?usp=sharing Linking Tumor with Personalized Medicine] - Rao
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*[https://drive.google.com/file/d/1eFBzOkXbNyaP4s0o7kemHVSbhgxfqUmz/view?usp=sharing Humanist Approach to Data Science] - Schutt
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*[https://drive.google.com/file/d/1kuDFENM8UwzxL_ve70jwca717RTDjzXA/view?usp=sharing Big Data in the Social Sciences] - Titunik
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*[https://drive.google.com/file/d/19bnSFP9xPQg7i6lQ1bdO439Gj7iyf1R9/view?usp=sharing Detecting Epistasis in Large Scale Genetic Mapping] - Zhou
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'''2018 Student Poster Presentations'''
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*[https://drive.google.com/file/d/1TGNqkCAV9eBJ_-zHbiU-yo3N4Aowm_HB/view?usp=sharing Imaging Group Presentation]
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*[https://drive.google.com/file/d/1S01_WV6wfJ6BE2Op-01byw0WFUZadPjR/view?usp=sharing Machine Learning Group Presentation]
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*[https://drive.google.com/file/d/1LlZgR4TAlyYaS88bQ6qgZncWFuS0lFuC/view?usp=sharing Genetics Group Presentation]
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*[https://drive.google.com/file/d/1HqWZFGjHgIYOoqqlpQxc0qn9y7PTa4hD/view?usp=sharing Data Mining Presentation]
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'''2017 Student Poster Presentations'''
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*[https://drive.google.com/file/d/0B2ht_TCS6xC-WFNPZzd5TndqZ0U/view?usp=sharing Data Mining/ Machine Learning]
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*[https://drive.google.com/file/d/0B2ht_TCS6xC-S2xrUFM0ZEI3dGM/view?usp=sharing Electronic Health Records (EHR)]
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*[https://drive.google.com/file/d/0B2ht_TCS6xC-NEZ1YnQyVW0tREE/view?usp=sharing Genomics]
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*[https://drive.google.com/file/d/0B2ht_TCS6xC-cDVJNUtIcjRjcFE/view?usp=sharing Imaging]
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=====2017 Symposium Reference Files=====
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*[https://drive.google.com/file/d/1zwuVp6_sIRIlKx79-i0uZRp6Gtooi6g8/view?usp=sharing 2017 Symposium Program]
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*[https://drive.google.com/file/d/18FfpzqxwPSunJfHM3pHDxYYggAPlKgWX/view?usp=sharing 2017 Symposium Flyer]
 +
======2017 Symposium Projects======
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*[https://drive.google.com/file/d/0B2ht_TCS6xC-Zm5RWHByeWdUd2M/view?usp=sharing A Time-to-Event Analysis of Heart Failure via Electronic Health Records]
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*[https://drive.google.com/file/d/0B2ht_TCS6xC-UEIwRVNZaVJXRFk/view?usp=sharing Melanoma Detection by Classifying Skin Lesion Images]
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*[https://drive.google.com/file/d/0B2ht_TCS6xC-VEk4RExSSkV3NGM/view?usp=sharing Classifying Skin Lesions Images Using Adaptive Boosting]
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*[https://drive.google.com/file/d/0B2ht_TCS6xC-RDR1UmtsV3hFUVk/view?usp=sharing Machine Learning Classification of Skin Lesion Images]
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*[https://drive.google.com/file/d/0B2ht_TCS6xC-YWs0alJGdTA3UE0/view?usp=sharing Genomics: Genome Storage and Assembly]
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*[https://drive.google.com/file/d/0B2ht_TCS6xC-SU1KWFdPcWZzMEk/view?usp=sharing Predicting the Transcriptome from the Genome]
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*[https://drive.google.com/file/d/0B2ht_TCS6xC-VGhDZlZZeHAyRDQ/view?usp=sharing Classification of Cell Types from Peripheral Mononuclear Blood Cells]
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*[https://drive.google.com/file/d/0B2ht_TCS6xC-bzRTUTlQek9JRGM/view?usp=sharing EHR-Based Study of Long-Term Infectious Diseases]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-VjRsZkJfalVNbVk/view?usp=sharing Visualizing Lab and Phenotype Associations Using PheWAS and Electronic Health Records]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJoemNibTFxZXc/view?usp=sharing Data Mining: Microenvironment Microarray Spot Based Approach for Cell Prediction]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-VDdJQmtOZHR6RE0/view?usp=sharing Estimating Cell Growth with Machine Learning and Data Mining]
 +
 
 +
== Additional Resources ==
 +
* [[DataCamp Resources]]
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* [[https://drive.google.com/file/d/15pPcBQrTBj9ze9VthpTZLmkEa3yRaz8T/view?usp=sharing Daily Schedule]] - Last update July 3, 2018

Revision as of 00:39, 4 June 2019

Welcome to the U-M Big Data Summer Institute 2019 Wiki!

Contents

Reading Material

Machine Learning Group

Research Lecture Slides

Lecture Notes

Readings

Genomics Group

Lectures
Intro Exercises
Papers
Population Genetics
Single Cell RNA
Transcriptomics

Online videos to better understand genetics and genomics

Genetics
Useful 3D Animations
Gene Regulation and Epigenetics
Sequencing Technologies

Data Mining on Large Complex Datasets

Papers

2019 Presentations

Week 1

Day 1: June 17

Day 2: June 18

Recorded Lectures

Day 3: June 19

Recorded Lectures

Day 4: June 20

Recorded Lectures

Day 4: June 21

Recorded Lectures

Day 5: June 22

Recorded Lectures

Week 2

Day 6: June 25

Recorded Lectures

Day 7: June 26

Recorded Lectures

Day 8: June 27

Day 9: June 28

Recorded Lectures

Day 10: June 29

Recorded Lectures

Week 3

Day 11: July 2

Recorded Lectures

Day 12: July 3

Recorded Lectures

Day 13: July 4 (NO CLASS)

Day 14: July 5

Recorded Lectures

Day 15: July 6

Recorded Lectures

Week 4

Day 16: July 9

Recorded Lectures

Day 17: July 10

Recorded Lectures

Day 18: July 11

Recorded Lectures

Day 19: July 12

Day 20: July 13

Recorded Lectures

Week 5

Day 21: July 16

Recorded Lectures

Day 22: July 17

Recorded Lectures

Day 23: July 18

Recorded Lectures

Day 24: July 19

Recorded Lectures

Day 25: July 20

Recorded Lectures

Day 29: Symposium

2019 Professor Lectures Presentations

2019 Student Poster Presentations

2018 Professor Lectures Presentations

2018 Student Poster Presentations

2017 Student Poster Presentations

2017 Symposium Reference Files
2017 Symposium Projects

Additional Resources

Retrieved from "http://bigdatasummerinst.sph.umich.edu/wiki2019/index.php?title=Main_Page&oldid=2"