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WikiSysop: Created page with " '''REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES''' Lectures and exercises will take place on Discord (https://discord.gg/FBb2edFW). Please register with your full name. Will use Discord for online classes and collaboration with your project partners. The course has two main parts, the first half is lectures and exercises and the last half is project work ending with the exam on '''Friday 21st of January'''. <!-- This term, we will be using Piazza for class disc..."
2024-03-19T16:03:30Z
<p>Created page with " '''REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES''' Lectures and exercises will take place on Discord (https://discord.gg/FBb2edFW). Please register with your full name. Will use Discord for online classes and collaboration with your project partners. The course has two main parts, the first half is lectures and exercises and the last half is project work ending with the exam on '''Friday 21st of January'''. <!-- This term, we will be using Piazza for class disc..."</p>
<p><b>New page</b></p><div><br />
'''REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES'''<br />
<br />
<br />
Lectures and exercises will take place on Discord (https://discord.gg/FBb2edFW). Please register with your full name. Will use Discord for online classes and collaboration with your project partners.<br />
<br />
The course has two main parts, the first half is lectures and exercises and the last half is project work ending with the exam on '''Friday 21st of January'''.<br />
<br />
<!--<br />
This term, we will be using Piazza for class discussion. The system is highly catered to getting you help fast and efficiently from classmates, the TA, and myself. Rather than emailing questions to the teaching staff, I encourage you to post your questions on Piazza [https://piazza.com/class/kjernxm6wre7ck here]<br />
--><br />
<br />
=== Course Program - January 2022 ===<br />
<br />
<br />
<HR><br />
'''Monday, January 3'''<br />
<HR><br />
''Introduction - Next Generation Sequencing''<br />
<DL><br />
<DT>9:00am-9:30am</DT> <br />
<DD>Introduction to course & Pre-test<br />
([https://teaching.healthtech.dtu.dk/material/22126/2022/11_Introduction_to_course_GR.pdf Lecture slides])<br />
([https://teaching.healthtech.dtu.dk/material/22126/2021/1_pre-test_2021.pdf Pre-test])</DD><br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>9:30am-10:00am</DT><br />
<dd>Introduction to NGS <br />
([https://teaching.healthtech.dtu.dk/material/22126/2022/12_Introduction_to_NGS_GR.pdf Lecture slides]) </DD><br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>10:00am-10:45am</DT><br />
<DD>2nd and 3rd generation NGS Technologies <br />
([https://teaching.healthtech.dtu.dk/material/22126/2022/13_Introduction_to_NGS_technology_GR.pdf Lecture slides])</DD><br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>10:45am-11:00am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>11:00am-12:00pm</DT><br />
<DD>Tech talk group formation and group work <br />
([https://teaching.healthtech.dtu.dk/material/22126/2022/14_Tech_Talks_GR.pdf Lecture slides])<br />
([https://docs.google.com/spreadsheets/d/1yY6HH10z_OTOTHQUiZehCUrya4u-N2xyUWSeM-EE__o/edit?usp=sharing Student Groups 2022]) </DD><br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>12:00pm-1:00pm</DT> <br />
<DD>''Lunch Break''</DD><br />
<br />
<DT>1:00pm-1:30pm</DT><br />
<DD>Exercise: Logging on to our Computerome cloud ([[Logging on to Cloud system]])</DD><br />
<DD>Peter Wad Sackett,Josh Rubin, Nicola Vogel, Gabriel Renaud, </DD><br />
<br />
<DT>1:30pm-2:15pm </DT><br />
<DD>Introduction to UNIX <br />
([https://teaching.healthtech.dtu.dk/36610/index.php/UNIX Video lectures to watch from "Unix intro.." to "Touching upon..."]) <br />
([https://teaching.healthtech.dtu.dk/36610/index.php/UNIX Exercises] possible answers [[Unix_answers|here]]) <br />
([http://teaching.healthtech.dtu.dk/material/36610/UnixInstructions36610.pdf Unix Notes])</DD><br />
<DD>Peter Wad Sackett, Josh Rubin, Nicola Vogel </DD><br />
<br />
<DT>2:15pm-2:30pm</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>2:30pm-3:30pm </DT><br />
<DD>Introduction to UNIX (continued)<br />
([https://teaching.healthtech.dtu.dk/36610/index.php/UNIX Video lectures to watch from "Unix intro.." to "Touching upon..."]) <br />
([https://teaching.healthtech.dtu.dk/36610/index.php/UNIX Exercises] possible answers [[Unix_answers|here]])<br />
([http://teaching.healthtech.dtu.dk/material/36610/UnixInstructions36610.pdf Unix Notes])</DD><br />
<DD>Peter Wad Sackett, Josh Rubin, Nicola Vogel </DD><br />
<br />
<DT>3:30pm-4:00pm </DT><br />
<DD>First look at data<br />
([[First look exercise]])<br />
<DD>Peter Wad Sackett, Josh Rubin, Nicola Vogel</DD><br />
</DL><br />
<br />
<BR><br />
<br />
<HR><br />
'''Tueday, January 4'''<br />
<HR><br />
''Data pre-processing & Alignment''<br />
<br />
<DL><br />
<DT>9:00am-10:45am </DT><br />
<DD>Data basics ([https://teaching.healthtech.dtu.dk/material/22126/2021/2_Data_Basics_SG.pdf Lecture slides]) ([[Data basics exercise]]) ([[Data basics exercise answers]])</DD><br />
<DD>Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel</DD><br />
<br />
<br />
<DT>10:45am-11:00am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>11:00am-12:00pm </DT><br />
<DD>Data pre-processing ([https://teaching.healthtech.dtu.dk/material/22126/2021/2_Data_preprocessing_SG.pdf Lecture slides]) ([[Data Preprocess exercise]]) ([[Data Preprocess exercise answers]])</DD><br />
<DD>Shyam Gopalakrishnan </DD><br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break'' </DD><br />
<br />
<br />
<DT>1:00pm-2:15pm</DT><br />
<DD>Alignment ([https://teaching.healthtech.dtu.dk/material/22126/2022/23_Alignment_GR.pdf Lecture slides]) </DD><br />
<DD>Gabriel Renaud </DD><br />
<br />
<DT>2:15pm-2:30pm</DT><br />
<DD>''Break'' </DD><br />
<br />
<br />
<DT>2:30pm-2:45pm</DT><br />
<DD>Brief reminder on probabilities and Bayesian theory ([https://teaching.healthtech.dtu.dk/material/22126/2022/24_Bayesian_reminder_GR.pdf Lecture slides]) </DD><br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>2:45pm-4:00pm</DT><br />
<DD>Exercise: Alignment ([[Alignment exercise]]) ([[Alignment exercise answers]])</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Nicola Vogel</DD><br />
</DL><br />
<br />
<BR><br />
<br />
<HR><br />
'''Wednesday, January 5'''<br />
<HR><br />
<br />
''Alignment & Genotyping''<br />
<DL><br />
<DT>9:00am-9:30am</DT><br />
<DD>Functional Human Variation</DD><br />
<DD>Shyam Gopalakrishnan, ([https://teaching.healthtech.dtu.dk/material/22126/2021/FunctionalHumanVariation_SG.pdf Lecture slides])</DD><br />
<br />
<DT>9:30am-10:15am</DT><br />
<DD>Alignment postprocessing & variant calling ([https://teaching.healthtech.dtu.dk/material/22126/2022/41_post_alignment_variantcalling_GR.pdf Lecture slides])</DD><br />
<br />
<DD>Gabriel Renaud</DD><br />
<br />
<DT>10:15am-10:30am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>10:30am-12:00pm</DT><br />
<DD>Exercise: Postprocessing & variant calling ([[Postprocess exercise]]) ([[Postprocess_exercise_answers]]) ([[SNP calling exercise]]) ([[SNP_calling_exercise_answers]])</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Nicola Vogel </DD><br />
<br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break'' </DD><br />
<br />
<br />
<DT>1:00pm-1:45pm </DT><br />
<DD>Lecture: de novo assembly ([https://teaching.healthtech.dtu.dk/material/22126/2021/4_de_novo_assembly_course_SG.pdf Lecture slides])([http://teaching.healthtech.dtu.dk/material/22126/debruijn_handout.pdf Handout (TODO)]) </DD><br />
<DD>Shyam Gopalakrishnan</DD><br />
<br />
<DT>1:45pm-2:00pm</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>2:00pm-4:00pm</DT><br />
<DD>Exercise: de novo assembly ([[denovo exercise]]) ([[denovo solution]]) </DD><br />
<DD>Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel</DD><br />
</DL><br />
<br />
<BR><br />
<br />
<HR><br />
'''Thursday, January 6'''<br />
<HR><br />
''Metagenomics''<br />
<DL><br />
<DT>9:00am-9:45am </DT><br />
<DD>Metagenomics & Binning ([https://teaching.healthtech.dtu.dk/material/22126/2022/Metagenomics_binning.pdf Lecture slides])</DD><br />
<DD>Gisle Vestergaard</DD><br />
<br />
<DT>9:45am-10:00am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>10:00am-12:00pm</DT><br />
<DD>Exercise: Kaiju: Taxonomic classification ([[Kaiju exercise]]) ([[Kaiju solution]]) </DD><br />
<DD>Gisle Vestergaard,Trine Zachariasen</DD><br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break'' </DD><br />
<br />
<DT>1:00pm-1:45pm</DT><br />
<DD>Lecture: Quantitative Metagenomics ([https://teaching.healthtech.dtu.dk/material/22126/2022/Quantitative_metagenomics_2.pdf Lecture slides])</DD><br />
<DD>Gisle Vestergaard</DD><br />
<br />
<DT>1:45pm-2:00pm</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>2:00pm-4:00pm</DT><br />
<DD>Exercise: Quantitative Metagenomics ([http://teaching.healthtech.dtu.dk/22126/index.php/QuantitativeMetagenomics Exercise]) ([http://teaching.healthtech.dtu.dk/22126/index.php/QuantitativeMetagenomicsSolution Solution]) </DD><br />
<DD>Gisle Vestergaard, Trine Zachariasen</DD><br />
</DL><br />
<br />
<BR><br />
<br />
<HR><br />
'''Friday, January 7'''<br />
<HR><br />
''Cell-free DNA and recap test''<br />
<DL><br />
<DT>9:00am-9:45am </DT><br />
<DD>Cell-free DNA ([https://teaching.healthtech.dtu.dk/material/22126/2021/cfDNA_lecture_2020_SB.pdf Lecture slides])</DD><br />
<DD>Søren Besenbacher</DD><br />
<br />
<DT>9:45am-10:00am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>10:00am-12:00am</DT><br />
<DD>Exercise: Cell free DNA ([[cfDNA exercise]])([[CfDNA_exercise_answers]])</DD><br />
<DD>Søren Besenbacher, Josh Rubin, Nicola Vogel</DD><br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break'' </DD><br />
<br />
<br />
<DT>1:00pm-1:45pm</DT><br />
<DD>Recap Test ([https://teaching.healthtech.dtu.dk/material/22126/2021/test_2021.pdf Test 2021])([https://teaching.healthtech.dtu.dk/material/22126/2021/test_2021_withA.pdf answers])</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Nicola Vogel </DD><br />
<br />
<DT>1:45pm-2:00pm</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>2:00pm-4:00pm</DT><br />
<DD>Time to work on this week's exercises</DD><br />
<DD>Gabriel Renaud, Josh Rubin, Nicola Vogel</DD><br />
</DL><br />
<br />
<BR><br />
<br />
<br />
<HR><br />
'''Monday, January 10'''<br />
<HR><br />
<br />
''RNA-seq and Cancer-seq''<br />
<DL><br />
<br />
<DT>9:00am-9:45am</DT><br />
<DD>Lecture: RNAseq ([https://teaching.healthtech.dtu.dk/material/22126/2022/RNA-seq_10-01-2022.pdf Lecture slides])</DD><br />
<DD>Francesca Bertolini</DD><br />
<br />
<DT>9:45am-10:00am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>10:00am-12:00pm</DT><br />
<DD>Exercise: RNAseq ([[Rnaseq_exercise]]) ([[Rnaseq_exercise_answers]]) </DD><br />
<DD>Francesca Bertoloni, Josh Rubin, Nicola Vogel </DD><br />
<br />
<DT>12:00pm-1:00pm</DT> <br />
<DD>''Lunch Break'' </DD><br />
<br />
<DT>1:00pm-1:45pm </DT><br />
<DD>Lecture: Cancer-seq ([https://teaching.healthtech.dtu.dk/material/22126/2021/CancerGenomics_Izarzugaza%20copy.pdf Lecture slides]) </DD> <br />
<DD>Elena Papaleo </DD><br />
<br />
<DT>2:00pm-4:00pm</DT><br />
<DD>Exercise: Cancer-seq ([[Cancerseq_exercise]]) ([[Cancerseq_exercise_answers]])</DD><br />
<DD>Adrian Otamendi, Josh Rubin, Nicola Vogel </DD><br />
</DL><br />
<br />
<BR><br />
<br />
<HR><br />
'''Tuesday, January 11'''<br />
<HR><br />
<br />
''Genomic Epidemiology and tech talk''<br />
<br />
<DL><br />
<DT>9:00am-9:55am</DT><br />
<DD>Exercise: Genomic Epidemiology ([[Genomic epidemiology exercise]]) ([[Genomic epidemiology solution]])</DD><br />
<DD>Shyam Gopalakrishnan</DD><br />
<br />
<DT>9:55am-10:10am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>10:10am-12:00pm</DT> <br />
<DD>Case story: Genomic Epidemiology ([https://teaching.healthtech.dtu.dk/material/22126/2021/Genomic_epidemiology_NGScourse_Jan2021.pdf Lecture])</DD><br />
<DD>Pimlapas Leekitecharoenphon (Shinny)</DD><br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break'' </DD><br />
<br />
<DT>1:00pm-2:00pm </DT><br />
<DD>Tech talk work</DD><br />
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel </DD><br />
<br />
<DT>2:00pm-4:00pm </DT><br />
<DD>TechTalks Presentations</DD><br />
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel </DD><br />
<br />
</DL><br />
<br />
<BR><br />
<br />
<HR><br />
'''Wednesday, January 12'''<br />
<HR><br />
''Ancient DNA & Project work''<br />
<br />
<DL><br />
<DT>9:00am-10:00am</DT><br />
<DD>Ancient DNA ([https://teaching.healthtech.dtu.dk/material/22126/2021/dtu_adna_2021.pdf Lecture slides])</DD><br />
<DD>Martin Sikora</DD><br />
<br />
<DT>10:00am-10:15am</DT><br />
<DD>''Break''</DD><br />
<br />
<DT>10:15am-12:00pm</DT><br />
<DD>Exercise: Ancient DNA ([[Ancient DNA exercise]]) ([[Ancient_DNA_exercise_answers]])</DD><br />
<DD>Martin Sikora, Josh Rubin, Nicola Vogel</DD><br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break'' </DD><br />
<br />
<DT>1:00pm-1:45pm </DT> <br />
<DD>Projects & Group formation ([https://teaching.healthtech.dtu.dk/material/22126/2021/82_Projects_GR.pdf Lecture slides] [http://teaching.healthtech.dtu.dk/material/22126/2022/posters.tar.gz Examples from previous courses]) </DD><br />
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel</DD><br />
<br />
<DT>1:45pm-4:00pm </DT> <br />
<DD>Projects & Group formation, prepare your presentation for tomorrow. please write group names in the [https://docs.google.com/document/d/11OudbQ1DGY9GwCoFXtU29rAZmhlBokmPify5b0uOb5Q/edit?usp=sharing document for 2022]</DD><br />
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel</DD><br />
</DL><br />
<br />
<br />
<BR><br />
<br />
<HR><br />
'''Thursday, January 13'''<br />
<HR><br />
''Project presentation''<br />
<DL><br />
<DT>9:00am-12:00pm</DT> <br />
<DD>Project work/Prepare presentations for this afternoon</DD><br />
<DD>Please go to Discord for help, we will be available.</DD><br />
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel</DD><br />
<br />
<DT>12:00pm-1:00pm </DT><br />
<DD>''Lunch Break''</DD><br />
<br />
<DT>1:00pm-2:00pm <DT><br />
<DD>Project Presentations (what you will do) /Project work</DD><br />
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel</DD><br />
<br />
<DT>2:00pm-4:00pm </DT><br />
<DD>Project work</DD><br />
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel</DD><br />
</DL><br />
<br />
<BR><br />
<br />
'''Friday, January 14'''<br />
<HR><br />
''Project work''<br />
<DL><br />
<DT>9:00am-4:00pm</DT><br />
<DD>Project work</DD><br />
<br />
<DT>1:00pm-3:00pm</DT><br />
<DD>Project work/Office hours</DD><br />
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel</DD><br />
</DL><br />
<br />
<BR><br />
<br />
'''Monday, January 17'''<br />
<HR><br />
''Project work''<br />
<DL><br />
<DT>9:00am-4:00pm</DT><br />
<DD>Project work</DD><br />
<br />
<DT>1:00pm-3:00pm</DT><br />
<DD>Project work/Office hours</DD><br />
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel</DD><br />
</DL><br />
<br />
<BR><br />
<br />
'''Tuesday, January 18'''<br />
<HR><br />
''Project work''<br />
<DL><br />
<DT>9:00am-4:00pm</DT><br />
<DD>Project work</DD><br />
<br />
<DT>1:00pm-3:00pm</DT><br />
<DD>Project work/Office hours</DD><br />
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel</DD><br />
</DL><br />
<br />
<BR><br />
<br />
'''Wednesday, January 19'''<br />
<HR><br />
''Project work''<br />
<DL><br />
<DT>9:00am-4:00pm</DT><br />
<DD>Project work</DD><br />
<br />
<DT>1:00pm-3:00pm</DT><br />
<DD>Project work/Office hours</DD><br />
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel</DD><br />
</DL><br />
<br />
<BR><br />
<br />
'''Thursday, January 20'''<br />
<HR><br />
''Project Work & Poster Printing''<br />
<DL><br />
<br />
<DD>Produce a PDF of your poster, presentation will online this year.</DD><br />
<DD>[http://teaching.healthtech.dtu.dk/material/22126/Posters.pdf Poster guide & requirements]</DD><br />
<br />
<DT>10:00am-12:00pm</DT><br />
<DD>Q&A: Practical information about the [http://teaching.healthtech.dtu.dk/material/22126/exam.pdf Exam]</DD><br />
<DD>Project work/Office hours</DD><br />
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Josh Rubin, Nicola Vogel</DD><br />
</DL><br />
<br />
<BR><br />
<br />
'''Friday, January 21'''<br />
<HR><br />
''Poster session - Online''<br />
<DL><br />
<DT>9:00am-4:00pm</DT><br />
<DD>Poster session part ('''exam''')</DD><br />
</DL></div>
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