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Created page with " '''REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES''' Lectures and exercises will take place at the Section for Bioinformatics at the Technical University of Denmark, '''Building 210, Room H162''' in Lyngby ([https://goo.gl/maps/hyifvFrZ5cPLroCv8 map]). The courses has two main parts, the first half is lectures and exercises and the last half is project work ending with the exam on Friday 24th of January. This term we will be using Piazza for class discussion. The..."

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'''REMEMBER TO BRING A LAPTOP COMPUTER FOR EXERCISES'''

Lectures and exercises will take place at the Section for Bioinformatics at the Technical University of Denmark, '''Building 210, Room H162''' in Lyngby ([https://goo.gl/maps/hyifvFrZ5cPLroCv8 map]).

The courses has two main parts, the first half is lectures and exercises and the last half is project work ending with the exam on Friday 24th of January.

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/danish_technical_university/summer2019/1 here]

=== Course Program - January 2020 ===

<HR>
'''Monday, January 6'''
<HR>
''Introduction - Next Generation Sequencing''
<DL>
<DT>9:00am-9:30am
<DD>Introduction to course & Pre-test
([http://teaching.healthtech.dtu.dk/material/22126/2020/1_Introduction_to_course_GR.pdf Lecture slides])
([http://teaching.healthtech.dtu.dk/material/22126/2020/1_pre-test_2020.pdf Pre-test])</dd>
<DD>Gabriel Renaud

<DT>9:30am-10:00am
<dd>Introduction to NGS
([http://teaching.healthtech.dtu.dk/material/22126/2020/1_Introduction_to_NGS_GR.pdf Lecture slides]) </dd>
<DD>Gabriel Renaud

<DT>10:00am-10:45am
<dd>2nd and 3rd generation NGS Technologies
([http://teaching.healthtech.dtu.dk/material/22126/2020/1_Introduction_to_NGS_technology_GR_2.pdf Lecture slides])
<DD>Gabriel Renaud

<DT>10:45am-11:00am
<DD>''Break''

<DT>11:00am-12:00pm
<DD>Tech talk group formation and group work
([http://teaching.healthtech.dtu.dk/material/22126/2020/1_Tech_Talks_GR.pdf Lecture slides])
([https://docs.google.com/spreadsheets/d/1awQ_-KiYC7r3IZXevJSCJ-gDMD8BNye4VOq98zy3z3U/edit?usp=sharing Student Groups]) </dd>
<DD>Gabriel Renaud

<DT>12:00pm-1:00pm
<DD>''Lunch Break''

<DT>1:00pm-1:30pm
<DD>Exercise: Logging on to our Computerome cloud
([[Logging on to Cloud system]])</dd>
<DD>Peter Wad Sackett, Bernadette Kofoed Christiansen, Nanna Møller Barnkob

<DT>1:30pm-2:15pm
<DD>Introduction to UNIX
([http://teaching.healthtech.dtu.dk/material/36610/UnixIntroduction.ppt Lecture slides])
([http://teaching.healthtech.dtu.dk/36610/index.php/UNIX Exercise])
([http://teaching.healthtech.dtu.dk/material/36610/UnixInstructions36610.pdf Unix Notes])
<DD>Peter Wad Sackett, Bernadette Kofoed Christiansen, Nanna Møller Barnkob

<DT>2:15pm-2:30pm
<DD>''Break''

<DT>2:30pm-3:30pm
<DD>Introduction to UNIX
([http://teaching.healthtech.dtu.dk/material/36610/UnixIntroduction.ppt Lecture slides])
([http://teaching.healthtech.dtu.dk/36610/index.php/UNIX Exercise])
([http://teaching.healthtech.dtu.dk/material/36610/UnixInstructions36610.pdf Unix Notes])
<DD>Peter Wad Sackett, Bernadette Kofoed Christiansen, Nanna Møller Barnkob

<DT>3:30pm-4:00pm
<DD>First look at data
([[First look exercise]])
<DD>Peter Wad Sackett, Bernadette Kofoed Christiansen, Nanna Møller Barnkob

</DD>
 
</DL>

<HR>
'''Tueday, January 7'''
<HR>
''Data pre-processing & Genomic Epidemiology''
<DL>
<DT>9:00am-10:45am
<DD>Data basics
([http://teaching.healthtech.dtu.dk/material/22126/Data_Basics.pdf Lecture slides])
([[Data basics exercise]])
([[Data basics solution]])
<DD>Shyam Gopalakrishnan, Bernadette Kofoed Christiansen, Freja Dahl Hede

<DT>10:45am-11:00am
<DD>''Break''

<DT>11:00am-12:00pm
<DD>Data pre-processing
([http://teaching.healthtech.dtu.dk/material/22126/Data_preprocessing.pdf Lecture slides])
([[Data Preprocess exercise]])
([[Data Preprocess solution]])
<DD>Shyam Gopalakrishnan, Bernadette Kofoed Christiansen, Freja Dahl Hede

<DT>12:00pm-1:00pm
<DD>''Lunch Break''

<DT>1:00pm-2:15pm
<DD>Alignment
([http://teaching.healthtech.dtu.dk/material/22126/2020/2_Alignment_GR.pdf Lecture slides])
<DD>Gabriel Renaud

<DT>2:15pm-2:30pm
<DD>''Break''

<DT>2:30pm-4:00pm
<DD>Exercise: Alignment
([[Alignment exercise]])
([[Alignment solution]])
<DD>Gabriel Renaud, Bernadette Kofoed Christiansen, Freja Dahl Hede
</DD>
 
</DL>

<HR>
'''Wednesday, January 8'''
<HR>

''Alignment & Genotyping''
<DL>
<DT>9:00am-9:30am
<DD>Functional Human Variation
<DD>Adrian Otamendi Laspiur, ([http://teaching.healthtech.dtu.dk/material/22126/2020/Intro_to_variation.pdf Lecture slides])

<DT>9:30am-10:00am
<DD>Alignment postprocessing & variant calling
([http://teaching.healthtech.dtu.dk/material/22126/2020/3_post_alignment_variantcalling_GR.pdf Lecture slides])

<DD>Gabriel Renaud

<DT>10:00am-10:15am
<DD>''Break''

<DT>10:15am-12:00pm
<DD>Exercise: Postprocessing & variant calling
([[Postprocess exercise]])
([[Postprocess solution]])
([[SNP calling exercise]])
([[SNP calling solution]]) </dd>
<DD>Gabriel Renaud, TBA

<DT>12:00pm-1:00pm
<DD>''Lunch Break''

<DT>1:00pm-2:15pm
<DD>Ancient DNA
([http://teaching.healthtech.dtu.dk/material/22126/2020/3_ancientDNA2020.pdf Lecture slides])
<DD>Gabriel Renaud

<DT>2:15pm-2:30pm
<DD>''Break''

<DT>2:30pm-4:00pm
<DD>Exercise: Ancient DNA
([[Ancient DNA exercise]])

<DD>Gabriel Renaud, TBA
</DD>
 
</DL>

<HR>
'''Thursday, January 9'''
<HR>
''de novo assembly & Metagenomics''
<DL>

<DT>9:00am-9:45am
<DD>Lecture: de novo assembly
([http://teaching.healthtech.dtu.dk/material/22126/de_novo_assembly_course.pdf Lecture slides])
([http://teaching.healthtech.dtu.dk/material/22126/debruijn_handout.pdf Handout]) </dd>
<DD>Shyam Gopalakrishnan

<DT>9:45am-10:00am
<DD>''Break''

<DT>10:00am-12:00pm
<DD>Exercise: de novo assembly
([[denovo exercise]])
([[denovo solution]]) </dd>
<DD>Shyam Gopalakrishnan, Nanna Møller Barnkob

<DT>12:00pm-1:00pm
<DD>''Lunch Break''

<DT>1:00pm-1:45pm
<DD>Metagenomics & Binning
([http://teaching.healthtech.dtu.dk/material/22126/Metagenomics_assembly.pdf Lecture slides])
</dd>
<DD>Gisle Vestergaard

<DT>1:45pm-2:00pm
<DD>''Break''

<DT>2:00pm-4:00pm
<DD>Exercise: Metagenomic de novo assembly
([[Metagenomic assembly exercise]])
([[Metagenomic assembly solution]]) </dd>
<DD>Gisle Vestergaard

</DD>
 
</DL>

<HR>
'''Friday, January 10'''
<HR>
''Quantitative Metagenomics and Test''
<DL>

<DT>9:00am-9:45am
<DD>Lecture: Quantitative Metagenomics
([http://teaching.healthtech.dtu.dk/material/22126/quantitative_metagenomics.pdf Lecture slides])</dd>
<DD>Gisle Vestergaard

<DT>9:45am-10:00am
<DD>''Break''

<DT>10:00am-12:00pm
<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>
<DD>Gisle Vestergaard

<DT>12:00pm-1:00pm
<DD>''Lunch Break''

<DT>1:00pm-1:45pm
<DD>Recap Test
([http://teaching.healthtech.dtu.dk/material/22126/Recap_test_2019.pdf Test])
<DD>Gabriel Renaud, Line Egerod Lund

<DT>1:45pm-2:00pm
<DD>''Break''

<DT>2:00pm-4:00pm
<DD>Time to work on this week's exercises
<DD>Gabriel Renaud, Line Egerod Lund

</DD>
 
</DL>

<HR>
'''Monday, January 13'''
<HR>
''RNA-seq and Cancer-seq''
<DT>9:00am-9:45am
<DD>Lecture: RNAseq
([http://teaching.healthtech.dtu.dk/material/22126/2020/RNA-seq%2013-01-2020.pdf Lecture slides])</dd>
<DD>Francesca Bertolini

<DT>9:45am-10:00am
<DD>''Break''

<DT>10:00am-12:00pm
<DD>Exercise: RNAseq
([http://teaching.healthtech.dtu.dk/material/22126/2020/RNAseq_excercise_2020.docx Exercise])
([http://teaching.healthtech.dtu.dk/material/22126/2020/RNAseq_answers_2020.txt Solution]) </dd>
<DD>Francesca Bertoloni, Nanna Møller Barnkob, Bernadette Kofoed Christiansen

<DT>12:00pm-1:00pm
<DD>''Lunch Break''

<DT>1:00pm-1:45pm
<DD>Lecture: Cancer-seq
([http://teaching.healthtech.dtu.dk/material/22126/2020/CancerGenomics_Izarzugaza.pdf Lecture slides])
<DD>Adrian Otamendi Laspiur, Nanna Møller Barnkob, Bernadette Kofoed Christiansen

<DT>2:00pm-4:00pm
<DD>Exercise: Cancer-seq
([https://github.com/nannabarnkob/dtu-cancer/blob/master/cancer_seq_exercise.md])
<DD>Adrian Otamendi Laspiur, Nanna Møller Barnkob, Bernadette Kofoed Christiansen

</DD>

<HR>
'''Tuesday, January 14'''
<HR>
<DT>9:00am-9:55am
<DD>Exercise: Genomic Epidemiology
([[Genomic epidemiology exercise]])
([[Genomic epidemiology solution]])
<DD>Shyam Gopalakrishnan
<DT>9:55am-10:10am
<DD>''Break''
<DT>10:10am-12:00pm
<DD>Case story: Genomic Epidemiology
([http://teaching.healthtech.dtu.dk/material/22126/2020/Genomic_epidemiology_NGScourse_Jan2020.pdf Lecture])
<DD>Pimlapas Leekitecharoenphon (Shinny)
</DD>
<DT>12:00pm-1:00pm
<DD>''Lunch Break''
<DT>1:00pm-4:00pm
<DD>Tech talk work & [http://teaching.healthtech.dtu.dk/material/22126/TechTalks.tar Presentations]
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Line Egerod Lund
</DD>

<HR>
'''Wednesday, January 15'''
<HR>
''Project work'' 
<DL>

<DT>9:00am-9:45am
<DD>Projects & Group formation
([http://teaching.healthtech.dtu.dk/material/22126/2020/9_Projects_GR.pdf Lecture slides] [http://teaching.healthtech.dtu.dk/material/22126/posters.tar.gz Examples from previous courses])
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Line Egerod Lund

<DT>9:45am-10:45am
<DD>Projects & Group formation, please write group names in the [https://docs.google.com/document/d/1MUkqNE9GSzTupR3ro4EQEybF5UR1TKQ4Dw5usi22tz4/edit?usp=sharing document]
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Line Egerod Lund

<DT>10:45am-11:00am
<DD>''Break''

<DT>11:00am-12:00pm
<DD>Project work
<DD>Gabriel Renaud, Shyam Gopalakrishnan, Line Egerod Lund

<DT>12:00pm-1:00pm
<DD>''Lunch Break''

<DT>1:00pm-4:00pm
<DD>Project work/Prepare presentations for tomorrow
How to get to Gabriel/Shyam/Gisle office: first go to 202, go to the 3rd floor and go to building 204 via the skyway. We are in 252/251
</DD>
 
</DL>
<HR>
'''Thurday, January 16'''
<HR>
''Project work & Project Presentations''
<DL>

<DT>9:00am-12:00pm
<DD>Project work
<DD>Gabriel Renaud, Shyam Gopalakrishnan, TBA

<DT>12:00pm-1:00pm
<DD>''Lunch Break''

<DT>1:00pm-2:00pm
<DD>Project Presentations
<DD>Gabriel Renaud, Shyam Gopalakrishnan, TBA

</DD>
 
</DL>
<HR>
'''Friday, January 17'''
<HR>
''Project work''
<DL>

<DT>9:00am-4:00pm
<DD>Project work
<DD>

<DT>1:00pm-3:00pm
<DD>Project work/Office hours
<DD>Gabriel Renaud, Shyam Gopalakrishnan, TBA

</DD>
 
</DL>
<HR>
'''Monday, January 20'''
<HR>
''Project work''
<DL>

<DT>9:00am-4:00pm
<DD>Project work
<DD>

<DT>1:00pm-3:00pm
<DD>Project work/Office hours
<DD>Gabriel Renaud, Shyam Gopalakrishnan, TBA

</DD>
 
</DL>
<HR>
'''Tueday, January 21'''
<HR>
''Project work''
<DL>

<DT>9:00am-4:00pm
<DD>Project work
<DD>

<DT>1:00pm-3:00pm
<DD>Project work/Office hours
<DD>Gabriel Renaud, Shyam Gopalakrishnan, TBA

</DD>
 
</DL>
<HR>
'''Wednesday, January 22'''
<HR>
''Project work''
<DL>

<DT>9:00am-4:00pm
<DD>Project work
<DD>

<DT>1:00pm-3:00pm
<DD>Project work/Office hours
<DD>Gabriel Renaud, Shyam Gopalakrishnan, TBA

</DD>
 
</DL>
<HR>
'''Thurday, January 23'''
<HR>
''Project Work & Poster Printing''
<DL>

<DD>Print your poster, it is possible to print in DTU library for 16-30kr.
<DD>[http://teaching.healthtech.dtu.dk/material/22126/Posters.pdf Poster guide & requirements]

<DT>10:00am-12:00pm
<DD>Q&A: Practical information about the [http://teaching.healthtech.dtu.dk/material/22126/exam.pdf Exam]
<DD>Project work/Office hours
<DD>Gabriel Renaud, Shyam Gopalakrishnan, TBA

</DL>
 
<HR>
Friday, January 24 
<HR>
''Poster session - in the hall of TBA''
<DL>

<DT>10:00am-2:00pm
<DD>Poster session part ('''exam''')

</DD>
 
</DL><HR>

Program 2020 - Revision history