BIMM 143 - Bioinformatics Laboratory - Schiffer [WI22]

Course Modules

Week 1: January 3-7

Week 1: January 3-7 Week 1: January 3-7

Assignment

Video: Welcome to BIMM 143 Winter 2022 Video: Welcome to BIMM 143 Winter 2022 5 1

assignment 1133546 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Video: What is DataCamp? Video: What is DataCamp? 2 2

assignment 1133547 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Video: Should I learn Python or R? Video: Should I learn Python or R? 5 3

assignment 1133548 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Entrance Survey Entrance Survey 5 4

quiz 1133549 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Video: #PODlife Video: #PODlife 3 5

assignment 1133550 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Downloading and an Introduction to Anaconda Navigator (Python) and R Studio (R) Downloading and an Introduction to Anaconda Navigator (Python) and R Studio (R) 10 6

assignment 1133551 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Project 1A: Choose a Journal Article Project 1A: Choose a Journal Article 25 7

quiz 1133552 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Journal Articles For Project 1 Journal Articles For Project 1 0 8

assignment 1133556 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

IntroductoryLecture_Winter2022.pdf IntroductoryLecture_Winter2022.pdf 9

attachment 1205716 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

Overview of Bioinformatics Methods.pptx Overview of Bioinformatics Methods.pptx 10

attachment 1170279 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Page

Lecture 1: (JAMIE) Introduction to Bioinformatics Lecture 1: (JAMIE) Introduction to Bioinformatics 11

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Page

Lecture 2: (JAMIE) Challenge Problem #1 Lecture 2: (JAMIE) Challenge Problem #1 12

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Page

Challenge Problem #1 - R Studio Challenge Problem #1 - R Studio 13

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Attachment

Challenge_Problem_1- R [W22].html Challenge_Problem_1- R [W22].html 15

attachment 1217659 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

ChallengeProblem_1-python.html ChallengeProblem_1-python.html 16

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Page

Challenge Problem #1 - Python Challenge Problem #1 - Python 19

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Week 2: January 10-14

Week 2: January 10-14 Week 2: January 10-14

Assignment

How to Read a Scientific Article How to Read a Scientific Article 5 1

assignment 1133564 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Data Camp - Introduction to Python and R Data Camp - Introduction to Python and R 20 2

assignment 1133554 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Challenge Problem #1: Printing Strings and History of Bioinformatics Challenge Problem #1: Printing Strings and History of Bioinformatics 15 3

assignment 1133555 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Challenge Problem #1: Printing Strings and History of Bioinformatics - Individual Submission Challenge Problem #1: Printing Strings and History of Bioinformatics - Individual Submission 0 4

assignment 1214539 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

EC: EBI Bioinformatics Course EC: EBI Bioinformatics Course 0 5

assignment 1133575 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Project 1D Rubric Project 1D Rubric 5 6

assignment 1151780 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

DataCamp_1_PYTHON-Intro_AnswerKey.html DataCamp_1_PYTHON-Intro_AnswerKey.html 9

attachment 1212364 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

DataCamp_1_R-Intro_AnswerKey.nb.html DataCamp_1_R-Intro_AnswerKey.nb.html 10

attachment 1216851 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

Lecture 3: (JAMIE) Project 1 & Project 2 Overview.pdf Lecture 3: (JAMIE) Project 1 & Project 2 Overview.pdf 11

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Page

Lecture 3: Introduction to Projects Lecture 3: Introduction to Projects 12

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Page

Outline of Lectures This Quarter Outline of Lectures This Quarter 13

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Lecture 4: (JAMIE) Data Camp Intro & Challenge Problem Review Lecture 4: (JAMIE) Data Camp Intro & Challenge Problem Review 14

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Attachment

Lecture 4_DataCamp#1_ChallengeProblem#1.pdf Lecture 4_DataCamp#1_ChallengeProblem#1.pdf 15

attachment 1221067 0

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Attachment

Lecture video (Kelly - R) - Challenge Problem 1 Lecture video (Kelly - R) - Challenge Problem 1 16

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete

Week 3: January 17-21

Week 3: January 17-21 Week 3: January 17-21

Assignment

Data Camp - Intermediate Python & R Data Camp - Intermediate Python & R 20 1

assignment 1133563 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Challenge Problem #2: Sequence Strings, Analysis, and Bioinformatics Databases Challenge Problem #2: Sequence Strings, Analysis, and Bioinformatics Databases 20 2

assignment 1133562 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Project 1B: Review Article, Describe Figures, Present Code - Submit as POD Project 1B: Review Article, Describe Figures, Present Code - Submit as POD 50 3

quiz 1133565 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Example Video from Jamie for Project 1D Example Video from Jamie for Project 1D 0 4

assignment 1133576 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

DataCamp_2_R-Intermediate_AnswerKey.nb.html DataCamp_2_R-Intermediate_AnswerKey.nb.html 7

attachment 1220989 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Page

Data Camp Lab #2 - R Intermediate Video Lecture (JAMIE) Data Camp Lab #2 - R Intermediate Video Lecture (JAMIE) 8

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Attachment

DataCamp_2-IntermediatePython_AnswerKey.html DataCamp_2-IntermediatePython_AnswerKey.html 9

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

ChallengeProblem2_R_AnswerKey.nb.html ChallengeProblem2_R_AnswerKey.nb.html 10

attachment 1221649 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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ChallengeProblem_2-python_AnswerKey.html ChallengeProblem_2-python_AnswerKey.html 11

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Page

Lecture 5: (JAMIE) video lecture on DataBases Lecture 5: (JAMIE) video lecture on DataBases 12

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Attachment

Lecture 5: (JAMIE) Bioinformatics DataBases.pdf Lecture 5: (JAMIE) Bioinformatics DataBases.pdf 13

attachment 1227139 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

Kelly Discussion: Challenge_Problem_2 [W22].Rmd Kelly Discussion: Challenge_Problem_2 [W22].Rmd 14

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

Video Lecture (Kelly - R) - Challenge Problem 2 Video Lecture (Kelly - R) - Challenge Problem 2 15

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

DataCamp_Python_Intermediate (JAMIE)_overview.mp4 DataCamp_Python_Intermediate (JAMIE)_overview.mp4 16

attachment 1227306 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete

Week 4: January 24-28

Week 4: January 24-28 Week 4: January 24-28

Assignment

Data Camp - Data Importing with pandas or R Data Camp - Data Importing with pandas or R 20 1

assignment 1133605 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Challenge Problem #3: From Dot Plots to BLAST Challenge Problem #3: From Dot Plots to BLAST 45 2

assignment 1133572 1

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Quiz

Project 1C: Draft 1 of Video and Self-Assessment Project 1C: Draft 1 of Video and Self-Assessment 50 3

quiz 1133574 1

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Attachment

DataCamp3_ImportingwithR_AnswerKey.nb.html DataCamp3_ImportingwithR_AnswerKey.nb.html 4

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DataCampLab3_ImportingwithPython_AnswerKey.html DataCampLab3_ImportingwithPython_AnswerKey.html 5

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Attachment

ChallengeProblem_3-python.html ChallengeProblem_3-python.html 6

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ChallengeProblem3_R.nb.html ChallengeProblem3_R.nb.html 7

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Page

Lecture 6 (JAMIE) Dot Plots, Sequence Alignments, p-values & more Lecture 6 (JAMIE) Dot Plots, Sequence Alignments, p-values & more 8

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Attachment

Lecture 6_Dot Plots, Sequence Alignments, p-values, BLAST.pdf Lecture 6_Dot Plots, Sequence Alignments, p-values, BLAST.pdf 9

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Attachment

ChallengeProblem3VideoLecture_PythonJAMIE.mp4 ChallengeProblem3VideoLecture_PythonJAMIE.mp4 10

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Kelly Discussion: Challenge_Problem_3-[W22].html Kelly Discussion: Challenge_Problem_3-[W22].html 11

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Attachment

Video Lecture (Kelly - R) - Challenge Problem 3 Video Lecture (Kelly - R) - Challenge Problem 3 12

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Week 5: January 31 - February 4

Week 5: January 31 - February 4 Week 5: January 31 - February 4

Assignment

Data Camp - Python Toolbox (pt 1) or RNA-Seq with Bioconductor Data Camp - Python Toolbox (pt 1) or RNA-Seq with Bioconductor 20 1

assignment 1133573 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Project 1D: Final Draft of Video Project 1D: Final Draft of Video 100 2

quiz 1133583 1

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External Url

POD anonymous feedback form POD anonymous feedback form 3

external_url 1133591 0

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Assignment

EC Video: Bioimaging EC Video: Bioimaging 0 4

assignment 1133585 1

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Assignment

Alternative Project 2!! Alternative Project 2!! 0 5

assignment 1133597 1

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Attachment

DataCamp_RNAseq_AnswerKey_R.nb.html DataCamp_RNAseq_AnswerKey_R.nb.html 6

attachment 1236001 0

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Attachment

Python_Toolbox_Lab_AnswerKey.html Python_Toolbox_Lab_AnswerKey.html 7

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Attachment

Lecture 7_ RNAseq.pdf Lecture 7_ RNAseq.pdf 8

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Page

Lecture 7: (JAMIE) Introduction to RNAseq Lecture 7: (JAMIE) Introduction to RNAseq 9

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Attachment

PythonistasLecture7_(JAMIE)_0131_NeedlemanWunsch.mp4 PythonistasLecture7_(JAMIE)_0131_NeedlemanWunsch.mp4 10

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Attachment

Lecture 8_ Diving Deep into RNA-seq.pdf Lecture 8_ Diving Deep into RNA-seq.pdf 11

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Page

Lecture 8: (Jamie) Deep Dive into RNAseq Lecture 8: (Jamie) Deep Dive into RNAseq 12

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Assignment

EC - Lecture 8 EC - Lecture 8 0 13

assignment 1238878 1

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Week 6: February 7-11

Week 6: February 7-11 Week 6: February 7-11

Assignment

Challenge Problem #4: RNAseq analysis and differential RNA expression Challenge Problem #4: RNAseq analysis and differential RNA expression 40 1

assignment 1133615 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Project 1E: Review your Peer's Final Videos Project 1E: Review your Peer's Final Videos 125 2

assignment 1133594 1

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Assignment

EC: POD-mate feedback EC: POD-mate feedback 0 3

assignment 1133595 1

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Assignment

Cheat Sheets! Cheat Sheets! 0 4

assignment 1133596 1

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Page

Lecture 9: (JAMIE) RPKM versus FPKM Lecture 9: (JAMIE) RPKM versus FPKM 5

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Attachment

Lecutre 9_ RNASeq - RPKM versusFPKM Lecutre 9_ RNASeq - RPKM versusFPKM 6

attachment 1247384 0

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Page

Lecture 10: (JAMIE) GEO datasets and GO analysis Lecture 10: (JAMIE) GEO datasets and GO analysis 7

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Attachment

Lecture 10_ RNASeq Lecture 3 - GEO & GO models.pdf Lecture 10_ RNASeq Lecture 3 - GEO & GO models.pdf 8

attachment 1247383 0

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Attachment

ChallengeProblem4_RNAseq_R.nb.html ChallengeProblem4_RNAseq_R.nb.html 9

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Attachment

Challenge Problem 4-RNAseq _python.html Challenge Problem 4-RNAseq _python.html 10

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Attachment

Kelly Discussion: Challenge_Problem_4-[W22].html Kelly Discussion: Challenge_Problem_4-[W22].html 11

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Attachment

Video Lecture (Kelly - R) - Challenge Problem 4 Video Lecture (Kelly - R) - Challenge Problem 4 12

attachment 1245290 0

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Attachment

Video_ChallengeProblem4_(Jamie-python).mp4 Video_ChallengeProblem4_(Jamie-python).mp4 13

attachment 1252982 0

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Week 7: February 14-18

Week 7: February 14-18 Week 7: February 14-18

External Url

How to Write a Scientific Hypothesis How to Write a Scientific Hypothesis 1

external_url 1133598 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Data Camp - Unsupervised Learning in Python & R Data Camp - Unsupervised Learning in Python & R 20 2

assignment 1133584 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Challenge Problem #5: Unsupervised Learning on Biopsy Data Challenge Problem #5: Unsupervised Learning on Biopsy Data 40 3

assignment 1151842 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Project 2A: Draft 1 of your Scientific Hypothesis Project 2A: Draft 1 of your Scientific Hypothesis 25 4

quiz 1133599 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

Project2_BIMM143_Fall2021.pdf Project2_BIMM143_Fall2021.pdf 5

attachment 1133603 0

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Assignment

EC Video: Single Cell Sequencing EC Video: Single Cell Sequencing 0 6

assignment 1133600 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

Lecture 10B_ RNASeq Lecture - Pathway analysis & Reactome.pdf Lecture 10B_ RNASeq Lecture - Pathway analysis & Reactome.pdf 8

attachment 1247506 0

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Attachment

Lecture 10B PathwayAnalysis_Python.html Lecture 10B PathwayAnalysis_Python.html 9

attachment 1247389 0

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Page

Lecture 11: (JAMIE) Project 2, PCA, Clustering, Pathway Analysis, Reactome Lecture 11: (JAMIE) Project 2, PCA, Clustering, Pathway Analysis, Reactome 10

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Lecture 11_ Project 2 Overview & Machine Learning (1).pdf Lecture 11_ Project 2 Overview & Machine Learning (1).pdf 11

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Attachment

Video_DataCamp_Week5_Python.mp4 Video_DataCamp_Week5_Python.mp4 12

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Page

Lecture 12: (JAMIE) Project 2 & Challenge Problem #5 (PCA & Clustering) Lecture 12: (JAMIE) Project 2 & Challenge Problem #5 (PCA & Clustering) 13

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Attachment

ChallengeProblem5_R.html ChallengeProblem5_R.html 14

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ChallengeProblem5_python.html ChallengeProblem5_python.html 15

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Attachment

Kelly Discussion: Challenge_Problem_5-[W22].html Kelly Discussion: Challenge_Problem_5-[W22].html 16

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Attachment

Video Lecture (Kelly - R) - Challenge Problem 5 Video Lecture (Kelly - R) - Challenge Problem 5 17

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Video-ChallengeProblem5(Jamie_python).mp4 Video-ChallengeProblem5(Jamie_python).mp4 18

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Week 8: February 21-25

Week 8: February 21-25 Week 8: February 21-25

Attachment

Methods and Databases that you need to use for Project 2 Methods and Databases that you need to use for Project 2 1

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Assignment

Challenge Problem #6: Proteomic Profiling & PCA Challenge Problem #6: Proteomic Profiling & PCA 40 2

assignment 1133609 1

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Quiz

Project 2B: Refining your Hypothesis & Annotated Bibliography Project 2B: Refining your Hypothesis & Annotated Bibliography 75 3

quiz 1133606 1

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Assignment

Project 2 Example Project 2 Example 15 4

assignment 1133607 1

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Assignment

EC: DataCamp EC: DataCamp 0 5

assignment 1133618 1

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Attachment

Lecture 12_ Proteomics & Expression Atlas.pdf Lecture 12_ Proteomics & Expression Atlas.pdf 6

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Page

Lecture 12: (JAMIE) Proteomics & Expression and Project 2 reviews Lecture 12: (JAMIE) Proteomics & Expression and Project 2 reviews 7

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Attachment

ChallengeProblem6_R.nb.html ChallengeProblem6_R.nb.html 8

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Attachment

ChallengeProblem6_python_answerkey.html ChallengeProblem6_python_answerkey.html 9

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Week 9: February 28 - March 4

Week 9: February 28 - March 4 Week 9: February 28 - March 4

Quiz

Project 2C: Draft 1 of your Jupyter Notebook and Self-Assessment Project 2C: Draft 1 of your Jupyter Notebook and Self-Assessment 50 1

quiz 1133610 1

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Assignment

Challenge Problem #7: Searching the PDB and Viewing Protein Structures Challenge Problem #7: Searching the PDB and Viewing Protein Structures 30 2

assignment 1133593 1

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Assignment

Video: README files and GitHub Video: README files and GitHub 5 3

assignment 1133616 1

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Assignment

EC: Internship Applications EC: Internship Applications 0 4

assignment 1133611 1

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Attachment

Overview of Bioinformatics Methods.pptx Overview of Bioinformatics Methods.pptx 5

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Page

Alternative Problem 2 Rubric Alternative Problem 2 Rubric 6

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Attachment

Lecture 13_ Project 2 Example Review & Structural Bioinformatics.pdf Lecture 13_ Project 2 Example Review & Structural Bioinformatics.pdf 7

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Attachment

Lecture 13: (JAMIE) Introduction to Structural Bioinformatics Lecture 13: (JAMIE) Introduction to Structural Bioinformatics 8

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Assignment

Lecture 14: Structural Bioinformatics ACE2 PyMol Video Lecture 14: Structural Bioinformatics ACE2 PyMol Video 0 9

assignment 1269428 1

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Lecture 14: (JAMIE) Structural Bioinformatics with PyMol Lecture 14: (JAMIE) Structural Bioinformatics with PyMol 10

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ChallengeProblem7_python_answerkey.html ChallengeProblem7_python_answerkey.html 11

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Week 10: March 7-11

Week 10: March 7-11 Week 10: March 7-11

Quiz

Project 2D: Submit Final Jupyter or R Notebook Project 2D: Submit Final Jupyter or R Notebook 100 1

quiz 1133617 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Exit Survey Exit Survey 10 2

quiz 1133620 1

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Assignment

EC Video: Drug Discovery EC Video: Drug Discovery 0 3

assignment 1133621 1

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Attachment

Lecture 15_ Structural Bioinformatics & Drug Discovery.pdf Lecture 15_ Structural Bioinformatics & Drug Discovery.pdf 4

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Attachment

Lecture15:[JAMIE]SWISS_Model&MovieImbedding.mp4 Lecture15:[JAMIE]SWISS_Model&MovieImbedding.mp4 6

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Attachment

DrugDiscoveryPresentations_Winter2022.mp4 DrugDiscoveryPresentations_Winter2022.mp4 7

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Attachment

Maestro Tutorial.mp4 Maestro Tutorial.mp4 8

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Attachment

Save.mov Save.mov 9

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete