Course Modules: CMSC423-0101: Bioinformatic Algorithms, Databases, and Tools-Fall 2016 mpop

Logistics

Logistics Logistics

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Class resources Class resources 2

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Clarification of grading policy Clarification of grading policy 4

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Rosalind Rosalind 5

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Good learning practices Good learning practices 6

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Student Grouping Student Grouping 7

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Attachment

grouping.xlsx grouping.xlsx 8

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Intro to Biology and Informatics

Intro to Biology and Informatics Intro to Biology and Informatics

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Introduction to Lesson plan and Bioinformatics Introduction to Lesson plan and Bioinformatics 0

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Assignment

Reading: introduction to biology Reading: introduction to biology 0 1

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Quiz

Reading quiz: Introduction to biological sequences Reading quiz: Introduction to biological sequences 4 2

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Page

More introduction: Central Dogma of Biology and Terminology More introduction: Central Dogma of Biology and Terminology 3

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Patterns in DNA - Z and KMP algorithm, Frequent Patterns (Compeau and Pevzner Ch 1)

Patterns in DNA - Z and KMP algorithm, Frequent Patterns (Compeau and Pevzner Ch 1) Patterns in DNA - Z and KMP algorithm, Frequent Patterns (Compeau and Pevzner Ch 1)

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Z algorithm and KMP algorithm - Lesson plan Z algorithm and KMP algorithm - Lesson plan 1

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Assignment

Reading: Z and KMP algorithms. Reading: Z and KMP algorithms. 2

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Attachment

Exact matching with the Z and KMP algorithms Exact matching with the Z and KMP algorithms 3

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Z-algorithm walk-through Z-algorithm walk-through 5

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Assignment

Reading: Chapter 1 from Compeau and Pevzner Reading: Chapter 1 from Compeau and Pevzner 0 7

assignment 8729379 1

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Quiz

Reading Quiz: Compeau and Pevzner Chapter 1 Reading Quiz: Compeau and Pevzner Chapter 1 5 8

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Assignment

Exit ticket - Chapter 1 Exit ticket - Chapter 1 1 9

assignment 8732353 1

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Motif search (Compeau and Pevzner Ch 2)

Motif search (Compeau and Pevzner Ch 2) Motif search (Compeau and Pevzner Ch 2)

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Motif finding - lesson plan Motif finding - lesson plan 0

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Assignment

Reading: Chapter 2 from Compeau and Pevzner - part 1 Reading: Chapter 2 from Compeau and Pevzner - part 1 0 1

assignment 8587833 1

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Quiz

Reading Quiz: Compeau and Pevzner Chapter 2: part 1 Reading Quiz: Compeau and Pevzner Chapter 2: part 1 5 2

quiz 8734839 1

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Assignment

Exit Ticket: Motif Search (Introduction) Exit Ticket: Motif Search (Introduction) 1 3

assignment 8734531 1

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Assignment

Exit Ticket: Median Motif Search, Greedy Motif Search Exit Ticket: Median Motif Search, Greedy Motif Search 1 4

assignment 8738223 1

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Page

Resources: greedy motif Search Resources: greedy motif Search 5

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Assignment

Reading: Chapter 2 from Compeau and Pevzner - part 2 Reading: Chapter 2 from Compeau and Pevzner - part 2 0 6

assignment 8734506 1

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Quiz

Reading Quiz: Compeau and Pevzner Chapter 2: part 2 Reading Quiz: Compeau and Pevzner Chapter 2: part 2 5 7

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Attachment

Gibbs sampler example.pdf Gibbs sampler example.pdf 8

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Assignment

Exit Ticket: Motif Search-chapter 2 Exit Ticket: Motif Search-chapter 2 1 9

assignment 8739616 1

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Assignment

Rosalind: Build a Motif-Finder Rosalind: Build a Motif-Finder 10 10

assignment 8739617 1

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Attachment

motif-1.html motif-1.html 11

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Midterm 1 and Ethics

Midterm 1 and Ethics Midterm 1 and Ethics

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Exam questions Exam questions 0

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Page

Ethics: lesson plan Ethics: lesson plan 1

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Assignment

Ethics readings Ethics readings 1 2

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Genome assembly - Compeau and Pevzner Chapter 3

Genome assembly - Compeau and Pevzner Chapter 3 Genome assembly - Compeau and Pevzner Chapter 3

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Genome assembly - Lesson Plan Genome assembly - Lesson Plan 0

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Assignment

Reading: Genome assembly part1 Reading: Genome assembly part1 0 1

assignment 8587841 1

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Additional resources on genome assembly Additional resources on genome assembly 2

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Quiz

Reading quiz: Assembly Reading quiz: Assembly 6 3

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Assignment

Exit ticket: assembly 2 Exit ticket: assembly 2 1 4

assignment 8745441 1

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Quiz

Exit ticket - Genome Assembly Exit ticket - Genome Assembly 1 5

quiz 8587844 1

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Attachment

de-bruijn-test.pdf de-bruijn-test.pdf 7

attachment 8587847 0

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Attachment

eulerian-graph.pdf eulerian-graph.pdf 8

attachment 8587848 0

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Assignment

Rosalind: Assembly part 1 Rosalind: Assembly part 1 10 9

assignment 8745438 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

Rosalind: Assembly part 2 Rosalind: Assembly part 2 5 10

assignment 8745439 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

Sequences from class Sequences from class 11

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Proteomics - Peptide Sequencing (Compeau and Pevzner Ch 4)

Proteomics - Peptide Sequencing (Compeau and Pevzner Ch 4) Proteomics - Peptide Sequencing (Compeau and Pevzner Ch 4)

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Proteomics - lesson plan Proteomics - lesson plan 1

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Assignment

Reading: Proteomics - Chapter 4 in Compeau and Pevzner Reading: Proteomics - Chapter 4 in Compeau and Pevzner 0 2

assignment 8587826 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

Reading Quiz: Proteomics Reading Quiz: Proteomics 6 3

quiz 8587827 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

Rosalind on proteomics Rosalind on proteomics 5 4

assignment 8587828 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

Sequence indexing - Compeau and Pevzner chapter 9

Sequence indexing - Compeau and Pevzner chapter 9 Sequence indexing - Compeau and Pevzner chapter 9

Page

Genome indexing - lesson plan Genome indexing - lesson plan 0

wiki_page 8587862 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

Reading: String indexing - Chapter 9 [volume 2] Reading: String indexing - Chapter 9 [volume 2] 0 1

assignment 8587863 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

Reading quiz: String indexing Reading quiz: String indexing 5 2

quiz 8587864 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 ticket - Genome indexing Exit ticket - Genome indexing 1 3

quiz 8587865 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
Page

Resources Resources 4

wiki_page 8755186 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

Rosalind: Invert Burrows-Wheeler Transform Problem Rosalind: Invert Burrows-Wheeler Transform Problem 1 5

assignment 8587866 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

Sequence alignment - Compeau and Pevzner Chapter 5

Sequence alignment - Compeau and Pevzner Chapter 5 Sequence alignment - Compeau and Pevzner Chapter 5

Page

Sequence alignment - Lesson plan Sequence alignment - Lesson plan 1

wiki_page 8587849 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

Reading: Sequence Alignment (Chapter 5) Reading: Sequence Alignment (Chapter 5) 0 2

assignment 8587850 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

Reading quiz: sequence alignment Reading quiz: sequence alignment 6 3

quiz 8587851 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 ticket: Sequence Alignment Exit ticket: Sequence Alignment 1 4

quiz 8587852 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

Rosalind: Longest common subsequence Rosalind: Longest common subsequence 5 5

assignment 8587853 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

Clustering

Clustering Clustering

Page

Clustering - Lesson Plan Clustering - Lesson Plan 0

wiki_page 8766021 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

Reading: clustering Reading: clustering 0 2

assignment 8587869 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

Reading quiz: clustering Reading quiz: clustering 5 3

quiz 8587870 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 ticket: clustering Exit ticket: clustering 1 4

quiz 8587871 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

Mid-semester evaluation

Mid-semester evaluation Mid-semester evaluation

Assignment

Expectation survey - Midterm 1 Expectation survey - Midterm 1 0 1

assignment 8587830 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

Rate your team-mates - midterm 1 Rate your team-mates - midterm 1 1 2

quiz 8587831 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

Mid-semester evaluation 2

Mid-semester evaluation 2 Mid-semester evaluation 2

Attachment

Grades after midterm 2.pdf Grades after midterm 2.pdf 2

attachment 8762378 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
Quiz

Rate your team-mates - midterm 2 Rate your team-mates - midterm 2 1 3

quiz 8762568 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