Course Modules

START HERE!

START HERE!
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START HERE! 1547383    
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    Get started Get started
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  • Quiz
    Getting to know you Getting to know you
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  • Quiz
    Class policy quiz Class policy quiz
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Logistics

Logistics
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Logistics 1547384    
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    Planned class schedule Planned class schedule
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    Grading and deadlines Grading and deadlines
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    Submitting programming assignments Submitting programming assignments
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    FAQ: programming assignments FAQ: programming assignments
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    Class resources Class resources
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    Good learning practices Good learning practices
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Intro to Biology and Informatics

Intro to Biology and Informatics
Prerequisites: Logistics, START HERE!
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Intro to Biology and Informatics 1547385    
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    Intro to biology: learning outcomes Intro to biology: learning outcomes
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  • Assignment
    Reading: introduction to biology Reading: introduction to biology
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  • Quiz
    Reading quiz: Intro to biology Reading quiz: Intro to biology
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  • External Url
    Video: Introduction to biology part 1 Video: Introduction to biology part 1
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  • Attachment
    Slides: Part1_Intro_to_Biology_and_Bioinformatics.pdf Slides: Part1_Intro_to_Biology_and_Bioinformatics.pdf
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  • Quiz
    Quiz: Introduction to DNA Quiz: Introduction to DNA
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  • External Url
    Video: Introduction to biology part 2 Video: Introduction to biology part 2
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  • Attachment
    Slides: Part2_Intro_to_Biology_and_Bioinformatics.pdf Slides: Part2_Intro_to_Biology_and_Bioinformatics.pdf
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  • Quiz
    Quiz: Sequencing technologies Quiz: Sequencing technologies
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  • External Url
    Video: Introduction to biology part 3 Video: Introduction to biology part 3
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  • Attachment
    Slides: Part3_Intro_to_Biology_and_Bioinformatics.pdf Slides: Part3_Intro_to_Biology_and_Bioinformatics.pdf
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  • Page
    More information about biology and sequencing More information about biology and sequencing
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  • Assignment
    Programming assignment: count DNA letters Programming assignment: count DNA letters
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  • Page
    ORFs and Central dogma ORFs and Central dogma
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  • Quiz
    End of module assessment: Intro to biology End of module assessment: Intro to biology
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Chapter 1: Patterns in DNA

Chapter 1: Patterns in DNA
Module Completed Module In Progress Module Locked
Chapter 1: Patterns in DNA 1547386    
  • Page
    Chapter 1: learning outcomes Chapter 1: learning outcomes
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  • Assignment
    Reading: Chapter 1 - Finding patterns Reading: Chapter 1 - Finding patterns
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  • Quiz
    Reading quiz: Chapter 1 Reading quiz: Chapter 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   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 lectures - Patterns in DNA Video lectures - Patterns in DNA
    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
  • External Url
    Video: Finding biological signals, Part 1 Video: Finding biological signals, Part 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   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
    Slides: Part1_Finding_Biological_Signals.pdf Slides: Part1_Finding_Biological_Signals.pdf
    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
    Quiz: Introduction to biological signals Quiz: Introduction to biological signals
    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
  • External Url
    Video: Finding biological signals, Part 2 Video: Finding biological signals, Part 2
    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
    Slides: Part2_Finding_Biological_Signals.pdf Slides: Part2_Finding_Biological_Signals.pdf
    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
  • External Url
    Video: Finding biological signals, Part 3 Video: Finding biological signals, Part 3
    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
    Slides: Part3_Finding_Biological_Signals.pdf Slides: Part3_Finding_Biological_Signals.pdf
    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
    Quiz: Strings and numbers Quiz: Strings and numbers
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  • External Url
    Video: Finding biological signals, Part 4 Video: Finding biological signals, Part 4
    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
    Slides: Part4_Finding_Biological_Signals.pdf Slides: Part4_Finding_Biological_Signals.pdf
    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
    Quiz: More DNA replication Quiz: More DNA replication
    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
    Programming assignment: Tools for DNA replication Programming assignment: Tools for DNA replication
    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
    More on replication More on replication
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  • Quiz
    End of module assessment: Patterns in DNA End of module assessment: Patterns in DNA
    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
    Practice: patterns in DNA Practice: patterns in DNA
    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

Z and KMP algorithm

Z and KMP algorithm
Module Completed Module In Progress Module Locked
Z and KMP algorithm 1547387    
  • Page
    Z algorithm and KMP algorithms: Learning outcomes Z algorithm and KMP algorithms: Learning outcomes
    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: Z and KMP algorithms. Reading: Z and KMP algorithms.
    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
    Exact matching with the Z and KMP algorithms Exact matching with the Z and KMP algorithms
    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: Z and KMP algorithms Reading quiz: Z and KMP algorithms
    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 lectures: Z and KMP algorithms Video lectures: Z and KMP algorithms
    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
  • External Url
    Video: Introduction to exact matching Video: Introduction to exact matching
    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
    Slides: Introduction to exact matching Slides: Introduction to exact matching
    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
    Quiz: Introduction to exact matching Quiz: Introduction to exact matching
    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
  • External Url
    Video: Introduction to the Z algorithm Video: Introduction to the Z algorithm
    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
    Slides: Introduction to the Z algorithm Slides: Introduction to the Z algorithm
    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
  • External Url
    Video: Computation of the Z values Video: Computation of the Z values
    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
    Slides: Computation of the Z values Slides: Computation of the Z values
    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
    Quiz: The Z algorithm Quiz: The Z algorithm
    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
    Z-algorithm walk-through Z-algorithm walk-through
    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
  • External Url
    Video: Introduction to the KMP algorithm Video: Introduction to the KMP algorithm
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  • Attachment
    Slides: Introduction to the KMP algorithm Slides: Introduction to the KMP algorithm
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  • External Url
    Video: Computation of the KMP sp values Video: Computation of the KMP sp values
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  • Attachment
    Slides: Computation of KMP sp values Slides: Computation of KMP sp values
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  • Quiz
    Quiz: The KMP algorithm Quiz: The KMP algorithm
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  • Page
    Sp-value-computation-KMP Sp-value-computation-KMP
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  • External Url
    Video: Aside on data compression Video: Aside on data compression
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  • Attachment
    Slides: Aside on data compression Slides: Aside on data compression
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  • Assignment
    Programming assignment: Exact matching with KMP and the Z algorithm Programming assignment: Exact matching with KMP and the Z algorithm
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  • Page
    Suffixes and prefixes Suffixes and prefixes
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  • Quiz
    z z
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  • Quiz
    End of module assessment: Z and KMP End of module assessment: Z and KMP
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  • Quiz
    KMP KMP
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  • Quiz
    Z to sp Z to sp
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Chapter 2: Motif search

Chapter 2: Motif search
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Chapter 2: Motif search 1547388    
  • Page
    Learning outcomes: motif finding Learning outcomes: motif finding
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  • Assignment
    Reading: Chapter 2 - Motif finding Reading: Chapter 2 - Motif finding
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  • Attachment
    Motif finding.pdf Motif finding.pdf
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  • Quiz
    Reading quiz: Motif finding Reading quiz: Motif finding
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  • Assignment
    Video lectures: motif finding Video lectures: motif finding
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  • External Url
    Video: Introduction to motif finding Video: Introduction to motif finding
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  • Attachment
    Slides: Introduction to motif finding Slides: Introduction to motif finding
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  • Quiz
    Quiz: Introduction to motif finding Quiz: Introduction to motif finding
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  • External Url
    Video: Defining motifs Video: Defining motifs
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  • Attachment
    Slides: Defining motifs Slides: Defining motifs
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  • Quiz
    Quiz: defining motifs Quiz: defining motifs
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  • External Url
    Video: Searching for motifs Video: Searching for motifs
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  • Attachment
    Slides: Searching for motifs Slides: Searching for motifs
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  • Quiz
    Quiz: Searching for motifs Quiz: Searching for motifs
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  • External Url
    Video: Gibbs sampler in practice Video: Gibbs sampler in practice
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  • Attachment
    Slides: Gibbs sampler in practice Slides: Gibbs sampler in practice
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  • Page
    Resources: greedy motif Search Resources: greedy motif Search
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  • Attachment
    Gibbs sampler example.pdf Gibbs sampler example.pdf
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  • Attachment
    Some tools used to find and catalog motifs Some tools used to find and catalog motifs
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  • Assignment
    Independent study - motif finding exercise Independent study - motif finding exercise
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  • Assignment
    Programming assignment: Greedy motif search with Laplace Programming assignment: Greedy motif search with Laplace
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  • Page
    Another way to look at motif finding Another way to look at motif finding
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  • Quiz
    End of module assessment: Motif search End of module assessment: Motif search
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Chapter 9: Sequence indexing

Chapter 9: Sequence indexing
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Chapter 9: Sequence indexing 1547392    
  • Page
    Learning outcomes: Chapter 9 - string indexing Learning outcomes: Chapter 9 - string indexing
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  • Assignment
    Reading: String indexing part 1 Reading: String indexing part 1
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  • Quiz
    Reading quiz: String indexing part 1 Reading quiz: String indexing part 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   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
  • External Url
    Video: Introduction to suffix trees Video: Introduction to suffix trees
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  • Attachment
    Slides: Introduction to suffix trees Slides: Introduction to suffix trees
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  • Quiz
    Quiz: Introduction to suffix trees Quiz: Introduction to suffix trees
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  • External Url
    Video: Using suffix trees Video: Using suffix trees
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  • Attachment
    Slides: Using suffix trees Slides: Using suffix trees
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  • Quiz
    Quiz: Using suffix trees Quiz: Using suffix trees
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  • External Url
    Video: Building suffix trees Video: Building suffix trees
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  • Assignment
    Programming assignment: Construct a suffix tree (BA9C) Programming assignment: Construct a suffix tree (BA9C)
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  • Page
    Clarifications on suffix trees Clarifications on suffix trees
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  • Assignment
    Reading: Sequence indexing part 2 Reading: Sequence indexing part 2
    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 indexing part 2 Reading quiz: Sequence indexing part 2
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  • External Url
    Video: Suffix arrays Video: Suffix arrays
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  • Attachment
    Slides: Suffix arrays Slides: Suffix arrays
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  • Quiz
    Quiz: Suffix arrays Quiz: Suffix arrays
    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
  • External Url
    Video: The Burrows Wheeler Transform Video: The Burrows Wheeler Transform
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  • Attachment
    Slides: The Burrows Wheeler Transform Slides: The Burrows Wheeler Transform
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  • Quiz
    Quiz: The Burrows Wheeler Transform Quiz: The Burrows Wheeler Transform
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  • Attachment
    Ben Langmead's lecture slides on BWT and the FM index Ben Langmead's lecture slides on BWT and the FM index
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  • Assignment
    Programming assignment: Inverting the Burrows Wheeler transform (BA9J) Programming assignment: Inverting the Burrows Wheeler transform (BA9J)
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  • Quiz
    Practice: suffix arrays Practice: suffix arrays
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  • Quiz
    End of module assessment: Sequence indexing End of module assessment: Sequence indexing
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Chapter 5: Sequence alignment

Chapter 5: Sequence alignment
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    Learning outcomes: Chapter 5 - sequence alignment Learning outcomes: Chapter 5 - sequence alignment
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  • Assignment
    Reading: Chapter 5 - Sequence Alignment part 1 Reading: Chapter 5 - Sequence Alignment part 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   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 part 1 Reading quiz: sequence alignment part 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   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
  • External Url
    Video: Introduction to inexact alignment Video: Introduction to inexact alignment
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  • Attachment
    Slides: Introduction to inexact alignment Slides: Introduction to inexact alignment
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  • Quiz
    Quiz: Introduction to inexact alignment Quiz: Introduction to inexact alignment
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  • External Url
    Video: Longest common subsequence, alignments, and graphs Video: Longest common subsequence, alignments, and graphs
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  • Attachment
    Slides: Longest common subsequence, alignments, and graphs Slides: Longest common subsequence, alignments, and graphs
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  • Quiz
    Quiz: Longest common subsequence, alignments, and graphs Quiz: Longest common subsequence, alignments, and graphs
    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
  • External Url
    Video: Solving LCS with dynamic programming Video: Solving LCS with dynamic programming
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  • Attachment
    Slides: Solving LCS with dynamic programming Slides: Solving LCS with dynamic programming
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  • Quiz
    Quiz: Solving LCS with dynamic programming Quiz: Solving LCS with dynamic programming
    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
  • External Url
    Video: Local alignment Video: Local alignment
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  • Attachment
    Slides: Local alignment Slides: Local alignment
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  • Quiz
    Quiz: Local alignment Quiz: Local alignment
    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
    Programming assignment: Find the highest scoring alignment of two strings (BA5E) Programming assignment: Find the highest scoring alignment of two strings (BA5E)
    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
    Alignment_challenge Alignment_challenge
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  • Assignment
    Reading: Chapter 5 - sequence alignment part 2 Reading: Chapter 5 - sequence alignment part 2
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  • Quiz
    Reading quiz: Chapter 5 - sequence alignment part 2 Reading quiz: Chapter 5 - sequence alignment part 2
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  • External Url
    Video: Affine gap penalties Video: Affine gap penalties
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  • Attachment
    Slides: Affine gap penalties Slides: Affine gap penalties
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  • Quiz
    Quiz: Affine gap penalties Quiz: Affine gap penalties
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  • External Url
    Video: Sequence alignment in linear space Video: Sequence alignment in linear space
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  • Attachment
    Slides: Sequence alignment in linear space Slides: Sequence alignment in linear space
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  • Quiz
    Quiz: Sequence alignment in linear space Quiz: Sequence alignment in linear space
    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
    Programming assignment: Find a highest-scoring local alignment of two strings (BA5F) Programming assignment: Find a highest-scoring local alignment of two strings (BA5F)
    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
    More details on dynamic programming alignment More details on dynamic programming alignment
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  • Attachment
    Intro to dynamic programming.pdf Intro to dynamic programming.pdf
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  • Quiz
    End of module assessment: Sequence alignment End of module assessment: Sequence alignment
    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

Chapter 4: Proteomics - Peptide Sequencing

Chapter 4: Proteomics - Peptide Sequencing
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  • Page
    Learning outcomes: proteomics/mass-spectrometry Learning outcomes: proteomics/mass-spectrometry
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  • Assignment
    Reading: Chapter 4 - Mass-spectrometry, branch and bound, leaderboard search Reading: Chapter 4 - Mass-spectrometry, branch and bound, leaderboard search
    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: Mass-spectrometry, branch and bound, leaderboard search Reading quiz: Mass-spectrometry, branch and bound, leaderboard search
    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
  • External Url
    Video: Introduction to mass-spectrometry Video: Introduction to mass-spectrometry
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  • Attachment
    1. Introduction to mass-spectrometry.pdf 1. Introduction to mass-spectrometry.pdf
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  • Quiz
    Quiz: Introduction to mass-spectrometry Quiz: Introduction to mass-spectrometry
    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
  • External Url
    Video: Solving perfect spectra Video: Solving perfect spectra
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  • Attachment
    2. Solving perfect spectra.pdf 2. Solving perfect spectra.pdf
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  • Quiz
    Quiz: Solving perfect spectra Quiz: Solving perfect spectra
    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
  • External Url
    Video: Solving imperfect spectra Video: Solving imperfect spectra
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  • Attachment
    3. Solving imperfect spectra.pdf 3. Solving imperfect spectra.pdf
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  • Quiz
    Quiz: Solving imperfect spectra Quiz: Solving imperfect spectra
    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
  • External Url
    Video: Implementation details Video: Implementation details
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  • Attachment
    4. Implementation details.pdf 4. Implementation details.pdf
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  • Assignment
    Independent study: Proteomics Independent study: Proteomics
    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
    Programming assignment: Branch and bound solving of mass spectra (BA4E) Programming assignment: Branch and bound solving of mass spectra (BA4E)
    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
    Cyclopeptide sequencing walk-through Cyclopeptide sequencing walk-through
    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
    End of module assessment: Peptide sequencing End of module assessment: Peptide sequencing
    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

Ethics

Ethics
Module Completed Module In Progress Module Locked
Ethics 1547395    
  • Page
    Learning outcomes: Ethics Learning outcomes: Ethics
    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 and quiz: Ethics Reading and quiz: Ethics
    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
  • External Url
    Video: Ethics part 1 Video: Ethics part 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   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
  • External Url
    Video: Ethics part 2 Video: Ethics part 2
    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
  • External Url
    Video: National Library of Medicine video on the Belmont report Video: National Library of Medicine video on the Belmont report
    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
    Ethical conundrums Ethical conundrums
    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
    End of module assessment: Ethics End of module assessment: Ethics
    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

Chapter 8: Clustering

Chapter 8: Clustering
Module Completed Module In Progress Module Locked
Chapter 8: Clustering 1547394    
  • Page
    Learning outcomes: Chapter 8 - clustering Learning outcomes: Chapter 8 - clustering
    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: Chapter 8 - Clustering Reading: Chapter 8 - Clustering
    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: Chapter 8 - clustering Reading quiz: Chapter 8 - clustering
    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
  • External Url
    Video: Introduction to clustering Video: Introduction to clustering
    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
    Slides: Introduction to clustering Slides: Introduction to clustering
    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
    Quiz: Introduction to clustering Quiz: Introduction to clustering
    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
  • External Url
    Video: K-means clustering Video: K-means clustering
    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
    Slides: K-means clustering Slides: K-means clustering
    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
    Quiz: K-means clustering Quiz: K-means clustering
    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
  • External Url
    Video: Hierarchical clustering Video: Hierarchical clustering
    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
    Sildes: Hierarchical clustering Sildes: Hierarchical clustering
    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
    Quiz: Hierarchical clustering Quiz: Hierarchical clustering
    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
    Programming assignment: K-means clustering, Lloyd's algorithm (BA8C) Programming assignment: K-means clustering, Lloyd's algorithm (BA8C)