Course modules
Preparation
Preparation
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Overview PageOverview OverviewScore 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 completed Must mark this module item done in order to complete Marked completed 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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Pre-course PagePre-course Pre-courseScore 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 completed Must mark this module item done in order to complete Marked completed 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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Data pre-processing PageData pre-processing Data pre-processingScore 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 completed Must mark this module item done in order to complete Marked completed 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
Day 1: Introduction, ML view of omics integration, introduction to Unsupervised Integration
Day 1: Introduction, ML view of omics integration, introduction to Unsupervised Integration
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Introduction PageIntroduction IntroductionScore 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 completed Must mark this module item done in order to complete Marked completed 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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Machine Learning view of Integration PageMachine Learning view of Integration Machine Learning view of IntegrationScore 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 completed Must mark this module item done in order to complete Marked completed 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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Unsupervised Integration PageUnsupervised Integration Unsupervised IntegrationScore 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 completed Must mark this module item done in order to complete Marked completed 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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Lab: Unsupervised Integration through MOFA2 PageLab: Unsupervised Integration through MOFA2 Lab: Unsupervised Integration through MOFA2Score 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 completed Must mark this module item done in order to complete Marked completed 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
Day 1: Unsupervised Integration through MOFA
Day 1: Unsupervised Integration through MOFA
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Multi-Omics Factor Analysis - MOFA PageMulti-Omics Factor Analysis - MOFA Multi-Omics Factor Analysis - MOFAScore 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 completed Must mark this module item done in order to complete Marked completed 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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Lab: MOFA for personalized medicine PageLab: MOFA for personalized medicine Lab: MOFA for personalized medicineScore 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 completed Must mark this module item done in order to complete Marked completed 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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Bonus materials: mofa PageBonus materials: mofa Bonus materials: mofaScore 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 completed Must mark this module item done in order to complete Marked completed 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
Day 2: Supervised Integration through Mixomics
Day 2: Supervised Integration through Mixomics
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Your instructor PageYour instructor Your instructorScore 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 completed Must mark this module item done in order to complete Marked completed 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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Preliminary background on PCA PagePreliminary background on PCA Preliminary background on PCAScore 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 completed Must mark this module item done in order to complete Marked completed 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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Lecture PageLecture LectureScore 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 completed Must mark this module item done in order to complete Marked completed 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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Lab: Application to a microarray data set PageLab: Application to a microarray data set Lab: Application to a microarray data setScore 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 completed Must mark this module item done in order to complete Marked completed 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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Bonus materials: mixomics PageBonus materials: mixomics Bonus materials: mixomicsScore 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 completed Must mark this module item done in order to complete Marked completed 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
Day 2: Deep Learning and UMAP integration
Day 2: Deep Learning and UMAP integration
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Deep Learning for Omics integration PageDeep Learning for Omics integration Deep Learning for Omics integrationScore 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 completed Must mark this module item done in order to complete Marked completed 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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Lab: Deep learning PageLab: Deep learning Lab: Deep learningScore 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 completed Must mark this module item done in order to complete Marked completed 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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UMAP for data integration PageUMAP for data integration UMAP for data integrationScore 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 completed Must mark this module item done in order to complete Marked completed 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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Lab: UMAP for data integration PageLab: UMAP for data integration Lab: UMAP for data integrationScore 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 completed Must mark this module item done in order to complete Marked completed 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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Bonus lab: dimensionality reduction PageBonus lab: dimensionality reduction Bonus lab: dimensionality reductionScore 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 completed Must mark this module item done in order to complete Marked completed 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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Bonus lab: integration at single-cell level PageBonus lab: integration at single-cell level Bonus lab: integration at single-cell levelScore 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 completed Must mark this module item done in order to complete Marked completed 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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Bonus materials: deep learning PageBonus materials: deep learning Bonus materials: deep learningScore 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 completed Must mark this module item done in order to complete Marked completed 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
Day 3: Network Analysis
Day 3: Network Analysis
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Introduction to network analysis PageIntroduction to network analysis Introduction to network analysisScore 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 completed Must mark this module item done in order to complete Marked completed 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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Network inference and properties PageNetwork inference and properties Network inference and propertiesScore 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 completed Must mark this module item done in order to complete Marked completed 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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Community analysis PageCommunity analysis Community analysisScore 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 completed Must mark this module item done in order to complete Marked completed 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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Lab: Network construction and analysis of a transcriptomic and metabolomic dataset PageLab: Network construction and analysis of a transcriptomic and metabolomic dataset Lab: Network construction and analysis of a transcriptomic and metabolomic datasetScore 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 completed Must mark this module item done in order to complete Marked completed 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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Bonus lab: Feature selection PageBonus lab: Feature selection Bonus lab: Feature selectionScore 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 completed Must mark this module item done in order to complete Marked completed 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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Bonus lab: data pre-processing in python PageBonus lab: data pre-processing in python Bonus lab: data pre-processing in pythonScore 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 completed Must mark this module item done in order to complete Marked completed 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
Day 4: Similarity Network Fusion and Non-negative Matrix Factorization
Day 4: Similarity Network Fusion and Non-negative Matrix Factorization
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Non-negative Matrix Factorization PageNon-negative Matrix Factorization Non-negative Matrix FactorizationScore 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 completed Must mark this module item done in order to complete Marked completed 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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Similarity Network Fusion PageSimilarity Network Fusion Similarity Network FusionScore 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 completed Must mark this module item done in order to complete Marked completed 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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Lab: Non-negative Matrix Factorization PageLab: Non-negative Matrix Factorization Lab: Non-negative Matrix FactorizationScore 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 completed Must mark this module item done in order to complete Marked completed 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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Lab: Similarity Network Fusion PageLab: Similarity Network Fusion Lab: Similarity Network FusionScore 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 completed Must mark this module item done in order to complete Marked completed 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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Bonus material: NMF and SNF PageBonus material: NMF and SNF Bonus material: NMF and SNFScore 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 completed Must mark this module item done in order to complete Marked completed 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
Day 4: Genome-scale metabolic modeling
Day 4: Genome-scale metabolic modeling
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Constraint-based modeling of metabolism PageConstraint-based modeling of metabolism Constraint-based modeling of metabolismScore 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 completed Must mark this module item done in order to complete Marked completed 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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Lab: constraint-based modeling of metabolism (in Python with cobrapy) PageLab: constraint-based modeling of metabolism (in Python with cobrapy) Lab: constraint-based modeling of metabolism (in Python with cobrapy)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 completed Must mark this module item done in order to complete Marked completed 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
Day 5: Gene set analysis, reporter features and network-meta analysis
Day 5: Gene set analysis, reporter features and network-meta analysis
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Network meta-analysis - Lecture PageNetwork meta-analysis - Lecture Network meta-analysis - LectureScore 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 completed Must mark this module item done in order to complete Marked completed 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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Network meta-analysis - lab PageNetwork meta-analysis - lab Network meta-analysis - labScore 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 completed Must mark this module item done in order to complete Marked completed 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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Gene set analyses - Lecture PageGene set analyses - Lecture Gene set analyses - LectureScore 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 completed Must mark this module item done in order to complete Marked completed 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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Gene set analysis and reporter features - lab PageGene set analysis and reporter features - lab Gene set analysis and reporter features - labScore 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 completed Must mark this module item done in order to complete Marked completed 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
Bonus material
Bonus material
Module completed
Module in progress
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Multi Omics Data Management PageMulti Omics Data Management Multi Omics Data ManagementScore 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 completed Must mark this module item done in order to complete Marked completed 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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Visualization with Cytoscape PageVisualization with Cytoscape Visualization with CytoscapeScore 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 completed Must mark this module item done in order to complete Marked completed 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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Circos & Hive visualization PageCircos & Hive visualization Circos & Hive visualizationScore 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 completed Must mark this module item done in order to complete Marked completed 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
Additional Materials
Additional Materials
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Additional reading PageAdditional reading Additional readingScore 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 completed Must mark this module item done in order to complete Marked completed 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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Open seminars PageOpen seminars Open seminarsScore 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 completed Must mark this module item done in order to complete Marked completed 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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FAQs PageFAQs FAQsScore 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 completed Must mark this module item done in order to complete Marked completed 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