System Biology and Biotechnology Specialization

About Course

Systems Biology and Biotechnology Specialization, Design systems-level experiments using appropriate cutting edge techniques, collect big data, and analyze and interpret small and big data sets quantitatively. The Systems Biology Specialization covers the concepts and methodologies used in systems-level analysis of biomedical systems. Successful participants will learn how to use experimental, computational and mathematical methods in systems biology and how to design practical systems-level frameworks to address questions in a variety of biomedical fields. In the final Capstone Project, students will apply the methods they learned in five courses of specialization to work on a research project.

Course Content

01. Introduction to Systems Biology

001 01_required-reading-list_instructions.html

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006 02_overview-of-systems-level-reasoning-molecules-to-pathways.mp4

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009 01_systems-level-reasoning-i.mp4

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012 02_systems-level-reasoning-ii.mp4

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015 03_lecture-slides_instructions.html

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018 01_molecules-to-pathways-camp-and-g-protein-pathways-i.mp4

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021 02_molecules-to-pathways-camp-and-g-protein-pathways-ii.mp4

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024 03_lecture-slides_instructions.html

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029 01_pathways-to-networks-map-kinase-pathways-network-i.mp4

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032 02_pathways-to-networks-map-kinase-pathways-network-ii.mp4

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035 03_lecture-slides_instructions.html

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038 01_mechanical-forces-in-cell-biology.mp4

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040 02_lecture-slides_instructions.html

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043 01_electrical-activity-in-cell-biology.mp4

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045 02_lecture-slides_instructions.html

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049 01_mathematical-representations-of-cell-biological-systems-i.mp4

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051 02_lecture-slides_instructions.html

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054 01_mathematical-representations-of-cell-biological-systems-ii.mp4

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056 02_lecture-slides_instructions.html

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059 01_simulations-of-cell-biological-systems-i.mp4

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062 02_simulations-of-cell-biological-systems-ii.mp4

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065 03_lecture-slides_instructions.html

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069 01_experimental-technologies.mp4

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071 02_lecture-slides_instructions.html

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074 01_analyzing-large-data-sets.mp4

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076 02_lecture-slides_instructions.html

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079 01_network-building-analysis-and-data-organization.mp4

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081 02_lecture-slides_instructions.html

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084 01_building-networks.mp4

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086 02_lecture-slides_instructions.html

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091 01_analysis-of-networks-i.mp4

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094 02_analysis-of-networks-ii.mp4

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097 03_lecture-slides_instructions.html

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100 01_from-topology-to-function-directed-sign-specified-graphs-i.mp4

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102 02_lecture-slides_instructions.html

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105 01_from-topology-to-function-directed-sign-specified-graphs-ii.mp4

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107 02_lecture-slides_instructions.html

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111 01_strengths-and-limitations-of-different-types-of-models-i.mp4

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113 02_lecture-slides_instructions.html

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116 01_strengths-and-limitations-of-different-types-of-models-ii.mp4

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118 02_lecture-slides_instructions.html

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121 01_identifying-emergent-properties-bistability-i.mp4

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123 02_lecture-slides_instructions.html

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126 01_identifying-emergent-properties-bistability-ii.mp4

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128 02_lecture-slides_instructions.html

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132 01_ultrasensitivity.mp4

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134 02_lecture-slides_instructions.html

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137 01_robustness-and-scaffolds.mp4

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139 02_lecture-slides_instructions.html

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142 01_case-studies-i.mp4

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144 02_lecture-slides_instructions.html

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147 01_case-studies-ii.mp4

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149 02_lecture-slides_instructions.html

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153 01_case-studies-iii.mp4

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155 02_lecture-slides_instructions.html

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158 01_case-studies-iv.mp4

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160 02_lecture-slides_instructions.html

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163 01_systems-biomedicine.mp4

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165 02_lecture-slides_instructions.html

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168 01_systems-pharmacology-and-therapeutics.mp4

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170 02_lecture-slides_instructions.html

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173 01_perspective.mp4

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02. Experimental Methods in Systems Biology

005 02_lecture-slides_instructions.html

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008 01_lecture-2-biological-model-systems.mp4

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010 02_lecture-slides_instructions.html

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013 01_lecture-3-experimental-perturbations.mp4

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015 02_lecture-slide_instructions.html

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018 01_lecture-4-measuring-nucleic-acids.mp4

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020 02_lecture-slides_instructions.html

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023 01_lecture-5-measuring-protein-and-protein-states.mp4

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025 02_lecture-slides_instructions.html

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030 01_lecture-1-history-of-sequencing.mp4

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033 02_lecture-2-2nd-and-3rd-generation-sequencing.mp4

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036 03_lecture-slides_instructions.html

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039 01_lecture-3-illumina-based-mrna-sequencing.mp4

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041 02_lecture-slides_instructions.html

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044 01_lecture-4-lab-based-video.mp4

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049 02_lecture-slides_instructions.html

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054 01_lecture-1-basics-of-mass-spectrometry-1.mp4

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057 02_lecture-2-basics-of-mass-spectrometry-2.mp4

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060 03_lecture-slides_instructions.html

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063 01_lecture-3-quantification-in-proteomics.mp4

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065 02_lecture-slides_instructions.html

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068 01_lecture-4-lab-based-video-proteomics-day-1.mp4

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071 02_lecture-5-lab-based-video-proteomics-day-2.mp4

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074 03_lecture-6-lab-based-video-analysis.mp4

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082 01_lecture-1-flow-cytometry-1.mp4

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087 02_lecture-2-flow-cytometry-2.mp4

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090 03_lecture-slides_instructions.html

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093 01_lecture-3-mass-cytometry.mp4

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095 02_lecture-slides_instructions.html

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098 01_lecture-4-cytometry-data-analysis.mp4

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100 02_lecture-slides_instructions.html

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103 01_lecture-5-lab-based-video-flow-cytometry-acquisition.mp4

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106 02_lecture-6-lab-based-video-flow-cytometry-analysis.mp4

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109 01_lecture-7-lab-based-video-mass-cytometry.mp4

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121 02_lecture-2-types-of-imaging.mp4

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124 03_lecture-slides_instructions.html

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129 01_lecture-3-visualizing-molecules-in-living-cells-fluorescent-tools.mp4

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131 02_lecture-slides_instructions.html

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136 01_lecture-4-quantification.mp4

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139 02_lecture-5-lab-based-video.mp4

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141 03_lecture-slides_instructions.html

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146 01_lecture-1-omics-data-and-network-model-analyses.mp4

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148 02_lecture-slides_instructions.html

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151 01_lecture-2-single-cell-time-course-data-and-dynamical-model-analyses.mp4

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153 02_lecture-slides_instructions.html

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157 01_lecture-3-dynamical-model-case-study.mp4

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159 02_lecture-slides_instructions.html

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160 01_reading-list_instructions.html

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links.txt

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003 01_lecture-1-scope-and-overview.mp4

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03. Network Analysis in Systems Biology

002 02_grading-policy_instructions.html

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005 03_resources-and-links-to-additional-materials_6768.html

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032 04_matlab-license_instructions.html

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036 01_design-principles-of-complex-systems.mp4

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037 02_introduction-to-complex-systems_exam.html

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041 01_introduction-to-cell-biology.mp4

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042 02_introduction-to-cell-biology_exam.html

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046 03_introduction-to-molecular-biology.mp4

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047 04_introduction-to-molecular-biology_exam.html

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051 01_small-world-and-scale-free-networks.mp4

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052 02_rich-get-richer_exam.html

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056 01_duplication-divergence-and-network-motifs.mp4

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057 02_duplication-divergence-and-network-motifs_exam.html

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061 01_large-size-motifs-and-complex-models-of-network-evolution.mp4

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062 02_large-size-motifs_exam.html

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066 01_network-properties-of-biological-networks.mp4

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067 02_topological-properties-of-biological-networks_exam.html

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071 01_types-of-biological-networks.mp4

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072 02_types-of-biological-networks_exam.html

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076 01_genes2networks-and-network-visualization.mp4

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077 02_genes2networks-and-network-visualization_exam.html

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081 01_sets2networks-creating-functional-association-networks.mp4

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082 02_functional-association-networks-with-sets2networks_exam.html

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086 01_genes2fans-analyzing-gene-lists-with-functional-association-networks.mp4

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087 02_functional-association-networks-with-genes2fans_exam.html

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091 01_data-normalization.mp4

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092 02_data-normalization_exam.html

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096 01_characteristic-direction-method-part-1.mp4

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100 02_characteristic-direction-method-part-2.mp4

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104 03_characteristic-direction-method-part-3.mp4

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108 04_characteristic-direction-method-part-4.mp4

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109 05_characteristic-direction_exam.html

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113 01_enrichment-analysis-and-enrichr.mp4

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114 02_the-fisher-exact-test-and-enrichr_exam.html

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119 01_geo2enrichr-a-google-chrome-extension-for-gene-set-extraction-and-enrichment.mp4

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124 02_gene-set-enrichment-analysis-gsea-part-1_exam.html

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128 03_gene-set-enrichment-analysis-gsea-part-2.mp4

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129 04_gene-set-enrichment-analysis-gsea-part-2_exam.html

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133 01_principal-angle-enrichment-analysis-paea.mp4

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134 02_principal-angle-enrichment-analysis-paea_exam.html

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138 01_network2canvas-n2c-and-enrichment-analysis-with-n2c.mp4

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139 02_gate-and-network2canvas_exam.html

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141 03_gate-desktop-software-tool_instructions.html

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145 01_expression2kinases-inferring-pathways-from-differentially-expressed-genes.mp4

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146 02_expression2kinases_exam.html

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150 01_drugpairseeker-and-the-new-cmap.mp4

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151 02_drugpairseeker-and-the-new-cmap_exam.html

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155 01_classifying-patients-tumors-from-tcga.mp4

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156 02_classifying-patients-from-tcga_exam.html

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160 01_rna-seq-analysis-preliminaries.mp4

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161 02_rna-seq-and-unix-linux-commands_exam.html

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165 01_rna-seq-analysis-using-tophat-and-cufflinks.mp4

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166 02_rna-seq-pipeline_exam.html

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170 01_rna-seq-analysis-r-basics.mp4

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171 02_cummerbund-and-r-programming_exam.html

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175 03_rna-seq-analysis-cummerbund.mp4

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176 04_cummerbund-demo_exam.html

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180 01_star-an-ultra-fast-rna-seq-aligner.mp4

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181 02_rna-seq-star_exam.html

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185 01_chip-seq-analysis-part-1.mp4

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186 02_chip-seq-analysis-part-1_exam.html

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190 03_chip-seq-analysis-part-2.mp4

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191 04_chip-seq-analysis-part-2_exam.html

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195 01_principal-component-analysis-pca-part-1.mp4

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196 02_principal-component-analysis-pca-part-1_exam.html

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200 03_principal-component-analysis-pca-part-2.mp4

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201 04_principal-component-analysis-pca-part-2_exam.html

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208 05_principal-component-analyis-pca-plotting-in-matlab.mp4

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209 06_principal-component-analysis-pca-with-matlab_exam.html

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210 07_matlab-license_instructions.html

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214 01_clustergram-in-matlab.mp4

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215 02_hierarchical-clustering-hc-with-matlab_exam.html

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219 01_self-organizing-maps.mp4

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220 02_self-organizing-maps_exam.html

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224 01_network-based-clustering.mp4

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225 02_network-based-clustering_exam.html

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229 01_big-data-in-biology-and-data-integration.mp4

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230 02_big-data-in-biology-and-data-integration_exam.html

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234 01_resources-for-data-integration-part-1.mp4

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238 02_resources-for-data-integration-part-2.mp4

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242 03_resources-for-data-integration-part-3.mp4

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246 04_resources-for-data-integration-part-4.mp4

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247 05_resources-for-data-integration_exam.html

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251 01_crowdsourcing-in-bioinformatics.mp4

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255 02_crowdsourcing-tasks-for-this-course.mp4

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256 03_crowdsourcing-microtasks-and-megatasks_exam.html

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257 01_final-exam_exam.html

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links.txt

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04. Dynamical Modeling Methods for Systems Biology

001 01_syllabus_instructions.html

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002 02_supplemental-files_instructions.html

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015 01_lecture-1-introduction.mp4

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016 02_matlab-licenses_instructions.html

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019 03_lecture-2-computing-with-matlab-part-1.mp4

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020 04_lecture-slides_instructions.html

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025 01_lecture-3-computing-with-matlab-part-2.mp4

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026 02_lecture-slides_instructions.html

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028 03_supplementary-files_instructions.html

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036 01_lecture-4-computing-with-matlab-part-3.mp4

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039 02_lecture-5-computing-with-matlab-part-4.mp4

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040 03_just-in-time-matlab-tutorials_instructions.html

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041 04_assignment-1_exam.html

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042 05_lecture-slides_instructions.html

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045 06_supplementary-files_instructions.html

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053 01_lecture-6-introduction-to-dynamical-systems-part-1.mp4

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054 02_lecture-slides_instructions.html

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058 01_lecture-7-introduction-to-dynamical-systems-part-2.mp4

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059 02_lecture-slides_instructions.html

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063 01_lecture-8-introduction-to-dynamical-systems-part-3.mp4

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064 02_lecture-slides_instructions.html

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068 01_lecture-9-introduction-to-dynamical-systems-part-4.mp4

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069 02_assignment-2_exam.html

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070 03_lecture-slides_instructions.html

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074 01_lecture-10-bistability-in-biochemical-signaling-models-part-1.mp4

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077 02_lecture-11-bistability-in-biochemical-signaling-models-part-2.mp4

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078 03_lecture-slides_instructions.html

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083 01_lecture-12-bistability-in-biochemical-signaling-models-part-3.mp4

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084 02_lecture-slides_instructions.html

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088 01_lecture-13-bistability-in-biochemical-signaling-models-part-4.mp4

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089 02_lecture-slides_instructions.html

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093 01_lecture-14-bistability-in-biochemical-signaling-models-part-5.mp4

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096 02_lecture-15-bistability-in-biochemical-signaling-models-part-6.mp4

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097 03_assignment-3_exam.html

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098 04_lecture-slides_instructions.html

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103 01_lecture-16-computational-modeling-of-the-cell-cycle-part-1.mp4

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104 02_lecture-slides_instructions.html

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108 01_lecture-17-computational-modeling-of-the-cell-cycle-part-2.mp4

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109 02_lecture-slides_instructions.html

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113 01_lecture-18-computational-modeling-of-the-cell-cycle-part-3.mp4

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116 02_lecture-19-computational-modeling-of-the-cell-cycle-part-4.mp4

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117 03_assignment-4_exam.html

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118 04_lecture-slides_instructions.html

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123 01_lecture-20-mathematical-models-of-action-potentials-part-1.mp4

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124 02_lecture-slides_instructions.html

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128 01_lecture-21-mathematical-models-of-action-potentials-part-2.mp4

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129 02_lecture-slides_instructions.html

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133 01_lecture-22-mathematical-models-of-action-potentials-part-3.mp4

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134 02_lecture-slides_instructions.html

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138 01_lecture-23-mathematical-models-of-action-potentials-part-4.mp4

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141 02_lecture-24-mathematical-models-of-action-potentials-part-5.mp4

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142 03_lecture-slides_instructions.html

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147 01_lecture-25-mathematical-models-of-action-potentials-part-6.mp4

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148 02_assignment-5_exam.html

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149 03_lecture-slides_instructions.html

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153 01_lecture-26-modeling-with-partial-differential-equations-part-1.mp4

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154 02_lecture-slides_instructions.html

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158 01_lecture-27-modeling-with-partial-differential-equations-part-2.mp4

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161 02_lecture-28-modeling-with-partial-differential-equations-part-3.mp4

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162 03_lecture-slides_instructions.html

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167 01_lecture-29-stochastic-modeling-part-1.mp4

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170 02_lecture-30-stochastic-modeling-part-2.mp4

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171 03_lecture-slides_instructions.html

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05. Integrated Analysis in Systems Biology

001 01_syllabus_instructions.html

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002 02_general-overview_instructions.html

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017 03_supplemental-files_instructions.html

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020 04_lecture-1-experimental-design.mp4

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023 01_lecture-2a-introduction-to-research-article-1-part-1.mp4

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026 02_lecture-2b-introduction-to-research-article-1-part-2.mp4

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027 03_problem-set-1_exam.html

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030 01_lecture-3-issues-of-reproducibility-in-systems-biology.mp4

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034 02_matlab-access-and-tutorials_instructions.html

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035 03_problem-set-2_exam.html

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038 01_lecture-5a-introduction-to-research-article-3-part-1.mp4

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041 02_lecture-5b-introduction-to-research-article-3-part-2.mp4

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042 03_problem-set-3_exam.html

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06. Systems Biology and Biotechnology Capstone

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About Course

What Will You Learn?

Course Content

01. Introduction to Systems Biology

001 01_required-reading-list_instructions.html

006 02_overview-of-systems-level-reasoning-molecules-to-pathways.mp4

009 01_systems-level-reasoning-i.mp4

012 02_systems-level-reasoning-ii.mp4

015 03_lecture-slides_instructions.html

018 01_molecules-to-pathways-camp-and-g-protein-pathways-i.mp4

021 02_molecules-to-pathways-camp-and-g-protein-pathways-ii.mp4

024 03_lecture-slides_instructions.html

029 01_pathways-to-networks-map-kinase-pathways-network-i.mp4

032 02_pathways-to-networks-map-kinase-pathways-network-ii.mp4

035 03_lecture-slides_instructions.html

038 01_mechanical-forces-in-cell-biology.mp4

040 02_lecture-slides_instructions.html

043 01_electrical-activity-in-cell-biology.mp4

045 02_lecture-slides_instructions.html

049 01_mathematical-representations-of-cell-biological-systems-i.mp4

051 02_lecture-slides_instructions.html

054 01_mathematical-representations-of-cell-biological-systems-ii.mp4

056 02_lecture-slides_instructions.html

059 01_simulations-of-cell-biological-systems-i.mp4

062 02_simulations-of-cell-biological-systems-ii.mp4

065 03_lecture-slides_instructions.html

069 01_experimental-technologies.mp4

071 02_lecture-slides_instructions.html

074 01_analyzing-large-data-sets.mp4

076 02_lecture-slides_instructions.html

079 01_network-building-analysis-and-data-organization.mp4

081 02_lecture-slides_instructions.html

084 01_building-networks.mp4

086 02_lecture-slides_instructions.html

091 01_analysis-of-networks-i.mp4

094 02_analysis-of-networks-ii.mp4

097 03_lecture-slides_instructions.html

100 01_from-topology-to-function-directed-sign-specified-graphs-i.mp4

102 02_lecture-slides_instructions.html

105 01_from-topology-to-function-directed-sign-specified-graphs-ii.mp4

107 02_lecture-slides_instructions.html

111 01_strengths-and-limitations-of-different-types-of-models-i.mp4

113 02_lecture-slides_instructions.html

116 01_strengths-and-limitations-of-different-types-of-models-ii.mp4

118 02_lecture-slides_instructions.html

121 01_identifying-emergent-properties-bistability-i.mp4

123 02_lecture-slides_instructions.html

126 01_identifying-emergent-properties-bistability-ii.mp4

128 02_lecture-slides_instructions.html

132 01_ultrasensitivity.mp4

134 02_lecture-slides_instructions.html

137 01_robustness-and-scaffolds.mp4

139 02_lecture-slides_instructions.html

142 01_case-studies-i.mp4

144 02_lecture-slides_instructions.html

147 01_case-studies-ii.mp4

149 02_lecture-slides_instructions.html

153 01_case-studies-iii.mp4

155 02_lecture-slides_instructions.html

158 01_case-studies-iv.mp4

160 02_lecture-slides_instructions.html

163 01_systems-biomedicine.mp4

165 02_lecture-slides_instructions.html

168 01_systems-pharmacology-and-therapeutics.mp4

170 02_lecture-slides_instructions.html

173 01_perspective.mp4

02. Experimental Methods in Systems Biology

005 02_lecture-slides_instructions.html

008 01_lecture-2-biological-model-systems.mp4

010 02_lecture-slides_instructions.html

013 01_lecture-3-experimental-perturbations.mp4

015 02_lecture-slide_instructions.html

018 01_lecture-4-measuring-nucleic-acids.mp4

020 02_lecture-slides_instructions.html

023 01_lecture-5-measuring-protein-and-protein-states.mp4

025 02_lecture-slides_instructions.html

030 01_lecture-1-history-of-sequencing.mp4

033 02_lecture-2-2nd-and-3rd-generation-sequencing.mp4

036 03_lecture-slides_instructions.html

039 01_lecture-3-illumina-based-mrna-sequencing.mp4