The [course_title] course teaches the analysis and design of integrated biological systems using analytical, graphical, and numerical methods. Emphasizes will be given on the modularity and abstraction in biological systems, mathematical encoding of detailed physical problems, statistical methods for solving the dynamics of continuous and discrete chemical systems. Other topics covered in the course are statistics and probability in dynamic systems and pattern recognition, applied local and global optimisation, simple feedback and control analysis, etc.
This course does not involve any written exams. Students need to answer 5 assignment questions to complete the course, the answers will be in the form of written work in pdf or word. Students can write the answers in their own time. Each answer need to be 200 words (1 Page). Once the answers are submitted, the tutor will check and assess the work.
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Course Credit: MIT
|Introduction to Phylogenetic Inference; Case Studies; Phylogenetic Trees; Quick Review of Recursion||00:15:00|
|Review of UPGMA; Purpose of Phylogenetics; Newick Notation||00:15:00|
|Phylogenetic Trees: Overview, Possible Trees||00:30:00|
|Parsimony; Sankoff Downpass Algorithm||00:30:00|
|Downpass (cont.); Fitch’s Up Pass||00:30:00|
|Parsimony (cont.); Overall Strategy; Maximum Likelihood (ML); Jukes-Cantor; Evolutionary Model||00:15:00|
|Greedy Algorithm for Trying Trees||00:30:00|
|Introduction to The Protein Design Problem. What Makes Proteins Fold? Entropy||00:16:00|
|Dihedrals, Build Order||00:15:00|
|When to Use Computational Methods vs. Exact Methods; The Physics Model Underlying Exact Methods||00:30:00|
|Physics Model Underlying Exact Methods (cont.); Using Physics Model to Compute When a Reaction will Take Place.||00:30:00|
|Review of How Physics Model Leads to Computational Method; The Complete Computational Method||00:30:00|
|Difference Between Reaction Rate and Reaction Propensity; Achieving Faster Computation||00:30:00|
|Next Reaction Method Algorithm; Application to Genetic Memory (Latch)||00:30:00|
|Review of Key Concepts||00:30:00|
|Submit Your Assignment||00:00:00|
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