Class Time: Tuesday (10:00-11:00 am) , Wednesday (12:00-1:00 pm) and Friday (10:00-11:00 am)
Place: CEP 108
First Class: Tuesday, January 5, 2016 (Only class in first week)
You must fill this if you are unable to come to lecture for reasons beyond your control.
4 January - 10 January
Introduction and History
Lecture 1: Introduction to synthetic biology and headlines
11 January - 17 January
Lecture 2: Introduction to molecular biology
Leccture 3: Human Genome Project and Vedio of Life 2.0
Lecture 4: Central Dogma of Life and Extract your DNA!
18 January - 24 January
Lecture 5: ORF Finder and Genetic Code
Lecture 6: Challenges in Molecular Biology
Lecture 7: Handson Matlab for sequence analysis using bioinformaticss toolbox
25 January - 31 January
Lecture 8: Introduction to protein structures, protein domains and motifs
Lecture 9: Demo on BLAST and PDB.
1 February - 7 February
Lecture 10: Introduction to differential equation, SPiM simulator and Pi Calculus.
Lecture 11: Abstract Machines of systems biology: Gene Machine, protein machines and membrane machines, molecular interaction maps.
Lecture 12: Gene Machines: Gene Regulatory Networks.
8 February - 14 February
Lecture 13: Membrane Machines
15 February - 21 February
Lecture 14: Modeling With SPIM, Hybrid Model
Lecture 15: The Logistic Equation
22 February - 28 February
Lecture 13: Phase plane analysis, Steady state analysis
Lecture 14: Bifurcation analysis, Transcitical Bifurcation
Lecture 15: Pitchfork bifurcation
29 February - 6 March
This is the list of tool assigned to each student for presentation. Each student have to explain the tool and give the demo of tool. Presentation dates will be declared soon. It will be held before second insem so that you can prepare for project.
Lecture 16: Enzymatic Reactions and Law of mass action
Lecture 17: Michaelis–Menten equation, Hills Equation, conservation law
Lecture 18: Stochastic Pi Calculus introduction
7 March - 13 March
Lecture 19: Presentation
Lecture 20: Presentation
Lecture 21: Presentation
If you think your course project have potenital, you can bring it to world by participating in the synthetic biology competion. Click on the link to know more about the competition Indian Biological Engineering Competition (iBEC).
14 March - 20 March
21 March - 27 March
Mid term break
28 March - 3 April
Lecture 22: Genetic Switch
Lecture 23: Genetic Switch Modeling
Lecture 24: Nonlinear Dynamics for Modeling the Genetic Switch
4 April - 10 April
Lecture 25: Central Dogma Modeling
Lecture 26: GEC: Towards Programming Language for Genetic Engineering of Living Cells
Lecture 27: Structural Synthetic Biology
11 April - 17 April
Lecture 28: Structural Synthetic Biology Applications
Lecture 29: Synthetic Data Storage
18 April - 24 April
Lecture 30: Synthetic Data Storage models
For Synthetic Biology Project Submission :Deadline April 26. Submit the following for the project.
1. Report in latex format (including all source files such as figures, .tex file and pdf files)
2. Link to youtube video (The video should contain your presentation of the project. You can use any software to create the video. Video presentation can also have slides. There is no limitation on the time length of the video however 1 one hour video should be good enough to explain the project.)
3. The ppt file of the presentation used in the video.
4. If you reach up to developing a software than please include a complete source code and help file including a manual on how to use the software.
Lecture 31: Synthetic data stroage models
Lecture 32: Selected Applications of synthetic biology