Course Syllabus

BENG/CHEM/PHAR/MATH 276
Numerical Analysis for Multi-Scale Biology

HHMI/NIBIB Interfaces Graduate Training Program Laboratory 2

Winter Quarter, 2021

Tuesdays and Thursdays 3:30 pm - 4:50 pm, Online only via Zoom

January 5th - March 11th, 2021

https://ucsd.zoom.us/j/99161269648

Password: MSM

Course Objectives

This hands-on laboratory course introduces students to numerical methods and computational tools for multi-scale biophysical modeling at the molecular, sub-cellular, whole cell, tissue and organ scales. 

Instructors

Prof. Andrew McCulloch, Department of Bioengineering, email: amcculloch@ucsd.edu

Prof. Rommie Amaro, Department of Chemistry and Biochemistry, email: ramaro@ucsd.edu

Prof. Terry Sejnowski, Salk Institute for Biological Studies and Neurobiology Section, Division of Biological Sciences, email: terry@salk.edu

Dr. Gary Huber, Department of Chemistry and Biochemistry, email: gahuber95@gmail.edu

Dr. Robert Konecny, Department of Chemistry and Biochemistry, email: rok@ucsd.edu

Dr. Tom Bartol, Salk Institute for Biological Studies, email: bartol@salk.edu

Dr. Kevin Vincent, Department of Bioengineering, email: kpvincen@ucsd.edu

Dr. Miriam Bell, Mechanical and Aerospace Engineering PhD Program, mkbell@eng.ucsd.edu

Ariel Wang, Department of Bioengineering, email: arw020@eng.ucsd.edu

Shulin Cao, Department of Bioengineering, email: shc131@eng.ucsd.edu

Graduate Student Instructors

Abby Teitgen, Bioengineering PhD program, ateitgen@eng.ucsd.edu

Office hours Wednesdays 3:30 - 5:00 pm https://ucsd.zoom.us/j/91512744942

Software Tools

• Adaptive Poisson-Boltzmann Solver, http://www.poissonboltzmann.org/
• Download available at: https://apbs.readthedocs.io/en/latest/
• pdb2pqr, https://pdb2pqr.readthedocs.io/en/latest/
• PyMol viewer, https://www.pymol.org  
• StochSS and StochKit, https://cse.cs.ucsb.edu/software 
• MCell, http://www.mcell.cnl.salk.edu/
• Blender, https://www.blender.org
• Virtual Cell, http://www.nrcam.uchc.edu/index.html
• Continuity, https://continuity.ucsd.edu/
• Biomedical Big Data Training Collaborative, https://biobigdata.ucsd.edu/resources/57/about

Contact information for each software tool 

Instructions for accessing each software tool

Course Schedule

• Visit the course schedule page 

Grading

Homework assignments	40%
Final project	60%

See examples of past projects. 

Grading Policy

Every effort will be made to accept homework assignments that are handed in a little late. However, all late homework, whether an extension was approved or not, may be subject to a late penalty at the sole discretion of the grader. We cannot guarantee that late assignments will be returned on time, and they may not be eligible for regrading. Homeworks received after worked solutions have been handed out will receive no credit. Regrades: In fairness to all students, work is only regraded when there is evidence of grading error. We reserve the right to regrade an entire piece of work. 

Late Homework Policy

Although we attempt to accept late homework, assignments submitted after the beginning of class on the day the homework is due, and the TA has left, may only receive partial credit. After solutions or design grading summaries are posted, late homework will not be accepted. A doctor's note or other written explanation will be required for exceptions to this policy. 

Integrity of Scholarship

The Department of Bioengineering adheres to the UCSD Policy on Integrity of Scholarship. This Policy states that "Students are expected to complete the course in compliance with the instructor's standards. No student shall engage in any activity that involves attempting to receive a grade by means other than honest effort ..." Pertinent university policies are described in abbreviated form at  http://ugr8.ucsd.edu/judicial/22_00.html. The full descriptions of these polices, as well as others regarding exams, grading policies, etc, are given in full in the General Catalogue at:  http://www.ucsd.edu/catalog/pdfs/regulations.pdf or http://infopath-1.ucsd.edu/catalog/front/AcadRegu.html as well as in the quarterly Schedule of Classes. 

Students are not discouraged from discussing homework assignments among themselves or engaging in group study. However, individual homework assignments must be the sole work of the submitting student. Specific guidance will be given in the case of group projects. When submitted coursework incorporates material authored by a third party, the source should always be attributed according to the accepted standards of scholarly endeavor. Material taken from the internet or other forms of electronic media are subject to the same requirements of attribution applicable to printed reference sources or materials. Work suspected of being tainted by plagiarism will receive no credit. All cases of suspected academic dishonesty including collaboration, plagiarism and cheating as defined by UCSD regulations will be referred to the UCSD Academic Integrity Coordinator.

In cases of suspected academic dishonesty including cheating in an examination or altering graded work and resubmitting it, the student will be handed a copy of the student conduct code, and the case will be referred to the appropriate dean. The academic penalty for serious academic dishonesty will generally be a grade of F. 

Interfaces Graduate Training Program

This lab course is offered as part of the Interfaces Graduate Training Program at UCSD and the Interdisciplinary PhD Specialization in Multi-Scale Biology.