COURSE CONTENT AND TENTATIVE SCHEDULE

 (due dates are given within each assignment document)

 

WEEK

TOPICS

ASSIGNMENTS

01/26, 01/28

Introduction to computers, operating systems and the Internet

  1. Accessing and using your student email account and your student computer accounts
  2. File Transfer Protocols for transferring large data streams
  3. File formats
  4. Publishing information on the WWW: mechanics, publication “rules” and legal aspects

Databases- Access, Search and Retrieval

Molecular Modeling 1- Sketching Molecules and Reaction Schemes

  1. Internet search engines; intelligent searching; engines specific to science
  2. Electronic chemical and biochemical databases, including ChemWeb, PDB, NCBI, BRENDA, KEGG
  3. Electronic literature databases, including ACS, Science Direct, JSTOR, etc…
  4. Search and Retrieval: saving files; copyright issues
  5. Sketching molecules and reaction schemes with Isis/Draw
  1. Your instructor will ask you to send an email from the account you will use during this course and attach to it a word file containing a short biographical sketch about yourself.
  2. You instructor will ask you to retrieve specific information about a chemical problem or molecular system from the WWW, a database, and from the literature. Skills assignment
  3. You will correctly draw the structure of your molecular system with Isis/Draw, save the file and insert the graphic into your document reporting on your molecular system.
  4. You will be asked to construct a reaction scheme of your choice. Molecules and Chemical Databases assignment; Molecules and Chemical Databases rubric

       

 

02/02 - 02/04

Spreadsheets

  1. Review of data entry, formatting and algorithms
  2. Graphical representations
  3. Statistics

     

     

 
  1. You will be asked to solve several chemical problems based on concepts from 120AB, using Excel. Some of these problems will involve creating suitable graphical representations of the data, as well as performing statistical analysis of the data. Excel assignment; Excel rubric
  2. Note: Resources on statistics are found on the course CD.

 

02/09 - 02/11

Molecular Modeling 2-  Computation and Visualization

  1. Basic computation of molecular and macromolecular properties: introduction to the tools of the molecular scientist, such as CaChe, DeepView, ICM, etc

  2. Visualizing molecular and macromolecular properties

 
  1. In silico, build a model of a particular molecular system.
  2. Compute some basic physical properties (to be announced by your instructor) of your molecular system.
  3. Interrogate properties of your molecular system using the visualization tools you have learned.
  4. Note: CAChe software, tutorials and exercises are found on the course CD. Jaguar/Macromodel assignment; Jaguar/Macromodel rubric

 

 

02/16 - 02/18

Introduction to Programming with Higher Order Languages

(NOTE: 02/16 CAMPUS CLOSED - Presidents' Day)

  1. Algorithm development

  2. Basic porgramming using one of several applications such as Mathematica.
  1. You will be asked to solve several chemical problems based on concepts from 120AB, using Mathematica. Some of these problems will involve creating suitable graphical representations of the data, as well as performing statistical analysis of the data.
  2. For this portion of the course, you should refer to the Mathematica resources on your course CD. Mathematica assignment; Mathematica rubric

 

02/23, 02/25

FINAL EXAM

 
  1. If the schedule runs a bit behind, the second class meeting this week will tie up loose ends, and  you will be completing your assignments.
  2. The final exam will consist of four integrated "problems", which you will solve using the skills learned in this class. You will each have a separate, distinct exam. You must electronically turn in the files associated with the final, well organized and clearly named, no later than Friday, March 6. Use email, box.net or collegebrain.net as appropriate.