http://bioquest.org/scaleit2012/files/2012/01/BioQuest-2012.pptx

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We may also direct students to protein structure information for the APC gene. This gene is the focus of a colon cancer case on Case-It and would lead to interesting discussions about determining protein structure because it is an instrinsically unstructured protein.

We would like to build a bioinformatics approach that will search databases for other SNP data sets that could be implemented in the Case-It simulation.

Initially, students would perform a small search manually. Next, they would write a simple program using Python that would find SNPs of interest.

Finally, the project would be extended to include a module called ‘Concepts in Bioinformatics Programming’.

Concepts in Bioinformatics Programming

To help students acquire the skills needed to do data mining, we propose to develop a course in bioinformatics programing concepts. Instructional components of this course would include:

1) Programming techniques (e.g., in C/C++, Java, Perl, Python).

2) Basic molecular biology concepts; e.g., DNA (4 nucleotides), amino acids, codons, the genetic code, etc.

By the end of the course the students would be able to do things such as:

1) Create random sequences

2) Work with dynamic programming and backtracking

3) Scoring matrices

4) Apply local and global alignment

5) Use sum of pairs or minimum entropy

6) MSA like: pairwise , tree, progressive , star alignments

7) Building profiles from MSA.

8) Work with Blossum matrices

9) Suffix trees for MSA.

Potential homework projects:

1) Create random sequences

2) Use of hashes for simplification in programming

3) Matching of sequences

4) Translation codons into am amino acid

5) Use regular expression for searching

6) Suffix trees

7) Multiple sequence alignment (MSA) implementations using other methods.

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We plan to develop a mathematical biology module using Dengue Fever as a case study.

The mathematical models can be a compartmental models with the susceptible, exposed,

infected, and recovered humans and susceptible, exposed, and infected mosquitos.

We will start with a simple model with a few compartments, using either deterministic

ordinary differential equations or stochastic models to show the disease transmission dynamics.

The course will serve as a starting point for students asking questions and

expand the simple model to explore the answers.

One of the questions is:

What is the likelihood of a person developing Dengue Hemorrhagic Fever?

Drew Kohlhorst

Tammy Longta

Arlin Toro-Martinez

Tamah Fridman

]]>Step 1: Using population data of US from year 1820 to 1870 (50 years), fit it to an exponential model

Step 2: Extend the data to year 1920 (100 years) and student will see that exponential model won’t fit very well. Then we introduce Logistic model and ask them to try to fit the data again.

Step 3: Extend further to data up to year 2010. Discuss the drawback of Logistic model and how we can improve it.

Then as an assignment, students will be divided into groups to fit data from different countries. Data from Sweden can be used as another example since there are enough population data from Gapminder.

As a longer term project, students can be asked to develop an ODE model to take the other parameters such as birth rate, motality, and life expectancy into consideration.

Update: Here is the file for some slides I made for this project.

BioQuest2012Project_ycao_GapMinder_DataFitting