Csci 3003 Midterm Exam #1 Review
Ive put together several topics that will be covered on the Midterm #1 exam and a list of example
questions to help in your studying. The exam will consist of a mix of questions about short pieces of
code (e.g. whats wrong
Overview of today
Today:
Review of concepts from last time
Statistics for differential expression analysis
Formatted printing
Reading from and writing to files in Matlab
Start on visualizing data in Matlab
Next week:
- More visualizing data in Matla
Midterm 1 grade summary
> = 74
>= 72
>= 70
>= 66
>= 64
>= 62
>= 58
>= 56
>= 54
>= 50
>= 48
A
AB+
B
BC+
C
CD+
D
D-
Mean: ~ 70/80
Max: 80/80
Min: 33/80
A brief overview of bioPerl
A collection of Perl modules for processing data
for the life sciences
A pr
Overview of today
Today:
Review of concepts from last time
Formatted printing
Reading from and writing to files in Matlab
- Visualizing data in Matlab
- Functions vs. scripts
Next time:
- Methods for clustering gene expression data
Intuitive idea behi
Midterm 1 grade summary
> = 74
>= 72
>= 70
>= 66
>= 64
>= 62
>= 58
>= 56
>= 54
>= 50
>= 48
A
AB+
B
BC+
C
CD+
D
D-
Mean: ~ 70/80
Max: 80/80
Min: 33/80
A brief overview of bioPerl
A collection of Perl modules for processing data
for the life sciences
A pr
Overview of today
Today:
Review of concepts from last time
Visualizing data in Matlab
- Functions vs. scripts
- Introduction to clustering
Plotting in Matlab
Visualizing your data is important!
Matlab supports almost any type of graph you
can think of
Introduction to Matlab
Today:
Review of Matlab environment
Variables and expressions
Loading/viewing your data
Matrices and common matrix tasks
Next week: Spring break!
Following week
Introduction to probability/statistics
More matlab:
Functions
Overview of today
Today:
Review of clustering
- More on clustering:
- K-means clustering
- Validating clusters
Introduction to clustering
What is clustering?
Process of grouping a set of objects (e.g. tumor
samples or genes) into classes of similar obj
Overview of today
Today:
Review of concepts from last time
Matlab environment
Loading/viewing data
Variables expressions
Using matrices in Matlab
More on handling matrices
Functions for matrices
Loops and conditional statements in Matlab
Matlab scrip
Overview of today
Today:
Quick review of functional analysis of clusters
Introduction to protein-protein interaction networks
Why are they important?
How can we measure them?
How are they useful?
Next week:
Go over Midterm #2 results
More protein
Overview of today
Today:
Review of concepts from last time
Matrices and matrix functions in Matlab
Functions for matrices
Loops and conditional statements in Matlab
Conditional statements
How
do we control the flow of a program based on the
state of
Overview of today
Today:
Review of concepts from last time
Matrix functions and conditional statements
conditional statements
For and While loops in Matlab
Statistical measures for differential gene
expression
Conditional statements
How
do we contr
Csci 3003: Introduction to Computing in Biology (Spring 2010)
Overview of wholegenome sequencing
technology
Prof. Chad Myers
Department of Computer Science and Engineering
University of Minnesota
cmyers@cs.umn.edu
The start of the genomic revolution:
sequ
Csci 3003: Introduction to Computing in Biology (Spring 2010)
Introduction to
programming
Prof. Chad Myers
Department of Computer Science and Engineering
University of Minnesota
cmyers@cs.umn.edu
What is a computer?
Central Processing Unit
Memory
Input De
Name: _
Csci 3003 Midterm Exam #1, Part I
Thursday, February 26, 2009
Guidelines (read carefully!)
The exam will have two parts. Part I will be written and will ask you to interpret short sections of code, state the value of variables, and write very shor
Csci 3003 Midterm Exam #2 Review
To help in your studying, weve put together several topics that will be covered on the exam. The exam
format will be similar to Midterm #1, and will consist of a mix of questions about short pieces of code
(e.g. whats wron
Name: _
Csci 3003 Midterm Exam #2
Thursday, April 16, 2009
Guidelines (read carefully!)
The exam will only consist of one section, and you are allowed to use your notes, lab solutions, the
internet, Matlab, or any other resource other than your neighbor.
CSci 3003: Introduction to Computing in Biology
Lab Assignment #1
5 points
Assigned: 1/20/10
Due: 1/26/10, 2pm
Goals of this lab:
Get practice using the Linux environment for writing and running Perl scripts.
See and run your first Perl script and begin u
CSci 3003: Introduction to Computing in Biology
Lab Assignment #2
15 points
Assigned: 1/27/10
Due: 2/2/10
Goals of this lab:
Become familiar with using public databases for browsing gene information, obtaining
sequence data.
Get practice using the Linux e
CSci 3003: Introduction to Computing in Biology
Lab Assignment #3
15 points
Assigned: 2/3/10
Due: 2/9/10, before midnight
Goals of this lab:
(1)
(2)
(3)
(4)
Practice Perl syntax rules covered in class.
Use numeric and string operations to manipulate varia
CSci 3003: Introduction to Computing in Biology
Lab Assignment #4
30 points
Assigned: 2/10/10
Due: 2/23/10 (before midnight)
Goals of this lab:
Practice manipulating arrays.
Become familiar with using conditional statements and loops.
Practice reading in
CSci 3003: Introduction to Computing in Biology
Lab Assignment #5
20 points
Assigned: 3/3/10
Due: 3/19/10 (before midnight)
Goals of this lab:
Practice writing programs to accomplish complex tasks.
Practice regular expressions.
Learn about gene expression
CSci 3003: Introduction to Computing in Biology
Lab Assignment #6
10 points
Assigned: 3/10/10
Due: Tuesday, 3/23/10 (before midnight)
Goals of this lab:
Become familiar with the Matlab interface.
Run/modify a simple Matlab script.
Part I: Instructions for
CSci 3003: Introduction to Computing in Biology
Lab Assignment #7
20 points
Assigned: 3/24/10
Due: Tuesday, 4/6/10 (before midnight)
Goals of this lab:
Practice using Matlab to load/analyze data.
Learn about statistical analyses of gene expression data.
L
CSci 3003: Introduction to Computing in Biology
Lab Assignment #8
20 points
Assigned: 4/7/10
Due: Tuesday, 4/27/10 (before midnight)
Goals of this lab:
Practice using Matlab to load/analyze expression data.
Practice using software tools to explore and int
Csci 3003: Introduction to Computing in Biology (Spring 2010)
Course Overview
Prof. Chad Myers
Department of Computer Science and Engineering
University of Minnesota
cmyers@cs.umn.edu
Welcome to CSci 3003
Course: Introduction to Computing in Biology
Instr
Overview of today
Today:
Quick review of k-means
clustering
More on clustering:
- Validating clusters
- Midterm #2 review
Hierarchical vs. k-means
clustering
Hierarchical:
K-means:
Samples
Method #2: K-means clustering
1. Define k = number of clusters