Bioinformatics - Hennig-Online.net

clumpfrustratedΒιοτεχνολογία

2 Οκτ 2013 (πριν από 3 χρόνια και 10 μήνες)

75 εμφανίσεις

1

Bioinformatics for

“Gene Expression Analysis

in Diagnostic Medicine”

Follow
-
up Course, 20 to 25 November 2006


CAS
-
MPG Partner Institute for

Computation Biology, Shanghai

2

1. Goals of this Course

2. Course Outline

3. TIGR Software Suite TM4

4. Using Apple computers

3

Goals

1.
Obtain raw expression values from
scanned slides

2.
Perform quality checks

3.
Produce comparable expression values
through normalization

4.
Explore data with clustering methods

5.
Find significantly expressed genes

4

1. Goals of this Course

2. Course Outline

3. TIGR Software Suite TM4

4. Using Apple computers

5

Outline



| Monday Tuesday Wednesday Thursday Friday

--------------------
+
------------------------------------------------------------------------------------------------


8:30 Computer
-

| Seminar room: Practise with Practise with Practise with Practise with


room |
-

Welcome Manila data: Manila data: MeV on: drosophila data:


|
-

Introduction
-

Get raw values
-

Get expression
-

Differential
-

Clustering

10:30 (Coffee) | Computer room: (Spotfinder) data (MIDAS) expression (Mev)


|
-

using Macs
-

Clustering (MeV)
-

Multiple
-

Compare to


|
-

starting testing Angela's work


| Spotfinder

--------------------
+
------------------------------------------------------------------------------------------------

13:30 Lunch |

--------------------
+
------------------------------------------------------------------------------------------------

14:30 Seminar
-

| Lectures: Lectures: Lectures Lectures Final:


room |
-

Image processing
-

Normalisation (Christ.+Dennis): (Angela):
-

Demo of


| (Spotfinder) (MIDAS software)
-

Differential
-

Identification databases

16:00 (Coffee) |
-

Quality checks
-

Clustering Expresssion of glial gene
-

General


|
-

Workflow and methods
-

Multiple in drosophila discussion


| data file types (MeV software) Testing
-

Discussion of


| experiment design

--------------------
|
------------------------------------------------------------------------------------------------

17:30 End |

6

1. Goals of this Course

2. Course Outline

3. TIGR Software Suite TM4

4. Using Apple computers

7

TIGR Software Suite TM5

Image
Analysis

Raw Gene Expression
Data

Normalized Data with
Gene Annotation

Interpretation of
Analysis Results

.tiff Image File

Gene Annotation

Scanner

Printer

Normalization /
Filtering

Expression
Analysis

8

1.

Goals of this Course

2. Course Outline

3. TIGR Software Suite TM4

4. Using Apple computers


(and viewing MA slides)

9

Using Apple computers

10

Using Apple computers

The
Menu bar

of the current application

Two
Finder
windows

(like Windows Explorer)

The
Dock

holds running and most used applications

The

Finder
Sidebar
provides
links to
important
folders

11

Using Apple computers

The
Apple menu

holds general
items, such as:

Logout

Here is all our course data:

/picb/course/

Finder

Preferences

Safari
Webbrowser

Activity Monitor

12

Using Apple computers

Practising steps:

1.
Obtain
login account

and password from lecturer

2.
Login and familiarize with
Finder

3.
Locate
/Applications/System Preferences.app

and use it to enable right
mouse button

4.
Remove unneeded items from
Finder Sidebar

and from
Dock

5.
Locate
/Applications/Utilities/Activity Monitor.app

and activate Memory
Usage and CPU Monitor

6.
Locate
/picb/course/Applications
and add it to Finder Sidebar

7.
Start
TIGR
-
Spotfinder311.app

(through Sidebar)

8.
In Spotfinder, view some
Microarray slides from Manila
, located in

/picb/course/10
-
Manila
-
Slides/