Difference between revisions of "UNIST Bioinformatics course syllabus"

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            <div style="text-align: center; line-height: 160%; -ms-word-break: keep-all" align="center"><b><span style="font-size: 14pt; color: black; line-height: 160%">Syllabus</span></b></div>
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><strong><span style="color:black; font-size:14pt">Syllabus</span></strong></div>
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<div style="word-break: keep-all; line-height: 160%"><strong><span style="color:black">Course Information&nbsp; Bioinformatics</span></strong></div>
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<p><strong><span style="color:black">Instructor Information [[Dugwoo Nam]] &amp; [[Jong Bhak]]</span></strong></p>
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<div style="line-height: 160%; -ms-word-break: keep-all">&nbsp;</div>
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<div style="word-break: keep-all; line-height: 160%">&nbsp;</div>
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<div style="line-height: 160%; -ms-word-break: keep-all"><span style="font-size: 12pt; color: black; line-height: 160%">Weekly Schedule</span></div>
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black; font-size:12pt">Weekly Schedule</span></div>
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<p>&nbsp;</p>
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            <div style="text-align: center; line-height: 160%; -ms-word-break: keep-all" align="center"><span style="color: black; line-height: 160%"><font size="2">Week</font></span></div>
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            <div style="text-align: center; line-height: 160%; -ms-word-break: keep-all" align="center"><span style="color: black; line-height: 160%"><font size="2">Contents</font></span></div>
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black">Week</span></div>
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black">Contents</span></div>
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            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">01</font></span></div>
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            <p style="text-align: left; -ms-word-break: keep-all" align="left"><span style="serif: "><font size="2">Introduction to Bioinformatics, Introduction to Microarray, RNA-seq</font></span></p>
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<div style="word-break: keep-all; text-align: center"><span style="color:black">01</span></div>
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<p style="text-align: left">Introduction to Bioinformatics, Introduction to Microarray, RNA-seq</p>
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            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">02</font></span></div>
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            <p style="line-height: 115%"><span style="serif: "><font size="2">Microarray &amp; gene data analysis I: Normalization, Identification of DEGs (R language), Gene list analysis with DAVID and STRING(web)</font></span></p>
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<div style="word-break: keep-all; text-align: center"><span style="color:black">02</span></div>
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<p>Microarray &amp; gene data analysis I: Normalization, Identification of DEGs (R language), Gene list analysis with DAVID and STRING(web)</p>
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            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">03</font></span></div>
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            <p style="line-height: 115%"><span style="serif: "><font size="2">Microarray &amp; gene data analysis II: Clustering, (R, cluster, treeview), Dimension Reduction (PCA), survival analysis</font></span></p>
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<div style="word-break: keep-all; text-align: center"><span style="color:black">03</span></div>
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<p>Microarray &amp; gene data analysis II: Clustering, (R, cluster, treeview), Dimension Reduction (PCA), survival analysis</p>
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            <td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 42.75pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: black 1pt solid; padding-right: 1.4pt; background-color: transparent; border-image: none" width="71">
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            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">04</font></span></div>
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            <div style="line-height: 115%"><span style="serif: "><font size="2">Test 1</font></span></div>
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<div style="word-break: keep-all; text-align: center"><span style="color:black">04</span></div>
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<div style="line-height: 115%">Test 1</div>
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            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">05</font></span></div>
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            <p style="text-align: left; -ms-word-break: keep-all" align="left"><span style="serif: "><font size="2">Gene-set and pathway analysis with GSEA, Introduction to classification analysis (SVM)</font></span></p>
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<div style="word-break: keep-all; text-align: center"><span style="color:black">05</span></div>
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<p style="text-align: left">Gene-set and pathway analysis with GSEA, Introduction to classification analysis (SVM)</p>
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            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">06</font></span></div>
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            <div style="line-height: 115%"><span style="serif: "><font size="2">RNA-seq, ChIP-seq data analysis</font></span></div>
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<div style="line-height: 115%">RNA-seq, ChIP-seq data analysis</div>
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            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">07</font></span></div>
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            <p style="text-align: left; -ms-word-break: keep-all" align="left"><span style="serif: "><font size="2">Introduction to NCBI databases: data and literature search</font></span></p>
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<p style="text-align: left">Introduction to NCBI databases: data and literature search</p>
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            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">08</font></span></div>
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            <div style="text-align: left; -ms-word-break: keep-all" align="left"><span style="color: black; serif: "><font size="2">Test 2</font></span></div>
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<div style="word-break: keep-all; text-align: left"><span style="color:black">Test 2</span></div>
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            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">09</font></span></div>
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            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">(2015.May 1st</font></span></div>
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<div style="word-break: keep-all; text-align: center"><span style="color:black">09</span></div>
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            <div style="text-align: left; -ms-word-break: keep-all" align="left"><span style="color: black; serif: "><font size="2">&nbsp;[[Principles of Bioinformatics]]</font></span></div>
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<div style="word-break: keep-all; text-align: left"><span style="color:black">&nbsp;[[Principles of Bioinformatics]]</span></div>
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            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">10</font></span></div>
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<div style="word-break: keep-all; text-align: center"><span style="color:black">10</span></div>
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            <div style="text-align: left; -ms-word-break: keep-all" align="left"><span style="color: black; serif: "><font size="2">&nbsp;[[Bioprogramming]]</font></span></div>
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<div style="word-break: keep-all; text-align: left"><span style="color:black">&nbsp;[[Bioprogramming]]</span></div>
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            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">11</font></span></div>
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<div style="word-break: keep-all; text-align: center"><span style="color:black">11</span></div>
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            <div style="text-align: left; -ms-word-break: keep-all" align="left"><span style="color: black; serif: "><font size="2">&nbsp;[[Genomics]]</font></span></div>
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<div style="word-break: keep-all; text-align: left"><span style="color:black">&nbsp;[[Genomics]]</span></div>
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        </tr>
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</td>
−
        <tr style="height: 35.65pt">
+
</tr>
−
            <td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 42.75pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: black 1pt solid; padding-right: 1.4pt; background-color: transparent; border-image: none" width="71">
+
<tr>
−
            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">12</font></span></div>
+
<td style="height: 35.65pt; width: 42.75pt; background-color: transparent">
−
            </td>
+
<div style="word-break: keep-all; text-align: center"><span style="color:black">12</span></div>
−
            <td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 462pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent" width="770">
+
</td>
−
            <div style="text-align: left; -ms-word-break: keep-all" align="left"><span style="color: black; serif: "><font size="2">&nbsp;[[Transcriptomics]]</font></span></div>
+
<td style="height: 35.65pt; width: 462pt; background-color: transparent">
−
            </td>
+
<div style="word-break: keep-all; text-align: left"><span style="color:black">&nbsp;[[Transcriptomics]]</span></div>
−
        </tr>
+
</td>
−
        <tr style="height: 35.65pt">
+
</tr>
−
            <td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 42.75pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: black 1pt solid; padding-right: 1.4pt; background-color: transparent; border-image: none" width="71">
+
<tr>
−
            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">13</font></span></div>
+
<td style="height: 35.65pt; width: 42.75pt; background-color: transparent">
−
            </td>
+
<div style="word-break: keep-all; text-align: center"><span style="color:black">13</span></div>
−
            <td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 462pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent" width="770">
+
</td>
−
            <div style="text-align: left; -ms-word-break: keep-all" align="left"><span style="color: black; serif: "><font size="2">&nbsp;[[Proteomics]]</font></span></div>
+
<td style="height: 35.65pt; width: 462pt; background-color: transparent">
−
            </td>
+
<div style="word-break: keep-all; text-align: left"><span style="color:black">&nbsp;[[Proteomics]]</span></div>
−
        </tr>
+
</td>
−
        <tr style="height: 35.65pt">
+
</tr>
−
            <td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 42.75pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: black 1pt solid; padding-right: 1.4pt; background-color: transparent; border-image: none" width="71">
+
<tr>
−
            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">14</font></span></div>
+
<td style="height: 35.65pt; width: 42.75pt; background-color: transparent">
−
            </td>
+
<div style="word-break: keep-all; text-align: center"><span style="color:black">14</span></div>
−
            <td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 462pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent" width="770">
+
</td>
−
            <div style="text-align: left; -ms-word-break: keep-all" align="left"><span style="color: black; serif: "><font size="2">&nbsp;[[Epigenomics]]</font></span></div>
+
<td style="height: 35.65pt; width: 462pt; background-color: transparent">
−
            </td>
+
<div style="word-break: keep-all; text-align: left"><span style="color:black">&nbsp;[[Epigenomics]]</span></div>
−
        </tr>
+
</td>
−
        <tr style="height: 35.65pt">
+
</tr>
−
            <td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 42.75pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: black 1pt solid; padding-right: 1.4pt; background-color: transparent; border-image: none" width="71">
+
<tr>
−
            <div style="text-align: center; -ms-word-break: keep-all" align="center"><span style="color: black"><font size="2">15</font></span></div>
+
<td style="height: 35.65pt; width: 42.75pt; background-color: transparent">
−
            </td>
+
<div style="word-break: keep-all; text-align: center"><span style="color:black">15</span></div>
−
            <td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 462pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent" width="770">
+
</td>
−
            <div style="text-align: left; -ms-word-break: keep-all" align="left"><span style="color: black; serif: "><font size="2">&nbsp;[[Canceromics and Geromics]]</font></span></div>
+
<td style="height: 35.65pt; width: 462pt; background-color: transparent">
−
            </td>
+
<div style="word-break: keep-all; text-align: left"><span style="color:black">&nbsp;[[Canceromics and Geromics]]</span></div>
−
        </tr>
+
</td>
−
    </tbody>
+
</tr>
 +
</tbody>
 
</table>
 
</table>
−
</p>
+
 
−
<div><font size="2">&nbsp;</font></div>
+
<div>&nbsp;</div>
 +
 
 
<hr />
 
<hr />
−
<p>[[UNIST Bioinformatics course]]</p>
+
<p>[[UNIST Bioinformatics course]]&nbsp; [http://bioinformatics.ws Bioinformatics.ws]</p>
 +
 
 +
<p>&nbsp;</p>
 +
 
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>

Revision as of 12:43, 11 May 2016

 

Syllabus
Course Information  Bioinformatics

Instructor Information Dugwoo Nam & Jong Bhak

Course Code
BIO43101
Instructor
Dugwoo Nam,

Course Title
Bioinformatics
Office

Room 701-8, EB1 (DN)

Room 215, Bldg 103 (JB)
Year/Semester
2015/1st
Telephone
010 4644 6754 (JB)
School
SLS
E-mail

Course Classification
TE-BIO/TE-BME/TE-BMS

Office Hours
TBA

Classroom/Class Time
FRI 13:00-15:30 (NSB S205)

Grading Type
Letter grade
Course Objectives & Description

Bioinformatics course contains introductory information in how to process biological data using computers.

The first part of the course taught by Dougu Nam covers the basic computational methods used for biological data analysis. During the class, students will learn the concepts by short lectures and hands-on experiences. So, please bring a laptop computer to the class from the second week.

 

The second part of the course taught by Jong Bhak will focus on:

1)     What Bioinformatics is

2)     How to independently read research papers

3)     How to critically analyze research papers and topics

4)     How to choose a research topic in bioinformatics and design an experiment and perform research

5)     How to write research report(paper) to make the results known to the public.

6)     The course will be done through active action-oriented learning method(AAO)

7)     Students are required to motivate themselves and bring their research topics after reading research papers.
Grading

Midterm( Two tests: 50 %) / Final Exam( Team project: 50%)
 
 
 
 
 
 
Text
Category

Book and PPT files, on-line links
 
Title
Bioinformatics
 
Author
Jong Bhak
 
ISBN
 
 
Remarks
 
 

Course Reserves Designation
 
 
References
Category
Book, on-line links
 
 
Title
Bioinformatics
 
 
Author
Jong Bhak
 
 
ISBN
 
 
 
Remarks
 
 
 

Course Reserves Designation
 
 
 
 
Weekly Schedule

 

Week
Contents
01

Introduction to Bioinformatics, Introduction to Microarray, RNA-seq
02

Microarray & gene data analysis I: Normalization, Identification of DEGs (R language), Gene list analysis with DAVID and STRING(web)
03

Microarray & gene data analysis II: Clustering, (R, cluster, treeview), Dimension Reduction (PCA), survival analysis
04
Test 1
05

Gene-set and pathway analysis with GSEA, Introduction to classification analysis (SVM)
06
RNA-seq, ChIP-seq data analysis
07

Introduction to NCBI databases: data and literature search
08
Test 2
09
10
11
12
13
14
15
 

UNIST Bioinformatics course  Bioinformatics.ws

 

 

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