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Created page with "<p> <strong>UNIST UNDERGRADUATE SCHOOL</strong></p> <p><strong> School of Life Science</strong></p> <p> </p> <p> </p> <p><..."
<p> <strong>UNIST UNDERGRADUATE SCHOOL</strong></p>
<p><strong> School of Life Science</strong></p>
<p> </p>
<p> </p>
<p><strong>RESEARCH INTERNSHIP REPORT</strong></p>
<p> </p>
<p> </p>
<p> </p>
<p><em>Student: </em> <u>___20132023___</u>_ <u>___Madina </u> <u>_ Seidualy____</u></p>
<p> Student ID First name Last name</p>
<p> </p>
<p><em>Track: </em> <u>____BIO ___ _</u> <u>_____BME_ ___</u> Grade: <u>__Senior ___</u></p>
<p> 1 Track 2 Track</p>
<p> </p>
<p><em>Advisor: </em><u>____SLS_ ___ __</u> <u>___Jong Hwa_____</u> <u>____Bhak ____</u></p>
<p> School First name Last name</p>
<p> </p>
<p> </p>
<p><em>Starting Date:</em> <u> 12/26/2016 </u>(mm/dd/yyyy)</p>
<p><em>Ending Date:</em> <u> 02/20/2017 </u>(mm/dd/yyyy)</p>
<p> </p>
<p> </p>
<p> </p>
<p> </p>
<p> </p>
<ul>
<li>
<h1><strong><u>The Genomic Lab</u></strong></h1>
</li>
</ul>
<p><strong> The Genomics lab was established in July 2014 by a group of researchers in Korea.</strong></p>
<p><strong>The genomics lab is a team of dedicated people who want to understand the structure and function of the genomes on Earth. The main application area is anti-cancer and anti-aging. The topics are unlimited. TGL belongs to BME (Biomedical Engineeing department of UNIST) in SLS (School of Life Science).</strong></p>
<p><strong>Professor Bhak Jong Hwa is a director of the The genomic Institute in the UNIST. I had a chance to get an experience in this lab for two months. The Genomic Institute run diverse projects like whole genome sequencing, transcriptome analysis and etc..</strong></p>
<p><strong> Currently, TGI doing genome sequencing analysis of whale shark, coral genome and jellyfish. Moreover, TGI is not confined on sequencing of the living species, either do relevance projects concerning problems in society, and trying to identify some genetic markers for those characteristic issues.</strong></p>
<p> </p>
<p> </p>
<p> </p>
<ul>
<li>
<h1><u><strong>Performance in the Lab</strong></u></h1>
</li>
</ul>
<table align="center" border="1" cellpadding="0" cellspacing="0" style="width:657px">
<tbody>
<tr>
<td style="width:219px">
<p><strong>Time</strong></p>
</td>
<td style="width:219px">
<p><strong>Tasks</strong></p>
</td>
<td style="width:219px">
<p><strong>Accomplishment</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>1<sup>st</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Introduction to Lab, learning general tools, introduction to genomic databases</strong></p>
</td>
<td style="width:219px">
<p><strong>I’ve learned basic multiple alignment programs, and compute protein alignments. I’ve constructed phylogenetic tree and studied about genome browsers.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>2<sup>nd</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Literature search about candidate genes of the Whale shark</strong></p>
</td>
<td style="width:219px">
<p><strong>By using information from genome browsers (DAVID, Ensembl, NCBI, Unipot) have collected data about positively selected genes of Whale Shark. I’ve found out fascinating facts about whale shark through protein analysis.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>3<sup>rd</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Literature search about candidate genes of the Whale shark</strong></p>
</td>
<td style="width:219px">
<p><strong>Close search about HP1BP3, and did multiple sequence alignments via MEGA7. I’ve recognized W2 domain gain in HP1BP3 through InterPro database.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>4<sup>th</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Introduction to Bioinformatics, learning Perl</strong></p>
</td>
<td style="width:219px">
<p><strong>I’ve introduced to Linux Terminal, and started study on Perl.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>5<sup>th</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Perl coding, constructing HeatMap using R</strong></p>
</td>
<td style="width:219px">
<p><strong>Doing simple calculations in DNA, protein data in terminal through by writing my own coding scripts. Learned and build HeatMap in R studio.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>6<sup>th</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Calculation of the length of each scaffolds with certain gene in it from whale shark genome data.</strong></p>
</td>
<td style="width:219px">
<p><strong>Through tasks improved coding skills, and got used to genomic data. I’ve started using BioPerl.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>7<sup>th</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Mapping paired end reads to the reference genome of the Whale Shark</strong></p>
</td>
<td style="width:219px">
<p><strong>Study on DNA sequencing processes. In order to sequence alignment against a large reference genome learned about BWA and corresponding steps.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>8<sup>th</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Learning about various integrative analyses for multi omics data</strong></p>
</td>
<td style="width:219px">
<h1><strong><span style="font-size:14px">Read paper about “Integrated Genomic Characterization of Papillary Thyroid Carcinoma”. I’ve learned about Circos program and other tool for integrating genomic data.</span></strong></h1>
</td>
</tr>
</tbody>
</table>
<div style="clear:both;"> </div>
<p> </p>
<p style="margin-left:.75in"> </p>
<p style="margin-left:.75in"> </p>
<p style="margin-left:.75in"> </p>
<p style="margin-left:.75in"> </p>
<p style="margin-left:.75in"> </p>
<p> </p>
<p> </p>
<ul>
<li>
<h1><u><strong>Self-Evaluation</strong></u></h1>
</li>
</ul>
<p> During the two month of internship in The Genomic Institute I’ve learned important values of the genomics. Before doing internship, I had known diverse things and learned plenty of stuffs in research area but I had had difficulties in correlating them. All seemed to me complicated. However, after having internship experience, I organized every research step in sequential order, and I could make whole picture of it. Now I know well how genome analysis have done. As an example, in below table I provided brief summary of the main genomic analysis I’ve learned so far:</p>
<table border="1" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td style="width:219px">
<p>STEPS</p>
</td>
<td style="width:219px">
<p>EXPLANATION</p>
</td>
<td style="width:219px">
<p>FORMATS&TOOLS</p>
</td>
</tr>
<tr>
<td style="width:219px">
<p> Raw Data</p>
</td>
<td style="width:219px">
<p> From Illumina sequencing</p>
</td>
<td style="width:219px">
<p> .bcl format (base cells per cycle)</p>
</td>
</tr>
<tr>
<td style="width:219px">
<p> Demultiplexing</p>
</td>
<td style="width:219px">
<p> Changing format from .bcl -> fastq</p>
</td>
<td style="width:219px">
<p> .fastq (+quality scores)</p>
</td>
</tr>
<tr>
<td style="width:219px">
<p>Downstream alignment</p>
</td>
<td style="width:219px">
<p> Sequence alignment to reference genome or creating de novo assembly.</p>
</td>
<td style="width:219px">
<p> Fastq->SAM</p>
<p> Sam ->bam (univercal file format for mapped seq. reads)</p>
<p>BWA, SOAPdenovo</p>
</td>
</tr>
<tr>
<td style="width:219px">
<p> Variant Calling</p>
</td>
<td style="width:219px">
<p> find SNP,SNV,INDELS</p>
</td>
<td style="width:219px">
<p> SAMtools, GATK</p>
</td>
</tr>
<tr>
<td style="width:219px">
<p>Visualization of DATA</p>
</td>
<td style="width:219px">
<p>Integrative genomic viewer,</p>
<p>UCSC Genome browser</p>
</td>
<td style="width:219px">
<p> Circos,Heatmap,etc</p>
</td>
</tr>
</tbody>
</table>
<p> </p>
<p>In above table, in each step there are plenty of tools used for, which I have to learn in detail in near future.</p>
<p> In addition, I’ve acknowledged that Bioinformatics is the main tool in genomic analysis. I cannot imagine how would researches in big mass of information of the DNA and protein would computed without programming codes. I have strong desire to fortify my bioinformatics skill further in order to do rewarding researches, and correctly interpret biological data.</p>
<p> Since DNA carries all genetic instructions used in growth, development, functioning and reproduction of all living organisms, fascinating thing is that, while conducting researches in genomic lab you learn, work and know about everything every day. Compare to laboratories, where researches are confined in specific topic Genomic department researchers observe everything and create big pictures of the life. For a student like me who has big passion in learning about living organisms it was best experiences. </p>
<p> </p>
<p> </p>
<p><strong> School of Life Science</strong></p>
<p> </p>
<p> </p>
<p><strong>RESEARCH INTERNSHIP REPORT</strong></p>
<p> </p>
<p> </p>
<p> </p>
<p><em>Student: </em> <u>___20132023___</u>_ <u>___Madina </u> <u>_ Seidualy____</u></p>
<p> Student ID First name Last name</p>
<p> </p>
<p><em>Track: </em> <u>____BIO ___ _</u> <u>_____BME_ ___</u> Grade: <u>__Senior ___</u></p>
<p> 1 Track 2 Track</p>
<p> </p>
<p><em>Advisor: </em><u>____SLS_ ___ __</u> <u>___Jong Hwa_____</u> <u>____Bhak ____</u></p>
<p> School First name Last name</p>
<p> </p>
<p> </p>
<p><em>Starting Date:</em> <u> 12/26/2016 </u>(mm/dd/yyyy)</p>
<p><em>Ending Date:</em> <u> 02/20/2017 </u>(mm/dd/yyyy)</p>
<p> </p>
<p> </p>
<p> </p>
<p> </p>
<p> </p>
<ul>
<li>
<h1><strong><u>The Genomic Lab</u></strong></h1>
</li>
</ul>
<p><strong> The Genomics lab was established in July 2014 by a group of researchers in Korea.</strong></p>
<p><strong>The genomics lab is a team of dedicated people who want to understand the structure and function of the genomes on Earth. The main application area is anti-cancer and anti-aging. The topics are unlimited. TGL belongs to BME (Biomedical Engineeing department of UNIST) in SLS (School of Life Science).</strong></p>
<p><strong>Professor Bhak Jong Hwa is a director of the The genomic Institute in the UNIST. I had a chance to get an experience in this lab for two months. The Genomic Institute run diverse projects like whole genome sequencing, transcriptome analysis and etc..</strong></p>
<p><strong> Currently, TGI doing genome sequencing analysis of whale shark, coral genome and jellyfish. Moreover, TGI is not confined on sequencing of the living species, either do relevance projects concerning problems in society, and trying to identify some genetic markers for those characteristic issues.</strong></p>
<p> </p>
<p> </p>
<p> </p>
<ul>
<li>
<h1><u><strong>Performance in the Lab</strong></u></h1>
</li>
</ul>
<table align="center" border="1" cellpadding="0" cellspacing="0" style="width:657px">
<tbody>
<tr>
<td style="width:219px">
<p><strong>Time</strong></p>
</td>
<td style="width:219px">
<p><strong>Tasks</strong></p>
</td>
<td style="width:219px">
<p><strong>Accomplishment</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>1<sup>st</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Introduction to Lab, learning general tools, introduction to genomic databases</strong></p>
</td>
<td style="width:219px">
<p><strong>I’ve learned basic multiple alignment programs, and compute protein alignments. I’ve constructed phylogenetic tree and studied about genome browsers.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>2<sup>nd</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Literature search about candidate genes of the Whale shark</strong></p>
</td>
<td style="width:219px">
<p><strong>By using information from genome browsers (DAVID, Ensembl, NCBI, Unipot) have collected data about positively selected genes of Whale Shark. I’ve found out fascinating facts about whale shark through protein analysis.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>3<sup>rd</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Literature search about candidate genes of the Whale shark</strong></p>
</td>
<td style="width:219px">
<p><strong>Close search about HP1BP3, and did multiple sequence alignments via MEGA7. I’ve recognized W2 domain gain in HP1BP3 through InterPro database.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>4<sup>th</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Introduction to Bioinformatics, learning Perl</strong></p>
</td>
<td style="width:219px">
<p><strong>I’ve introduced to Linux Terminal, and started study on Perl.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>5<sup>th</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Perl coding, constructing HeatMap using R</strong></p>
</td>
<td style="width:219px">
<p><strong>Doing simple calculations in DNA, protein data in terminal through by writing my own coding scripts. Learned and build HeatMap in R studio.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>6<sup>th</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Calculation of the length of each scaffolds with certain gene in it from whale shark genome data.</strong></p>
</td>
<td style="width:219px">
<p><strong>Through tasks improved coding skills, and got used to genomic data. I’ve started using BioPerl.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>7<sup>th</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Mapping paired end reads to the reference genome of the Whale Shark</strong></p>
</td>
<td style="width:219px">
<p><strong>Study on DNA sequencing processes. In order to sequence alignment against a large reference genome learned about BWA and corresponding steps.</strong></p>
</td>
</tr>
<tr>
<td style="width:219px">
<p><strong>8<sup>th</sup> Week</strong></p>
</td>
<td style="width:219px">
<p><strong>Learning about various integrative analyses for multi omics data</strong></p>
</td>
<td style="width:219px">
<h1><strong><span style="font-size:14px">Read paper about “Integrated Genomic Characterization of Papillary Thyroid Carcinoma”. I’ve learned about Circos program and other tool for integrating genomic data.</span></strong></h1>
</td>
</tr>
</tbody>
</table>
<div style="clear:both;"> </div>
<p> </p>
<p style="margin-left:.75in"> </p>
<p style="margin-left:.75in"> </p>
<p style="margin-left:.75in"> </p>
<p style="margin-left:.75in"> </p>
<p style="margin-left:.75in"> </p>
<p> </p>
<p> </p>
<ul>
<li>
<h1><u><strong>Self-Evaluation</strong></u></h1>
</li>
</ul>
<p> During the two month of internship in The Genomic Institute I’ve learned important values of the genomics. Before doing internship, I had known diverse things and learned plenty of stuffs in research area but I had had difficulties in correlating them. All seemed to me complicated. However, after having internship experience, I organized every research step in sequential order, and I could make whole picture of it. Now I know well how genome analysis have done. As an example, in below table I provided brief summary of the main genomic analysis I’ve learned so far:</p>
<table border="1" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td style="width:219px">
<p>STEPS</p>
</td>
<td style="width:219px">
<p>EXPLANATION</p>
</td>
<td style="width:219px">
<p>FORMATS&TOOLS</p>
</td>
</tr>
<tr>
<td style="width:219px">
<p> Raw Data</p>
</td>
<td style="width:219px">
<p> From Illumina sequencing</p>
</td>
<td style="width:219px">
<p> .bcl format (base cells per cycle)</p>
</td>
</tr>
<tr>
<td style="width:219px">
<p> Demultiplexing</p>
</td>
<td style="width:219px">
<p> Changing format from .bcl -> fastq</p>
</td>
<td style="width:219px">
<p> .fastq (+quality scores)</p>
</td>
</tr>
<tr>
<td style="width:219px">
<p>Downstream alignment</p>
</td>
<td style="width:219px">
<p> Sequence alignment to reference genome or creating de novo assembly.</p>
</td>
<td style="width:219px">
<p> Fastq->SAM</p>
<p> Sam ->bam (univercal file format for mapped seq. reads)</p>
<p>BWA, SOAPdenovo</p>
</td>
</tr>
<tr>
<td style="width:219px">
<p> Variant Calling</p>
</td>
<td style="width:219px">
<p> find SNP,SNV,INDELS</p>
</td>
<td style="width:219px">
<p> SAMtools, GATK</p>
</td>
</tr>
<tr>
<td style="width:219px">
<p>Visualization of DATA</p>
</td>
<td style="width:219px">
<p>Integrative genomic viewer,</p>
<p>UCSC Genome browser</p>
</td>
<td style="width:219px">
<p> Circos,Heatmap,etc</p>
</td>
</tr>
</tbody>
</table>
<p> </p>
<p>In above table, in each step there are plenty of tools used for, which I have to learn in detail in near future.</p>
<p> In addition, I’ve acknowledged that Bioinformatics is the main tool in genomic analysis. I cannot imagine how would researches in big mass of information of the DNA and protein would computed without programming codes. I have strong desire to fortify my bioinformatics skill further in order to do rewarding researches, and correctly interpret biological data.</p>
<p> Since DNA carries all genetic instructions used in growth, development, functioning and reproduction of all living organisms, fascinating thing is that, while conducting researches in genomic lab you learn, work and know about everything every day. Compare to laboratories, where researches are confined in specific topic Genomic department researchers observe everything and create big pictures of the life. For a student like me who has big passion in learning about living organisms it was best experiences. </p>
<p> </p>
<p> </p>
