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George Washington Carver Internship Program
Iowa State University
By:
Danielle Nicole Charley
Northern Arizona University
Flagstaff, AZ
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Table of Contents:
Cover Page……………………………………………………………….….1
Table of Contents………………..…………………………...…….………..2
Proposal…………………………………………………………….….…….3
Abstract………………………………………………………….…………..4
Research Paper………………………………………..……………………..5
Acknowledgements………………………………….…..…………….……15
Bibliography……………………………...………………..………..……....16
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George Washington Carver Internship Program
Research Proposal, July 2, 2009
Danielle Charley
Northern Arizona University, Flagstaff, AZ
Plant Genome Outreach to Native Americans
Title:
Missouri 17 Sequencing Questioned And Importance Of World Wide Accessible Results
Description:
Genome sequencing projects have occurred all over the world involving species from single-celled
organisms to the human genome sequence. Many of the researchers on these various projects have
published many articles and abstracts about their findings, but without accessibility to the data
generated for genome sequencing and other research projects, much of the data generated would never
be utilized in future research projects of others for the simple reason of accessibility. While many
scholarly journals hold valuable data that could be used to prove a thesis correct, if the data reported are
simply embedded in text, they are not available for download in a computer-friendly format. The fact
remains that much of the research is at a loss because of the lack of a universal database.
A portion of my research is developing a website that will be available to people world wide displaying
the research done with the interns over the summer of 2009. Being able to access the data from research
worldwide is a very powerful asset. Not only will other researchers be able to access the data but people
all around the world will be able to browse the results of the work done this summer. I will be using the
website to display projects and data on four different topics developed by my summer colleges and me.
Using the HTML and Java Script languages I will be able to show data more efficiently to researchers
that this project might aid to in the future.
The second part of my summer research deals with discerning which accession of the Missouri17
(Mo17) inbred line of corn (maize) was sequenced by making use of molecular markers to discern
differences among three maize accessions: the one being sequenced, one being distributed by the North
Central Regional Plant Introduction Station, and one being distributed by the Maize Genetics
Cooperation – Stock Center. There is a chance that the sequenced line could have been derived from a
research laboratory’s stock rather than a stock currently being distributed by the National Plant
Germplasm System (NPGS). To determine whether what was sequenced is equivalent to a line
currently made available by the NPGS we are: extracting DNA and learning how to use the polymerase
chain reaction (PCR) to amplify genomic DNA, learning to separate DNA segments as bands on a gel
using sweet corn DNA and recording outcomes as images. We will compare the markers assessed for
sweet corn to Mo17, B73, the F1 hybrid, and once confident that the techniques work, will apply these
methods to the Mo17 samples in question.
Mentors:
Carolyn Lawrence, USDA
Ethy Cannon, ISU
Holly Tang, ISU Graduate Student
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Iowa State University
Abstract
The “Plant Genome Outreach Program for Native Americans” Research Website
by:
Danielle Charley
Northern Arizona University, Flagstaff, AZ
Dr. Carolyn Lawrence, USDA-ARS
Ethalinda Cannon, POPcorn Software Developer
Genome sequencing projects have occurred all over the world involving species from single-celled
organisms to the human genome sequence. Many of the researchers on these various projects have
published many articles and abstracts about their findings, but without accessibility to the data
generated for genome sequencing and other research projects, much of the data generated would never
be utilized in future research projects of others for the simple reason of accessibility. While many
scholarly journals hold valuable data that could be used to prove a thesis correct, if the data reported are
simply embedded in text, they are not available for download in a computer-friendly format. The fact
remains that much of the research is at a loss because of the lack of a universal database. For this
reason, a website is being developed that will be available to people world wide displaying the research
done with the interns over the summer of 2009. Being able to access the data from research worldwide
is a very powerful asset. Not only will other researchers be able to access the data but, the pubic all
around the world will be able to browse the results of the work done this summer. The website will
display projects and data on five different topics developed by four interns of the George Washington
Carver Internship Program. Using the HTML and Java Script languages the website will be able to
show data more efficiently to researchers that this project might aid to in the future.
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Danielle Charley
George Washington Carver Internship
Research Paper
27 July 2009
The “Plant Genome Outreach Program for Native Americans” Research Website
A database represents a collection of related records that are kept in a computer system that can
sort the record into a collection of similar data to make it increasingly accessible. Databases should be
made so the data can not only be accessible but can be managed and updated. There are many ways a
database can be organized depending on the data that needs to be projected such as bibliographies, text,
numbers, and images. A computer database is created using several different kinds of computer
languages such as C++, JavaScript, php, html, flash and several others. These languages are used to
organize the data by creating Database Management Systems (DBMS). There are several types of
databases; the one closest to the website being developed is called a Hyper Media Database which
includes a mix of several types of data.
In 1970, a theory of database was envisioned and recorded by Edgar Codd (IBM Research).
After this many other ideas where taken into consideration because of the general ideas of collections of
data. In the beginning the databases could only be accessed from the original computer it was created
on. ARPANET (the U.S. government’s Advanced Research Projects Agency’s Networking Project)
was being used in the early 1970s for linking databases. This project grew to becoming the internet.
Databases created were now able to be linked through the World Wide Web. Thus, giving the public
power to produce any kind of database needed available World Wide Web. Through rising technology
databases now pertain to anything from products for sale to genome sequencing data.
The website being developed is not an actual database but some pages are a mini version of an
actual database. The website is called “Plant Genome Outreach Program for Native Americans 2009.”
It was created for the very simple reason of projecting to the public the research and parts of the GWC
internship that took place in the summer of 2009. Given the limited time available, only the Native
American projects were included in the website.
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For this website three common Internet languages were used to develop the content; HTML,
CSS, and and JavaScript. The editor used is called Crimson Editor 3.72. It was used to create all the
pages used on the website. Images placed on the website were modified and scaled using the software
Gimp 2.6, an image editor. I used this program mainly to scale, crop and alter the pictures to fit into the
parts of the website that I needed it to fit to. I have had classes in C++ and classes dealing with HTML.
There was much information that was very new to me but most was a refresher course. I have never
worked with the JavaScript language before but the class I took on the C++ language was very similar
or at least the ideals were. Although I have taken a few classes, I have never created an entire web by
myself. It was very challenging, very educational to learn how to build an entire website. In the
beginning of creating the website I started out with examples and not actually working on my website. I
spent many hours trying to figure how to get different slideshow to work. Finally a month into playing
around with examples I felt I learned enough to start the website. I first started with my home page.
This took the longest because I had to develop the main menu, popup menus, background and official
format for the entire website. Then include the information I wanted on the page. From there I worked
on every page figuring out ways to organize the data that had to be projected. Creating new pages when
needed and adding images and slideshows where I thought would be most beneficial creating pages that
link back to papers and posters that come in computer friendly formats. The website took about a month
to create and will be available on the web at http://www.lawrencelab.org/Outreach/ .
Results:
The projects were not all completed in time to be put into the website, but instead place holders
were put up to make the data transition easier. Below is an image of the home page, where all the time
and effort went into making the menu, marquee, header, and basic format for the rest of the website.
This is the final outcome. I will show all the language that had to be used to set this basic home page
up.
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HTML code:
<html>
<head>
<title>Home Page</title>
<link rel="stylesheet" href="styles.css" type="text/css">
<script language=javascipt>
var mqAry1=['gwcwebsite/pics/Slideshow1.jpg','gwcwebsite/pics/Slideshow1.jpg'];
var mqAry2=['gwcwebsite/pics/Slideshow1.jpg','gwcwebsite/pics/Slideshow1.jpg'];
// setArrays(mqAry1, mqAry2);
</script>
<script type="text/javascript" src="gwc.js"></script>
</head>
<body background="gwcwebsite\background.jpg" leftmargin="100px" >
<table cellpadding=0 cellspacing=0 border=0>
<tr>
<td>
<marquee behavior="slide" align="left" loop="1" scrollamount="4" width="990" valign="top">
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<h1 style="vertical-align:top"><font color="grey"><span class="textborder">
Plant Genome Research Outreach Program For Native Americans</h1>
</marquee>
<div id="m1" class="marquee"></div>
</td>
</tr>
</table>
<table width="994" height="100%" cellpadding=0 cellspacing=0 border=0>
<tr>
<td bgcolor="#878791" valign="top" width="10%" onmouseover="clearOthers('')">
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</td>
<td bgcolor="#ECEDED" width="100%" bgcolor="black" onmouseover="clearOthers('')">
<font face="papyrus">
<div style="margin-left: 100px; margin-right: 50px; margin-top: 50px">
<a name=mission></a>
<h1>Overview: </h1>
The involvement of Native American students and researchers in plant genome research is minimal.
In an effort to increase their representation in the research community, a summer program to
mentor Native American/American Indian undergraduates in plant genomics research was started
on the Iowa State University campus. Participating students study the genetic sequence behind
Missouri 17 and B73 (types of field maize). They are also doing research of their own on the history
of these field plants, Native medicinal plants, and creating a website to document the summer.
One other student not involved in the original research project is studying cell culture and cell
life. Students work with USDA-ARS North Central Regional Plant Introduction scientists to carry out
field-work (to germinate and propagate the plants)and to collect and preserve plant material. As well
as using the many field houses that surround Iowa State University. The students are learning to use
PCRs, make gel for loading, and developing many lab skills that will aid them in their research. The
data from the PCRs are giving students an idea of how to identify patterns in sequencing.
This work is funded by the National Science Foundation, and all participating students' travel, health
care, room and board, and as well as a stipend were arranged by the Iowa State University George
Washington Carver Summer Research Internship program, which runs from June 6 to August 1. An
advisory council made up of Tribal Elders has been involved in this process, and each elder
traveled to Ames to work with the students. In this manner, the Elders' hopes for the students
have been conveyed alongside the outcomes anticipated by the researcher mentors.<br><br>
</font>
<font face="papyrus" size="25">
<div style="margin-left: 50px; margin-right: 50px" align="center">
<a name=2009></a>
~2009~
</div>
</font>
<div style="margin-left: 50px; margin-right: 50px" align="center">
<img src="gwcwebsite\pics\main.jpg" align="center">
<br>Top:Thurman Redhouse Jr. (participant), Sanzhen Liu (Graduate Assistant), Larry Morris Jr. (participant),
Bottom:Danielle Charley (participant), Leslie Nelson (participant), Holly Tang (Graduate Assistant)<br>
</div>
<br><br>
</table>
<div name="item1" id="item1" class="item1"
onmouseover="showPopup('popupdiv1', 'popupdiv1text')">
<a href="GWC.html">Home</a>
</div>
<div name="popupdiv1" id="popupdiv1" class="popup1">
<br>
</div>
<div name="popupdiv1text" id="popupdiv1text" class="popup1text">
<table height="100%" width="100%" border=0>
<tr>
<td></td>
<td valign="middle" align="left">
<b>
<a href="GWC.html#mission">Overview</a>
<br>
<a href="GWC.html#2009">2009 Participants</a>
</b>
</td>
</tr>
</table>
</div>
<div name="item2" id="item2" class="item2"
onmouseover="showPopup('popupdiv2', 'popupdiv2text')">
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<a href="research.html">Research</a>
</div>
<div name="popupdiv2" id="popupdiv2" class="popup2">
<br>
</div>
<div name="popupdiv2text" id="popupdiv2text" class="popup2text">
<table height="100%" width="100%" border=0>
<tr>
<td></td>
<td valign="middle" align="left">
<b>
Mo17 ??
<br>
<a href="research.html">-Problem</a>
<br>
<a href="timeline.html">-Timeline</a>
<br>
<a href="gelgenotyping.html">-genotyping(gel)</a>
<br>
<a href="snpgenotyping.html">-genotyping(SNP)</a>
<br>
<a href="results.html">-Results</a>
<br>
<a href="cellculture.html">Cell Culture</a>
<br>
<a href="cellcultureresults.html">-Results</a>
</b>
</td>
<tr>
</table>
</div>
<div name="item3" id="item3" class="item3"
onmouseover="showPopup('popupdiv3', 'popupdiv3text')">
<a href="participants.html?person=0">Participants</a>
</div>
<div name="popupdiv3" id="popupdiv3" class="popup3">
<br>
</div>
<div name="popupdiv3text" id="popupdiv3text" class="popup3text">
<table height="100%" width="100%" border=0>
<tr>
<td></td>
<td valign="middle" align="left">
<b>
<a href="participants.html?person=0"> Danielle</a>
<br>
<a href="participants.html?person=1">Leslie</a>
<br>
<a href="participants.html?person=2">Thurman</a>
<br>
<a href="participants.html?person=3">Larry</a>
</b>
</td>
<tr>
</table>
</div>
<div name="item4" id="item4" class="item4"
onmouseover="showPopup('popupdiv4', 'popupdiv4text')">
<a href="pictures.html">Pictures</a>
</div>
<div name="popupdiv4" id="popupdiv4" class="popup4">
<br>
</div>
<div name="popupdiv4text" id="popupdiv4text" class="popup4text">
<table height="100%" width="100%" border=0>
<tr>
<td></td>
<td valign="middle" align="left">
<b>
<a href="work.html">Research</a>
<br>
<a href="play.html">PLAY</a>
<br>
<a href="Elders.html">Elders</a>
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</b>
</td>
<tr>
</table>
</div>
<div name="item5" id="item5" class="item5"
onmouseover="showPopup('popupdiv5', 'popupdiv5text')">
<a href="sponsors.html">Sponsors</a>
</div>
<div name="popupdiv5" id="popupdiv5" class="popup5">
<br>
</div>
<div name="popupdiv5text" id="popupdiv5text" class="popup5text">
<table height="100%" width="100%" border=0>
<tr>
<td></td>
<td valign="middle" align="left">
<b>
<a href="http://www.ag.iastate.edu/diversity/gwc/">GWC</a>
<br>
<a href="http://www.iastate.edu/">ISU</a>
<br>
<a href="http://www.nsf.gov/">NSF</a>
<br>
<a href="http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=201687">USDA</a>
</b>
</td>
<tr>
</table>
</div>
</body>
</html>
JavaScript Code:
// Set 4 copies of same image for continuous scrolling:
if (Math.random() < .2) {
var mqAry1=['gwcwebsite/pics/Slideshow1.jpg','gwcwebsite/pics/Slideshow1.jpg'];
var mqAry2=['gwcwebsite/pics/Slideshow1.jpg','gwcwebsite/pics/Slideshow1.jpg'];
}
else if (Math.random() < .4) {
var mqAry1=['gwcwebsite/pics/Slideshow2.jpg','gwcwebsite/pics/Slideshow2.jpg'];
var mqAry2=['gwcwebsite/pics/Slideshow2.jpg','gwcwebsite/pics/Slideshow2.jpg'];
}
else if (Math.random() < .6) {
var mqAry1=['gwcwebsite/pics/Slideshow3.jpg','gwcwebsite/pics/Slideshow3.jpg'];
var mqAry2=['gwcwebsite/pics/Slideshow3.jpg','gwcwebsite/pics/Slideshow3.jpg'];
}
else if (Math.random() < .8) {
var mqAry1=['gwcwebsite/pics/Slideshow4.jpg','gwcwebsite/pics/Slideshow4.jpg'];
var mqAry2=['gwcwebsite/pics/Slideshow4.jpg','gwcwebsite/pics/Slideshow4.jpg'];
}else {
var mqAry1=['gwcwebsite/pics/Slideshow5.jpg','gwcwebsite/pics/Slideshow5.jpg'];
var mqAry2=['gwcwebsite/pics/Slideshow5.jpg','gwcwebsite/pics/Slideshow5.jpg'];
}
function setArrays(ma1, ma2) {
mqAry1 = ma1;
mqAry2 = ma2;
}
function start() {
// repeat for as many fields as required
new mq('m1', mqAry1, 990);
new mq('m2', mqAry2, 990);
mqRotate(mqr); // must come last
}
window.onload = start;
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// Continuous Image Marquee
// copyright 24th July 2008 by Stephen Chapman
// http://javascript.about.com
// permission to use this Javascript on your web page is granted
// provided that all of the code below in this script (including these
// comments) is used without any alteration
var mqr = [];
function mq(id, ary, wid) {
this.mqo = document.getElementById(id);
var heit = this.mqo.style.height;
this.mqo.onmouseout = function() {
mqRotate(mqr);
};
this.mqo.onmouseover = function() {
clearTimeout(mqr[0].TO);
};
this.mqo.ary = [];
var maxw = ary.length;
for (var i=0; i<maxw; i++) {
this.mqo.ary[i] = document.createElement('img');
this.mqo.ary[i].src=ary[i];
this.mqo.ary[i].style.position = 'absolute';
this.mqo.ary[i].style.left = (wid*i)+'px';
this.mqo.ary[i].style.width = wid+'px';
this.mqo.ary[i].style.height = heit;
this.mqo.appendChild(this.mqo.ary[i]);
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mqr.push(this.mqo);
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function mqRotate(mqr) {
if (!mqr) return;
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if (parseInt(y.left, 10) + parseInt(y.width, 10) < 0) {
var z = mqr[j].ary.shift();
z.style.left = (parseInt(z.style.left) + parseInt(z.style.width)*maxa) +
'px';
mqr[j].ary.push(z);
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}
mqr[0].TO = setTimeout('mqRotate(mqr)', 20); // set speed here
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var items = ['item1', 'item2', 'item3', 'item4', 'item5'];
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var popuptexts = ['popupdiv1text', 'popupdiv2text','popupdiv3text','popupdiv4text','popupdiv5text',];
function hidePopup(which) {
div = document.getElementById(which);
div.style.visibility = 'hidden';
}
function showPopup(which, which_text) {
clearOthers(which)
div = document.getElementById(which);
div.style.visibility = 'visible';
div_text=document.getElementById(which_text);
div_text.style.visibility = 'visible';
}
function clearOthers(which) {
for (i=0; i<popups.length; i++) {
if (popups[i] != which) {
hidePopup(popups[i]);
hidePopup(popuptexts[i]);
}
}
}
Style Sheet page:
Charley 12
body {
font-family:papyrus;
}
a:link,a:visited,a:active{
color:Black;
font-weight:900;
}
a:hover{
color:Aqua;
font-weight:600;
}
.marquee {
position:relative;
overflow:hidden;
width:990;
height:100px;
border:solid black 2px;
}
.item1 {
background-color:"#3090C7";
position:absolute;
top:250;
left:100;
width:100;
height:20;
text-indent:5px;
}
.popup1 {
background-color:#3090C7;
position:absolute;
top:250;
left:200;
width:150;
height:60;
visibility:hidden;
opacity:0.8;
filter:alpha(opacity=40);
border:2px solid black;
}
.popup1text {
position:absolute;
color:black;
top:250;
left:200;
width:150;
height:60;
visibility:hidden;
}
.item2 {
background-color:"#3090C7";
position:absolute;
top:300;
left:100;
width:100;
height:20;
text-indent:5px;
}
.popup2 {
background-color:#3090C7;
position:absolute;
top:300;
left:200;
width:160;
height:210;
visibility:hidden;
opacity:0.8;
filter:alpha(opacity=40);
border:2px solid black;
}
.popup2text {
position:absolute;
color:black;
top:300;
left:200;
width:150;
height:120;
visibility:hidden;
}
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.item3 {
background-color:"#3090C7";
position:absolute;
top:350;
left:100;
width:100;
height:20;
text-indent:5px;
}
.popup3 {
background-color:#3090C7;
position:absolute;
top:350;
left:200;
width:150;
height:115;
visibility:hidden;
opacity:0.8;
filter:alpha(opacity=40);
border:2px solid black;
}
.popup3text {
position:absolute;
color:black;
top:350;
left:200;
width:150;
height:120;
visibility:hidden;
}
.item4 {
background-color:"#3090C7";
position:absolute;
top:400;
left:100;
width:100;
height:20;
text-indent:5px;
}
.popup4 {
background-color:#3090C7;
position:absolute;
top:400;
left:200;
width:150;
height:80;
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border:2px solid black;
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position:absolute;
color:black;
top:400;
left:200;
width:150;
height:60;
visibility:hidden;
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background-color:"#3090C7";
position:absolute;
top:450;
left:100;
width:100;
height:20;
text-indent:5px;
}
.popup5 {
background-color:#3090C7;
position:absolute;
top:450;
left:200;
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visibility:hidden;
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filter:alpha(opacity=40);
Charley 14
border:2px solid black;
}
.popup5text {
position:absolute;
color:black;
top:450;
left:200;
width:150;
height:60;
visibility:hidden;
}
The text given was the HTML language, JavaScript language, and a page of the style sheet for
the entire website. This took a great amount of time. Not all the pages have this much detail but this is
an idea of what I dealt with when creating this website. I created fourteen pages in all and used many
images to create this website. Through all the trials and tribulations of developing a website with a few
mini versions of database within it, projects along with more info will now be available on the World
Wide Web. Not only will the student interns of 2009 be able to access it but also any who finds this
information relevant.
Charley 15
Acknowledgements:
I created a sponsors page, especially for the people who helped a great deal with our projects. I
also included the sponsors who funded us.
Charley 16
Work Cited
Cook, William R. and Ibrahim, Ali H., “Integrating programming languages and databases: What is the
problem.” CiteULike In ODBMS.ORG. 12 October 2005 Web. 21 July 2009.
http://www.citeulike.org/user/taroleo/article/5130582
Codd, E.F. (1970) A relational model of data for large shared data banks. Communications of ACM
13(6), 377-387.
“Database.” NTC Hosting: Kickstart Your Web Presence. www.ntchosting.com 2009. Web. 21 July
2009. http://www.ntchosting.com/databases/database.html
Lawrence, Carolyn J. and Ware, Doreen. “Databases and Data Mining.” In Handbook of Maize:
Genetics and Benomics, ed. Jeff Bennetzen and Sarah Hake. New York: Springer Science +
Business Media, LLC., 2009.
“Library Tutorial-Selection a database-What is a Database?” McConnell Library: RU Radford
University. McConnell Library. 14 September 2005. Web. 21 July 2009.
http://lib.radford.edu/tutorial/IV/index.asp