DREU in Bioinformatics and Genomics

Distributed Research Experiences for Undergraduates
University of North Carolina at Charlotte
Winona State University

Week 1 (Jun 1 - Jun 5, 2010)

I am study at Winona State University, which in Minnesota. The summer research college is at University of North Carolina at Charlotte. It took me 3h by flight from Winona to Charlotte. My advisor Dr. Jessica picked me up at airport, helped me set up dorm and baggage. She also drove me to grocery store to grab some food. I did appreciate her help.
I wanted use excited to describe the first week. My lab was in Bioinformatics Building which was a brand new building, so I had pretty well research environment. Because of my Computer Science major and research was about Bioinformatics and Genomics, I needed read book as well as papers to understand the background knowledge about genomics. I spend all the time in first week to know how legume evolution, how gene duplicate and so on. Finally, I had some basic idea about the genomics.

Week 2(Jun 6 - Jun 12, 2010)

I still spend most of time play with papers during the second week. I could not stop by only knowing general idea for gene what I need is the specific knowledge to overcome the project. Also I read some software manuals like BLAST and Vmatch, which all related to sequences analysis.
Another challenge for me was the desktop in lab. The operation system which I used before was Window, but now only having UNIX system. I had to familiar with the new desktop. Anyway, it was not a big deal for me.
There was a lot of restaurant in Charlotte, like Asian food, Mexico food, Italy food and Fast food. I tried Italy food this week, the name was Calzones. It was so delicious that I almost cannot stop eating.

Week 3(Jun 13 - Jun 19, 2010)

The third week study was more focus on research, like followed demos in Vmatch manual to compute some genomic sequences, run command through terminal, and familiar with the bioinformatics algorithm. After these times go through papers, I felt more confident about this project.
I was worked in Masters Lab, which near by the PHD lab. It was easy for me to ask questions from PHD students. They have more experience and knowledge which are professional than us. I learned a lot.
This week I went to Chinese buffet and Thai restaurant. To my surprise, Chinese buffet has sushi and Thai restaurant has fancy decoration. All in all, they all have wonderful food.

Week 4 (Jun 20 - Jun 26, 2010)

This week I met some problems about my project. It was easy to read software manual than to use it yourself. Same commands which followed demo in manual, however error always arose to my program. Huge difference among learn, understand, and familiar with a software. I think experience will improve this situation very well. I do enjoy the feeling of figure out a problem no matter how long time I took on that.
I had 413 sequences file so Vmatch seems perfect for me to deal with large scales sequences matching. Vmatch have lots of features, like persistent index, alphabet independency, efficient algorithms and data strunctures and so on. Those advantages list above can ensure the speed of matching sequences, which also need sacrifice huge memory. Nothing is perfect.
It is easy for store over 400 files matching result out of memory. I had to transfer files among local machine, remote machine, and portable hard drive back and forth. The drawback was did simple things wasting lots of time the benefit was I become familiar with shell command and sftp command.

Week 5(Jun 27 - Jul 3, 2010)

Time went so fast, now half of the research time was gone. I felt happy about what already learned from the past half time also felt a little nervous about how to finish my project in the left half time. All in all, how lucky I am to participate this DREU program.
This week most of time I was played with Vmatch and mySQL database. First used Vmatch to get match results which need two phases, like building index tree and sequence matching. Then stored match results to files, but I had to format results so that it can store in database directly. Due to over 400 sequence files need to done, I use perl script language to finish this circle. Unfortunately, perl program abort before successful deal with all the sequence files, at that time I knew check memory statue is necessary for play with too much data.
During weekend, I went to a Sushi restaurant. I felt sushi tasted much better than I though before. I saw Chinese couplet on the door of that restaurant, which means lucky and make more money. So cute it is. After dinner, we went to an Asian Store. Lot of vegetables, seasonings, seafood, snacks which I though only available in China. Walked around the store, it looks like back to my hometown.

Week 6(Jul 4 - Jul 10, 2010)

This week I was focus on Blast and mySQL. Blast is for sequence similarity searching, in other word, it is also for sequences matching. The speed of Blast is not as fast as Vmatch, however, it can save lots of space. When query against mySQL, I realize what I learned from database course was far enough to use. In order to speed up the query time, I needed consider build suitable index. In order to save memory, I needed care about data type. A tiny mistake will lead to huge error. Like I use “varchar” data type to store scientific number. So when query data between 1e-4 and 1e-8, I got empty set. Thank for my advisors, they are so brilliant to find and solve my stupid problem.
Now I had deep feeling of so powerful the mySQL it is. Only playing with it a lot, the mySQL magically store and query data will show up. Using the right query language can lead to efficient deal with data, also when bug appeared in query language will conduct program running long time and not enough RAM problems. Like I need join two tables and find the different data among them. Due to forget left join tables my query command ran one day and killed in the end. Haha, I did learn a lot.

Week 7(Jul 11 - Jul 17, 2010)

This week I did feel time was not enough and a little worried about finish my project in time. I checked “DMP student funding specifics and requirements” got information list below: for the third stipend the Progress Report is required, further more for the fourth stipend the Final Report is required. The lucky thing was now I only need done the Progress Report, however, the downside was Final Report is around the corner. Also near the end, we need formal presentation for our project. Too much things suddenly arose and needed to be done at the same time.
I began a Blast program at last Friday afternoon and it kept working till this Tuesday morning. What an awful speed of blast, but this was not the end because I got a ridiculous result. I realize that I tradeoff 4 days to wrong outcome. After talked to my advisor, she told me two students ran Blast on the server at the same time so the server crushed. So upset I was and I had to start over by Vmatch. After last weeks played with Vmatch and perl script language, the second time use them became much easy. All in all, every work will have fruit in the end.
By the help of high efficient Vmatch, I got result soon. When drew chart according to new result, I found the sum of different columns were no match the total. I felt so worried about maybe redo it from the beginning of second phase. I checked result carefully and hoped I can found the headstream of error. I was so lucky that I realize I miscount 2 types of sequences. So what I need to do was just format the Vmatch result again. Soon fix this problem and I felt very proud of myself.

Week 8(Jul 18 - Jul 24, 2010)

When checking calendar only two weeks left, I rushed myself all the time. I needed done the left part of research, I needed done a final report, and I needed done a final presentation. However, I was so in a hurry that can’t concentrate. I wrote script program and organized final paper at the same time, which I wanted speed up my project, however I forget correct part of script and had to redo it again. Then I realize this is hurry emotion only lead to slow down my process. I must adjust myself and came down to thing one by one. In fact this way was more efficient.
I used server to run Vmatch program, but too much people all busy with programs the RAM became not big enough again. I only got 4 Vmatch results whole night. What I could do was used this waiting time to get some ideas for final report and presentation.
I went to an Indian Restaurant. I tried Indian pancake, yummy! But it was really hard to describe the Indian sauce flavor, which seems like lots of ingredients mix together and came up with a wonderful taste.

Week 9(Jul 25 - Jul 31, 2010)

Busy week again. On Friday all students who had internship at UNCC no mater REU or DREU students needed final presentation. But my project hadn’t got final result yet I had to present part of research. Prepared PowerPoint was much harder than I though before, because explain Bioinformatics research to Computer Scientist was though to let them understand how and why we do it. I had to explained background knowledge at the beginning and used chart to convince them how overcame problems in my project. In fact, before presentation I was worried about audience question part, due to I do not know too much bioinformatics terminology to answer questions. However, the presentation went on very well. I learned a lot by other students explained their research. It was harvest time for all the students.
I found I fall in love with sushi, haha. What a magic food with wonderful favor and lots nutrition. I like sushi buffet, which I always have illusion of eatting sushi for free.

Week 10(Aug 1- Aug 7, 2010)

Time flew so fast the last week final came. I still needed Vmatch program running so that I can have some conclusion for my project. Due to use server to run Vmatch and other student busy with other programs, the speed of server was real slower. I was worried about can I have all the Vmatch results before due day. God bless me.
Thursday morning I was on my way to Bioinformatics Building. Lots leaves fell down and danced with wind, I wondered it was the end of summer or the beginning of fall. In fact, it was the end of my internship. What a wonderful summer I ever have. I did learn a lot, like how to work with graduate student and professor. Thankful and reluctant to depart was the feeling in my heart right now.
After internship my boyfriend flight to Charlotte, so it was the beginning of our four days vacation. The weather was extremely hot and no raining at all. We walked around campus and visited some landmarks in Charlotte downtown. Also we tried lots of delicious food. I have no hesitate to say Charlotte is a real wonderful city.