Week 5 - Placement 1

This week I was working with Paul once again on bioinformatics. Paul explained how he sequence the 2 reads in every lane as far as lane 16 over the course of the week while I was at school. 

Firstly we had to download all of the information form the servers in order to align the DNA. This was a very slow proses as the file was very large. While waiting for the file to load I looked at some more tutorials online about the history of genetics and DNA. The website that I was using went through all of the individual discoveries by different scientists over the years in relation to genetics. It also showed me some of the Nobel prizes won by scientist working in the field of genetics and what they discovered. A lot of what they discovered we kind of take for granted now but it was very interesting to see the experiments they had to perform in order to come to that conclusion.

 Once all of the Results from the DNA sequencing was downloaded we allied all of the files onto one program so that we could compare the lanes and reads equally. some parts of it were very interesting as not all of the lanes matched up. This indicated that there was either a mutation on that read if it may just be a fault. However for some of the mutations we went online to check and clarify. Unfortunately we found no new mutations, so we didn't get a paper published out of that ;) 

After our DNA was allied Paul showed me how to create a dot line graph to represent our results. 

Graph

Today I learnt that in science you need a lot of evidence in order to come to some sort of conclusion. i.e needing 16 lanes in order to compare the reads. You also cannot take anything for granted, you but check to see if you are correct first. Today has shown me that you must be very precise when researching and carrying out tests. 

Week 4 - Placement 1

It was very quite today as most of the staff were at a genetics conference in Germany, therefore I worked with Paul, who works with bioinformatics and sequencing DNA.

Over the coarse of the morning Paul introduced me to using the different commands on a different type of computer software called linux. He also taught me how to download and install new computer programmes on the computer. 

Command	Action
pwd	"Print working directory" - show what dir you're in.
ls	List the contents of a dir.
ls -l	List the contents of a dir and show additional info of the files.
ls -a	List all files, including hidden files.
cd	Change directory.
cd ..	Go to the parent directory.

A list of some of the commands used in linux.

He explained how the servers and the computer systems work at St.James's and how they are connected to Trinity aswell. Later on I looked at some youtube videos on the way in which the DNA is sequenced to make sure I fully understood how it worked. I also had to reseach different sites in order to explain the computer software behind it. 

Paul showed me a sample result of what the sequencing should look like at the end. We then began sequencing the first read of Lane 4 of the DNA. Once this was finished we sequenced the second read of DNA of lane 4. It is a quite slow process as it takes the server some time to process all of the information and pick out the correct information needed. While the computer/server sequenced all of the DNA smaple, I look at different programmes which anylsis the DNA sequencing result. You basically have to look for mutations in the DNA and compair it with a control. Some of the mutations can have an effect on the person and some cannot. The more reads you have to work with the surer you can be with your judgement. Paul discribed how he would continue running different reads over the coarse of the next week and then have them for me to work on next Wednesday.

http://www.genome.ucsc.edu/cgi-bin/hgTracks?hgsid=304466077

 Here is a link to the website used to analysis the DNA that is sequenced.

I really enjoyed today as it was a completely different experience for me working with different forms of software. I thuraly enjoyed working with Paul today as he not only taught me a great deal about computer science, he also explained to me about collage choices and job opportunities in the subject of science. 

Week 3 - Placement 1

Today I looked at the results from the genotyping experiment that I performed last week. Carol explained how the different types of DNA are sorted into three groups, AA, AG or AT. We then looked up the results on the internet also to see if they matched our results.

How the protein is produced from the DNA

Later I met with Game who explained the latest project that he is working on which is, growing cells from the very beginning and then taking the protein produced by the DNA in the cells and analgising the protein. However it is a very long and time consuming process. We mostly talked about X factor or One Direction to fill the the time! ;D We had to stylized everything and all of the work had to be conducted in a hood to prevent any enzymes coming in contact with the cells.  I was given my own flask to work with, is if i mucked up it wouldn't matter! ha :) 

After lunch I attended a seminar for a half an hour, however I missed the introduction so I didn't really have a clue what was being presented. After, Derek introduced me to Paul who works at sequencing the DNA on a computer, also know as bioinformatics. He showed me how the software he uses work. He also explained how to sequence the DNA properly. He then explained what I would working on with him over the next 2-3 weeks. All of the work I do with him I will have to present at the end of the work experience, wish me luck with that ;)

This week I really enjoyed working with new people and seeing different aspects of the lab.I think today I learnt the most by far.

Week 2 - Placement 1

First of all I met with Derek who told me what I would be doing today. He brought me up to where Ciara and Carol and other Ph.D. students work. I was given a computer for the day. Derek showed me a website called DNA from the Beginning which basically told you about the discovery of DNA and genes from the very beginning. I found the website extremely helpful and interesting as it linked into a lot of the Biology course that I studied for my Junior Cert.

http://www.dnaftb.org/ 

( Just in case you want to have a look) 

Just before lunch I went with Ciara to the lab to help me prepare my DNA and 5 others samples for a genotyping test I would be preforming after lunch with Carol.

Once I returned from lunch I went straight to the lab with Carol to set up the DNA to put in a machine which looks for mutations on the DNA which is also known as genotype. Once again Carol allowed me to pipette which was really fun and interesting. After completing the protocol for the preparation on the DNA we put the DNA samples in the machine for reading. 

This week I was trained how to pipette properly and how to use various machines with in the lab. 

Next week Derek said that I will be working with others form different labs. I look forward to see other aspects of the Institute. I can't wait for next week! 

This is basically what the genotyping machine looks like. Most of the machines in the lab are given nick names, the genotyping machine is called Patrick from Spongebob Squarepants :)