Bioinformatics 471V

Week 2: we did DQs but our main focused was to learn how to use/browse NCBI website. we also looked at Jmole to view a protein. we didn’t have any project to work on however we did some work together in class because not everyone knew what was going on. DQs most of them were easy and i answered them fine i know that because i received full credit on DQs.

Week 3 notebook: mainly discuss DQs from the book in class, because this was the first time we realized that book was out dated and instructions are not correct because those websites are updated. We started to consider maybe we shouldn’t use book anymore.
some people were still having problems with blog setting up blog.

Week 4: We finally decided we will no longer do the DQs from the book. This week we had lots of online stuff that did not work therefore we decided not to do the DQs from the book anymore. We discussed how celera and HGP differ; like celera didn’t use golden tiling path but HGP did. Overall results from both were really close except in two chromosome and that is because celera leaves out lots of repetitive sequence. I remember we had a figure on point and it was very easy to see the difference on chromosomes.

Week 5: Dr. Lewis and Dr. Loessor came to our class friday of that week and we learned how to use the online software. It was really exciting when learned about those software because we were understanding some of the stuff could be done easily. The same week we had to download excel file and work on it and for some of us download wasn’t available; direction in the book was not helpful.
we were assign to download sequencher and play with the limited version.

Week 10: This is when we decided that we will only blog once a week. We had some presentation for journal club in class. Also figures and table from HIV paper were explianed well by students because not everyone had understood everything at that time from the paper. So journal club was beneficial for everyone in that regard.
Also we watch the video and I love the whole genome replacing part; replacing all the genes from one bacterium and giving it a new identity by putting new genes in it. That was really cool.

Above was the summary of the blogs that i didn’t explained well throughout the semester. I think they are way more clear now.

Tags: bioinformatics

I am working on Chromosome one of all 10 subjects. I am mainly looking the same mutations found in chromosome one of different patients. I work with excel and it was very frustrated because the excel was not meant to be for the work Stephen did. I used UCSC genome browser to get more information about the mutations. I thought UCSC would have information on all the mutation because Stephen post the link to it however i was unable to find information for some of the mutation. What i found how exactly i did the work are in my paper. Overall i think this paper wasn’t that bad.
Fez

Tags: bioinformatics

I already blogged for last week yesterday, so i am blogging for today (monday). I personally didn’t find journal club to be that helpful today, but the mini discussion afterward was helpful. I am looking forward for the project; i just hope that its not very time consuming as the last one was. One big thing i notice for the last one was that it was lots of work therefore many things that i thought were clear weren’t as clear in my paper so i loss points. Therefore i hope this project is a smaller project so i can do a better job at explaining things.

Tags: bioinformatics

Stephen’s paper was very good; it wasn’t well written but his work was good. I liked how subjects’ detail was given in the paper but at the same time, he jump from place to place. So far journal club is been very helpful. My method section was hard to understand so I ask a friend for help and my friend was able to explain the gist of the method. I am looking forward to rest of the journal club on Monday. I hope we get sometime after finishing journal club to discuss and put pieces together since paper was not completely clear in explaining/describing everything.

Tags: bioinformatics

Everyone’s presentations were great, so far pretty much everyone had some sort of continuation idea if project was to continue. I found Tom’s presentation to be interested since it was similar to part of my project. He did stats in detail whereas i just did it percentage for part of my project. I think most people knew what they were talking about when giving presentation. I am looking forward for the next project and our last couple of presentations. Overall doing presentation brought closer understanding of the project as well as new ways to look at the project.

Tags: bioinformatics

Speaker’s talk was great. He was able to give thorough background and explain what he is doing. I wish we had more time to work with him because at the end we were rushing and trying to finish. if he had work on his data at the beginning of the class then things wouldn’t have made sense so the only way he could actually show/work on this data was give us the background which took most of the time. Overall i think it was great and he was really knowledgeable about the field. I love how at the end he was like do u all know what does phenotype means?
Also Andrew’s presentation was great, looks like he put great effort in gathering everything.I am working with cluster W and other methods to make my power point. I am also trying to do some allignments but things aren’t working the way i want them to work but hopefully i will figure out before my presentation and if not then i can everyone know that this method does not work. I also got some help from Ramsey and  I was able to help one person from our class.

Tags: bioinformatics

This week’s power point was some what helpful in understanding different types of phylogenic tree. Review for ortholog and paralog was also helpful and i think i will usiing these words in my project. I decided to make phylogenic trees for all the patients and analyze two trees one from slow progressor and one from rapid progressor. I upload data for patient 1 through 8 on workbench and i will upload the data for rest of the patient over this weekend and i am using cluster W to make trees. I will need to learn some techniques to copy the tree since i couldn’t find the option for that. I learned how to make tree on workbench from Ramsey and he was very helpful in explaining everything.

1. 2. 3 > > > already said above

Fez

Tags: bioinformatics

Finished Journal club on Monday. Working on phylo tree hleped me better understand the tree. I like the Questions ppl asked, it made me start thinking about it more; especially since the article didn’t explain the tree very well, just assumed reader would know what they are trying to show.
End of class on Wednesday, when were introduced to SWAMI, it looked really good, easy to use and convenient but when we worked on it on Friday it just wasn’t good. I think there are many gliches that they need to fix. And also, we need to have detail explanation on how to use it because some ppl can play with it for 10 mins and figure out everything whereas others can play with it for 2 hrs and still don’t find what they are looking for.

1,2 and 3: above in the discussion

Tags: bioinformatics

A. Friday’s class was very helpful. Figure 1 and table 1 were thoroughly explained. I think it was smart that Tom’s group made different graph for each section of the table. Also the break down of the outlier was very crucial (explain that HIV could have severe effects in some individuals). I think journal is great because it helped me clarify what i was thinking and it also brings different people thoughts together and force us to think more deeply.
1. 2. explained above
3. I need to work more on presenting figure 3 and 4. fig 3 and 4 looks hard but once you understand the description of it, it is very to interpret.

Tags: bioinformatics

A. Party!!!!!!!!!!!, we had chips, cookies, Pizzas and Sodas but the most interesting thing was the videos we watched. They were Awesome; both of them were similar in some parts but overall they were cool. the most fascinating part was when they did experiment and replace the entire genome of bacteria in experiment; whole appearance(phenotype & genotype) of the bacteria was change.
1. many different things; cool one i already said it above.
2. In his video, he explain everything very thoroughly so i understood everything, he even explain what transposon was; his videos were different for people with very little bio background.
3. I need to work on figure 3 and 4 for presentation.

Tags: bioinformatics