I miss it already

Wow, looking back now I can't believe we're all done! I really think that everybody did a great job this year! The website looks amazing! Great job everyone and have a fantastic summer!

Year Reflections

It took me forever to figure out how to post on this blog =].

Anyways, ever since last summer when I got the email saying that I was accepted into this lab, I was excited - maybe it was because of how exciting it sounded from the description or maybe it was because upcoming freshmen are excited about everything ;). I remember on the first day of class we were handed these awesome lab notebooks and then being told by the professors after giving a brief introduction to the class, "We have a long and busy schedule ahead of us, so lets get our hands dirty and find some phage!" Amazing.. it was only my first day in a college lab and we were already venturing out into the abyss to do fieldwork. After that, things started to get exciting. Fall term was marked with memories of using petri dishes, microcentrifuge tubes, micropipettes, and the incubator, day in and day out. Every week I would give myself a pat on the back for hitting another checkpoint in the process. Spring term, I got to run a gel for the first time (I remember using the super tiny tubes) and I got to watch the operation of an electron microscope. This term, we got to experience first hand what genome analysis was like. Finally, after having a wonderful year, we met in class for the last time today.

Even though a lot was accomplished, it doesn't even feel like the first day of class wast that long ago. Time flies when you're having fun :p

Today is our last day of the phage genomics laboratory; I have mixed feelings about it. Looking back as a whole, I am so proud of the work that was accomplished. This was an opportunity that I never imagined I would have when entering Oregon State University. I am very thankful to have had this chance to dive into a lab type setting such as this. I am also a little sad to be finished with this lab. I met many great people and had some great opportunities. Lastly, I wanted to thank everyone involved in this lab. It has been a great experience that I will not soon forget!

Last Lab

Tomorrow will be our last and final phage lab, we have gone trough so many SMEG and TA buffers to get where we are right now. Reflecting on the past months, it is incredible to think that we started out from a tiny sample of dirt, compost, or manure and now the final genome! Just shows what a team of dedicated students and experienced and passionate instructors can accomplish in a small amount of time. I am sure everyone have learned more than just the information, but also in some ways improved our communication, team work and time management skills, something’s that is very crucial to any career in the future. Lastly I would like to congratulate everyone and good luck with finals!!!

Roberto G. 

Colbert on Colbert

Hey guys - I just wanted to comment on Nick's post. I fully support the effort to try to get Stephen Colbert to recognize Mycobacteriophage Colbert on his show! I think this would be awesome and I am happy to help. I will definitely let you guys know when the GenBank file is accepted. I know that the file was submitted on May 15...it takes a little while to get accepted but it shouldn't be too long until we hear. Here is the address for the new phage lab website: http://biology.science.oregonstate.edu/courses/genomics-lab/
There is a link there called "Genome" that talks about Colbert a bit.

Let's chat about this in lab tomorrow!
~Christy

안녕 (means good bye)

Real world research experience. Great opportunity for first year students to develop skills that I did not learn till junior year. An educational environment in which you work closely with your teachers. These teachers are awesome and dedicate a lot of time and energy into helping develop the students skills and knowledge.

Dead Week!

So... It's dead week already. I must say these past three terms have been a whirlwind experience for me. This genomics lab was my first experience in a real lab, and it has been pretty awesome. Fall term was kind of a shock, having to come in so often and facing so many problems, but it was a learning experience that helped me get very familiar with microbiology laboratory procedures. The rest of the year was a lot easier. Working with software was somewhat simpler, but I still learned a lot about genes.

I want to take this time to thank everyone for making this lab an enjoyable class. I made friends I probably wouldn't have made in a regular lab section, and I truly learned a lot, thanks largely to our advising faculty. Dr. Taylor, Dr. Denver, Christy, and Andrew, thank you very much for being so dedicated to helping all of us through this adventure of a research lab. :)

Sincerely,
Junghee

Hey everybody,

So, I figured this would be a good place for updates on, as well as a sounding board for, getting Colbert (the phage) recognized by Colbert (the TV show host). Right now, my current plan is to wait until the GenBank entry has been finished and published (as that is the real legitimate proof if there being a mycobacteriophage named after Stephen Colbert), then posting the info to the Colbert Nation forum site, and hoping it gets seen by the right people, including links to our website, this blog, a contact email (I can either just create one, or we can make some sort of contact email for the lab at large), and some pictures. Thus, whoever gets informed about the GenBank entry, they should let me know, and we can get this ball rolling. Any other comments / suggestions are welcome as well.

Nick

Thanks and Farewell

Hi guys! I couldn't agree more with Rachel- it's crazy how this lab is really coming to an end. I feel like I have learned SO much over the course of this year not only in terms of phage genomics and working with these highly specialized computer programs like Phamerator and Mega4 but also in terms of wet lab protocol which will be particularly useful for me in future science courses (i.e Microbiology and Cell Molec). In particular, I really enjoyed the DNA extraction process when we used the centrifuge and syringe/column apparatus to remove impurities from the DNA sample. And even though certain aspects of this lab may have been...less optimal to say the least (haha j/k), I appreciate the challenges that this lab presented me with because I know that they have influenced how I will approach problems in the future. I've had a blast this year working with you all and getting to know many of you very well. Lets stay in touch...facebook, of course haha. Special thanks to Dr. Denver, Dr. Taylor, Christy and Andrew; without all of you, none of this would have been possible.

Best to you all, and take care!

Lauren

pham 1419

i found that about 4 of the 6 genes i looked at in class last time were in pham 1419, which had a total of over 600 members...and yet, the pham that contained my tapemeasure protein only had 6 members. i'd have thought that one tapemeasure protein would perhaps have more in common with other tapemeasure proteins...any thoughts on that?

-anjali

Wow! I can't believe that we're almost done with this lab :( I have learned so much about genetics and bioinformatics! For the microbiology task force, we're currently investigating if the phage that has been sitting on the bench top for the past month is still alive and active! We're also starting a DNA prep, to see if we can improve the yield.

Pham 1432

I don't know about all of you but I am curious about the infamous pham 1432. Which if you don't remember has the largest number of members, 792 total.

I am wondering if this lab has access to a more powerful computer that has the Phamerator on it? I would really like to see this pham circle myself and I am sure others would also.

Anyway everyone have a good long weekend!

~Jon S.

Well - there's only 2 weeks to go in the Phage Lab! We've made it all the way through Sequencher, Apollo, GBrowse, BLAST, and Phamerator with our Colbert genome. The map of Colbert is at the right. It is pretty fun to see how it turned out and to compare it to other phage genomes - especially ones that have been discovered this year by other schools in the SEA - like UncleHowie. I hope that everyone has enjoyed this voyage of discovery as much as I have! 

Also - we are looking for students to help out with the lab next year as undergraduate teaching interns. You can get credit for this. If you are interested - come talk to me!  

FML

...my phamily has 792 members.

Update

We still only have 8 followers! We're are all the people in this lab? I know you guys are out there, I've seen you in lab.

Anyways,

We have a website url now: http://biology.science.oregonstate.edu/courses/genomics-lab

It's still under construction but should be up to running standards pretty soon-ish.

See you guys next Tuesday!

- Tamsen.

Phage Lab Thus Far

For many of us Phage Labbers, this has been the first time that we have truly been thrust out into the world of science without really having any idea what the outcome would be at the end of our journey. For the first time, questions arose that didn't necessarily have clear cut answers, and at that point we all heard the resounding words of Dr. Denver's coined phrase, "That's Science." Although some of us may have forgotten how we arrived where we are today, analyzing the base pairs of the Colbert genome, others are reminded of the hours a week we spent in Fall Term. Occasionally up to 7 hours a day for a few of the ambitious ones. The countless number of titrations, purification rounds, etc. that led us all where we are today. I, personally, feel quite lucky that although as a class we had a few minor setbacks, we really have gotten the job done quite nicely. Everyone stepped up when they needed to, and in the end, although only one phage was chosen to be sequenced, we were all able to make our own contributions. I just thought I would take some time to encourage people to look back the long path that we've traveled over this year. Think back to our dough-eyed expressions trying fervently to decide whether to choose the manure pile or the recycling bin. It's been a truly outPHAGEous class, wouldn't you agree?

--Erica

Lab This Week

This week was Jamboree week. We got to present all of our annotated genome segments to the class and add them to the main file. This will allow us to ask the class if they agree with what we called and put all the called genes onto one genome.

We only got through a couple group presentations (maybe half) so next week will probably be the same. It is rather difficult to make this part of the class interesting because we're going through each gene called at a time, and explaining our reasoning.

Hope everyone is enjoying the weather,
Tamsen.

First Post

This is the first post in the genomics blogs.

Using this to let me know how to set up the template. :)

- Tamsen.