Bears In The SEA

Today in lab we worked on our final gene presentation. It was a little stressful because we did not know where to start, but after we started it became much easier. I’m glad that we were able to finish most of it during class because this week is crazy! Less than two more weeks until summer, everyone!

I’m DONE with my functional annotations… YEYYYY. Although….they weren’t that hard. None of my genes had any known functions, and I only had one conserved domain, and that also had an unknown function. Most of my genes were shared with genes in other A cluster phages. One of my genes, Glimmer Gene 13, blasted one to one with a bunch of genes. I just finished the powerpoint for the functional annotation presentation and now I have to do the presentation for in class on Friday.

That’s right, people, we are done with functional annotations, my wonderful lab group just finished up our beautiful final presentation, and corn genes are being finished up! WOW! We have done a lot this semester, way to go class!!

I hope everyone enjoyed their Easter break! It was so relaxing, but unfortunately it is time to go back to work now .

I am already overwhelmed with everything these week, but seeing all of my friends again (and the fact that we only have two weeks left of school) are going to help me get through it. I wish everyone the best of luck with their finals and all of their presentations. I am looking forward to the functional annotation presentations on Thursday and the biome presentations on Friday. I annotated the end sequence of Benedict, which unfortunately did not have ANY interesting genes. All of my genes did not have significant BLAST results (if they did, the e-values were too high), there were no conserved domains, and therefore I could not determine the function of any genes. I am curious as to the interesting genes other groups found!

I am excited because I managed to finish my maize annotations. It went a lot easier than I expected due to help from Dr. Gibbon, Dr. Adair, Luke, and Bayless before Easter break. I really appreciate their patience in answering all of my questions! Only three more presentations in this class (functional annotation presentation, biome presentation, and honors presentation) and one more final… I am not excited about these coming two weeks, but we will soon be able to recuperate during the summer!

Well…not really, but almost.  We have finished our functional annotations and now we are working on our presentations that go over our interesting genes.  It should go pretty fast though, mostly because most genes were either interesting or not, as in some had known functions and others didn’t.  Somehow I feel like we are not finishing our job as researchers.  I wish we could go back into the lab and actually find the function of these genes for which there is no known function. I guess that’s a job for someone else……….

The class has finally, basically … kind of? finished.

Lab is basically done.  We have completed our functional annotations of our sections.   We’re now beginning to work on the corn genome – well, some of us.  Hopefully, this shall be a lot easier – because we’ve already done it before.  And, this isn’t all relying on unreliable internet sources – it is based on cold, hard facts.

only two more lab days and i will miss everyone so much. even though learning all of these new computer programs has been difficult and i now have all of this information in my head about how to functionally annotate genes in micobacteriaphages that i most likely will never use again. it has been a good semester and i am glad that i took this class.

I have finally finished my functional annotations for Benedict!!!! YAY!!!! I thought I would never finish this but the process became really easy after the first few. Now on to corn annotations. I am sure that this will go just as smoothly as Benedict…that is after I suffer and become frustrated with the first few.

I’ve been swamped with tests the last couple weeks so that has been consuming my time, so i haven’t written to the blog in a while. We are now done with phamerator and nearing the end of year long course! It has been a long and fulfilling year thats been a great experience! Everyone in our class has learned so much it is unbelievable! I had no idea i would be sitting in the position I am now at the beginning of last semester a much more mature and smarter person than i was, but i still don’t know that much! so much to learn, so little time!

Tomorrow we begin calling corn genes and finish up annotating phage genes.  It’s weird to think that we only have 3 more classes left in Bio Lab, and will be finishing up a year long project.  Only 5 more school days left too. I hope everyone has a good Easter Break.

Everything in science should be approached with an open mind, right? I will need that kind of mindset for lab tomorrow…

so it seems like everyone is expressing a similar sentiment, but where on earth has the semester gone?! and the year, for that matter. i wasn’t with you all last semester so maybe that’s part of why this semester has flown by… wish i could have known you all longer! looking back: i feel like this has been hands down the most challenging bio class ever. buuuuut… totally the most rewarding. i keep having to step back and evaluate when i get frustrated with all of the work  that we have to do and how totally stressful this class is. and when i step back and evaluate i realize that this has been such an awesome opportunity and totally worth the extra work/stress/sleeplessness/confusion/etc… really totally is.

anyways, class is almost done for the year, so super bittersweet there. mostly sweet i think, with just a touch of the bitterness. sort of like a good cup of coffee! now with that witty comparison, i believe i shall end this.

Where has all of the time gone? I am glad and sad that we are almost done with Benedict’s annotations. We had ZERO known functions for our set of genes which was frustrating so hopefully, like Dr. Gibbon said, the maize annotations will be more rewarding. I am also confused on how I feel about the lab “final” that we will be having. On one hand it was a surprise, especially because I asked if we would have a final during the final slots and was told, no that it would be during class hours if we had one and it will take away some much needed study time for the actual bio test. But on the other hand, it doesn’t interfere with my leaving time for the summer and it will be a lot of fun to have a party! That’s a good last hoorah before the bio final, right?

After finishing the functional annotations after lab today, it finally fully dawned on me that the year is almost over. While yes, I am excited to see all of the work that our class has done throughout the year come to a cumulation, I am also saddened to know that after this year our class of twenty-four amazing people will scatter throughout Baylor. (However it does seem like there is a fairly large percentage in my chemistry class next semester!) Anyway, good luck to everyone as we finish with Benedict and start work on the corn genomic honors project!

Today in lab Chelsea and I were able to finish our functional annotations. It felt weird turning them in because it felt like we didn’t do a whole lot on some of the genes. Our section fell towards the end of Benedict so many of our genes had no match, no conserved domains, or poor matches on Blast. Overall, I think we found 2 genes with known functions.
I’m excited to do a bit of research with the corn genes. It will be neat to search for the genes and to get solid results when we compare the sequences against other sequences.

The only frustration that phamerator has ever caused in the past has been due to the slow speed of the virtual box. Well…that all changed today. It seems that I just wasn’t meant to do any work in the lab today. The first computer wouldn’t start virtual box, the second computer didn’t have virtual box downloaded, the third and fourth refused to log me in. Finally, I stole Bayless’s computer but then caused her to go around the computer lab….(sorry Bayless >.<) I hope the computer will be more cooperative next time. Or else there are other ways to deal with computer problems……

This is bittersweet… I am finished with my Benedict annotations and am now ready to begin annotating corn! I am going to miss working with Benedict, but I am looking forward to continuing to practice gene annotations with the corn genome. After going through the process today, I feel a little less stressed. I was quite worried at first, but I think that our experience with Benedict will help us greatly. I am so excited that we have been offered this opportunity for an Honors project instead of a ten-page paper. This way, we will be continuing to apply the research we have been doing for the last semester.

I was very happy to hear that instead of having a lab final, we will be having a lab party! I know it is before the biology final, but it will be nice to get together for the last time before we leave for summer. I can’t believe that after Easter, we will have only two more weeks left of school. We will have officially completed our Freshman year at Baylor!!! It is all going so fast… I feel like I just met all of you yesterday. We have been through a lot, but we have learned so much, built many friendships, and have hopefully contributed in some way to finding a cure for Tuberculosis!

Like everyone else, I can’t believe that this semester is ending! Freshmen year has flown by! I’m also sad that our year together is ending The best part of this class has definitely been the people in it  and I don’t know what I’m going to do without y’all and bacteriophage next year! Reunions all of the time, please! Today in lab we spent half the time talking about the honors project and although I’m a little stressed out with the idea of another project on my plate, it actually seems pretty interesting!

The class is coming to an end, and we’re still working on Benedict. It is a tad aggravating because it takes half the class to open the programs needed to work on the annotations, and then I am still not 100% sure what I am doing, so I am hoping I am doing it right.

On a slightly better note, I am excited for summer and to spend time back home with my brothers and sisters for one last summer before taking off to Europe next summer and then who knows what after that!

It’s a tad bittersweet, but it’s been fun guys! 6 more class days … Shocking, right!

Today Frank and I are going to finish our functional annotations!  We’ve been working together and it actually really helps to use two computers.  Other people are already finished but we’ll get our’s done soon.   I don’t care if we still have quite a few left.  We are going to fly right through them, while still doing an awesome job, of course!!!  Then I can get started on my maize genes!!!

Well, HOPEFULLY, today I will finish my final annotations with the lovely Ellie! It’s so exciting to be so close to the end, but I think I’ll miss Benedict a little bit; he was a good phage while he lasted! Now, on to corn!

I think that Morgan and I will be able to finally finish our functional annotations today. Some of our genes are actually kind of cool. One is a phage portal protein so it creates a hole in the nuclear envelope. While it has been fun to learn how to work these programs I am definitely glad to be almost finished.

These last few days have been creepily stress free. I only have on test and 2 quizzes this week that I am ridiculously prepared for. I’m kind of worried that I’m forgetting something…

We had our last bio test and are finishing up in lab. I’m not quite sure what we are going to do now that most of the annotations are finished. We’ll just have to see!

One more class presentation!!!! I am quite glad because they are time consuming, but I will miss my quality time with Esther and Kristie We’ll just have to hang out ALL THE TIME next year

I’m pretty sure it is time to start studying for finals- especially in Bio because there is so much to review- but I realllly don’t want to. It just sounds so ominous…

I do believe I am just experiencing the calm before the storm…

I haven’t realized how much time has gone by until I read Meredith’s blog about how there are only 8 more days left. AHHHHHHH! This means that finals are closer and our time together is coming to an end. I feel like I might be a little (actually A LOT) depressed when the new semester begins and I don’t see all the familiar faces again every single day. I felt like I was back in Korea again with our biology class because in Korea the students stay together as one class until graduation. It sounds terrible but it was actually wonderful to become really bonded to each other by studying, plyaing, and going on vacation together. sigh…..