Where did the time go?

How can it be the end of WEEK 9?! I knew this day would come, but am still not prepared for the internship to be over. This week I worked on my paper and presentation, all while finalizing my sequences and deciding which trees are the best to build- BTW, they take forever! This weekend is going to be a busy one!

I can't wait to see everyones' presentations on Wednesday. It's always great to hear about what everyone did over the summer.

Now, back to work...

Hi everyone,

I don't have much to report since my data collection has been finished since last week. I have just been working on the paper and presentation which should be finished in plenty of time before the internship is over. Open House was a blast (Cubelets were probably the highlight in my opinion) and I'm looking forward to the seminar this afternoon. It finally hit me that the internship is over in a week which is a bummer, but it was an enjoyable summer and I'll try to make the most of this last week.

-David

Happy Thursday! Second-to-last confluence update - yikes!

It has been a somewhat slow week work-wise, but with so many great activities!
I went diving in the kelp forest exhibit at the Aquarium last Thursday. I wrote a blog post about, which I hope will be posted soon.
The open house was a lot of fun. I got talked into building my own ROV and attracted a small audience of aquarium volunteers as I was building; I think they were impressed, I did not tell them that I majored in physics... Anyway, I am very proud of my new ROV Engineering Certificate of Achievement, which is hanging in my cube.
NASA was totally cool, especially the fluid mechanics lab. There's a little part of me now that wouldn't mind being an astronaut - would that be like the opposite of diving?

I had a couple of frustrating days this week. My virtual machine ran out of hard disk space, and it took me a while to figure out how to expand it. Now that it is expanded, I am trying to load a massive database onto it and it's taking FOREVER - two days so far, and still going. I'm feeling the pressure, as I need this database in order to make the last couple of figures for my final presentation. I might have to resort to the back-up plan today.

Have a lovely weekend! Don't forget to take some time to relax.

Cheers,
Rachel

Heyyy there!

This week has gone pretty smoothly. I had such a good time on the NASA tour! I am still mind blown at all the the things we got to see while we were there. I finally finished pulse 66 yesterday, and have to do one more section before I am finished with pulse 67. I hope that I have time to finish it with enough time for analysis and to put together a good presentation, but I am remaining hopeful! Worst case scenario, I will just focus on pulse 66 for the presentation. Super nervous for next week but also excited to see everyone present! Hope everyone is having a great week! It is going to be a looooong work filled weekend for me haha.

• Danielle

Hi everyone!

Not too much to report this week. I've finished with all of my data collection and am currently extracting everything from VARs and compiling it together. Hopefully by the end of the day I can have it done so I can spend the weekend working on my paper and presentation! Other than that, I thought the Open House was super fun and had a great time working the booths and also walking around to see what everyone does -- the ROVs at the dock were super cool!! 

Have a great weekend everyone!

Victoria 

Wow. Ok so it's getting to the point where everything is happening like RIGHT NOW.

Remember last week when I said that everything would have to go perfectly for my project to be done by the final presentation? Haha. That didn't happen. But that's science, I know.

Our first round of cloning PCR yielded zero results, so I created some more specific primers, and while I was waiting for those to come, I digested my plasmid with my restriction sites and de-phosphorylated it, ran out my product on a gel to confirm, purified and quantified the DNA. My new cloning primers worked beautifully, and after amplifying all my sequences successfully, I digested the sequence/gene DNA, purified it, and ligated it to the plasmid DNA. My first transformation and plating of gene DNA into my plasmid DNA and then the E. coli was a fluke, so today we're troubleshooting/testing a bunch of the different steps to see what went wrong. So we'll be re-plating the rest of my transformed cells onto plates today, along with re-transformed E. coli cells from yesterday's ligations, and then additionally, we're re-doing our cloning PCR, and instead of digesting it and then putting it into the plasmid, we'll be ligating it into a different, intermediate plasmid, sequencing it maybe? And then digesting it out of the plasmid to transform it into our E. coli. Apparently this method is more reliable. Keep your fingers crossed for me!

If all goes well, I'll put my grown up, re-transformed colonies into the fridge tomorrow (to stop them from growing), picking colonies on Monday, and putting them into my expression vector later in the week. My project definitely won't be done by the presentation, so I'm extra glad I'll be staying here for a while so that I can finish it. If this turns out to work, and my sequence of interest is actually the gene for the luciferase in vampire squid, I'll be really, really, really excited. GAhh.

Anyways, hope y'all are doing alright, I'm so excited to hear about everyone's projects!

Chloe

Week 9 (or 7 in my case).

I started working in the pCO2 in air project, which was cool as I had to learn how to clean data for matlab to read it. It was a lot of figuring things out but I got some pretty cool atmospheric CO2 curves that I will be comparing to the measurements from our moorings. However, I was informed early this week that I was presenting today to my mentor, so my focus shifted to the presentation (won't complain as it had to happen at some point). I've spent most of this week polishing figures and getting everything to fit without being overwhelmingly technical--it has definitely been a challenge!

Oh, I also went diving with George last Friday at the kelp forest array. It took us a while to find the array but once we did we managed to do most of the work George had planned. It was good to go out on a work dive and be out in the field again! Also NASA was epic, I really enjoyed the tour and I'm thankful that we were able to go. It's crazy to think all these things happened in the last week--busy days!

On to finishing this presentation... at least I don't have to worry about the full paper just yet .

Diego

Wow, we have like 3 days after today. May all our original project goals rest in peace while we scramble to finish up what we can (;

I'm nearly finished, having completed all the content for Kelly-Benoit Bird's web page and the two brief news articles about her. Nancy is reviewing them now for grammar/style, and then Kelly will take one last look to make sure everything is correct. I'm now finishing up the remaining ESP pages that need to be written. About half have already been sent to Nancy and Jim for review, and I'm finishing up the last half now. I'm NEARLY done, and am hoping to have ALL of the ESP content written before I leave today and ready for review.

Paper and presentation are firmly weekend projects, but I'm not too worried yet about that! I've picked the layout and made the cover slide (which is what always takes me the longest ha) and have a good idea of how I want my presentation to go. Hopefully it will just be a lot of copying and pasting screenshots of different webpages. Sometime this weekend if I have time (and need a break from the paper) I'll finish up some blog things, but otherwise that can wait while the rest of my the project is racing to be finished.

Too long, didn't read: "AAAAH!!! (But everything is going to be okay)

P.S. The open house was wonderful and NASA blew my mind!

Aloha! Is anyone else as tired as I am? All this thinking. Well I am still finishing up little nit picky details to my projects. I need to stop being picky and move on to working on the presentation and paper stuff which are in very basic draft form. I guess I feel anxious about things and am starting to feel like oh geeze, what if my project sucks and I just dont know it. I am hopeful I will finish my list of edits and all my work will live up to my expectations. I am excited for next week and continuing to collaborate with my mentor after the intern program ends. Doing the paperwork now!
Mahalo
Alia

It has really been busy these past few days. It's really exciting to see all the products of all of our time and effort. Seeing the results are really what make time fly by as we wrap up the project. Other than preparing my presentation, I'm just doing some finishing touches on the network at the moment. There needs to be more false positives in order increase the and accuracy/precision of the model. I got some great feedback from my mentors today on my presentation. A lot needs to be simplified and a lot needs to be expanded on. The REUers will be getting a tour of MBARI tomorrow so I'm excited to show them the sound system. Other than showing them my (John's) desk, that is about all I can show them on my end. We'll see what happens though.

I'm getting sad that it's coming to end soon. I have really enjoyed working here. I do look forward to presenting my work to everyone though. A few of my teachers might be able to make it to the symposium too so that is exciting.

Daniel

Week 8 so I'm not scrambling to finish my papers quite yet

The NASA tour was probably the highlight of the week for me, the Fluid Mechanics lab was my favorite part. Back at MBARI I've been spending this week getting data from the IMU and trying to determine if it could be used in the way we were hoping. The answer is starting to look like a pretty clear no. The signal I'm chasing is far too small to be picked out from the general vibration of the motor. We've known since the start that this device would most likely not be sensitive enough. My mentor hopes top eventually try implementing this with a "tactical grade" sensor. At this point my goal with the project is to get some pretty signal plots and explain why it's not the data we're looking for.

Tired and looking forward to the long weekend.

Pierre

Hi all!

I finally finished up my growth-light experiment on Saturday! We continued growing the cultures to make sure their growth rates didn't increase as densities increased, and they didn't (hurray!). I gave a practice talk in my lab meeting on Wednesday, so I spent much of the week preparing for that. I've also spent a fair amount of time working on writing up my paper. Daily sampling of the chemostats has continued as the CO2 and nitrate experiment is continuing.

I'm looking forward to everyone's presentations next Wednesday!

Ellie

Week 9:

I was able to take a timelapse video of the Open House using SeeStar! Within a day, I had to debug and modify the SeeStar code and get it ready for the Open House. Thom and I also had to disturb Chris Scholin and ask permission to mount the SeeStar onto his balcony. On Monday, however, we noticed that there was a hardware problem with the Go Pro, as it created a thousand folders with one image in each folder. I had to write a few scripts on Python to move and enumerate all the images in one folder, and of course compose a timelapse from the images. It was exciting as I would have been happy if the SeeStar only managed to save a few images. As of right now the SeeStar is being used to monitor the Power Plant, Rachel Carson, and Rascal the cat.

As for my project, I performed a dry run for the presentation and received some great input from my mentors; I just need to polish the presentation, practice, and get started on the paper. I have been pre-occupied documenting my work by writing READme's and diagrams, which I think will help with the paper. Writing these manuals are probably one of the most important parts of the project because if they are well written then all the work can be continued, otherwise all the work are for naught. I really wish to have my work carried over, but since the project is open source, I suppose i can always ask for a pull request. 

I also added the checksum function I mentioned last week.

Hi all,
wow! its hard to believe how quickly the past nine weeks have passed by...week 10 here we come
this has been and interesting week for me..I started out Monday confident that my data had interesting results, only to find there wasn't no strong correlation. After meeting with my mentor to discuss the situation, we decided to look at the other data set and potentially find a stronger correlation, sadly after two days (Tuesday and Wednesday) of analysis we found the data to be less significant than the previous and so we went back to the original data. As for today, I spent my morning working on a pre-presentation to deliver to my mentors later in the day. My pre-presentation went well and I received really good feedback and suggestions which I'll be working on for the remainder of the day....and weekend!

Enjoy the rest of your days
Ash

The end is so close, and I still have so much to do! This week I've been working on tidying up my code for future use. Making sure all my data is saved properly and backed up. I've also been working on my presentation. At this point, I'm trying to strike a balance between giving enough background information that people can understand what I am talking about while still having enough time to talk about my actual project. I've also been working quite heavily on creating visualizations that really show what I'm doing. I think videos will play a pretty important role in my presentation. I'll link to one at the end of this post.

https://www.youtube.com/watch?v=7mJEaN2Kz2w