Still sorting data. The initial tidied results show good trends. Depending on time I'll do the transform faults. Though having processed the raw data it seems a shame not to use it.

This was an up and down week.  Early in the week I recreated the output of my matlab code running in real time using opencv on my embedded system.  I then tried to copy my other video files over to the target for testing.  It didn't work.  It also broke the graphical interface to the embedded system.  I then spent the rest of my week trying to fix it.  When that didn't work I refashed the firmware on the target, reloaded opencv and dependencies, and got back to where I was a couple of days ago. 

I enjoyed Ben's tour of the Moss Landing Marine Laboratories on Monday. On the coding front, BENTHIA generates the two data values accurately, which is rewarding. I'm comparing my data to that of Paul McGill, who did similar image analysis on pulses 59 through 61. Excited to tour NASA's Ames Research Center on Friday!

This week, John and I have been working with the SIMZ data from last fall. We are delving into the molecular results provided by Julio and the physical parameters collected by the AUV. We have also been working with Hans to alter the plumbing for the HOLO with hope that these changes will provide us with images that are more representative of the zooplankton community. To test these changes, am I joining the Carson cruise up in Bodega Bay next week. When we return, I will count the whole water samples to compare with images collected by HOLO.

Long week but promising results. I was having trouble getting the 3' and 5' extreme ends of my sequence, so we decided to go ahead and clone (as opposed to continued primer design). I'm looking at my cloning sequencing results now and they look very promising! I won't have time to completely analyze everything today, but hopefully I have sequence that covers the ends. If that's the case, I can work on expressing my isolated protein in E. coli and get some glowing bacteria. Which would be dope.

This week was slightly discouraging. I was planning on making 12 L of ASW and then 12 L of media on Monday... but we actually ran out of magnesium sulfate hepta-hydrate, so I had to delay my media making 2 days while I was waiting for the shipment to come in. Then, I had another disappointment. No matter what I did, I could not get CCMP1545 to grow. AT ALL. Each day it declined about a couple million cells/mL. CCMP1545 is known to be relatively healthy in natural sea water, but for my experiment, I want to use artificial sea water (ASW), and CCMP1545 is not tolerating it at all. I am SO frustrated because I wanted to use both RCC299 and CCMP1545 for my project and compare the results between the two strains since they're both micromonas.... but with VERY different genomes. So it would be interesting to compare the nutrient uptake results. But I can't use natural sea water for my experiment because I'm using ASW for RCC299... and it's best to stay consistent. So, after trying for the past couple weeks, I think I'm going to have to retire CCMP1545 and just focus on RCC299... but I'm not happy about it... so I'm going to keep trying to revive CCMP1545 in time for my major experiment... but the odds are against me. Attached is a logarithmic scale of one of my growth curves This is the control (replete) culture that I've been using for my preliminary experiment. It's been growing-out since July 10th and it's STILL growing. Today they reached 95 million cells/mL. P.S. it looks like it reached stationary phase on the logarithmic scale... but it hasn't yet.... not completely anyways.

My experiment is going great, the cultures are growing really well and my graphs look beautiful. On tuesday I am going to inoculate the main experiment and let it grow out. I am going to be taking samples at the lag, mid exponential,and stationary phases for cellular quotas of phosphorus, carbon and nitrogen, and dissolved nutrients which will eventually be shipped off to hawaii. Next week is going to be insanely busy but I am excited to finally start the main experiment.

1004 PCRs and 2540 sequencing reactions left! Hopefully doable within the next week (at least partly). Aside from this I am editing and quality checking my data at the moment.

Everything is starting to wrap up now. Trying to figure out how to organize all my data, or rather, which method would be most representative. Standardization? Transformation? All of this is made a little more complicated since none of the species I am looking are from separate phyla and inhabit different parts of the water column. I will be looking more into this statistical hoo-haw next week.

Been wrapping the control alg. into a state machine within the profiling float code. Just need to fix a bug that arises when the float is in ascent. From there will run through tests and collect data that will go in report and presentation.

Finishing up with videos, trying to get some diet information out of my dissected squid, and organizing my data. Also getting ready for the cruise in a week because I hope to get some nice fresh squid specimens.

This week I worked with the CalCOFI database, sorting data from 1951 to 2011. Made correlations between data corresponding larval Vs catching for USA for three species S. sagax, E. mordax and P. californicus. Also I worked ??in graphs sardine and anchovy catches corresponding to California, Japan and Humbolt from 1920-2013.

My week was fun! I went out on Weds and Thurs mornings to collect water samples from Hopkins. Next week, I'll be getting my final round on Monday. Other than that, I've been working on my powerpoint presentation. I had to build, calibrate, and deploy a new pH sensor also, because we were not getting data from one of the drifters.

Had a good week. LRAUV model I've been working on for the past couple of weeks is finally tuned and running. Malfunction classifier based on empirical data is complete. Next week I'll be producing figures and working on my presentation and paper. Two months flew by - wow.

Everything is moving along quite nicely. The main frame to suspend the model ROV from the ceiling has been welded together and is now a finished product. I have moved on to designing the components of the main drive shaft to allow the model ROV to rotate in the exhibit. I have been doing more 3D modeling, and computer aided as well as "old fashioned" by hand stress and deflection calculations for my component designs.

Sorry for the delay in posting! Got too distracted by the whales yesterday to remember to post!

So, finally I have finished logging (fanfare noises, cheering, etc etc...) and now have to spend time digitising them ready for the report. Luckily, for the grain sizing I ran every other core so need only to digitise those. I'm spending at least the first part of this week generating images for the report and presentation as from experience, those take an absolute age. I'll draft up a plan for the report this week and also spend time going through data so I have a clear idea about discussions and further work I will try to complete once back in Southampton and for when I'm back out in October/November.

There are more cores that i could log however... They are not part of my collection but I looked through the database and found an old transect further up the canyon. Luckily they are stored here at MBARI and I think would be nice to complete the study. That said, we are running short of time so may be something for future work. I also tried to get more time up in Santa Cruz but they were pretty booked up so that will have to wait.