Hi everyone, this is Michael and I've been working in Ware Lab at Rutgers. We focus on studying the body and shape of dragonflies and damselflies.
Coming back from the weekend, I started off with creating draft phylogenetic trees for my Orthetrum leg sample. This time, however, instead of a single cycle, I adjusted the program to create a draft tree for 100 cycles and pick the best tree. This would prove that I had not related my sample with Orthetrum by chance. This took a long time, since I was comparing my sample with about 20 other Odonata. Creating a tree for one cycle itself took about 15 minutes. Gettign a best tree, with 100 cycles, would took a couple hour; basically it was lots of waiting for the tree.
On Tuesday, I got to go on a field trip to catch some dragonflies for the lab. I was lucky since the day before had been raining the whole time, and now it was quite wet outside. Will taught me two basic ways of catching dragonflies: when they were resting on something, you can sneak up to them and and catch them with a net in a burst of action; the other way, when they are flying around, is to simply chase and swing your net around, hoping that you will catch one. (This way is especially exhausting - there was one dragonfly that totally drove my crazy; I was exhausted at the point when I decide to give it up). When you manage to catch one, there will be buzzing noise coming from the dragonfly trying to escape, so you can tell if you catch one. One thing to keep in mind is that be sure to fold your net and seal its opening; dragonflies can escape if you don't.
Anyway, at the end of the day, I caught about 9 dragonflies, including a lot of blue dashers (since they were literally everywhere for some reason), a couple other species, and a metal hawk, which people from my lab had never caught one before.
For the rest of the week, I made more draft trees for my other samples. My professor said that she will probably publish a paper on my discovery with the Orthetrum, and we were all excited about this news.
Overall, this has been a really nice experience for me. I got to experience the environment in college labs, and got some idea about what do people do in lab, how do they get money for research (for this, there was a grad students in the lab,Melissa , who was recruited by National Geographic by writing a proposal to them), how do they find topics to work with, etc. I'm really glad that my professor offered me this opportunity, and along with the lab members for guiding me through my works.
Saturday, August 3, 2013
Rutgers Ware Lab - Week 4
Hi everyone, this is Michael and I've been working in Ware Lab at Rutgers. We focus on studying the body and shape of dragonflies and damselflies.
Throughout the week, I worked on Will's wing scan project, and managed to finish scanning all of the wings he had given me earlier. Aside from that, most gene alignments were also completed. I also re-ran many PCR for the samples with poor quality.
At the end of the week, after numerous processes on organizing and comparing my dna sequences with the database online, I made an interesting discovery. The larva leg sample from Florida, which I got for a collector about 3 weeks ago, had thought to belong to the Libellula family. Now with my data, it showed that the sample was more closely related to the Orthetrum genus, a group that was not supposed to be found in the new world. On the next week, I would continue to work with this discovery.
Throughout the week, I worked on Will's wing scan project, and managed to finish scanning all of the wings he had given me earlier. Aside from that, most gene alignments were also completed. I also re-ran many PCR for the samples with poor quality.
At the end of the week, after numerous processes on organizing and comparing my dna sequences with the database online, I made an interesting discovery. The larva leg sample from Florida, which I got for a collector about 3 weeks ago, had thought to belong to the Libellula family. Now with my data, it showed that the sample was more closely related to the Orthetrum genus, a group that was not supposed to be found in the new world. On the next week, I would continue to work with this discovery.
Thursday, August 1, 2013
Week four: FlyVac Machine
Hi everyone. This is Sandra again. I am writing my forth week in the Evolution and Behavior Lab in Harvard University.This week is quite exciting for me. I've finally got the chance to use the FlyVac machine to measure the flies' photo-tactic behavior!!
The process was doing it was actually not as difficult as I thought. As you see in the picture, the FlyVac machine is connected to a computer that is used to collect the data. Lighter blue means a light choice and the darker blue means the dark choice. The white column is used for labeling the specific type of each fly. (Enriched or controlled, Canton.S or DGRP, Female or male). After doing the labeling and set up the computer, I have to load the flies that were in the second-staging tubes (Since they already been tested in Y-maze) into the choice tubes. There are 32 choice tubes in the FlyVac.Once the flies finished 40 choices (complete line in the computer), I would use a tube to suck the fly out(which is still alive inside the choice tube), and put another fly into the choice tube.
In this coming week I will start analyzing the data in both Y-maze and FlyVac machine. I can't wait!! Hope everyone is doing fine in their labs too!
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| FlyVac machine and the computer |
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| The data in the computer |
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| The tube I used to load the flies in and suck them out |
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| The place where the flies end their life..... |
Monday, July 29, 2013
Computer Networking Lab Week 8
Hi again, this is Sohan and I am working in a computer networking lab this summer at Columbia University.
Once again, my routine this past week was essentially the same as the weeks prior; try to run the test on the Orbit-lab, process the .pcap files, and graph the results. This last time, however, after several attempts, I was finally able to obtain some data as the test bed did not give too many insurmountable issues. With this new data, I am currently trying to run the Python scripts and MATLAB script to complete the post-processing of this new data set. instead of processing and graphing previous data sets. Given that this is a new data set, the post-processing also poses issues as some of the nodes from the test bed cannot properly create .pcap files and thus the Python script cannot process them. My new challenges include trying to figure out which .pcap files are causing the issues and to further develop the script and make adjustments to it so that it can process the .pcap files smoothly without any errors arising.
Also, this past week, we had a lab meeting where all the Ph.D students had to present their recent work, and a few had to practice their presentations for their posters in some upcoming gatherings. The most intriguing, and the one I could probably understand the most, was one on cascade power failures and how to predict which power lines will go out depending on which line fails. Since Varun was at Bell Labs that day (since our project is in conjunction with Bell Labs), me and Josiah had to present in his place. All the other Ph.D provided very constructive criticism and offered other solution to more efficiently process the .pcap files such as eliminating certain steps, like storing the values in an excel file, that can be avoided entirely and save some time without altering anything whatsoever.
Lastly, since our lab is under rennovation, we are currently working in another work area. However, this past Friday, some workers came to put in some cable trays, can be used to pass wires through and create a mini network of sorts. Instead of it taking them one hour to finish as they said it would, it took them five. Instead, the five of us working in this area went into the kitchen area and watched a few episodes of Breaking Bad to pass the time - one of my favorite days on the job!
Hi again, this is Sohan and I am working in a computer networking lab this summer at Columbia University.
Once again, my routine this past week was essentially the same as the weeks prior; try to run the test on the Orbit-lab, process the .pcap files, and graph the results. This last time, however, after several attempts, I was finally able to obtain some data as the test bed did not give too many insurmountable issues. With this new data, I am currently trying to run the Python scripts and MATLAB script to complete the post-processing of this new data set. instead of processing and graphing previous data sets. Given that this is a new data set, the post-processing also poses issues as some of the nodes from the test bed cannot properly create .pcap files and thus the Python script cannot process them. My new challenges include trying to figure out which .pcap files are causing the issues and to further develop the script and make adjustments to it so that it can process the .pcap files smoothly without any errors arising.
Also, this past week, we had a lab meeting where all the Ph.D students had to present their recent work, and a few had to practice their presentations for their posters in some upcoming gatherings. The most intriguing, and the one I could probably understand the most, was one on cascade power failures and how to predict which power lines will go out depending on which line fails. Since Varun was at Bell Labs that day (since our project is in conjunction with Bell Labs), me and Josiah had to present in his place. All the other Ph.D provided very constructive criticism and offered other solution to more efficiently process the .pcap files such as eliminating certain steps, like storing the values in an excel file, that can be avoided entirely and save some time without altering anything whatsoever.
Lastly, since our lab is under rennovation, we are currently working in another work area. However, this past Friday, some workers came to put in some cable trays, can be used to pass wires through and create a mini network of sorts. Instead of it taking them one hour to finish as they said it would, it took them five. Instead, the five of us working in this area went into the kitchen area and watched a few episodes of Breaking Bad to pass the time - one of my favorite days on the job!
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