Summer Research at The Foot Hills of The Rockies...

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Week 1: May 24th-28th: The Scary Week
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I met up with Prof. Strout on 24th May, '10. This was my first day on my summer research project. Day one is known to be scary, but this was more than I had expected. I was introduced to a variety of new topics and all I could think of was "How will I ever understand all this?!"
But after the initial shock things seemed to turn better. I read my first research paper on the topic "Parallelization of the Molecular Workbench" by Christina Williams. This very topic is my project for the summer.
Prof. Strout took us all out to lunch to a Mexican food place in old town Fort Collins. I met my partner Samantha Wood too and we befriended each other very quickly.
This week, I also studied Unix and familiarized myself with the Unix shell commands, since these will be primarily used to access and conduct all the work on the machines. I familiarized myself with the workings of the Molecular Workbench and drew some simulations (some with graphs attached to them).

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Week 2: May 31st-June 4th: The Stabilizing Week
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The second week seemed to put things into better perspective. I Learned to use Eclipse -  a Java editor and wrote some programs to test out my grasp on it.
I learnt about Subversion and made a repository and a working directory.
Apart from learning about these new concepts, I read more research papers and got acquainted with other topics and projects being undertaken at the moment in CSU. I had mentioned to my mentor about my interest in Mathematics-based researches and she had introduced me to one of the projects undergoing at the college currently.
And hence, I attended the 'Melange' meeting: A meeting held primarily for Graduate students working on more mathematics based research project (Polyhedral Model).

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Week 3: June 7th-11th: The Understanding Week
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For my third week, I read through the Molecular Workbench code. Compared some of the files mentioned in the MWCHANGES.txt by Christie. I also looked at the actual MW code of both the versions side by side. Also, tried to understand the XYGraph code.
I read a paper on the applicability of the polyhedral model - "The Polyhedral Model is more widely applicable than you think" by Bastoul et al..
I started working with LyX  -  a word editor that simplifies typing papers and is very interactive and requires the least amount of commands. LyX and it's numerous interactive and easy commands and objects help in writing a research paper in the accepted standard format.
For our group meeting with all research students, we read the paper: "So long and thanks for the Ph.D.!" by Ronald Azuma. This paper gives a detailed insight to those qualities and requirements that a graduate student should have, but no one lists them on the application form.

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Week 4: June 14th-18th: The Reality-Hits-Hard Week
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This week I learned about more Java classes and looked into the Molecular Workbench code some more and worked a little more in the Eclipse environment. The main classes I learned about were:
HashMap: Map is an object that stores key/volume pairs. Given a key, you can find its value. Keys must be unique, but values may be duplicated. The HashMap class provides the primary implementation of the map interface. I wrote a little program using HashMap and the GUI library, javax.swing, of Java. It worked!
GlobalTimer: The class is simple. It was short and easy to understand.
MW PageXYGraph: I stepped through the code with the debugger in Eclipse (after much struggling!). I now understand quite a bit of the code.
Apart from this, I worked on the prototypes for some worksheets on social networking and entertainment. I came up with some literature material and real-life examples for the social networking one. Entertainment is still half way through -- we are working on more defined outlines for this one. I have some examples on paper.
I am looking at the user's manual and code of the Molecular Workbench. Two of the science faculty members from Poudre High School from the Poudre School District joined us on the 4th week. They have worked with the Molecular Workbench and they will be helping with the new worksheets. I met up with them and looked at some of their previous work.

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Week 5: June 21st-25th: The Variety Week
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I got a lot of background research accomplished this week, all a variety of various things I am working on.
Survey student attitudes about CS: I read two papers by faculty members in the Colorado School of Mines. One of the papers dealt with the attitudes high school students towards computing. The paper described what high school studetnts think about taking up CS as a career. The second paper on the other hand, described the process used to develop an instrument to measure the attitude of first year (undergraduate level) science and engineering students towards computer science. This paper had actual questions and categories to be measured.
**MW Code:(Oh! dear...): I read the code more and differentiated between the functions in the code, I am still trying to figure the rest of it out.

Others: I looked up miscellaneous information on crime investigation techniques, simulations on natural disasters, multitasking abilities of electronics such as iPhones and about the entertainment industry. This information will help us in creating some new worksheets for high school students and introduce the concept of Computer Science and hopefully open that as a more interesting career option to be considered.

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Week 6: June 28th-July 2nd: The Disappointment Week
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Apart from spraining my waist and spending a lot of time trying to import pictures in MW, I finally was able to create three pages for the facebook worksheet. I read two papers about the security on facebook and other social networking sites. The papers describe the risk and how to compute the amount of risk a person can be under, but nothing that can be represented somehow, without having to explain tons of variables and calculations....I don't know if I should include that in a worksheet?!
I also talked to Tim(Poudre High School Teacher) about the HTML and connecting all the pages together. He also gave me his oil spill worksheet (5 pages of it, that he created last week).

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Week 7: July 5th-9th: The Stress-Tension-Revision Week
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I did not have a meeting last week, so I have had a lot of time in between my last meeting and the one tomorrow. I have worked on the facebook worksheet quite a bit and ran it through Kelly(Poudre High School Teacher), for any changes and more suggestions. I have been able to find graphs for facebook statistics but no simulations, I am still searching.
I also prepared a presentation on my project for the summer and it went well. The focus group brainstormed ideas and probable areas of question formation. This week was fun to work....except for the presentation maybe (it was scary!).

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Week 8: July 12th-16th: The Feedback Week
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I finished working on the Facebook Worksheet and the page for the Elements worksheet. I also worked on the Fingerprinting video and completed the page. Kelly, Tim and I went over the worksheets for feedback. I created a wave using Google wave and set up possible survey questions on the wave to share with everyone concerned with the project and finalize the questions. I also worked on my Final Paper and Presentation. This presentation will be a group presentation with Tim and Kelly!

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Week 9: July 19th-23th: The Almost-There Week
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I am almost done with the Facebook Worksheet barring a few touch-up changes. For the Entertainment worksheet I am to work on a page bout Fingerprinting. I also devised some questions for the survey that could be incorporated in the worksheet.

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Week 10: July26th-30th: The Goodbyes Week
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This week was mostly wrapping up everything and cleaning up the project. It feels good to complete something and know that it is valuable :)
I presented my entire 10 weeks worth of work on July 30th. It was our last day. On my last day in Colorado, my mentor took me and Sam to Boulder (just an hour away) for some presentations on atmospheric research and high performance computing. It was a beautiful day and Boulder's life and liveliness cheered all of us up! It is sad that I will be leaving right away, though I want to go home to my family, whom I have not seen in a year...