Archive for category Projects

Phylogenetic tools diigo page

Here is the Diigo page that contains links to all the programs we used in the presentation.


Lucky: Canine Parvovirus type 2

Our names are Joanna and Anna, and we have a puppy named Lucky.  Two weeks ago Lucky started vomiting and having diarrhea, so we took him to the vet.  He was diagnosed with having canine parvovirus type 2.  Because we are inquisitive scientists, we took it upon ourselves to research this disease and document our findings.  Here they are!

Don’t worry guys, Lucky is on the mend 😀


Comparison Between SIV and HIV: Shalanda and Raphael

We want to show differences between HIV and SIV as demonstrated by data we present. Using ImageJ we counted the number of spikes from tomograms of HIV-1 and SIVmac239 published in PNAS (Zhu, P. et al, PNAS, 100(26): 15812, 2003). We then looked at available PDB data for viral spikes and present PyMOL and Consurf images of SIV gp41, HIV gp41 and HIV gp120 protein components. Both SIV and HIV have gp120 and gp41 which is cleaved from gp160. Our concept map created with Cmap uses current data on SIV and HIV in Proteopedia.

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Drug Delivery Project (Stefan and Mauricio)

micelle measure


Project (Pawel and Tara)

Phylogenetic Tools presentation


Jennifer, Kate R, Anastasia A. Project



Group Project (Caroline and Sean)

“E. coli fear grips Hamburg hospitals”
“Mystery of Hamburg E. coli outbreak”

Hamburg Outbreak

We sought to make the original data of media events more accessible and dynamic so that people may interact with and better understand the basic information. We used tools from Google docs and PyMOL to visualize topics relevant to the Hamburg E. coli outbreak.

Google doc visualization reference

Walk the Line (Ben/Kyle/Thomas)

Walk the Line

Kinesin (3Kin)



-Kinesin is a type of motor protein found in eukaryotic cells

-Its structure is a dimer, it includes two heavy chains (which are called the motor domains) and two light chains (α-helical stalks)

-The image seen here is from PyMOL, and it was used to separate the individual chains/proteins from larger complexes

-PyMOL can be used to learn about molecular structures including molecular size, bond lengths/angles, and specific sites of inter/intramolecular forces (important for binding of ligands)


-The motor domains contain highly conserved regions, which is expected because these are the sites of microtubule and ATP (discussed later) binding.

-These regions cannot change much or binding would not commence.


-Kinesin proteins move across microtubules and its main functions include transport and motility

-The motor domains contain 2 binding sites, 1 for ATP and 1 for microtubules

-Movement along the microtubules is powered by hydrolysis of ATP to ADP

-Hydrolysis of ATP causes a conformational change which leads to “power strokes”

-Kinesintransport a wide range of structures including vesicles and organelles, and are also important in chromosome movement during cell division


– Spactic Paraplegia

– Polycystic Kidney Disease

– Alzheimer’s Disease

– Salmonella

Link to Powerpoint



Our project investigated our travels to knoxville through the use of wordle, Cmap Tools, and image J.  Cmap Tools shows all the potential modes of transportation we might have taken.  Wordle depicts the types of words we used when thinking about transportation to Knoxville.

Cmap Tools:

To work with image J we obtained google map directions from each state and created a screen shot.

Nashua, NH to Knoxville, TN

Morris Plains, NJ to Knoxville, TN

Tyler, TX to Knoxville, TN

Once screen shots were created they were imported into image J and each image was calibrated using the map scale in the bottom left corner.  Once that was complete measurements were taken using the line option in the drawing tools.  The measurements for each trip were then imported into excel and total distance was summed.  Percent error was calculated for each trip using google’s distance versus image J’s calculated distance.  For comparison each of us calculated the distance for each trip using image J and compared the percent errors.  This showed us the personal error that can occur within image J due to its subjectivity.

Jessica’s percent error:

NH to Knox:


Jersey to Knox:


TX to Knox:


Ann’s percent error:

NH to Knox:


Jersey to Knox:


TX to Knox:


Sara’s percent errror:

NH to Knox:


Jersey to Knox:


TX to Knox:


Looking at these percent errors you can see that there can be a large difference between individuals.  This further proves that mutliple measurements should be taken and averaged to obtain results.


Google Maps


Cmap Tools

image J


kate R. Jennifer O. and Anastasia A.

We used many of the resources taught to us in this seminar such as: google reader, diigo, mendeley, c map and pymol to create an interactive concept map that could be used to teach young college and high school students. This map could be used in class as a teaching tool as well as if posted to a blog site like blackboard, used as a tool for students to study or learn more about a specific topic. In this project we looked at luciferase which is a protein that catalyzes the production of light in fireflies.