This week, Tim and I, started analyzing the results for soil samples from the HD prime in depth. We analyzed a soil sample changing the type of the substrate we had been using through the HD prime keeping the soil sample consistent. The substrate that was used to analyze all the other soil samples through the HD prime was 'bulk paint'. Other substrates available were metal, wood, textile, plastic, leather, glass. This required us to compile all the data to one file for sake of comparison and presentation. We tried different presentation approaches including individual bar charts for each substrate with the corresponding elements and one bar chart with all the substrates and their elements. Then after Dr. Kolonko explained to me and Tim how bubble charts can be used to present the data we collected. He showed us an example of such via research poster by the Chemistry department regarding Chromatography. Hence we decided to present the results through a bubble chart, such that our x-axis is the substrate, y-axis is the atomic number of the element and the size of each bubble would represent the concentration of the corresponding element the HDPrime recorded.

We started out doing bubble charts in Excel, with the atomic number of the element in the x-axis, the concentration of the element in the y-axis and the color of the bubble to be the substrate. The size of the bubble represented the uncertainty of each concentration of element.

To continue with our original idea for the bubble chart, Dr. McColgan suggested to do the plotting in MatLab. MATLAB was new to me and Tim had some past experience with regards to it. We spent a couple of hours figuring it out and trying to familiarize the coding.

With help from Dr. McColgan regarding the code, Tim and I plotted the bubble graph of Substrate vs Atomic number with the size of the bubble to be the concentration. The color of the bubbles represented the substrate. Later, to obtain more clarity on the subject, we changed the color of the bubble for each color to represent a different element, which required a finger breaking amount of time re-working the code.

Concentration of each element for one substrate [wood]

Attempt for a Bubble graph with all substrates in one graph

Atomic number vs Concentration bubble chart with the size of the bubble the uncertainity

Data Collected through the HD prime for different substrate

Atomic Number	metal	wood	textile	plastic	leather	glass	bulk paint
14	23567	22818	21506	19798	23443	22527	21466
17	0	217	288	0	211	204	237
19	8143	5523	5409	4608	5624	5582	5603
20	4035	4034	4097	4646	3903	3989	4029
22	1334	1231	1211	1151	1233	1274	1219
23	47.9	0	0	0	0	0	0
24	35.5	32.4	40.6	34.3	38.8	38.1	35.2
25	297	288	289	221	290	286	286
26	34140	34586	34595	10082	34543	34165	34340
29	74.1	78.7	79.2	44.3	78.6	77.6	78.3
30	664	695	701	350	692	683	695
31	0	0	8.2	6	9.2	0	8.5
33	22.2	48.2	63.9	0	62.8	42.8	46.2
34	0	0	1.2	1	0	0	0
35	4.9	0	0	6.2	0	0	0
36	199	54.9	57.7	52.5	53.7	51.3	56.2
37	44.7	86.2	87.7	99.6	85.9	76.6	86.1
38	66.9	0	0	0	6.6	0	0
47	0	13	9.3	4.4	11.4	10	9.5
48	0	9.5	8.6	0	11.6	9.5	0
49	0	552	567	213	509	503	537
50	415	70.2	63.5	17	52.3	69	83.5
51	35.3	423	393	403	432	383	409
82	946	793	795	554	801	791	797
83	2	6.1	7.5	3.7	5.9	4.7	7.6

Substrate vs Atomic number bubble chart with the size of the bubble to be the concentration of the particular element. Color: particular element.

5/22 -Day 5
Today was a shortened work day because Dr.K needed to leave early.  Today Dr.K told Cham he would like him to create a protein with the 3D printer so Cham found a simple, single helix protein to print out.  Soon we learned that even the most simple things aren't simple with 3D printers.  Originally we made the protein lye on its side but after a couple attempts it became clear that it wasn't working.  We took a break to test a soil sample with different settings on the HDPrime.  After I suggested to stand up the molecule, instead of lying it down, it seemed for the first twenty minutes that it would work out great, but once the molecule was too tall for its supports the printer started ripping up the print. So we cut that and didn't have enough time in the lab to start another print but Cham came up the solution I believe.  Too lean the molecule so it can have supports throughout and still be built from the ground up.  Me and Cham stayed in the computer labs a little after Dr.K left to make some soil comparison graphs with error bars and that concluded our day.  

5/21-Day 4
   Not every day is great to be a scientist, sometimes there are walls that seem miles high.  But I guess you just need to keep climbing.  This happened to me and Cham when we moved the printrbot from one location to another and Cham needed to reinstall all the programs onto this new computer.  That was a minor setback, nothing to bad.  The next challenge that stopped us is how on the previous day we got the printer to work in less than fifteen minutes and now today no matter how many adjustments we made the printer still wouldn't make a good print.  After hours of aggravation me and Cham were both equally frustrated, I decided lunch was a good idea, even though it was a bit early if me and Cham had stayed any longer it wouldn't have been pretty.  After returning From lunch i made one last adjustment to the probe that detects the metal plate and of course the next print was spot on.  We decided the first usable thing that we make with the printer should be the fan shroud, a cover for the fan that was suggested to be something to make after finishing the Printbot.  The piece came out perfectly on our first attempt. Below are some pictures from the Fan cover being made.  Even after hours of aggravation the day still ended on a good note, after I tested some of the supplements that I take from GNC.

The beginning of the Fan hood 

The printbot finishing the Fan hood

     

5/20 -Day 3

The motherboard of the printer before wiring

     On the third day of working, me and Cham agreed together that we were determined to complete the Printrbot before we left for lunch... needless to say we ate a late lunch that day.  The teamwork and coordination necessary for me and Cham to build the printer in the short amount of time amazed me at how good of a team we are together.  By far the most challenging and time consuming part of this project was the wiring inside of the Printer.  But after some carefully placed zip-ties everything fell into place as it should have.  After completing the printer and eating lunch we returned to the lab to start printing.  This is where Cham took over, he knew everything necessary to get the printer going as fast as possible.  Our first print of a cube was a mess to say the least, but after I took on the responsibilities of physical calibrations our second print was spot on, this must be a rare occurrence because even Cham was amazed.  After printing another cube or two we decided to call it a day.  

Trying to find room for all the wires

Things became more and more messy with every wire plugged in

The printer just before adding the metal plate

The finished product.

5/19 -Day 2
       Over the course of the second day Cham and I were collecting data on soil samples in the HD Prime, the tests should have taken less than an hour, however, after deciding we needed to test the plastic bags, which were all different, we finished collecting data in a little less than two hours.  after lunch, Cham and I were blessed with the task of assembling a 3D printer.  I have had zero experience in this field however it seemed Cham knew what he was doing so we began to take all the parts from the box and start building.  Over the next three hours Cham and I finished one of the arms of our wooden Printrbot.  A picture of the resulting product of Day one is shown below.

The 3D printer after one day of assembly

Some of the wooden panels that created the frame for the printer

5/18- Day 1
On my first day back at Siena I was introduced and got familiar with the HD Prime and began running tests on water and soil samples.  After running about ten tests over the course of an hour or so, it became clear to me that this process needs to become autonomous one to streamline the process of collecting data in the most efficient way possible.  Me and my partner Cham finished the day by making some graphs on excel that compared the results we found from the water samples.