MC Chem Wiki - User contributions [en]

Alex L Boswell

2022-07-11T15:27:11Z

Bozz: /* Undergraduate Research Activities */

==Personal Information==
Monmouth College class of 2023
:'''''Chemistry Major; Physics Minor'''''

From Dixon, IL

Email: alboswell@monmouthcollege.edu

Phone Number: (1)815-677-1450

==Undergraduate Research Activities==

[[Exploring Underwater Environments_Drone_01|Exploring Underwater Environments with Fifish V6 Expert Drone]]

[[Data analyzation|Data analyzation]]

Alex Boswell

Exploring Under Water Environments

•Under water environments and the human body are similar in the fact that we are made mostly of water and have a microbiome. Science has mapped the human body, can obtain samples of the microbiome through fecal matter, and convey the information into a readable format. Under water environments have yet to be mapped, this is where SONAR becomes a very helpful tool as it maps the ground below the water. To collect samples a Fifish V6 Expert Drone was used which not only gave us a means of collecting samples but also gave access to exploring the water in a first-person view from the safety of land. Once the samples have been run through an instrument it will provide a text file, converting this file into images through the Qiime2 software gives easy to read and informative graphics such as bar plots.

==Presentations==
:Coming Soon

==Interests==

I am interested in chemistry, physics, coding, and teaching. I enjoy a challenge and the responsibility of leadership.

==Career Goals==

With these interest in mind I am excited to apply to Graduate School and possibly enter the work force in a lab or industrial setting after graduating from Monmouth College. With the experience I have so far from research and communicating with my Professors I can already sense that there are many options available to me in terms of education, research, and work.

I want to attend Graduate School and study more in the field of Physical Chemistry or a mix of Chemistry and Physics. I particularly want to focus on one of these two options as I have found a love for the physical side of chemistry and enjoy the hands on experience that is accustomed to it. Physics is something I did not start to learn till I was a Junior at Monmouth College, but since joining physics I have enjoyed learning how the universe works and the complicated questions and issues that physics ask or does not explain. During my hunt for schools I would like to attend my top priority will be how their Physical Chemistry department is and what they are currently doing with research as well as future projects they want to pursue.

Finding a job is also extremely important and although I do like using Instruments and learning about what they do I like to use my hands along with my brain. My preferred job would be teaching as a Professor at a college level institution. This would allow me to have lots of communication with others, being able to teach, and set up and perform research on a subject that I select.
I would also enjoy working in a lab as a managerial position where I am expected to know how things run in the facility but also take part in working with those that I am responsible for.

==Work Expierience==
August 2021-Current

'''Teaching Assistant|Teaching|Monmouth College Department of Chemistry'''

Working in the Analytical Chemistry Lab, I set up materials and instruments and helped students with questins they may have as well as understanding the concepts of each lab.

Alex L Boswell

2022-07-11T15:26:45Z

Bozz: /* Undergraduate Research Activities */

==Personal Information==
Monmouth College class of 2023
:'''''Chemistry Major; Physics Minor'''''

From Dixon, IL

Email: alboswell@monmouthcollege.edu

Phone Number: (1)815-677-1450

==Undergraduate Research Activities==

[[Exploring Underwater Environments_Drone_01|Exploring Underwater Environments with Fifish V6 Expert Drone]]

[[Data analyzation|Data analyzation]]

Alex Boswell
Exploring Under Water Environments
•Under water environments and the human body are similar in the fact that we are made mostly of water and have a microbiome. Science has mapped the human body, can obtain samples of the microbiome through fecal matter, and convey the information into a readable format. Under water environments have yet to be mapped, this is where SONAR becomes a very helpful tool as it maps the ground below the water. To collect samples a Fifish V6 Expert Drone was used which not only gave us a means of collecting samples but also gave access to exploring the water in a first-person view from the safety of land. Once the samples have been run through an instrument it will provide a text file, converting this file into images through the Qiime2 software gives easy to read and informative graphics such as bar plots.

==Presentations==
:Coming Soon

==Interests==

I am interested in chemistry, physics, coding, and teaching. I enjoy a challenge and the responsibility of leadership.

==Career Goals==

With these interest in mind I am excited to apply to Graduate School and possibly enter the work force in a lab or industrial setting after graduating from Monmouth College. With the experience I have so far from research and communicating with my Professors I can already sense that there are many options available to me in terms of education, research, and work.

I want to attend Graduate School and study more in the field of Physical Chemistry or a mix of Chemistry and Physics. I particularly want to focus on one of these two options as I have found a love for the physical side of chemistry and enjoy the hands on experience that is accustomed to it. Physics is something I did not start to learn till I was a Junior at Monmouth College, but since joining physics I have enjoyed learning how the universe works and the complicated questions and issues that physics ask or does not explain. During my hunt for schools I would like to attend my top priority will be how their Physical Chemistry department is and what they are currently doing with research as well as future projects they want to pursue.

Finding a job is also extremely important and although I do like using Instruments and learning about what they do I like to use my hands along with my brain. My preferred job would be teaching as a Professor at a college level institution. This would allow me to have lots of communication with others, being able to teach, and set up and perform research on a subject that I select.
I would also enjoy working in a lab as a managerial position where I am expected to know how things run in the facility but also take part in working with those that I am responsible for.

==Work Expierience==
August 2021-Current

'''Teaching Assistant|Teaching|Monmouth College Department of Chemistry'''

Working in the Analytical Chemistry Lab, I set up materials and instruments and helped students with questins they may have as well as understanding the concepts of each lab.

File:Abstract.docx

2022-07-11T15:16:18Z

Bozz: File uploaded with MsUpload

File uploaded with MsUpload

Alex L Boswell

2022-07-08T15:15:23Z

Bozz: /* Presentations */

==Personal Information==
Monmouth College class of 2023
:'''''Chemistry Major; Physics Minor'''''

From Dixon, IL

Email: alboswell@monmouthcollege.edu

Phone Number: (1)815-677-1450

==Undergraduate Research Activities==

[[Exploring Underwater Environments_Drone_01|Exploring Underwater Environments with Fifish V6 Expert Drone]]

[[Data analyzation|Data analyzation]]

==Presentations==
:Coming Soon

==Interests==

I am interested in chemistry, physics, coding, and teaching. I enjoy a challenge and the responsibility of leadership.

==Career Goals==

With these interest in mind I am excited to apply to Graduate School and possibly enter the work force in a lab or industrial setting after graduating from Monmouth College. With the experience I have so far from research and communicating with my Professors I can already sense that there are many options available to me in terms of education, research, and work.

I want to attend Graduate School and study more in the field of Physical Chemistry or a mix of Chemistry and Physics. I particularly want to focus on one of these two options as I have found a love for the physical side of chemistry and enjoy the hands on experience that is accustomed to it. Physics is something I did not start to learn till I was a Junior at Monmouth College, but since joining physics I have enjoyed learning how the universe works and the complicated questions and issues that physics ask or does not explain. During my hunt for schools I would like to attend my top priority will be how their Physical Chemistry department is and what they are currently doing with research as well as future projects they want to pursue.

Finding a job is also extremely important and although I do like using Instruments and learning about what they do I like to use my hands along with my brain. My preferred job would be teaching as a Professor at a college level institution. This would allow me to have lots of communication with others, being able to teach, and set up and perform research on a subject that I select.
I would also enjoy working in a lab as a managerial position where I am expected to know how things run in the facility but also take part in working with those that I am responsible for.

==Work Expierience==
August 2021-Current

'''Teaching Assistant|Teaching|Monmouth College Department of Chemistry'''

Working in the Analytical Chemistry Lab, I set up materials and instruments and helped students with questins they may have as well as understanding the concepts of each lab.

Alex L Boswell

2022-07-08T15:14:32Z

Bozz: /* Presentations */

==Personal Information==
Monmouth College class of 2023
:'''''Chemistry Major; Physics Minor'''''

From Dixon, IL

Email: alboswell@monmouthcollege.edu

Phone Number: (1)815-677-1450

==Undergraduate Research Activities==

[[Exploring Underwater Environments_Drone_01|Exploring Underwater Environments with Fifish V6 Expert Drone]]

[[Data analyzation|Data analyzation]]

==Presentations==
:Coming Soon

<div class="highlight-shell notranslate"> == $0
<button class="btn btn-default clipboard-btn" title="Click to copy the command block below" data-clipboard-text="qiime --help">
<span class="glyphicon glyphicon-copy">
</span>
</button>
<div class="highlight">
<pre>
<span></span>
qiime --help
</pre>
</div>
</div>

==Interests==

I am interested in chemistry, physics, coding, and teaching. I enjoy a challenge and the responsibility of leadership.

==Career Goals==

With these interest in mind I am excited to apply to Graduate School and possibly enter the work force in a lab or industrial setting after graduating from Monmouth College. With the experience I have so far from research and communicating with my Professors I can already sense that there are many options available to me in terms of education, research, and work.

I want to attend Graduate School and study more in the field of Physical Chemistry or a mix of Chemistry and Physics. I particularly want to focus on one of these two options as I have found a love for the physical side of chemistry and enjoy the hands on experience that is accustomed to it. Physics is something I did not start to learn till I was a Junior at Monmouth College, but since joining physics I have enjoyed learning how the universe works and the complicated questions and issues that physics ask or does not explain. During my hunt for schools I would like to attend my top priority will be how their Physical Chemistry department is and what they are currently doing with research as well as future projects they want to pursue.

Finding a job is also extremely important and although I do like using Instruments and learning about what they do I like to use my hands along with my brain. My preferred job would be teaching as a Professor at a college level institution. This would allow me to have lots of communication with others, being able to teach, and set up and perform research on a subject that I select.
I would also enjoy working in a lab as a managerial position where I am expected to know how things run in the facility but also take part in working with those that I am responsible for.

==Work Expierience==
August 2021-Current

'''Teaching Assistant|Teaching|Monmouth College Department of Chemistry'''

Working in the Analytical Chemistry Lab, I set up materials and instruments and helped students with questins they may have as well as understanding the concepts of each lab.

Alex L Boswell

2022-07-08T15:00:42Z

Bozz: /* Presentations */

==Personal Information==
Monmouth College class of 2023
:'''''Chemistry Major; Physics Minor'''''

From Dixon, IL

Email: alboswell@monmouthcollege.edu

Phone Number: (1)815-677-1450

==Undergraduate Research Activities==

[[Exploring Underwater Environments_Drone_01|Exploring Underwater Environments with Fifish V6 Expert Drone]]

[[Data analyzation|Data analyzation]]

==Presentations==
:Coming Soon
<button class="btn btn-default clipboard-btn" title="Click to copy the command block below" data-clipboard-text="qiime --help"><span class="glyphicon glyphicon-copy"></span></button>

==Interests==

I am interested in chemistry, physics, coding, and teaching. I enjoy a challenge and the responsibility of leadership.

==Career Goals==

With these interest in mind I am excited to apply to Graduate School and possibly enter the work force in a lab or industrial setting after graduating from Monmouth College. With the experience I have so far from research and communicating with my Professors I can already sense that there are many options available to me in terms of education, research, and work.

I want to attend Graduate School and study more in the field of Physical Chemistry or a mix of Chemistry and Physics. I particularly want to focus on one of these two options as I have found a love for the physical side of chemistry and enjoy the hands on experience that is accustomed to it. Physics is something I did not start to learn till I was a Junior at Monmouth College, but since joining physics I have enjoyed learning how the universe works and the complicated questions and issues that physics ask or does not explain. During my hunt for schools I would like to attend my top priority will be how their Physical Chemistry department is and what they are currently doing with research as well as future projects they want to pursue.

Finding a job is also extremely important and although I do like using Instruments and learning about what they do I like to use my hands along with my brain. My preferred job would be teaching as a Professor at a college level institution. This would allow me to have lots of communication with others, being able to teach, and set up and perform research on a subject that I select.
I would also enjoy working in a lab as a managerial position where I am expected to know how things run in the facility but also take part in working with those that I am responsible for.

==Work Expierience==
August 2021-Current

'''Teaching Assistant|Teaching|Monmouth College Department of Chemistry'''

Working in the Analytical Chemistry Lab, I set up materials and instruments and helped students with questins they may have as well as understanding the concepts of each lab.

Qiime2 Instructions

2022-07-07T15:23:16Z

Bozz: /* Command set 1 */

==Introduction==
Data sent to us by Frank Oliaro (foliaro@sheddaquarium.org) from Shedd Aquarium has the input format of the “Casava 1.8 paired-end demultiplexed fastq.” This data (.fastq vs .fast) also contains “Quality” information. In this format there are two data files per sample, one for the forward read (R1) and one for the reverse read (R2); the files are compressed and have the XXX_fastq.gz extension. Qiime2 can work with compressed files, so no need to convert the XXX.fastq.gz to XXX.fastq. This file format is described on the Qiime2 website (see importing link below) as:

“In Casava 1.8 demultiplexed (paired-end) format, there are two fastq.gz files for each sample in the study, each containing the forward or reverse reads for that sample. The file name includes the sample identifier. The forward and reverse read file names for a single sample might look like L2S357_15_L001_R1_001.fastq.gz and L2S357_15_L001_R2_001.fastq.gz, respectively. The underscore-separated fields in this file name are:

- the sample identifier,
- the barcode sequence or a barcode identifier,
- the lane number,
- the direction of the read (i.e. R1 or R2), and
- the set number.”

The amplicon to be sequenced was for the variable region 4 (V4) of the 16S gene which contains 254 base pairs. The HiSeq Lumina sequncing requires additional DNA referred to as adapters, sequencing binding sites, indices (or barcodes), and complements to the flow cell oligios. Therefore the DNA sequence has an overall length of >400 base pairs. Since the HiSeq instrument works best with ~200 base pairs, sequencing forward and reverse generates these two sequences which can be analyzed (ie. combined/joined together) to generate a final sequence containing the entire 254 (V4) base pairs.

==Analyzing the Data==
===STEP 1===
The first step in the processing of the two forward and reverse files (XXX_R1_YYY.fastq.gz and XXX_R2_YYY.fastq.gz) is to import then into qiime2. Prior to doing any qiime2 work we must place all data files in a single directory. For example, Frank O sent us a link to the data that was compressed into a single zip file. When downloaded and unzipped, the resulting folder contained 11 subfolders each with the R1 and R2 data file. A new folder was made called ‘reads’ and all R1/R2 data sets were put directly (ie, no subfolders) in this folder. The resulting ‘reads’ folder now contains 22 files with sequencing data for 11 samples. When importing data into qiime2, all data in the ‘reads’ folder will be processed at the same time.

===STEP 2===
Importing this data will be outlined below, but can be found on the Qiime2 website:
https://docs.qiime2.org/2021.8/tutorials/importing/
…scroll down under the heading of Casava 1.8 paired-end demultiplexed fastq

Let me remind you that this sequencing data has already been demultiplexed, meaning that the sequencing data has been sorted based on the indexes/barcodes; this is done by the HiSeq instrument.

====Command set 1====
The following commands must be executed using a terminal window/shell from the directory immediately above the ‘reads’ directory. The following assumes that Qiime2 has been installed on your computer. If you are just opening a terminal window, you must enter into the Qiime2 environment by typing:

For VR laptops...

conda activate qiime2-2022.2

conda activate qiime2-202X.X <—where the X.X is your installed version; this is qiime2-2021.4 or qiime2-2022.2 (MAC), qiime2-2021.8 on the PC in CSB 360.
- the above commend will then result in the terminal window showing a (quine2-2021.4) line header.

====Command set 2====
Now navigate to the proper directory; fyi, when working in a “window” environment we usually refer to folders, but when working in a terminal window/shell we often use the term directory. These terms have the exact same meaning. The UNIX commands cd XYZ for change directory to XYZ and ls for list directory contents are necessary to navigate within a terminal window.

Once in the proper directory, ie if you type ls you will see the reads directory listed, the following series of commands will be executed (do not type the word <enter> just hit the enter/return key):

qiime tools import \ <enter> <— this will launch the qiime application and the \ means wait, then
--type 'SampleData[PairedEndSequencesWithQuality]' \ <enter> <— this command identified the data type
--input-path reads/ \ <enter>
--input-format CasavaOneEightSingleLanePerSampleDirFmt \ <enter>
--output-path demux-paired-end.qza

====Command set 3====
Once the set of commands above have run successfully, you need to exam the sequence quality (QC) to determine how the data sequences should be trimmed. There is a plugin for graphing sequence quality that is run by the following commands (this command is run from the directory containing the .qza file):

qiime demux summarize \
--i-data demux-paired-end.qza \
--o-visualization demux-paired-end_viz.qzv

This output file, demux-paired-end_vis.qzv is then “dragged and dropped” into the https://view.qiime2.org window and data will be displayed.

Interpreting the .qzv data
The view.qiime.org webpage will display a window with 2 tabs:
- Overview
- Interactive Quality Plot

The information in the Interactive Quality Plot shows that the quality score (blk data) is between 40 and 20 and this data looks really good (some quality scores are in the 2-10 range). Based on this plot we will trim the front by 15 basepairs and the end at 230. Keep in mind that the V4 region is 256 base pairs and since we have ~ 220 forward reads and ~220 reverse reads, we will have a significant amount of end-overlap which will be discarded once we join the two sets of reads.

====Command set 4====
To do this trimming, execute the following commands:

qiime dada2 denoise-paired \
--i-demultiplexed-seqs demux-paired-end.qza \
--p-trim-left-f 15 \
--p-trim-left-r 15 \
--p-trunc-len-f 220 \
--p-trunc-len-r 220 \
--o-representative-sequences rep-seqs-dada2.qza \
--o-table table-dada2.qza \
--o-denoising-stats stats-dada2.qza

The above command generates 3 .qza files.

====Command set 5====
Next, we want to visualize the stats data (stats-dada2.qza) by entering the following command:

qiime metadata tabulate \
--m-input-file stats-dada2.qza \
--o-visualization stats-dada2.qzv

The resulting .qzv files contains information about how the data was processes…there is no real info to pull for this at this time.

Next, we want to visualize the FeatureTable data (table-dada2.qza) by entering the following command:

qiime feature-table summarize \
--i-table table-dada2.qza \
--o-visualization table.qzv

*******
the following command was listed in the tutorial, but was not used??? We do not have a metadata file…CORRECTION…the metafile .TSV file can be downloaded from the view.qiime.org…i don’t recall what visulization files showed this link???
--m-sample-metadata-file sample-metadata.tsv
*******

====Command set 6====
Next, we want to visualize the seq data (rep-seqs-dada2.qza) by entering the following command:

qiime feature-table tabulate-seqs \
--i-data rep-seqs-dada2.qza \
--o-visualization rep-seqs-dada2.qzv

====Command set 7====
Now we are ready to generate a tree for phylogenetic diversity using the following commands:

qiime phylogeny align-to-tree-mafft-fasttree \
--i-sequences rep-seqs-dada2.qza \
--o-alignment align-rep-seqs.qza \
--o-masked-alignment masked-aligned-rep-seqs.qza \
--o-tree unroot-tree.qza \
--o-rooted-tree rooted-tree.qza

not totally sure what the above commands have done for us, but…

====Command set 8====
For the next command you will need to acquire a "classifier" file from [https://data.qiime2.org/2022.2/common/gg-13-8-99-515-806-nb-classifier.qza here_1] or [https://data.qiime2.org/2022.2/common/gg-13-8-99-nb-classifier.qza here_2] <-- this file needs to be saved/relocated into the main working folder.

On to taxonomy…to determine the taxonomic composition of the samples use the following commands:

qiime feature-classifier classify-sklearn \
--i-classifier gg-13-8-99-515-806-nb-classifier.qza \ <-- us this line if using gg-13-8-99-515-806-nb-classifier.qza
--i-classifier gg-13-8-99-nb-classifier.qza \ <-- us this line if using gg-13-8-99-nb-classifier.qza
--i-reads rep-seqs-dada2.qza \
--o-classification taxonomy.qza

qiime metadata tabulate \
--m-input-file taxonomy.qza \
--o-visualization taxonomy.qzv

====Command set 9====
Now we want to visualize this data using the barplot…using these commands:

qiime taxa barplot \
--i-table table-dada2.qza \
--i-taxonomy taxonomy.qza \
--m-metadata-file sample-metadata.tsv \ <-- skip this line
--o-visualization taxa-bar-plots.qzv

====Visualizing the barplot====
Now drag and drop the taxa-bar-plots.qzv file into the view.qiime2.org/ window.

Alex L Boswell

2022-07-06T16:32:32Z

Bozz: /* Undergraduate Research Activities */

==Personal Information==
Monmouth College class of 2023
:'''''Chemistry Major; Physics Minor'''''

From Dixon, IL

Email: alboswell@monmouthcollege.edu

Phone Number: (1)815-677-1450

==Undergraduate Research Activities==

[[Exploring Underwater Environments_Drone_01|Exploring Underwater Environments with Fifish V6 Expert Drone]]

[[Data analyzation|Data analyzation]]

==Presentations==
:Coming Soon

==Interests==

I am interested in chemistry, physics, coding, and teaching. I enjoy a challenge and the responsibility of leadership.

==Career Goals==

With these interest in mind I am excited to apply to Graduate School and possibly enter the work force in a lab or industrial setting after graduating from Monmouth College. With the experience I have so far from research and communicating with my Professors I can already sense that there are many options available to me in terms of education, research, and work.

I want to attend Graduate School and study more in the field of Physical Chemistry or a mix of Chemistry and Physics. I particularly want to focus on one of these two options as I have found a love for the physical side of chemistry and enjoy the hands on experience that is accustomed to it. Physics is something I did not start to learn till I was a Junior at Monmouth College, but since joining physics I have enjoyed learning how the universe works and the complicated questions and issues that physics ask or does not explain. During my hunt for schools I would like to attend my top priority will be how their Physical Chemistry department is and what they are currently doing with research as well as future projects they want to pursue.

Finding a job is also extremely important and although I do like using Instruments and learning about what they do I like to use my hands along with my brain. My preferred job would be teaching as a Professor at a college level institution. This would allow me to have lots of communication with others, being able to teach, and set up and perform research on a subject that I select.
I would also enjoy working in a lab as a managerial position where I am expected to know how things run in the facility but also take part in working with those that I am responsible for.

==Work Expierience==
August 2021-Current

'''Teaching Assistant|Teaching|Monmouth College Department of Chemistry'''

Working in the Analytical Chemistry Lab, I set up materials and instruments and helped students with questins they may have as well as understanding the concepts of each lab.

Alex L Boswell

2022-07-06T14:53:55Z

Bozz: /* Undergraduate Research Activities */

==Personal Information==
Monmouth College class of 2023
:'''''Chemistry Major; Physics Minor'''''

From Dixon, IL

Email: alboswell@monmouthcollege.edu

Phone Number: (1)815-677-1450

==Undergraduate Research Activities==

[[Exploring Underwater Environments_Drone_01|Exploring Underwater Environments with Fifish V6 Expert Drone]]

Data analyzation

==Presentations==
:Coming Soon

==Interests==

I am interested in chemistry, physics, coding, and teaching. I enjoy a challenge and the responsibility of leadership.

==Career Goals==

With these interest in mind I am excited to apply to Graduate School and possibly enter the work force in a lab or industrial setting after graduating from Monmouth College. With the experience I have so far from research and communicating with my Professors I can already sense that there are many options available to me in terms of education, research, and work.

I want to attend Graduate School and study more in the field of Physical Chemistry or a mix of Chemistry and Physics. I particularly want to focus on one of these two options as I have found a love for the physical side of chemistry and enjoy the hands on experience that is accustomed to it. Physics is something I did not start to learn till I was a Junior at Monmouth College, but since joining physics I have enjoyed learning how the universe works and the complicated questions and issues that physics ask or does not explain. During my hunt for schools I would like to attend my top priority will be how their Physical Chemistry department is and what they are currently doing with research as well as future projects they want to pursue.

Finding a job is also extremely important and although I do like using Instruments and learning about what they do I like to use my hands along with my brain. My preferred job would be teaching as a Professor at a college level institution. This would allow me to have lots of communication with others, being able to teach, and set up and perform research on a subject that I select.
I would also enjoy working in a lab as a managerial position where I am expected to know how things run in the facility but also take part in working with those that I am responsible for.

==Work Expierience==
August 2021-Current

'''Teaching Assistant|Teaching|Monmouth College Department of Chemistry'''

Working in the Analytical Chemistry Lab, I set up materials and instruments and helped students with questins they may have as well as understanding the concepts of each lab.

File:Summer research computer help.docx

2022-07-06T14:50:07Z

Bozz: File uploaded with MsUpload

File uploaded with MsUpload

Dive Computer Application and Use

2022-06-30T19:36:28Z

Bozz: /* Installation and Manual */

==Use and Application==

In our Under-Water Microbiome research we are using the ''Cressi Dive Computer, Leonardo Addition''. Our motivation for using this dive computer is that it will allow us to receive information from the dive in a format that we can work with. This is necessary because the Fifish V6 Expert Drone that we use relays data such as time, depth, and temperature in the form as a watermark on the video captured, essentially whenever you are not recording you have no access to this information. Not only that but it doesn't save this data, it is only available through the images produced by the drones camera interface. The current computer and drone setup has the dive computer on top of the drone strapped down by wires hugging the side motors. This allows us to receive data from both the drone and dive computer without interfering with the performance of either.

Through the use of this dive computer and software program we are able to look at the data from the dive of the drone in a text format that will allow us to create graphs and quickly look through the data to see what temperature and depth the drone was at for any given moment recorded. This specific tab will also display the mode you were in (ex. air or nitride mix), pressure, and decompression information (information involving rising to the surface). The software along with this allows you to put a location on a map as to where a dive took place and write down notes involving the dive including weather and water conditions, visibility, and wind. You can take images taken from the drone and attach them to the specific dive and dive folder within the Cressi PC Interface.

'''Accessing a Dive File'''

To gain access to the dive information it only takes a few steps.

1) Open the Cressi PC Interface application and plug in the Cressi interface to the computer.

2) On the Cressi Dive Computer there is a button allowing you to change settings, set it to PCLINK.

3) Take the dive computer (dive watch) and place it on top of the Cressi interface.

4) Go to the settings tab, the connection status will say 'Active' when it is connected.

5) Go to the download tab, there is a folder named 'Dive Computer_logbook'. In this folder it will show on the right of the screen that reads "Dives in The Device" it will show all the dives on the Cressi Dive Computer.

6) Select the dive that you want to look at, a check mark will appear in the line. After selecting the dive, select download.

7) Go to the archive tab, in a box on the left of the screen will read archive path, by selecting the folder from before 'Dive Computer_logbook'. The dive will be in this folder.

8) Double clicking a dive will open a graph with all the information from the dive available in the 'Archive' tab. You can export the data from this tab as either an image or a text data file.

==Installation and Manual==

Download of Cressi PC Interface- https://www.cressi.com/software

Dive computer manual- https://s3-eu-west-1.amazonaws.com/cressielettronica/software/CressiPcInterface_2_0_1_ManualeUtente_ENG.pdf

https://www.manualslib.com/manual/764842/Cressi-Leonardo.html?page=31

SONAR Mapping

2022-06-30T19:10:00Z

Bozz: Created page with "https://youtu.be/WFzBSq8KCkg"

https://youtu.be/WFzBSq8KCkg

Exploring Underwater Environments Drone 01

2022-06-30T19:09:20Z

Bozz: /* Equipment */

==Motivation==

==Introduction==

==Equipment==
[[Dive Computer Application and Use|Dive Computer]]

[[Fifish V6 Expert Drone Arm Attachment|Fifish Arm Attachment]]

[[SONAR Mapping|SONAR Mapping]]

==Experimental==

==References==
[[Media:Bjorneras et al 2020.pdf|Inland blue holes of The Bahamas – chemistry and biology in a unique aquatic environment (2020)]]

Fifish V6 Expert Drone Arm Attachment

2022-06-24T19:23:06Z

Bozz: /* Use and Application */

==Use and Application==

When swimming or diving in water you may lose things and wish they could be recovered but they are just too deep. When trying to collect samples and/or material from the deep or in caves it may be hard to gain access to. A lack of equipment and or a lack of access to an area may require the use of a smaller body and set of hands. This is where the drone (body) and the arm attachment (hand) come into play. As we conduct research primarily in bodies of water and more specifically our interest in Blue Holes we need to think about what is needed to collect samples in these areas. Getting access to courses and learning to SCUBA Dive takes a good amount of money and time, not only that but the dangers that come with SCUBA Diving primarily in caves are not worth the risk of students and professors. So, we will use the Fifish V6 Expert Drone to explore and be the eyes of our research team.

The arm attachment gives us capabilities that the drone alone couldn't do. With this attachment there a number of things we can do. First, we can pick up things from within the water, but more importantly it can hold things. If we had an ''oxygen degredation or a salinity tube'' we can use the drone to dive down and run this expieriment without needing to buy a boat or expensive apparatus for getting down there. Next, the drone can hold things like a bottle which would allow us to go into the water and as a bottle facing down does not take in water we would then be able to flip the drone upside down collecting a water sample, saving hundreds of dollars.

==Attachment==

Fifish V6 Expert Drone Arm Attachment

2022-06-24T14:51:55Z

Bozz: /* Use and Application */

==Use and Application==

When swimming or diving in water you may lose things and wish they could be recovered but they are just too deep. When trying to collect samples and/or material from the deep or in caves it may be hard to gain access to. A lack of equipment and or a lack of access to an area may require the use of a smaller body and set of hands. This is where the drone (body) and the arm attachment (hand) come into play. As we conduct research primarily in bodies of water and more specifically our interest in Blue Holes we need to think about what is needed to collect samples in these areas. Getting access to courses and learning to SCUBA Dive takes a good amount of money and time, not only that but the dangers that come with SCUBA Diving primarily in caves are not worth the risk of students and professors. So, we will use the Fifish V6 Expert Drone to explore and be the eyes of our research team.

The arm attachment gives us capabilities that the drone alone couldn't do. With this attachment there a number of things we can do. First, we can pick up things from within the water, but more importantly it can hold things. If we had an ''oxygen degredation or a salinity tube'' we can use the drone to dive down and run this expieriment without needing to buy a boat or expensive apparatus for getting down there. Next, the drone can hold things like a bottle which would allow us to go into the water and as a bottle facing down does not take in water we would then be able to flip the drone upside downcollecting a water sample saving hundreds of dollars.

==Attachment==

Fifish V6 Expert Drone Arm Attachment

2022-06-23T20:58:26Z

Bozz: /* Use and Application */

Fifish V6 Expert Drone Arm Attachment

2022-06-23T20:58:10Z

Bozz: /* Use and Application */

Fifish V6 Expert Drone Arm Attachment

2022-06-23T20:17:12Z

Bozz: Created page with "==Use and Application== ==Attachment=="

==Use and Application==

==Attachment==

Exploring Underwater Environments Drone 01

2022-06-23T20:08:07Z

Bozz: /* Equipment */

==Motivation==

==Introduction==

==Equipment==
[[Dive Computer Application and Use|Dive Computer]]

[[Fifish V6 Expert Drone Arm Attachment|Fifish Arm Attachment]]

==Experimental==

==References==
[[Media:Bjorneras et al 2020.pdf|Inland blue holes of The Bahamas – chemistry and biology in a unique aquatic environment (2020)]]

Dive Computer Application and Use

2022-06-23T19:18:53Z

Bozz: /* Use and Application */

Dive Computer Application and Use

2022-06-23T19:18:19Z

Bozz: /* Use and Application */

==Use and Application==

In our Under-Water Microbiome research we are using the ''Cressi Dive Computer, Leonardo Addition''. Our motivation for using this dive computer is that it will allow us to receive information from the dive in a format that we can work with. This is necessary because the Fifish V6 Expert Drone that we use relays data such as time, depth, and temperature in the form as a watermark on the video captured, essentially whenever you are not recording you have no access to this information. Not only that but it doesn't save this data, it is only available through the images produced by the drones camera interface. The current computer and drone setup has the dive computer on top of the drone strapped down by wires hugging the side motors. This allows us to receive data from both the drone and dive computer without interfering with the performance of either.

Through the use of this dive computer and software program we are able to look at the data from the dive of the drone in a text format that will allow us to create graphs and quickly look through the data to see what temperature and depth the drone was at for any given moment recorded. This specific tab will also display the mode you were in (ex. air or nitride mix), pressure, and decompression information (information involving rising to the surface). The software along with this allows you to put a location on a map as to where a dive took place and write down notes involving the dive including weather and water conditions, visibility, and wind. You can take images taken from the drone and attach them to the specific dive and dive folder within the Cressi PC Interface.

'''Accessing a Dive File'''

To gain access to the dive information it only takes a few steps.

1) Open the Cressi PC Interface application and plug in the Cressi interface to the computer.
2) On the Cressi Dive Computer there is a button allowing you to change settings, set it to PCLINK.
3) Take the dive computer (dive watch) and place it on top of the Cressi interface.
4) Go to the settings tab, the connection status will say 'Active' when it is connected.
5) Go to the download tab, there is a folder named 'Dive Computer_logbook'. In this folder it will show on the right of the screen that reads "Dives in The Device" it will show all the dives on the Cressi Dive Computer.
6) Select the dive that you want to look at, a check mark will appear in the line. After selecting the dive, select download.
7) Go to the archive tab, in a box on the left of the screen will read archive path, by selecting the folder from before 'Dive Computer_logbook'. The dive will be in this folder.
8) Double clicking a dive will open a graph with all the information from the dive available in the 'Archive' tab. You can export the data from this tab as either an image or a text data file.

==Installation and Manual==

Download of Cressi PC Interface- https://www.cressi.com/software

Dive computer manual- https://s3-eu-west-1.amazonaws.com/cressielettronica/software/CressiPcInterface_2_0_1_ManualeUtente_ENG.pdf

Dive Computer Application and Use

2022-06-23T18:22:27Z

Bozz: /* Accessing the Dives */

Dive Computer Application and Use

2022-06-23T18:21:59Z

Bozz: /* Use and Application */

Dive Computer Application and Use

2022-06-23T16:51:50Z

Bozz: /* Use and Application */

Dive Computer Application and Use

2022-06-23T15:14:55Z

Bozz: /* Use and Application */

==Use and Application==

The Cressi Dive Computer ''Leonardo'' addition

==Installation and Manual==

Download of Cressi PC Interface- https://www.cressi.com/software

Dive computer manual- https://s3-eu-west-1.amazonaws.com/cressielettronica/software/CressiPcInterface_2_0_1_ManualeUtente_ENG.pdf

Dive Computer Application and Use

2022-06-23T15:11:08Z

Bozz: /* Installation and Manual */

==Use and Application==

==Installation and Manual==

Download of Cressi PC Interface- https://www.cressi.com/software

Dive computer manual- https://s3-eu-west-1.amazonaws.com/cressielettronica/software/CressiPcInterface_2_0_1_ManualeUtente_ENG.pdf

Dive Computer Application and Use

2022-06-23T15:10:04Z

Bozz: /* Installation and Manual */

==Use and Application==

==Installation and Manual==

Dive computer manual- https://s3-eu-west-1.amazonaws.com/cressielettronica/software/CressiPcInterface_2_0_1_ManualeUtente_ENG.pdf

Download of Cressi PC Interface- https://www.cressi.com/software

Dive Computer Application and Use

2022-06-23T15:07:59Z

Bozz: /* Installation and Manual */

==Use and Application==

==Installation and Manual==

[https://s3-eu-west-1.amazonaws.com/cressielettronica/software/CressiPcInterface_2_0_1_ManualeUtente_ENG.pdf| Dive computer manual]

[https://www.cressi.com/software| Download of Cressi PC Interface]

Dive Computer Application and Use

2022-06-23T15:07:25Z

Bozz: /* Installation and Manual */

==Use and Application==

==Installation and Manual==

[https://s3-eu-west-1.amazonaws.com/cressielettronica/software/CressiPcInterface_2_0_1_ManualeUtente_ENG.pdf|Dive computer manual]

[https://www.cressi.com/software|Download of Cressi PC Interface]

Dive Computer Application and Use

2022-06-23T15:06:24Z

Bozz: /* Installation and Manual */

==Use and Application==

==Installation and Manual==

[[https://s3-eu-west-1.amazonaws.com/cressielettronica/software/CressiPcInterface_2_0_1_ManualeUtente_ENG.pdf|Dive computer manual]]

[[https://www.cressi.com/software|Download of Cressi PC Interface]]

Dive Computer Application and Use

2022-06-23T15:05:04Z

Bozz: /* Installation and Manual */

==Use and Application==

==Installation and Manual==

[[Dive computer manual\https://s3-eu-west-1.amazonaws.com/cressielettronica/software/CressiPcInterface_2_0_1_ManualeUtente_ENG.pdf]]

[[Download of Cressi PC Interface|https://www.cressi.com/software]]

Dive Computer Application and Use

2022-06-23T15:03:56Z

Bozz: /* Installation and Manual */

Dive Computer Application and Use

2022-06-23T15:02:12Z

Bozz: Created page with "==Use and Application== ==Installation and Manual=="

==Use and Application==

==Installation and Manual==

Exploring Underwater Environments Drone 01

2022-06-23T15:00:29Z

Bozz: /* Equipment */

==Motivation==

==Introduction==

==Equipment==
[[Dive Computer Application and Use|Dive Computer]]

==Experimental==

==References==
[[Media:Bjorneras et al 2020.pdf|Inland blue holes of The Bahamas – chemistry and biology in a unique aquatic environment (2020)]]

Exploring Underwater Environments Drone 01

2022-06-23T15:00:06Z

Bozz: /* Equipment */

==Motivation==

==Introduction==

==Equipment==
[[Dive Computer Application and Use|Dive Computer]]
Dive computer manual- https://s3-eu-west-1.amazonaws.com/cressielettronica/software/CressiPcInterface_2_0_1_ManualeUtente_ENG.pdf

==Experimental==

==References==
[[Media:Bjorneras et al 2020.pdf|Inland blue holes of The Bahamas – chemistry and biology in a unique aquatic environment (2020)]]

Exploring Underwater Environments Drone 01

2022-06-22T18:06:43Z

Bozz: /* Equipment */

==Motivation==

==Introduction==

==Equipment==

Dive computer manual- https://s3-eu-west-1.amazonaws.com/cressielettronica/software/CressiPcInterface_2_0_1_ManualeUtente_ENG.pdf

==Experimental==

==References==
[[Media:Bjorneras et al 2020.pdf|Inland blue holes of The Bahamas – chemistry and biology in a unique aquatic environment (2020)]]

Alex L Boswell

2022-05-31T20:57:09Z

Bozz: /* Work Expierience */

==Personal Information==
Monmouth College class of 2023
:'''''Chemistry Major; Physics Minor'''''

From Dixon, IL

Email: alboswell@monmouthcollege.edu

Phone Number: (1)815-677-1450

==Undergraduate Research Activities==

Exploring Underwater Environments with Fifish V6 Expert Drone

[[Results and Discussion|Results and Discussion]]

==Presentations==
:Coming Soon

==Interests==

I am interested in chemistry, physics, coding, and teaching. I enjoy a challenge and the responsibility of leadership.

==Career Goals==

With these interest in mind I am excited to apply to Graduate School and possibly enter the work force in a lab or industrial setting after graduating from Monmouth College. With the experience I have so far from research and communicating with my Professors I can already sense that there are many options available to me in terms of education, research, and work.

I want to attend Graduate School and study more in the field of Physical Chemistry or a mix of Chemistry and Physics. I particularly want to focus on one of these two options as I have found a love for the physical side of chemistry and enjoy the hands on experience that is accustomed to it. Physics is something I did not start to learn till I was a Junior at Monmouth College, but since joining physics I have enjoyed learning how the universe works and the complicated questions and issues that physics ask or does not explain. During my hunt for schools I would like to attend my top priority will be how their Physical Chemistry department is and what they are currently doing with research as well as future projects they want to pursue.

Finding a job is also extremely important and although I do like using Instruments and learning about what they do I like to use my hands along with my brain. My preferred job would be teaching as a Professor at a college level institution. This would allow me to have lots of communication with others, being able to teach, and set up and perform research on a subject that I select.
I would also enjoy working in a lab as a managerial position where I am expected to know how things run in the facility but also take part in working with those that I am responsible for.

==Work Expierience==
August 2021-Current

'''Teaching Assistant|Teaching|Monmouth College Department of Chemistry'''

Working in the Analytical Chemistry Lab, I set up materials and instruments and helped students with questins they may have as well as understanding the concepts of each lab.

Alex L Boswell

2022-05-31T20:56:45Z

Bozz: /* Work Expierience */

==Personal Information==
Monmouth College class of 2023
:'''''Chemistry Major; Physics Minor'''''

From Dixon, IL

Email: alboswell@monmouthcollege.edu

Phone Number: (1)815-677-1450

==Undergraduate Research Activities==

Exploring Underwater Environments with Fifish V6 Expert Drone

[[Results and Discussion|Results and Discussion]]

==Presentations==
:Coming Soon

==Interests==

I am interested in chemistry, physics, coding, and teaching. I enjoy a challenge and the responsibility of leadership.

==Career Goals==

With these interest in mind I am excited to apply to Graduate School and possibly enter the work force in a lab or industrial setting after graduating from Monmouth College. With the experience I have so far from research and communicating with my Professors I can already sense that there are many options available to me in terms of education, research, and work.

I want to attend Graduate School and study more in the field of Physical Chemistry or a mix of Chemistry and Physics. I particularly want to focus on one of these two options as I have found a love for the physical side of chemistry and enjoy the hands on experience that is accustomed to it. Physics is something I did not start to learn till I was a Junior at Monmouth College, but since joining physics I have enjoyed learning how the universe works and the complicated questions and issues that physics ask or does not explain. During my hunt for schools I would like to attend my top priority will be how their Physical Chemistry department is and what they are currently doing with research as well as future projects they want to pursue.

Finding a job is also extremely important and although I do like using Instruments and learning about what they do I like to use my hands along with my brain. My preferred job would be teaching as a Professor at a college level institution. This would allow me to have lots of communication with others, being able to teach, and set up and perform research on a subject that I select.
I would also enjoy working in a lab as a managerial position where I am expected to know how things run in the facility but also take part in working with those that I am responsible for.

==Work Expierience==
August 2021-Current
'''Teaching Assistant|Teaching|Monmouth College Department of Chemistry'''
Working in the Analytical Chemistry Lab, I set up materials and instruments and helped students with questins they may have as well as understanding the concepts of each lab.

Alex L Boswell

2022-05-31T20:51:35Z

Bozz:

Alex L Boswell

2022-05-31T20:47:59Z

Bozz: /* Career Goals */

Alex L Boswell

2022-05-31T20:47:39Z

Bozz: /* Interests */

Alex L Boswell

2022-05-31T20:47:15Z

Bozz: /* Interests */

Alex L Boswell

2022-05-31T20:19:23Z

Bozz: /* Undergraduate Research Activities */

Alex L Boswell

2022-05-31T20:16:11Z

Bozz: /* Presentations */

Alex L Boswell

2022-05-31T20:15:13Z

Bozz: /* Personal Information */

Alex L Boswell

2022-05-31T16:48:53Z

Bozz: /* Personal Information */

==Personal Information==
Monmouth College class of 2023
:Chemistry Major; Physics Minor
:''Chemistry Major; Physics Minor''
:'''Chemistry Major; Physics Minor'''
:'''''Chemistry Major; Physics Minor'''''

''From Dixon, IL''''''''Bold

Email: alboswell@monmouthcollege.edu

Phone Number: (1)815-677-1450

==Undergraduate Research Activities==
==Presentations==
==Interests==
==Career Goals==

Alex L Boswell

2022-05-31T16:43:15Z

Bozz: /* Personal Information */

==Personal Information==
Monmouth College class of 2023
Chemistry Major; Physics Minor
From Dixon, IL
Email: alboswell@monmouthcollege.edu
Phone Number: (1)815-677-1450

==Undergraduate Research Activities==
==Presentations==
==Interests==
==Career Goals==

Alex L Boswell

2022-05-31T16:42:30Z

Bozz:

==Personal Information==
==Undergraduate Research Activities==
==Presentations==
==Interests==
==Career Goals==

Alex L Boswell

2022-05-31T16:42:05Z

Bozz: /* Personal Information */

==Personal Information==
=Monmouth College class of 2023=
=Chemistry Major; Physics Minor=
=From Dixon, IL=
=Email: alboswell@monmouthcollege.edu=
=Phone Number: (1)815-677-1450=

==Undergraduate Research Activities==
==Presentations==
==Interests==
==Career Goals==

Alex L Boswell

2022-05-31T16:37:40Z

Bozz:

==Personal Information==
==Undergraduate Research Activities==
==Presentations==
==Interests==
==Career Goals==