September 20, 2016

Done:

Today during my Independent Study time, I worked on the rubric for which I will be graded. I completed the presentation rubric given to me by the history department. As well as this, I set up my meeting with Dr.G for thursday at 4:00pm. As well as this setup, I also successfully setup an additional observership for Mondays at Mass General. I began reading a medical article called Genomic characterization of brain metastases reveals branched evolution and potential therapeutic targets. I began taking notes on the Research Doc about this article. I finished reading the Abstract section of this article and look forward to digging deeper into the findings of this study.

Next Step:

Tomorrow, I plan to finish the rubric for my independent study. I have to finish filling out the general portion of the rubric, as well as one for my daily summaries, which I will complete every Thursday. I also plan to continue my reading into the article of Genomic characterization of brain metastases reveals branched evolution and potential therapeutic targets, and taking notes as well.

September 21, 2016

Done:

Today I finished the Rubric for my project. I plan to make some edits down the road in order to improve it, however, I believe I have a solid outline of what I would like to be graded on. I also met with Ms. Wolf today and looked at some articles for me to research. The topics used to research these were given to me by Dr. Gerstner. The questions which were most important to research were How is an MRI acquired? why do we use it? What is the biology of the disease and why it spreads to the brain? How do we look for genetic mutations in tumors vs. normal cells? Why do you have to do CITI training to look at patient data? Ms. Wolf and I went over these articles and pulled out some key vocab word to focus on for my further research.

Next Step:

Tomorrow I plan to continue my research in the topics given. I plan to continue reading and taking notes on the article of Genomic characterization of brain metastases reveals branched evolution and potential therapeutic targets. I also plan to create a schedule for my work online to help organize my workload. I will meet with Dr. Gerster at 4:00 tomorrow and I plan to ask her a few questions about the work I have been doing so far.

Questions:

-On the IMAIOS webside (https://www.imaios.com/en/e-Courses/e-MRI) what is the most important program to look at for my own knowlege?

-How should I use dropbox?

September 22, 2016

Done:

Today I made an account for the IMAIOS, the interactive learning website suggested by Dr. Gerster. Later on today, I met with Dr. Gerster at her office in the MGH research facility. During our meeting, she shared with me the dropbox used to store anonymous patient data and showed me how to use it. We went over the first task of mine, which is to organize the patient data in a spreadsheet in the drop box in order to make the image reading easier. What I will be doing is taking a documented spreadsheet labeled Clinical%20info%20Summary and transferring the data to another spreadsheet labeled Melanoma_Pre_v_Pre. The data I will be transferring is the patient’s surgery dates and type of surgery. Dr. Gerster informed me that when she received the image from BWH, there was a virus in the program. Therefore, she had to send the images back and wait for the new image set to show up. However, while there may be a week or so delay on the images, I will be able to complete the spreadsheet as well as continue my personal research.

Answers to Questions:

-On the IMAIOS webside (https://www.imaios.com/en/e-Courses/e-MRI) what is the most important program to look at for my own knowlege?

It is important to view this website in chronological order. It is all beneficial information for this project, except: cardiac, functional MRI and MR spectroscopy (and perfusion imaging for now but we may look into some perfusion imaging later).

-How should I use dropbox?

The task with the use dropbox consists of taking a documented spreadsheet labeled Clinical%20info%20Summary and transferring the data to another spreadsheet labeled Melanoma_Pre_v_Pre

Next Step:

The next step of mine in this project is to complete the spreadsheet of patient information in the drop box. I also plan on continuing my own research alongside Ms. Wolf who will help guide me through medical journals. I plan on emailing Ms. Wolf a couple of sentences describing what I am primarily interested in searching/what stands out to me amongst the rest of the articles on the database. I will also continue reading the article sent to me by Dr. Gerster and will continue to take notes on that, as well as research any unknown terms.

September 23, 2016

Done:

Today I had a meeting with Ms. Shah and we discussed the advancements of my project. I showed her my schedule made from a program called Manage It, the complete rubric, and discussed with her the work I have been doing with Ms. Wolf in the bibliotech, and with Dr. Gerstner. I showed her the spreadsheets which I will be working on she showed me some tricks on how to use a spreadsheet more effectively. Unfortunately, there was a problem with my computer today so I had to take it to the apple store, which delayed my research slightly. However, now that my computer and dropbox are working well, I can continue the excitingness of my project.

Next Step:

My next step in the project is to email Dr. Gerstner in order to confirm the work I have to do for dropbox and the patient data. I would like to ask her again because this information is very important and it would be nice for everything to stay on track as planned. I plan on continuing my spreadsheet and research work at MGH and is still an amazing experience so far.

September 23, 2016

Done:

Today I finished reading the Introduction to the article Genomic characterization of brain metastases reveals branched evolution and potential therapeutic targets. After I finished this article, I heard back from Dr. Gerstner about the spread sheets. She explained where to find the proper spreadsheets and cleaned up my confusion.

Next Step:

Now that my confusion about the spread sheet has been cleared up, I plan to begin working on it. My next step would be to begin this data input, as well as do more Database research, which I will send to Ms. Wolf. I also plan to continue my reading on this scientific article sent to be my Dr. Gerster, as she describes as the most “dense” of the articles.

September 24, 2016

Done:

Today I was planning on working on the spreadsheet for Dr. Gerstner, however, I received an email that before I do so, I must completed the mandatory Observership Training online, which was emailed to me. This was to secure the work I will be doing at MGH, so that the security of MGH officially has my record of training in their system. The course objectives were

• Apply HIPAA Privacy and Security rules to protected health information at MGH both during and after observership,
• Differentiate and demonstrate responsibilities and limitations of being an observer, and
• Complete all necessary documentation to onboard observers successfully.

The main points of this training were to secure and enforce the following

Confidentiality

Security

Privacy

Patient Care

Next Step:

Next I plan to finally work on the spreadsheet given to me by Dr. Gerstner. I also plan to do research through the Beaver Database and find a time to collaborate with Ms. Wolf. I also plan to continue reading the article sent to me by Dr. Gerstner.

September 25, 2016

Done:

Today I worked on the spreadsheet. What I did was I looked at the Melanoma Pre v Post spreadsheet and sorted through the data to find the cranial surgical dates. The dates are sorted on the far right hand column, and the surgeries/procedures done on the patient are in the left hand column. The procedures are listed under Dx, which typically means diagnosis. However, because of the stage of the patient's illness, a biopsy is usually performed and taken to pathology at the hospital to test for the Dx, therefore, the diagnosis listed under “Dx” are also most likely surgical procedures.

Next Step:

My next step for this project is to continue my research and to look up any terms/words I am not familiar with to educate myself further on the disease and the medical field. Much like what I did with “Dx”. I also continue to work on the spreadsheet.

September 26, 2016

Done:

Today I continued to work on the spreadsheet. I am almost finished filling out the first surgical dates into the Cranial Mutation Breakdown-MRI data sheet. I also continued with my research for the article sent to me by Dr. Gerstner.

The objectives are:

• Determine whether clinically sampled brain metastases--find out whether or not the sampled brain metastases-- harbor distinct potentially clinically informative mutations--obtain specific, or clinically important mutations-- not detected in paired primary-tumor samples--that is not found in two of the same primary tumor samples
• Determine the extent to which--to see how much-- the mutations are shared among multiple regions--the mutations are shared in different regions-- of a single brain metastasis--of one brain metastasis--, anatomically distinct brain metastasis sites--the site of the brain metastasis in the body--, and temporally separated lesions--and in separated lesions in the brain-- (in cases which recurred following therapy)--in case these happen again after therapy
• Determine whether lymph nodes or extracranial metastases--determine if lymph nodes or metastases outside the brain-- are genetically similar to brain metastases--are genetically the same as the metastases inside the brain-- and might serve as their proxy--and might act as the agent-- for genomic* assessment and clinical decision making

*Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes (the complete set of DNA within a single cell of an organism)

Next Step:

My next step will be to finish the spreadsheet for Surgery Dates_1. Once this is finished, I plan to continue with my independent research.

Questions:

• Where is the Dx for the patient with the mrn number of 26444422?

September 27, 2016

Done:

Today I finished logging in the spreadsheet for Surgery Date_1. I still plan to ask Dr. Gerstner about the patient with the mrn number of 26444422 in order to find their information.

Next Step:

September 28, 2016

Done:

Next Step:

September 29, 2016

Done:

Today I spoke with Dr. Gerstner over the phone because she was unable to meet in person. We spoke about the work I have been doing and what is next. She explained to me that the images are planned to arrive next Monday if there are no issues and she is organizing for me to receive a hard drive of them as well. Aside from our hour meeting over the phone, I was able to complete the spreadsheet assigned. I put in all the Surgery_1 an 2 dates as well as the Dx. While I spoke on the phone with her, she was able to answer some questions that I had.

Answers to Questions:

• Where is the Dx for the patient with the mrn number of 26444422?

The Dx for the patient with the mrn number of 26444422 is on the spreadsheet. However, it is not as recognizable as the other ones. This is because the Dx for this mrn number is the image of the “insula” a very small, specific part of the brain, unlike the temporal, parietal, or cerebellar, and is much less common.

Next Step:

My next step in this project is to continue a week’s worth of dedicated independent research, now that the spreadsheet is finished on my end.

September 30, 2016

Done:

Today I spoke with Ms. Shah about my project so far during our weekly Friday meeting. We talked about my organization for this project and some next steps. We agreed that since the work with the spreadsheet is done, for now I will focus on my personal research. We talked about the final project and how I should explore different website templates for the final product of this project. As well as speaking with Ms. Shah, I continued my independent research on Genomics and how they relate to cancers such as Metastatic Melanoma.

Next Step:

I will continue with my independent research on Genomics as well as introduction research on a new article sent to me by Dr. Gerstner called Current approaches to the treatment of metastatic brain tumors

October 1, 2016

Done:

Today I started reading the article sent to me by Dr. Gerstner called Current approaches to the treatment of metastatic brain tumors. I read the abstract portion of it which stated the purpose of the article was to address the current disease, Metastatic Melanoma, and specifically addresses the imaging, surgery, radiation therapy, cytotoxic chemotherapy and targeted therapy regarding this disease.

Next Step:

My next step is to continue reading this article through the introduction and continue to take notes. I also plan on continuing the research on Genomics through the beaver database.

October 2, 2016

Done:

Today I read the introduction to the Article titled Current approaches to the treatment of metastatic brain tumors. I took notes on this introduction as it spoke about the basics of this disease and the new advances which are taking place.

Next Step:

My next step is to create a dissection of the last paragraph of the introduction section of this article to frame out, in layman's terms, what the article is about. After I finish the dissection, I will continue with my genomics research as well as the next article sent to me by Dr.Gerstner.  

October 3, 2016                                                

Done:

Today, I took the conclusion of the introductory section in the article of Current approaches to the treatment of metastatic brain tumors and dissected the main points of the review article. The review’s objectives are:

This Review provides an overview of current management modalities for brain metastases,--provides model examples of management of brain metastases-- with particular emphasis--with a main focus-- on therapies that specifically target the key biological mechanisms--that target the important biological system-- involved in cancer development and treatment resistance. The epidemiology--the branch of medicine that deals with the incidence, distribution, and possible control of diseases and other factors relating to health--, biology and diagnosis of brain metastases, factors which are relevant to the management of this condition, are also discussed.

Next Step:

My next step is to finish reading and taking notes the article regarding Genomics during my independent research time.                         

October 4, 2016

Done:

Today, I finished reading the article on the study of genomics. I completed taking important notes on this subject in the Data Base Document. I learned a lot about this scientific discipline and the divisions within the field of genomics, such as Structural Genomics, Functional Genomics and Comparative Genomics. I learned what each of these entail as well as how they differ from one another.

Next Step:

My next step in my personal research is to see how genomics relates to the disease, research, exploration or the disease Metastatic Melanoma. I will also begin to research more on genetic mutations and how that is used for medical discoveries.

October 5, 2016

Done:

Today I continued with my personal research of studying genomics regarding Melanoma patients. I discovered an article in the database which helped guide me toward new findings in my research. I began with the abstract portion of this article which states:

Over the last decade the molecular characterization--scientific explanation and discovery-- of melanoma has progressed. Since a majority of melanoma cases arise from repeated intermittent ultra violet radiation (UVR) exposure--since most of these cases are caused by an immense amount of UVR exposure--, the role of UVR has been evaluated extensively. Recent work has identified two mechanisms in which the carcinogenesis--the initiation of cancer formation-- of melanoma may result; Ultraviolet radiation has been demonstrated to lead to down regulation in immune responses and result in pyrimidine dimerization--molecular lesions formed from thymine or cytosine bases in DNA via photochemical reactions. Ultraviolet light induces the formation of covalent linkages by reactions localized on the C=C double bonds. Given these links and more significant immunogenic antigen--a molecule that is capable of eliciting an immune response by an organism’s immune system, whereas an antigen refers to a molecule that is capable of binding to the product of that immune response-- profile of melanoma, as compared to other malignancies--the state or presence of a malignant tumor; cancer--, there has been significant therapeutics breakthroughs based on these molecular pathways.

Next Step:

My next step in this project is to continue my independent research on this article and continue reading documents and taking notes while learning about the Genomics of Melanoma. I plan to meet with Dr. Gerstner tomorrow and hope to receive the  images and a new assignment.

October 6, 2016

Done:

Today I met with Dr. Gerstner in her office at 4:00 for our weekly meeting she showed me a new spreadsheet and the first five images of patients she received.  The new spreadsheet is the dates of when the mri took place (pre-op). She gave me an assignment to go through a spreadsheet with pre-op dates on it, find the correct one for the correct patient, and record it into the other spread sheet. After she taught me how to do this, I began my work. As well as this, Dr. Gerstner received the images of the Melanoma patients. She uploaded them onto a harddrive for me and together we made my computer able to access the hard drive and save new documents to it. We uploaded one image at a time to an imaging editor application. This applications allows one to upload an mri or ct scan and highlight the tumor clearly. After this is to be done with any/all of the photos, it is to be saved back to the hard drive.

Next Step

My next step in this project is to complete the spreadsheet assignment given to me by Dr. Gerstner, for this will help Dr. G collect further images from the lab. As well as this, I plan to complete the imaging edits by next Thursday.

October 7, 2016

Done:

Today I spent the majority of my day working on the spreadsheet as well as learning how to read it. My job by Thursday is to complete the spreadsheet in order for Dr. Gerstner to receive the next round of images. I completed approximately half of the Pre-Op MRI data dates as well as the second dates for the given MRN numbers, if there were any. My biggest challenge with this is finding the correct date to use in the MGH/BWH spreadsheet. The way to determine this is by finding the date that is closest to the surgical date.

Next Step:

My next step is to continue my work on the spreadsheet as well as looking at the MRI’s given to me on a hard drive. I also plan on looking back at my Genomics research and creating a list of questions for Ms. Shah and I to address at our next meeting.

October 8, 2016

Done:

Today I continued to work on the spreadsheet. Given that the process is not a short one, I got the majority of the sheet done with a few more to do. As well as this, I began looking at the images sent to me. Dr. Gerstner also sent me some additional images to add to the mix. I took these images and opened the first one in the slicer application. I was able to highlight the areas of the brain metastasis. However, I faced some difficulties while trying to save the image back on the hard drive. At least, I was able to figure out how the website worked in order to complete the assignment when the saving problem is fixed.

Next Step:

My next step is to work on the images and finish up the spreadsheet. I plan to contact Dr. Gerstner about the issue with the saving and hopefully get a better hold on that so I can continue my work. As I did not get a chance to, I also plan on creating a list of questions for Ms. Shah about genomics.

October 9, 2016

Done

Today I began creating a list of questions for Ms. Shah about Genomics and Genetics. My questions were:

What is non-coding DNA?

How does one determine the number, location, and order of genes on a particular chromosome?

How do the four different deoxyribonucleotides act within the DNA? Their jobs?

What can cause gene mutations?

How is a gene mutation detected?

Why do gene mutations cause cancer?

As well as this, I also worked on the images, without saving, only to get myself more familiar with the slicer application. As well as this, I was able to finish the spreadsheet and send it to Dr. Gerstner.

Next Step:

My next step for this Ip is finish the images in slicer and try to find a way to fix it and identify the problem.

October 10, 2016

Done

Today I emailed Dr. Gerstner the completed spreadsheet, making sure that the dates were correct before I added it to the dropbox. I had a couple of questions for her which I stated in my email. I ask her if FMRI (functional MRI) and MRI both applied for the Pre-Op MRI date column. As well as this, I also informed her about the dates I was unable to find on my own. I looked at the images again and figured out how to save them. The thing I was doing wrong was not changing the files to NiFti files, which is the correct file which the program “slicer” is able to open.

Next Step:

I plan to work on the images for Dr. Gerstner and save them to the hard drive. Now that I have figured out how to save them, my work should become much simpler.

October 11, 2016

Done:

Today I was able to get about halfway through drawing the images in Slicer. I was able to get into the program, pull up each of the images, and highlight the tumor in a green coloring. I saved them back to the hard drive for when I meet with Dr. Gerstner on Thursday, I will be able to show them to her. I did come across some challenges, however. Some of the images I pulled up already had been edited. This confused me slightly because I was not sure if I were suppose to be editing those. I decided to go through each of the images anyway and highlight some parts which had been left out. I plan to present this confusion to Dr. Gerstner on Thursday.

Next Step:

My next step is to continue highlighting the images in Slicer. I plan to finish them tomorrow, for I meet with Dr. Gerstner on Thursday and will give her the hard drive them.

October 12, 2016

Done:

Today I was able to find the time to finish the images for Dr. Gerstner. I completed each of the Post-contrast images, the ones that had not yet been edited. Today I came across a new challenge where on MRI #15981400_20080723 POST, I was unable to see any tumor. I plan to ask Dr. Gerstner about this tomorrow when I meet with her. I will also ask her about the images that were already completed and if I needed to do anything with those.

Next Step:

I plan to meet with Dr. Gerstner tomorrow in her office. I plan to return the hard drive to her with the completed images. I will ask her about the questions I had about the completed images and the one image where I was unable to see anything. I plan to go through their images with her and see if I made any mistakes. After I am given feedback I plan to receive another task, whether that is receiving any more images, editing the ones I already have, or something completely new.

October 13, 2016

Done:

Today I had a couple of meetings regarding  my independent study due to the day off on Friday, when I usually meet with Ms. Shah. I met with Ms. Shah and showed her the image work I had been doing as well as the spreadsheet which I completed. I presented her with the list of questions I create regarding genomics. We decided to spend this next week both researching the questions and next time we reconvene, discuss our findings given we will have two different perspectives (ie teacher/student perspective). As well as researching these answers, I also plan on speaking with my future genetics teacher, Mr. Micari, to see his perspective on the answers. The Questions are:

What is non-coding DNA

How does one determine the number, location, and order of genes on a particular chromosome

How do the four different deoxyribonucleotides act within the DNA? Their jobs?

What can cause gene mutations?

How is a gene mutation detected?

Why do gene mutations cause cancer?

As well as meeting with Ms. Shah, I also met with Dr. Gerstner at MGH. We discussed the images and she showed me how to properly save the images in order to avoid glitches with the “slicer” application. I successfully learned how to save, each image. As well as this, she informed me that she will receive a new batch of images tonight (yay!). With this I will be about to continue my work on image drawing.

Next Step:

The next step in this project is to re-save the images which I struggled with saving before. With this comes the job of redrawing the images and submitting them to the dropbox instead of the hard drive, which I gave back to Dr. Gerstner.

October 14, 2016

Done:

Today I finished the images given to me by Dr. Gerstner and re-saved the images properly. These images were re-sent to me through DropBox instead of the hard drive due to convenience. The proper images which I drew are presented below

1                                                2

You can see in these images below that the Tumor in image 2 is evident. I was given image 2 and highlighted the tumor, in a different color. When the image is saved under a NifTi file, the image (image 1) is left with only blurb of white.

Next Step:

My next step in this project is to continue my imaging work when they are added to the dropbox. I also plan on researching the questions listed in my previous log post in order to better educate myself on the topic and record my finding for a future discussion with Ms. Shah.

October 15, 2016

Done:

Today I began my work on the new set of MGH_Images which were emailed to me last night by Dr. Gerstner. There are approximately 12 sets of images with 1-2 POST contrast images. For each of the 1-2 surgeries of each image. Today I decided that an easy way to get started would be to create an organized spreadsheet of the images so that I know which images I have done and which need to be completed. The 5 columns I created were a list of MRN numbers, a list for the Surgery_1 Post contrast 1, Surgery_1 Post contrast 2, Surgery_2 Post contrast 1, Surgery_2 Post contrast 2. Click here to view the spreadsheet.

Next Step:

Given that I have created an organized spreadsheet to help with my work, my next step will be to begin the drawings for the images. I plan on using the spreadsheet to help me see what  have done and what needs to be done.

October 16, 2016

Done:

Today I worked on the new set of images given to be by Dr. Gerstner. I was able to get 6 of the 12 images drawn. As I worked on drawing these images I wrote down questions I had regarding a few. The challenge with these images oppose to the first set was that these images, most of them, had more than one metastasis in the image. This was challenging because they were not always clear and consistent.

Questions:

• I was unable to locate the tumor on image #1484422
• On image #3162742, there are several contrasted spots
• On image #3189507, the ring around the tumor, in some of the slices, is the only thing highlights, should that still be drawn?

• They are also saved as different files, is that ok? (AxT

Next Step:

My next step will be to continue and/or finish the the image set. By Thursday I plan to have all these images done, that way I will have an opportunity to discuss them with Dr. Gerstner and present her with the questions I had along the way.

October 17, 2016

Done:

Today I continued my work on the images. I was able to complete four more of the images. However, faced some difficulties with locating the correct one to edit. In the question about the image below, I had a bit of trouble locating some of the melanomas however will add this to the list of questions for Dr. Gerstner.

Questions:

1. Image #5098581

Next Step

My next step will be to finish the images tomorrow, and from there, email Dr. Gerstner the list of questions which I compiled I also plan on tackleing the questions which are kept in the Google keep, whether that is discussing them with Mr. Micari, or during my own independent research time.

October 18, 2016

Done:

Today I was able to finish my Image work for Dr. Gerstner for when we meet on Thursday. Below are some additional questions I wish to ask her. The mostly have to do with the initial labeling of the images, however, some had to do with the images themselves. As well as this, many of the images were already completed, making the organization slightly more difficult.

Questions:

1. I noticed some contrast in the image #5393805_20140318_AxT1Post.nii-label, is this a post-surgical image?
2. Image #5393805_20140415 has an earlier date, however it appears to be post-surgical

Next Step:

My next step will be to email Dr. Gerstner tomorrow so I am able to resolve all my questions by the next time we meet. Also I plan on researching the questions in the Google Keep in order to keep the research portion of my project on track.

October 19, 2016

Done:

Today I addressed the questions which were made in the google keep. I research them and was able to complete three of the six questions in this document. I plan to revisit these questions as my image work and knowledge progresses. Currently I have learned a lot about dna and how it acts in the body and it our biology class, its importance in our lives. As well as this, I plan on meeting with Dr. Gerstner tomorrow and figured I would wait to ask her the questions tomorrow. In the meantime, I compiled my questions into a neat list below:

Questions:

• I was unable to locate the tumor on image #1484422
• On image #3162742, there are several contrasted spots
• On image #3189507, the ring around the tumor, in some of the slices, is the only thing highlights, should that still be drawn?

• They are also saved as different files, is that ok? (AxT)

• Image #5098581?
• I noticed some contrast in the image #5393805_20140318_AxT1Post.nii-label, is this a post-surgical image?
• Image #5393805_20140415 has an earlier date, however it appears to be post-surgical

Next Step:

My next step in this project will be to meet with Dr. Gerstner tomorrow and discuss these questions about the images. I plan on continuing my research work with the Google Keep questions as well, finishing up the first three, and moving on to the next three.

October 20, 2016

Done:

Today I met with Dr. Gerstner in her office at MGH. The two of us discussed the images and the questions I had about the images as well

Questions:

• I was unable to locate the tumor on image #1484422

• Yes! Because there is no tumor! This image is one that was taken either after surgery, or the patient had a spinal cord metastasis and the brain image was send due to the condition category which it fell under.

• On image #3162742, there are several contrasted spots

• These several spots are most likely tumors as well. However, these small ones were not removed due to the lack of danger they caused to the patient’s health. Although the largest tumor spotted in the brain should be drawn because this is the one causing/potentially causing the most harm.

• On image #3189507, the ring around the tumor, in some of the slices, is the only thing highlights, should that still be drawn?

• This ring classifies this as a necrotic or cystic tumor. These tumors are interesting because they are related to the growth beyond the tumor’s blood supply as dead tissue builds up, which is what forms the white ring and the darker center. To answer the question of mine, yes, this should be drawn. And not only the ring, but the entire tumor. This is because when taken into surgery with one of these tumors, the entire thing is removed because it all contains cancer cells.  
• They are also saved as different files, is that ok? (AxT)

• These files are saved as AxT because they were taken at an “Axial” view point. All of these image slices are taken at this point, these were just more specified in the labeling.

• Image #5098581?

• This case, again, was one which involved a necrotic/cystic tumor.

• I noticed some contrast in the image #5393805_20140318_AxT1Post.nii-label, is this a post-surgical image?

• This is not a post-surgical image

• Image #5393805_20140415 has an earlier date, however it appears to be post-surgical

• Check the spreadsheet!

As well as addressing these questions, we were able to mark off the completed images in the spreadsheet which is sent to the imaging lab in order to receive a new batch of images. She taught me how to tell the difference between a melanoma tumor and a necrotic/cystic lesion, which is very similar shape but has a different contrast pattern. I was also given some more tips about how to better organize the tumors and tumor types. She informed me that color coding the different tumors within one image is extremely helpful, as well as color coding the different types of tumors, which I plan on doing.

Next Step:

My next step in this project is to go through all the images again and identify whether the tumor is a melanoma tumor or a cystic tumor, color coding each one. I also plan on going through the images again and color coding the different tumors within the same brain. As well as this I plan on my continued work tackling the questions which Ms. Shah and I created in the google keep, in addition I plan on keeping an eye out for the new batch of images which should arrive in the dropbox this week.

October 21, 2016

Done

Today I had a very productive meeting with Ms. Shah where we discussed the questions that are in the Google keep. Specifically the question regarding DNA/RNA structure, and briefly the cause of mutations. Together we looked at the image of the DNA below, and discussed its structural components. I learned a lot about the four types of deoxyribonucleotides (dATP, dCTP, dGTP and dTTP), and how they bond together through hydrogen bonds. As well as meeting with Ms. Shah and learning more about DNA, I personally worked on going back through the MGH images and editing the drawings. I color coded the different types of tumor in the brain as well as just the different ones.

Next Step:

The next step I plan on taking in this project is to finish the MGH images and color coding those, as well as organizing the colors used. So far, I have assigned green to be the main tumor, red to the necrotic/cystic tumors, and colors such as brown and blue to the extra tumors. As well as the imaging, I plan to do my own personal research on Genetics as well as compile information learned in my bio class, for information to share with Ms. Shah the next time we meet, to compare notes.

October 22, 2016

Done:

Today I worked a lot on the images. I was able to get all but one completed due to a bit of confusion about what colors to highlight in on the image 5023, so I just let it be. I also created a small spreadsheet to help myself organize the colors in a proper way. I had a busy day academic wise as well as active wise and was not able to get much done on the new images, but plan to look at them tomorrow.

Next Step:

The next thing I plan on doing is reviewing the new images sent to me by Dr. Gerstner. As well as this I plan on continuing my personal research on the google keep notes for next Friday’s meeting.

October 23, 2016

Done:

Today I was very productive with the images which were given to me by Dr. Gerstner in the dropbox. These are a new set of images sent from BWH of new patients. I saw the list of patients and realized that I would be much more efficient if I created an organized spreadsheet which I did for the set of patients before. So I did so. I was able to label the images that did not need to be done (either have been done or non existent) with an “x”, and the images which needed to be done left blank. As I continued my work, I began filling in the blank spots with”o”’s to help me understand what I have done, and what needed to be done. I got through a few of the images after I complete this spreadsheet and continued with the color coding system as before.

Next Step:

I plan to put these images as a top priority as they need to be done by Thursday. Therefore, my next step(s) will consist of finishing these images within the next couple of days. Tomorrow I plan on getting half, or even more than have completed/

October 24, 2016

Done:

Today I completed all of the images sent to me in the BWH file. These images were tricky because I encountered many necrotic ones as before. Therefore, I was sure to be even more precise with the coloring system. Many of the images had already been done, however, I did take the time to look through them for my own curiosity. I complete the Image Organizer spreadsheet as I completed all the images.

Next Step:

As I have the images done, which was my week’s priority, I plan to solely focus on the research portion of my project. As I am continually learning new concepts within my biology class relating to DNA and genetics, I am able to grasp more of an understanding on the material.

October 25, 2016

Done:

Today I worked on the research portion of my project and the questions which were stated in the google keep document. Today I mainly focused on genetic mutations and different components to that. In Biology class, we are also learning a great deal about this as well, which has been extremely interesting. I researched a keyword, which Ms. Shah gave me in our last meeting called transcription. In class as well as on my own time, I learned that this means the process by which the information in DNA is copied into messenger RNA (mRNA) for protein production. As well as this, I learned about mutations, what they are, how they are caused, and the different types, all in this document here. I will continue to work on this research over the next couple of days, continuing with the research of the splitting of DNA.

Next Step:

My next step in this project is to continue my research on this subject. My goal is to complete the research on mutations by tomorrow, and begin exploring the other questions on the keep. I will also continue to go more in depth with my science teacher and Ms. Shah, letting them know of any additional questions I have which may benefit my research and understanding.

October 26, 2016

Done:

Today I finished addressing the questions from the google keep in my Keep Question’s Doc. I addressed the last two questions as well as going more in depth for the first couple questions. In my biology class, I have been learned a lot about DNA and its structure. We have been learning about the important components as well as how copies of the DNA (RNA) is sent out into the cytoplasm, and how DNA is contained in chromosomes. Independently I have researched chromosomes and learned about their patterns and their structure. I learned about how cancer cells are developed, through faulty splitting. One big larger aspect of my research today was learning about the different types of mutations.

Next Step:

My next step is to continue my research, however much more specific research regarding Metastatic Melanoma and how it develops, and more specifically, how it spreads to the brain. I plan on using my time to research this and come up with more questions to ask Ms. Shah for our meeting on Friday.

October 27, 2016

Done:

Today I met with Dr. Gerstner at MGH and we discussed the next steps for this project. I showed her the image work and was pleased to have it all completed. Although she is still waiting on 5 more images from the image lab, she will begin reviewing and approving the drawn roi’s. After this is completed, she will begin making a chart, generally represented as a scatter plot graph, or the heterogeneity in correlation with the mutation rate. This graph would be predicted to increase at a positive correlation, however, there could be some outliers which were not predicted.

Next Step:

Because I finished at the images in a good amount of time, and am not behind on any work I plan on continuing my research into mutation of this disease. This is especially important now because the next step of this project will be in regards to the mutation rate, which I will research over the next week. The next five images are expected to show up in the dropbox over the next week and then, I will continue drawing them.

October 28, 2016

Done:

Today I had a meeting with Ms. Shah and discussed the progress I have been making so far with my work. I informed her about the work/images I have finished and the future work I will be doing with the remaining images and research. We discussed what my next steps should be research wise as well as brained stormed for my final project. We talked about the website which I will roughly create by the end of the term as well as continuing my independent study. Therefore, I will be adding to the website through the next term as well, and will hopefully be able to continue my Independent Study throughout this time. The new topics which Ms. Shah gave me to research were:

Cell cycle

Checkpoints- proteins

Oncogenes

Strength of correlation between two variable- stats

Genetic markers- particular genes

Different Alleles 

Next Step:

Given the new guidance, I will continuing researching the topics above. As I continue doing this I will start to put together my end-term project (website) and send Ms. Shah the outline for said website between now and our next meeting. I will also plan on meeting with Ms. P, my advisor about a possible course switch into anatomy this spring due to my interest in the subject. Also I plan on contacting Ms. McKnight to possibly continue this independent project into the winter due to my open schedule and my interest in this project. Because this project will technically last for a couple of years, I plan on giving a final presentation closer to the end of my winter term due to the further completing of this project.

October 29, 2016

Done:

Today was quite productive in that I was able to work on the final project which will be slightly finished at the end of this term. I emailed both Ms. P and Ms. McKnight on trying to set up meetings to a) set up a meeting to try and switch into an anatomy class for the spring term, and b) try and extend this independent study for the next term, winter. As I sent those emails out, I was also able to start and complete an outline for the website which I will be creating. This was an interesting process because, on paper, I was able to see all the work I had done so far throughout this term (roughly). It was great to organize myself that way and I am looking forward to improving the Website Outline throughout this week and wrapping up this term of the project.

Next Step:

The next step in this project will be to continue refining the Website Outline. As well as this, I will continue working on the research which I discussed with Ms. Shah. I look forward to hearing back from Ms P and Ms. McKnight regarding this project in my future terms.

October 30, 2016

Done:

Today I was able to begin some more research on the given topics by Ms. Shah. I began with studying cell cycle, which is a complicated process leading to DNA duplication. This process consists of multiple phases such as G1, Synthesis, G2, and Mitosis. I learned a lot about what each phase does and its importance to cell division. This is an important subject to learn because this is how a mutation in a gene occurs and spreads throughout the body. With this, the spread of cancer occurs. Through G1, G2, and M, there are certain “checkpoints” which asses the quality and accuracy of DNA.

Next Step:

My next step in this project is to continue researching these “checkpoints” and learn more in depth about the cell cycle throughout the body. I plan to research more about the importance of this cycle and how cancer can spread due to this cycle. I also plan to address the other subjects in the keep.

October 31, 2016

Done:

Today I scheduled a meeting with Ms. Shah regarding my independent study. Together we will look at the outline for the website which I have created and refine it together. We will only keep the important information. Today I was able to refine my outline myself, creating a much easier outline to follow. The way I set this up was having about 8 main sections, the topics which I mainly focused on throughout this project. Within those sections, I have sub-sections, and for some, within those I have even narrower sections. This was extremely help for me to see the work I have done so far as well as some work I wish to do and continue. In my outline, I not only include content about information on the genetics of the disease, but I also include my experience. I realized that this outline could be universal in that it could apply to any final project, and not only a website. Therefore, when I complete this project at the end of the year, most likely, I will have the option of writing a paper, doing a presentation, or any other final interest of mine.

As well as refining this outline, I was able contact Mr. Adjout as well as Ms. Monasterios about my project and possible continuing it. Though a few emails which were sent out, it has been accepted to extend my project through the winter term, and possibly the spring term depending on my schedule. I am extremely happy about this and look forward to continuing my work.

Next Step:

Because I have a meeting with Ms. Shah on Wednesday to go over my outline, I plan to step away from the outline for a day to focus on my research and addressing some of the questions in the google keep doc.

November 1, 2016

Done:

Today I worked a little bit more on the outline for the website I will be creating. It is still a rough draft, however, it so far gives me a much better understanding for the topics, organization wise. As well as this, I work a lot more on the research portion of my project. I was able to get through and understand a majority of the google keep questions. I researched a lot today on the cell cycle and understanding its basics including the different parts of the cycles and the important checkpoints which a healthy cell must be checked as and hopefully pass through. Contributing to this research, I learned a great deal about cancer cells and how that act within the cell cycle, basically passing through the necessary checkpoints without a problem when there is a mutation. When they are able to pass through this cycle, the replicate out of control, creating more cancer cells. As these build up, a tumor is created of fast growing cells.

Next Step:

Tomorrow I plan on meeting with Ms. Shah about the semi-final project of mine. We will go over my refined outline and hopefully refine it even more! I hope to speak with her about the research I have been doing on cell cycle. Until the end of the term, I plan to work mostly on my semi-final project (website). And the outline for that. I plan on choosing a template and beginning the actual work post-meeting.

November 2, 2016

Done:

Unfortunately today I was unable to meet with Ms. Shah. However, I was able to make some progress for the website. I started researching some options for the layout as I wait for some feedback on the outline which I made. I looked at several different sites which offer templet to make a free website. The website template which stood at to me the most was Wix. I have previously used this template in other classes for class projects and it has worked well. I explored the different tools one can use and the different features in order to prepare myself for when I begin my final work.

Next Step:

My next step will be to receive and take some feedback for my outline for my website and possibly begin mocking up on paper what I would like it to look like, given the fact that I know what the template offers. I also plan on working in the drop box Dr. Gerstner updated the other day and checking my ROI drawings for accuracy.

November 3, 2016

Done:

Today I met with Dr. Gerstner over the phone and we talked about the next steps for this project. She sent me a couple of more images which I drew the ROIs for after our meeting. These images were a few of the ones which were not yet in the dropbox. So, now there are only a couple more needed until we begin the next big step. We talked about the importance of drawing the Regions Of Interest (ROI) and how it an extremely helpful tool within research. She said she has begun to review the ROIs and they look as though I have drawn them in the right place, (yay!). However there are still a handful more that need to be reviewed. She said that it would be productive to have me check my own drawings with the spreadsheet which has the given information of the specific number paired with the specific location of the tumor and see if I drew them correctly and in the right spot. Before starting this process, I took initiative and created a spreadsheet in order to organize the drawn data: Image Organizer: ROI Review. This will ultimately help me organize myself into what I did correctly and what I did not.

Next Step:

My next step in this project will be to use the spreadsheet which I created to check my work on the ROI drawings. I will label the ones in the spreadsheet that I did correctly, and the ones that I didn’t do correctly I will make not of so that I may correct my error. I also plan on continuing my work for the final and adding to the outline which I made for my website.

November 4, 2016

Done:

Today I was able to continue my work for Dr. Gerstner in regards to the checking of the ROI drawings. I Went through all of the scans and compared the location which I drew, to the location where the tumor was located. All of the drawings matched the location of interest. However, there were some areas where I drew multiple tumors (including the tumors which did not need to be drawn. In the spreadsheet, I made note of that so that I am able to go back through the images and edit the ones which need to be changed slightly.

Next Step:

My next step will be to go over the spreadsheet and change the the images which need to be changed. I will update my spreadsheet and review the images one more time to make sure I have all the images drawn correctly.

November 5, 2016

Done:

Today I was able to complete approximately half of the corrections which I had to do on the locations of some of the tumors I had drawn. There weren’t many corrections to make, however, I did improve some of the ones which were correct by making the drawing more accurate and/or neater so the eye could follow them. I was able to also color code the ones which I did not do in the beginning, for the ones with multiple metastases. I also found a pattern within the  location of the tumors. The main locations which all the tumors were in are the following: Occipital, Frontal, Cerebellum, Temporal, Insula (only 1), Parietal. While looking at all these images and knowing their locations, I was able to familiarize myself with the name of the locations so that I automatically was able to tell if the tumor which I had drawn was in the right place.

Next Step:

Now that I am familiar with the locations of the brain, I hope to quickly go through the rest of the corrections and clear-ups on the images. After this is complete, I will meet with Ms. Shah of Monday to review the website and my outline for my final project.

November 6, 2016

Done:

Today I was able to finish up all the image corrections/clean-ups and I recorded them all in the spreadsheet. Some interesting things that I noticed while perusing this was that I was automatically able to see if the tumor was in the right space or not just by looking at the image and the location it was suppose to be in. As well as this, I went through and was able to color code the images I had not before and catch any additional mistakes I made. However, there were still a few images which were not in the dropbox which I will ask Dr. Gerstner about on Thursday.

Next Step:

Tomorrow, I plan to meet with Ms. Shah and talk about the final project of mine. I will soon begin putting together the website after my outline is approved. I hope to talk with Ms. Shah about what I have so far and what I could possibly add to the outline. I also plan to go over what I have been doing research wise as it has been awhile since we have met about that, especially because we have officially wrapped up our genetics unit in biology class and I will be beginning my DNA and Genetics class next term.

November 7, 2016

Done:

Due to the delay in meeting with Ms. Shah, I was able to spend some more time of research today. I continued with  my research of Oncogenes and refreshed myself on what I had already learned given that it had been awhile since I have done some research. After I watched a couple videos on the cell cycle, I dove into the research of the oncogene. I watched a video on Oncogenes and took notes in the research doc. I learned about how an oncogene can transform from a proto oncogene, and also the different kinds of Oncogenes.This was extremely helpful because it clears my understanding of cancer and how the proteins grow uncontrollably.

Next Step:

My next step will be to hopefully schedule a meeting time with Dr. Gerstner sometime this week to meet about my final project. In the meantime I will continue with the research on Oncogenes as well as Metastatic Melanoma in general to help myself get to the next level of research for the next term.

November 8, 2016

Done:

Today I continued my research. However, today, I focused more on research regarding Metastatic Melanoma specifically, rather than cancer in general. I started by defining “Melanoma”. After this I started to look at more of the specifics such as mutations which cause this disease. I learned about the common mutations in this disease and how the certain proteins act within a cell. It was interesting to see the pattern of RAS genes which play a role in this disease. In my research, if I came across a word or phase I was not familiar with I would begin to research that word or phase so that I would be able to understand the facts entirely.

Next Step:

My next step will be to continue my research this week. I received some feedback from Dr. Gerstner on the ROIs so I will look through that and make any changes which need to be made. I also look forward to meeting with Ms. Shah on Friday and discussing the end result to this project and my next steps to continue it.

November 9, 2016

Done:

Today I focused more on my independent research. I focused, again, on the specific disease of Metastatic Melanoma. However I focused much more on the brain and the act of the cancer spreading to the brain. I learned some statistics about cancer spreading to the brain and how usually when a metastasis is found in the brain, it is also somewhere else in the body and usually began at a separate location. I learned that how the majority of brain tumors are found in the cerebrum and some in the cerebellum, but not as many. I found this also with the research I was doing.

Next Step:

My next step will be to meet with Dr. Gerstner to review the images which need to be worked on. I also plan on continuing my research as much as I can and speaking with Ms. Shah about the Final project on Friday.

November 10, 2016

Done:

Today I met with Dr. Gerstner at MGH. We talked about the scans and went through each one of them individually to look at the brain tumor and the image drawing. She showed me a couple of improvements I could make and I could change to a couple of the images which I drew. She showed me how she lays out the images to see if they were drawn correctly. What she does is creates a collage of the images at different stages and then looks at the ROIs which I drew and compares them. Another thing we talked about during our meeting was the next steps of this project. After she gets a couple of more images back from the imaging lab, and after I complete the corrections/improvements for the ROIs, the images will be run through the “pipeline”, which is a program which will generate a chart of categorized tumor characteristics. These are important for gathering the data because once these characteristics are gathered, they will be able to be graphed on a scatter-plot graph along with the specific tumor’s mutation rate and hopefully, the characteristics will match the certain mutation rate which is consistent with the one found in the biopsy of the brain metastasis.

Next Step:

My next step will be to complete the corrections/suggestions made for the specific images. I also plan to continue my research so that when I do meet with Dr. Gerstner again, after Thanksgiving, we will be able to continue data analysis. Also, a more long-term “next step” will consist of reviewing/writing an abstract for this research project which will eventually be submitted to the American Brain Tumor Association Conference this coming January or May.

November 11, 2016

Done:

Today was a very important day in my Independent Study. Today I finally met with Ms. Shah to discuss my final, which we decided should be officially due on Friday, or at least a solid draft. Ms. Shah and I went over my outline for the website and tweaked a couple of things. We created a more organized outline which goes almost chronologically in how my project went, ending with the “next steps”. We talked about and organized the sections and what should make up on of the bigger sections, and what sub-sections to include. I will also be implementing my research into this website, which I will keep adding to as well as the next term goes on. As well as meeting with Ms. Shah today, I was able to begin the ROI corrections which are in the spreadsheet. I was able to clear up one of the tumor’s images and was able to be more detailed with drawing and the important aspects.

Next Step:

Now that I have more specific instruction from Ms. Shah, I will take a short break from my personal research as this term comes to an end. I will begin working on my website (draft due next wednesday) and transferring information from my existing docs into that. As well as this I will be doing more ROI corrections for Dr. Gerstner this week so that the research may continue smoothly.

November 12, 2016

Done:

Today I was able to complete the corrections for Dr. Gerstner. There were about 5 images which needed to be changed slightly. I was able to clean up a few and make a couple a little more clear. After I did the corrections on each of the images, I saved them back to their proper files. As well as this, I was able to get started on my website which is due on Wednesday. I took the rough outline that I had and started to organize it with the template I chose. With the template, I was able to customize each of the different categories for what I will have my website be about. There are lots of picture options for the website so I am excited to start taking some screenshots and posting those up there. It looks good so far, but is still a very rough draft. I will begin to add content soon and add in my own pictures.

Next Step:

My next step will be to only work on the website as I need to add many more images and content to it to make it full. I plan on doing this over the next couple of days as a draft of it will be due on Wednesday.

November 13, 2016

Done:

Today I was able to revise the site and add some more content to the cover page of it. For example, I wrote an intro paragraph describing my projects and headings for each of the sections which needed one. I was able to reorganize the pages to a better looking format and add sub-pages to all the ones which had additional content. I worked a lot on organizing the home page and the other pages as well and made sure it was easy to navigate for any type of user. I also tried my best to make it creative and well put together.

Next Step:

My next step in this project will be to find all the images. Now that I have a good outline of the home page, it is important to have images to make it easier to navigate. I also plan on adding in content to the sub-pages. This will be a helpful source of information for the viewer

November 14, 2016

Done:

Today I was able to go back through some of the data and imaging work that I did and take necessary screenshots. I was also able to go online and find relevant photos for each of the subject. I worked on the outline a bit and worked on trying to find relevant content for the pages so that I will be able to cut and paste the research I already have to my website.

Next Step:

My next step for this will be my last one as well. I will need to add content to the subpages. As most of my content is organized already, this should not not be so difficult/time consuming. I will prepare for my meeting with Ms. Shah on Wednesday and show her what I have done and take some notes on things I can improve on for Friday, when it is technically due.

November 15, 2016

Done:

Today I continued with progress on the website. I was able to take the work that I had in my research on google docs and create a more condensed research doc on my outline page, for what I will be adding to the website. I focused mainly on the “What is Cancer” section. I organized the outline doc a bit more and was able to create some nice descriptions for the science behind what cancer is, as well as refining the sub-sections.

 November 16, 2016

Done:

Today I was able to take the organized information on the outline doc and place it into the made up website. This worked, however, the website is starting to lag a lot more than it did before, making it almost impossible to manage within a short amount of time causing great frustration.

 November 17, 2016

Done:

Today I was unable to open up the website:(. I am able to preview the old website but none of the changes had saved. As a result, I had to completely redo the website on a new template, from scratch. I was able to get the new website to the same place as the old website.

WEBSITE WORK:

 November 17, 2016- November 22, 2016

Term 2:

November 29, 2016

Done:

Now that the term is starting back up, it is time to fill my time with new assignments regarding my project. I contacted Ms. Shah about possible next steps (for until we discuss it in more detail in person). One suggestion was, until our meeting on friday, to continue with research. I proceeded to do so until I received an email from Dr. Gerstner about some new images which needed to be drawn. I then took my time to draw the ROI’s for half of these images

Next Step:

My next step in this project, until further instruction on possible corrections on the website, I will continue, and hopefully finish the new image set as well as research where I left off before Fall term ended. When I meet with Ms. Shah, I indent to discuss with her areas where I could improve. I also plan to meet with Dr. Gerstner on Thursday and discuss our next steps in this project as it continues.

November 30, 2016

Done:

Today I was able to revisit the images which were sent to the dropbox by Dr. Gerstner. I finished these as well as one more which she sent separately (one she did not have yesterday). These were less difficult to complete compared to the ones before because along with the images which were sent, were the locations as well. Another aspect which made these images slightly more simple were that there were usually only one metastasis, so I did not have to use many different colors.

Next Step:

Now the images have been finished, I plan on continuing my research for a day, unless assigned otherwise by Dr. Gerster tomorrow, or Ms. Shah on Friday. I look forward to reconvening with both now that the new term has started.

 December 1, 2016

Done:

Today I had my first meeting with Dr. Gerstner since before Thanksgiving break. We reviewed the images which I had done and ones which I had done before break as well. A couple of them needed adjusting by other than that most of the images were correctly drawn. As we looked at the images she pointed out a pattern where most all of the tumors were toward the outside rim and very few were toward the center of the brain. She explained that this is because when the mutation travels to the brain, the tumor is most likely to grown among the thinner blood vessels around the rim of the brain because it is simply easier for the cancer to develop. After we spoke about this, we discussed how that now the images are in the system (after I complete only two more), she will run the images through the pipeline and then she will get the chart of the different mutation rates in order to correlate them with the location of the tumors.

Next Step:

My next step is to complete the last two images which I need to do a couple clarifying details on. After this I will begin my research, specifically studying the braf mutation, suggested by Dr. Gerstner. Tomorrow, I will meet with Ms. Shah to discuss some of my next steps for this project in more detail.

 December 2, 2016

Done:

Today was very helpful for myself and Ms. Shah. The two of us reconnected in our first meeting of the term. We discussed the rubric which she filled out over break. As we went through it, as well as her comments and suggestions, we were able to discuss what ways I could improve the project. We also talked about my strengths and how they helped me throughout this project as well as ways I developed. Ms. Shah also showed me an email she received from Dr. Gerstner with her feedback of the previous term and the website as well. I took all the information gathered and created an organized document of my Game Plan and what I wish to do over these next few weeks.

Next Step:

My next step in this project is to make my way through this list of next steps which I created. Every now and then it is good to step back and see what just needs improving from the existing content, which I will begin to do. I plan to show as much work as I can on the website and in my weekly logs.

 December 3, 2016

Done:

Today I began the process of refining my work from last term. I used my “Game Plan” document as a guide to help me get started. My first step was to make sure my weekly logs were is grammatically good shape. I went about this by pasting all of my weekly logs into Grammarly and making the corrections which needed to be made. This was helpful for me to see the areas, writing wise, that I needed to improve. This is also very necessary because soon I will be creating a section in my website for my weekly logs.

Next Step:

My next step in this project will be to continue with the “Game Plan” list. Now that I have my weekly logs grammatically checked, I will create a page  on my website specifically for “Meetings and Logging”. This section will include my weekly and daily logs as well as my bi-weekly meetings with both Ms. Shah and Dr. Gerstner.

 December 4, 2016

Done:

Today, I was able to begin the process of setting up a new page in my website for the Meetings and Logging portion of my project. I created an extra page on my website where I have begun to write about my weekly meetings. I have two boxes, one which discusses my meetings at MGH and another to discuss my meetings at Beaver. I feel as though by doing this, other have a good idea about the work I put into this project. Especially after I begin to add in information about my daily and weekly logging.

Next Step:

My next step in this project is to continue of this page. I plan to finish this page, publish my weekly logs, and embed or link them into the correct section. This way, other people will have an idea about not only what I did that specific week, but what I learned.

 December 5, 2016

Done:

Today I continued my progress on the website. I added in the sections dedicated to my logging--both daily and weekly log. Here I included what I logged, why, and how this helped me throughout my project. As well as this, I published my daily and weekly log and linked them to the website so that anyone can access them if they are interested.

Next Step:

My next step in this project, now I have finished linking my logs to my site, is to go back through some old emails and find the information on the training I had to do prior to the beginning of the project and write about that on my website, as another component of creating this opportunity. As well as this, I plan to emphasize more learning points from the research project - i.e. trouble shooting and how we circumvented problems.

 December 6, 2016

Done:

Today I was able to look back through my emails and find the observership training which I did earlier this year, as well as the process I went through before beginning my observership at MGH in the neuro-oncology unit. This training consisted of, as explained on my website, a long background check process, lots of extensive paper work which disclosed patient's information, and an online “quiz” to make sure I was suitable for the environment. I posted on my website a screenshot of the end of the quiz and put this process under the section called “My Observership” given that this was the root to my current opportunity.

Next Step:

My next step in this project will, again, be to refer back to my “Game Plan” document. This will consist of emphasizing more learning points from the research project - i.e. troubleshooting and how we circumvented problems. This will also consist of the reviewed ROIs and the corrections which I made and this repetitive process.

 December 7, 2016

Done:

Today I began refining my “Imaging” page on the website. Before, I had it as mostly an into to slicer with some hints of what I did along the way. Now, however, I have reworded the page to begin talking about slicer, then another section with a button leading to more specific work which I did regarding the imaging. I plan to create this separate page in a similar format, however mentioning less about what slicer is, and more about how I specifically used it and how it is benefitting this project as a whole. Given that this project has been based mostly around imaging, I find that this should be one of the most important pages, showing the many images which I drew the ROIs for as well as the troubleshooting and corrections along the way.

Next Steps:

My next step is to continue this portion of my project and continue designing and creating this imaging page. As well as this, I will meet with Dr. Gerstner tomorrow about some next steps now that all the images have been collected and drawn.

 December 8, 2016

Done:

Today was a very productive day. I met with Dr. Gerstner at MGH and we discussed the project and what the next steps will be now that all the images have been drawn and corrected. She explained to me that all the images have been sent through the pipeline and the data sheet has been sent to her. She shared with me the data sheet through dropbox and it looks like this

As this chart is filled with data, Dr. Gerstner has highlighted four primary columns to look at these volumes are represented as the following

• Contrast-supposed to correlate with extreme differences in pixel intensities

•  i.e. very bright to very dark.

• Dissimilarity- supposed to correlate with frequent differences in pixel intensities

• i.e. very grainy to very smooth.

• Homogeneity-supposed to be the opposite of contrast, while ASM and Energy are supposed to be the opposite of dissimilarity
• Correlation-supposed to be the degree to which one pixel's intensity value correlates with the next

This information will next be taken and graphed along its mutation rate and plotted on the same graph as other images (shown on the far left of the chart). Here, a pattern will hopefully be exposed between the location and description of the tumor and its mutation rate.

Next Step:

As assigned by Dr. Gerstner, my next steps in this project will be do make sure the images within this chart match with the images which were drawn and recorded in the spreadsheet. After this (putting the website aside for a bit), I will plan to start compiling the data into an excel spreadsheet to begin the data collecting. I also plan to work on the website and do corrections for that as much as I can.

 December 9, 2016

Done:

Today I had my weekly meeting with Ms. Shah about my project. I presented to her the spreadsheet/data-sheet which was sent to me by Dr. Gerstner. I explained my task in a way which I hope was clear: to find patterns, and become familiar with the numbers of the four components which we will look at. Ms. Shah and I organized this by turning the spreadsheet which was in the drop-box into an excel, where there are a lot more options. As well as this, we talked about the ways these would be graphed in comparison to each other as well as the mutation rates. What we did to help organize this data was color code the four charts from green (low/small number) to red (high/big number). With this, I was able to see which characteristic were most similar, and had the most similar patterns with each other. Even though this is prior to mutation graphing, it is important for me to understand these numbers inside and out.

Next Steps:

My next step in this project, as encouraged by Dr. Gerstner, will be to make sure all the images within the sheet are the correct ones and the correct images. As well as this, I continue to play around with data and take notes as I do so. I also plan to learn more about the mutation rates and how this mutation graphing may look.

 December 10, 2016

Done:

Today I was able to spend some more one-on-one time with the data, trying to understand the patterns within the initial data. I went about this by creating a doc called Initial Data Impression: Pre Mutation Analysis. With this, I created a space for me to put six different charts which would tell me the relationships between the descriptions within the imaging data. After I, one by one, paired them with another, I created a chart for each and pasted them into this document. This was really helpful for me to see some patterns within the data even before seeing the patterns with the mutation rates.

Next Steps:

Now that I have completed my curiosity with what the charts may look like, I will go about checking the images to make sure they are the correct ones within the document. As well as this, I would like to continue working on my data impressions document and adding descriptions of what I see and notice while I wait to hear back from Dr. Gerstner about when the mutation data analysis will begin.

December 11, 2016

Done:

Today I was able to go through approximately half of the images on the chart to make sure they matched the MRI data sheet which we worked off of to help us organize the images. A lot of which were not on the MRI data sheet, which I put in bold and commented on. Either this, or their date was not correct. By doing, this, I will have a good idea about how many images I will need to ask Dr. Gerstner about through email. Because we will not be meeting this Thursday, I will construct and email to her of my findings within the data and also the questions which I had about certain image numbers and their location.

Next Step:

After I finish completing the chart of image numbers, I plan to write an email to Dr. Gerstner with any questions I have about the images. As well as this, I think it would be cool to start researching/playing around with the mutation rates and start seeing patterns within the data.

December 12, 2016

Done:

Today I was able to finish checking and confirming the images on the spreadsheet. Despite some repeats and dates which were only slightly off, and two which did not appear in the chart, most of the images were correct. There were, as I just stated, two images which were on the spreadsheet and not on the chart which was created to organize the images. With this information, I will let Dr. Gerstner know of these two in order to clear up any confusion

Next Step:

My next step in this project is to wait to hear back from Dr. Gerstner about the two images which did not match with the mutation rate sheet. After this, I plan to continue both on the website and playing around with the mutation rate data to see what I can infer prior to meeting with Dr. Gerstner about this specifically.

December 13, 2016

Done:

Today I received an email back from Dr. Gerstner about the two images. She agreed that they were peculiar and that they may want to just be taken off the sheet given the fact that we do not have properly drawn mutation data from them. As well as this, I decided to continue a little bit on the website. I continued with the task of better showing what I have been doing this term and what I did this past term. I am still finding ways to represent my imaging work and have begun a page on the website dedicated to the work which I did regarding the imaging.

Next Steps:

I plan on continuing my work on the website. Also, before I begin playing around with the mutation data, I plan on doing some more, extensive research on mutation rates and how to read them properly. This is in order to educate myself on the subject so the mutation correlation portion of this project goes much smoother.

December 14, 2016

Done:

Today I was able to work on the website a bit more. I got done the layout and wrote an outline of what I wanted the new page to look like. I am happy with the way it is turning out and looking forward to continuing it. Due to the business of the end of the week, I was only able to work on it for a little bit, but I was able to get a solid outline done of what I would like it to look like.

Next Steps:

Tomorrow, as Dr. Gerstner is out of town, I plan on continuing my work on the website and hopefully finishing the imaging page and possibly beginning a page of troubleshooting and my process/experience with that.

December 15, 2016

Done:

Today was a productive day in that I was able to finish the website page which I was working on and begin a little bit of the troubleshooting page. I am looking forward to showing Ms. Shah tomorrow what I have done with the website as well as the imaging data which I worked on earlier this week. As well as meeting with Ms. Shah tomorrow, I was able to set up a meeting with Mr. Adjout for 7:40am tomorrow to discuss my project and the progress I have made so far.

Next Steps:

Tomorrow I plan to meet with Mr. Adjout in the morning and Ms. Shah in the evening. With both  meetings I plan on discussing what I did this week in relation to the image data which was sent me. I am looking forward to speaking with Ms. Shah about the graphs which I made and taking suggestions for next steps while I am on break.

Post-break

January 4, 2017

Done:

Today I was able to speak with Dr. Livingston about switching my spring class of Organic Chem to Anatomy and Physiology. This is extremely helpful for my further research due to my further interest in anatomy. As well as this, I spoke with Mr. Micari about a question I had regarding the mutation rates within the data-set. She explained to me the units of Megabase and how the mutation rates (total) are written in scientific notation. One of them, for example, was .09. He explained to me where this number came from and how this is .09 out of 1,000,000 sequences of DNA. He suggested to me to continue the research of mutation rates and informed me of our future study of this in class. As well as this, today I was able to meet with Dr. Livingston not only about my class which I will be dropping, but she was able to answer a few questions I had about my data and why it was showing up differently when I copy-pasted the mutation rate. She help me understand the problem and I now understand that this data will be much more difficult to plot than I thought. As well as this, I have a few questions for Dr. Gerstner about the data and how it matches with the mutation rates.

Next Steps:

My next step will be to continue with my research and start researching more about mutations and mutation rates. This is very interesting to me and I look forward to learning more about this topic. As well as this, I plan to keep trying to brainstorm ways to put this data together into graphs before I meet with Dr. Gerstner. When I meet with Dr. Gerstner, I plan to ask her some questions about the mutation data and it that is the correct data to use.

January 5, 2017

Done:

Today I began reviewing an article which was sent to me a couple months ago by Dr. Gerstner. I looked at the article and it’s main points and began to make sense of the information. I started a document under the article’s name and began summarizing the key points of it for myself and others as I will eventually post this on my website under “Current Research”. I really enjoyed this article’s main points because it is a lot like what I am doing with my current research: identifying characteristics, and seeing specific patterns helping to identify key factors such as diagnosis and survival time.

Next Step:

My next step in my project will be to complete this summary sheet and finish reading the article I also plan on writing a “Key Terms” section in this document for others to help understand the specific language used.

January 6, 2017

Done:

Today I was able to finish my summarizing sheet for the article which I was reviewing. I was also able to create a “Key Terms” section which I wanted to do. I also found out what the “Karnofsky performance score” was, which was really interesting and seems crucial for any type of medical research.

Next Step:

My next step in this project will be to continue my research on mutations, specifically the bRaf mutation, and add more information to my running document.

January 7, 2017

Done:

As today I was busy again with competition in Ohio, I was able to review my website and make some changes with the Current Research section. I fixed the problems with the buttons which read “Read More”, and was able to link them to the current page.

Next Step:

My next step will be to continue editing the website and doing as much article research and genetic research that I can with my limited time. I plan on connecting with Ms. Shah when I get back from my trip and hopefully solving the problem I have been having with Tableau.

January 8, 2017

Done:

Due to my day of competition and travel, I was unable to connect to the internet making any work difficult for this day.

Next Step:

January 9, 2017

Done:

Luckily, today was extremely productive! I met with Ms. Shah and we discussed the research I have been doing so far as well as the struggles I have been coming across with Tableau. We discussed these problems and how I was unable to even log into my tableau account. Ms. Shah concluded that I would most likely need to download Tableau Public, oppose to just Tableau. As well as this, she showed me how to transfer the data from a separate spreadsheet to a Google Spreadsheet, without copying the equation used to accumulate the numbers. The two of us also discussed to questions which I should ask Dr. Gerstner for our next meeting this Thursday. These questions regarded the spreadsheet with the mutation rates and the MRN numbers.

Next Step:

 I greatly look forward to meeting with Dr. Gerstner on Thursday and asking her the questions I had about the mutation rates. In the meantime, I plan to keep working on my website and receiving feedback from Ms.Shah on set-up and content.

January 10, 2017

Done:

College Night

January 11, 2017

Done:

Today I was able to continue the research I aimed to continue. I talked to Mr. Micari who let me know of a really great website to use for extra information I might want to know about Mutations. He informed me that we will be learning about mutation later on in the term but if I wanted to start studying it now for my project, I should do so. I went to the website he suggested and watched a video on mutation basics and took notes in this document.  The video has some really great images on it which I used in my research document. I learned about different types of mutations and the different causes of mutations, and that not all mutations are bad. The video used a recipe analogy to help describe the different types of mutations, which was really helpful to me.

January 12, 2017

Done:

Today I was able to have a couple meetings. I met with Ms. Shah an we discussed some of the research I have been doing in mutations. We talked about the meeting i would have later that day with Dr. Gerstner and understood that once I get my questions for her answered, I would be put on the right track with the data. Therefore, Ms. Shah suggested that I meet with a stats teacher at Beaver and present him or her with my data. By doing this I will have a better idea of what to do with the data, how to read it, and what further questions to ask. As well as this, I met with Dr. Gerstner later on that day. During our meeting, we discussed the questions which I had. Dr. Gerster showed me that the mrn numbers which didn’t match up were assigned different numbers because they came from a different hospital. She showed me where to find the numbers which the other ones correlated with. Now that I have this information I will be able to match the correct total mutation rates to the correct MRN.

Next Steps:

Now that I have all my questions answered from Dr. Gerstner, I plan to start compiling the data and graphing it correctly. As well as this, I will speak with a stats teacher at beaver when I get back to school and start reviewing my findings with them.

January 13, 2017

Done:

Today I was able to go into the mutation data and feature data and pull the proper mutation rate from each image and paste it into the feature data with the correct mrn. This took awhile, but it really helped me familiarize myself with the data. I was able to transfer all the proper mutation rates to the feature data and complete the spreadsheet which Dr. Gerstner set up for me.

Next Steps:

Now that  I have completed transferring all the mutation data, I will begin to make the charts for the data, in hopes to see some patterns in the color coding of the mutation data. I look forward to do this, as this is what my project has been leading up to.

January 14, 2017

Done:

Today I was able to begin the graphing for the mutation and feature data. I was able to play around with Tableau public and familiarize myself with the program before importing my data. I was then able to import my data from Google Sheets as taught to me by Ms. Shah. After I finished this, I began graphing each feature against another and assigning the Mutation Rate to “color”. After I did this, I was able to see some results. As it did not look to me as if there were major patterns with the mutation rates, we are still unsure, given that I will be talking to one of Beavers stats teachers for a second opinion.

Next Step:

My next step will be to keep playing around with the data in order to try and find some more patterns. I plan to write an “Initial data report” on my first impressions of the data. I also plan to update my website with my latest research and findings. As well as this, I hope to reach out to a stats teacher at Beaver to help me understand this data a little better.

January 15, 2017

Done:

Today I was able to go through my data results and really analyze it as best I could. I looked at the features and definitely saw patterns within those. The mutations however, were more difficult to see patterns in given the lack of data. I was able to record a description of each of the charts which I created and state what I observed. Because it was more difficult to see pattern in the mutations, I plan on meeting with a stats teacher at beaver in hopes to show them the data and get a second opinion on the mutation section.

Next Step:

As a next step, I plan to meet with a stats teacher at beaver to try and get a second opinion on the data, especially on the mutations. I also look forward to updating the website a bit on the work I have done so far.

January 16, 2017

Done:

Today I was able work on the website. I was able to add the article notes which I wrote up on the article called An Accurate and Facile Diagnosis-Specific Tool to Estimate Survival for Patients With Brain Metastases. I was able to transfer the summaries of the different sections which I wrote up, to the website with an attached link to the article itself. I also added a section at the bottom for vocabulary and key terms which are important to know while reading the article.

Next Steps:

My next step in this project is to continue adding content to the website as well as getting in touch with a stats teacher, hopefully Thursday, as well as meet with Ms. Shah for our weekly meeting to show her the work I have been doing so far.

January 17, 2017

Done:

Today I was able to work on my website some more. I was able to add my bRaf research to the “The Science of Metastatic Melanoma” page. I added some more details on mutations as well as the bRaf gene plays a significant role in the mutation given that it is the gene we are dealing with in the majority of the patients.

Next Steps:

My next step in this project will be to continue adding information to the website. I will also set up a meeting with Mr. MacDonald to go over the data I have graphed. I will review my research and continue adding and editing.

January 18, 2017

Done:

Today I was a little busy, but was able to continue making edits to the website. I ran it through for spelling and grammar check, making sure everything was correct. I also looked it through for places I could add more information which was great to be able to see areas of improvement.

Next Steps:

I plan to continue making edits to the website. Tomorrow I will meet with Ms. Shah and speak with Dr. Gerstner over the phone about the data and next steps. Looking forward to meeting with these teachers!

January 19, 2017

Done:

Today I was able to meet with Ms. Shah as well as speak with Dr. Gerstner over the phone. Ms. Shah and I looked at the data together and discussed some of the data patterns. We saw that on a couple, there were some very evident patterns, and others there were none at all. We looked at the mutation rates and discussed how it is difficult to tell if there is a pattern or not. I also spoke with Dr. Gerstner later that day and we discussed the data as well. I sent her the graphs and we talked about possibilities regarding those. She agreed that it was difficult to see patterns regarding the mutations, however suggested an alternative approach. She suggested inputting a median line, and color graphing the mutations based on whether they are above or below that line.

Next Steps:

My next steps for this project include playing around with tableau, trying to implement the suggestions given to my by Dr. Gerstner. As well as this, I plan to continue working on the website, editing, and adding information to it. I plan to meet with Mr. Adjout about my project again, so I look forward to sharing with him the updates in my project.

January 20, 2017

Done:

Today I was able to read an article which Ms. Shah sent me yesterday. This article was called The Fine Art of Sniffing Out Crappy Science By Steve Kolowich. This article was able a new course at University of Washington which introduces the idea of “Bullshit Data”, and most importantly, how to recognize, and avoid both using it and creating it. “BS Data” is technically data which has been taken, and reshaped in order to please/deceive the viewers, thinking they see something that is not actually there. This is just as important to recognize as it is to avoid doing. This article was helpful to me because it helped me understand how to avoid BS-ing my data so it looks like something it’s not.

Next Steps:

My next step for this project is to continue working on my website, correcting some existing errors as well as adding some content, as well as this article if possible. As well as this, I would like to continue exploring my data, looking for significant patterns within the mutation data.

January 21, 2017

Done:

Today I was able to work on my website. I was under the section of “treatments”, I have begun to put more detail of the treatments which I state. I have started with the treatment of surgery, as that is one which people are most familiar with when it comes to more severe cases of cancer. I was able to create a button for it, and a web page stating what cancer surgery is as well as a video link. I spent a lot of my time trying to find a video that would best work for what I am trying to explain, and I found one that does it well. It shows the precise incisions and the suctioning out of the tumor.

Next Step:

My next step is to continue working on this treatment page on the surgery section. I plan to finish that up and create pages for the other treatment options as well. As this will take awhile to complete, I will also be examining my data, taking in the suggestions from Dr. Gerstner.

January 22, 2017

Done:

Today I was able to continue adding to the website. I am currently putting the treatment pages on hold and have been focusing mainly on updating the website of the progress I have been making as well as my new goals for this project. I have added another page, discussing the retrieving of Data from the pipeline after I sent in the images. On this page I discuss where the data came from, and what the numbers represent, as well as what is next after this step.

Next Step:

My next step for this project is to continue updating my website with what I have done so far. I also plan on adding a page describing what happened after I retrieved this data and compiled it all onto one spreadsheet for further investigation.  

January 23, 2017

Done:

Today I was able to finish my data retrieving page, and add another page about my use of Tableau and graphing. I have begun working on this page, adding a slide show of the steps I took in this process, and will look forward to adding the actual graphs. I will also discuss on this page how I analyzed the data and the suggestions I got from Dr. Gerstner about how to look at it.

Next Steps:

My next step in this project is to inform Ms. Shah on the progress I have made on the website. I plan to finish up the Graphing and Discoveries page, and return to working with the actual data itself, in order to keep working and updating the website. I also plan to hopefully meet with Mr. MacDonald soon as I will try and contact him again to get a second opinion on the data.

January 24, 2017

Done:

Today I was able to complete a lot of things regarding my website. I received an email from Ms. Shah about improvements I should make regarding structure and grammar. I went ahead and saw her remarks regarding the need for more subject matter on the spreading of cancer, and I created a document with information on that, as well as the start of a new page on my website. As well as this, I saw her remarks on grammar and began going through each page with a fine-tooth comb, looking for grammar mistakes myself, and with the help of Grammarly.

Next Steps:

My next steps in this project is to take a small break from the website portion and begin to make changes to the data regarding how it is viewed on the graphs. I plan on finding out how, on Tableau, to make a median bar, raising some mutations above and below that bar.

January 25, 2017

Done:

Today I had a productive meeting with Mr. MacDonald where we discussed the statistics portion of my project, as I am dealing with data and graphing. I was able to discuss with him the importance of knowing stats when it comes to collecting data. We talked about the R value in statistics and the way the ‘best fit’ line is calculated. He suggested that for some of my data, which I showed to him, might be interesting to see the graph in form of numbers instead of visual display, and might be able to get a better sense of the correlation and comparing the different sets of data. I also received an email from Dr. Gerstner about another website which graphs the data and adds in the best fit line. I look forward to exploring this more as well as more of the math side of things.

Next Steps:

My next steps for this project will be to explore this website which Dr. Gerstner sent me and see how the data differs from the graphs in tableau. I will also explore more of the math side of things as I use a website Mr. MacDonald sent me to calculate the correlation. As well as this, I plan on continuing to improve my website and look forward to meeting with Ms. Shah on Friday.

 January 26, 2017

Done:

Today I was able to explore the graphs which were sent to me on a new program by Dr. Gerstner, made by her friend, Andrew Lawrence Beers. I looked at the graphs and reported the patterns I recognized in my initial data report: 2, document. I noticed a few patterns although would like to show them to Ms. Shah to get a second opinion on the slight patterns I noticed. As well as this, I continued to make spelling and grammar corrections to my website, which I hope to review with Ms. Shah tomorrow as well.

Next Steps:

My next steps for this project will be to begin coming up with conclusions for the data before my next meeting with Dr. Gerstner. I was unable to meet with her today, so I plan on continuing drawing my conclusions on my own and with Ms. Shah, as well as exploring more of the math side of things with the help of Mr. MacDonald.

 January 27, 2017

Done:

Today I was able to meet with Ms. Shah to discuss the work I have done and what I should look forward to doing going forward. I spoke with her about my meeting with Mr. MacDonald and how that went successfully. I showed her the new charts and graphs that I will be looking at. I asked her about the data in the graphs and whether or not that is enough data to draw a conclusion. She informed me that she has a friend who specializes in stats like these and would be a good resource for that kind of information. As well as this, we discussed next steps for the data. We agreed that the more data the better in order to draw a conclusion and I proposed combining some of the different sets of data of the same/similar characteristics, in order to get a better visual.

Next Steps:

My next steps in the project will consist of connecting with Ms. Shah’s friend to go over some of the statistics, as well as combining some of the data to help draw some better conclusions. As well as this, I still plan on improving the website as much as I can before the end of this term.

January 28, 2017

Done:

Today I received an email from Ms. Shah regarding her friend who works in the field of statistics. Ms. Shah explained that her friends suggested I speak with some statisticians at MGH about the data in order to draw a more efficient conclusion from the data. As well as this, I was able to begin compiling all the different data sets together (all the contrasts in one column, dissimilarities in another, and so on). This will be a helpful way of seeing some clearer results because I will have more data for each of the characteristics.

Next Steps:

My next step in the data is to finish compiling the data in the new spreadsheet and begin to graph it. This will be interesting to see if the same patterns/ suspected patterns occur with more data. As well as this, I plan to connect with Dr. Gerstner about the data and whether or not anyone from MGH should look at it before a conclusion is drawn.

January 29, 2017

Done:

Today I was able to finish up the spreadsheet of the compiled data. After I finished this, I was able to import the sheet into tableau to see some conclusions. From this, I was able to see the same patterns as I did before, but much more obvious. I was able to see (in contrast and dissimilarity especially), that the higher the mutation rate, the lower the contrast and so on. This is an interesting pattern and I look forward to presenting these graphs to Dr. Gerstner to see if this is beneficial in any way.

Next Step:

My next steps in this project will be to continue to look at my data both visually, and mathematically. This will be helpful for when I meet with Dr. Gerstner on Thursday. As well as this, I am looking forward to continuing to work on my website and updating it with my progress so far.

January 30, 2017

Done:

Today I focused on my website once again. I realized that I have more stuff than expected to put into my website so I aim to work on it a little everyday. I have just completed the page where I talk about my experience with Tableau and my initial graphing experience. I talk about the program as well as the steps I took to use it, and the steps I took to initially look at my data.

Next Steps:

My next steps in this project will be to continue to work on my website as much as I can before this term ends. By the end of this week, I aim to be caught up with where my work is now. I also plan to write up an initial data report for my “full” data sets and show them to Ms. Shah during our next meeting.

January 31, 2017

Done:

Today I was able to work on my website, on the “My Graphs” pages, which is linked to my “Graphing and Discovery” page. I worked on adding in my graphs and setting up this page with a slideshow and information bar on each of the slides where I will place my data analysis. As well as this, I was able to organize a phone call meeting with Dr. Gerstner on Thursday where I will talk to her about the work I have been doing with combining my graphs.

Next Steps:

My next steps I plan to continue working on my website, perfecting my graphing pages and adding additional information about the additional data I added to the graphs. I will also add in the math portion of the graphs and show a data analysis for those.

February 1, 2017

Done:

Today I was able to continue working on my website before my meeting call with Dr. Gerstner tomorrow. I was able to complete most of the graphing page and return an email from Dr. Gerstner regarding the accuracy of the mutation rates and their mrn numbers.

Next Steps:

My next steps for this project are to speak with Dr. Gerstner tomorrow and talk about the next steps in the project regarding the data. I also plan to talk with Ms. Shah tomorrow about these next steps. I also plan to talk with Dr. Gerstner about possible summer opportunities.

February 2, 2017

Done:

Today went very well speaking with Dr. Gerstner over the phone. We discussed the progress so far and how to make improvements to the accuracy of the data. We began by talking about the charts I had done, and although the additional data I added shows different information, the trend was the same as the one without the additional data, only further confirming the trend. This is important because typically, the opposite of this trend would be expected, and having this unexpected data is an interesting factor in this project. As well as discussing this interesting factor, we talked about cleaning up the data a bit and clearing up some duplicates as well as taking some irrelevant/ “no good” data out. This will hopefully clear up any outliers in the data set and when we return to graphing, we will see a crisper trend line.

Next Steps:

The next steps for me in this project is to run through the data, making sure we have all the data for the roi’s and making sure, with the help of Dr. Gerstner, that there are no duplicates that could mess up the data. As well as this, Dr. Gerstner informed me that there is a deadline on Tuesday for abstracts to be submitted. With this in mind, we are both hoping to have all these questions cleared up by then and have a clear hypothesis written. In the meantime, as well as cleaning up data, Dr. Gerstner is hoping to present this data to some data experts at MGH to help create a clear conclusion around what it is showing.

February 3, 2017

Done:

Today I met with Ms. Shah and we discussed the next steps for the data and the next steps for the project as a whole. I explained to her that the next steps for the data will be to check it over and make sure there are no mistakes which could be contributing to some of the outliers in the graphs. We also talked about the website and the parts I should improve with that, regarding the articles and article summaries. Also, we talked about the program for students interested in medicine offered at Harvard. Ms. Shah suggested that more research is done about it, and to get Ms. Hutton, the head of school, involved.

Next Steps:

My next steps will include cleaning up, and double checking the data to make sure there are no mistakes with dates etc.. Also, I plan on continuing my work on the website and creating more understandable summaries for the articles I have.

February 4, 2017

Done:

Today I received an email from Dr. Gerstner asking me to check over the pre-surgery dates, and making sure that the dates in the data were in fact, before the surgery date. As I did so, I added a column to one of the spreadsheet with the pre-surgery information on it, and made sure that each of the dates were immediately before the surgery date. Dr. Gerstner stated that this could have been the result of some of the discrepancies in the graph.

Next Steps:

My next steps, as requested by Dr. Gerstner, will be to double check each of the dates and make sure the dates which we have as our pre-surgery dates, are in fact the immediate date before the surgery. As well as this, I will make sure that each of the images have a correctly drawn ROI.

February 5, 2017

Done:

Today I was able to review all the data and double check each of the dates to make sure the dates which we have as our pre-surgery dates are before the surgery dates. As I reviewed the dates, I noticed that the dates, except that one, are all correctly before the surgeries. However, I noticed some were a little too far before the surgeries. As I noticed this, I composed an email to Dr. Gerstner explaining what I observed while checking over this data.

Next Steps:

My next steps in this project are to hear back from Dr. Gerstner for her opinion on the matter. Also, I plan on working on my website and making sure the summaries of the abstracts are better worded in a more understandable way.

February 6, 2017

Done:

Today I was able to work some more on my website. What I did was looked at my abstract interpretations and edit them to be put in my words, easier to understand. I mainly worked on one abstract and began another that I may need help from Ms. Shah with due to its content heavy form. The one that I worked on and finished, Ms. Shah and I reviewed prior to me writing it, so I had a general idea about what to write, but I am finding it easier to have a second set of eyes.

Next Steps:

My next steps will be to meet with Ms. Shah tomorrow because she cannot meet on Friday and discussing the abstract I was having difficulty with. Also, I plan on talking with Dr. Gerstner on Thursday about the spreadsheets and the next steps for those.

February 7, 2017

Done:

Today I continued working on my website. I was able to complete the graphing  page which I started a couple of days ago, where displayed both graphs used and an analyzation of the data. This is great because I have almost officially caught up to where I am suppose to be, website wise.

Next Steps:

My next steps will be to continue working on the website and catching up on where I am now. I will also prepare for my meeting with Dr. Gerstner by reviewing the data and exploring the spreadsheets which I have been working on. I am excited to speak with Dr. Gerstner about the next steps for this project, and talk to Ms. Shah on Friday about the progression of the project as well.

February 8, 2017

Done:

Today I was able to continue working on the website, on the graphing page. As well as this, I was told by Dr. Gerstner to clean up the data sheets so we could discuss them tomorrow. As well as this, I went through all the scans on the combined charts sheet and confirmed their appearance on the data analysis as well as the accuracy of the mutation rates. As I completed this, there were only two which appeared on the combined spreadsheet and not on the data analysis sheet, but I will plan to discuss this with Dr. Gerstner tomorrow.

Next Steps:

My next steps will be to meet with Dr. Gerster and discuss the “cleaned up” data. I plan on discussing with her the two which showed up in one sheet and not in the other, and talk about our next meeting time now that all the data sheets have been officially completed.

February 9, 2017

Done:

Today I was able to speak with Dr. Gerstner about all the spreadsheets and the completion and confirmation of the data collection. Now that all the data has been completed, it is time to see how the cleaned data will play out in the graphs and will plan to meet in Charlestown MA for a more formal meeting with other doctors and neuro-oncologists. Dr. Gerstner explained to me that now is the time to begin finalizing the material and getting second opinions.

Next Steps:

Other than meeting in Charlestown, and waiting to receive the graphs in full form, my next steps for this project will be to proceed finalizing everything. I look forward to meeting with other doctors for second opinions on the data. As well as this, I will proceed planning a final presentation for a select group of upper schoolers and teachers to present the work I have done in this project.

February 10, 2017

Done:

Today I was able to refine the graph section on my website and begin thinking about my next steps for the website. I also received an email from Dr. Gerstner today, forwarded from a friend of hers who designed the graphing website. With these new graphs from the cleaned up data, it is evident that the conclusions which were drawn before still rein true. With this in mind, we can now be confident in our results.

Next Steps:

My next steps for this project will be to draw up a final data analysis and continue adding the new and improved graphs to my website. I also plan to meet with Ms. Shah, as we were not able to today, and go over what I have been doing lately regarding cleaning up the data and next steps.