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# System prepended metadata

title: Meeting Notes I

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# Meeting Notes I
With a [Jamboard here](https://jamboard.google.com/d/1cgR0qUb7ZOFeMZ1tKXCKFM4z6YJ1fKc3GA5Jytc3Sm4/edit?usp=sharing)
## Analytics
- Everyone has a poster to make
- Also a presentation
    - Not necessarily just on this
## Exploratory Data Analysis
[Follow this](https://www.tutorialspoint.com/exploratory-data-analysis-in-python)
## Goals
We will be working on Down syndrome in rats. With the following papers (and data):

- [This data set](https://archive.ics.uci.edu/ml/datasets/Mice+Protein+Expression)
- [Protein Dynamics Associated with Failed and Rescued Learning in the Ts65Dn Mouse Model of Down Syndrome](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119491#pone.0119491.s003)
- [Self-Organizing Feature Maps Identify Proteins Critical to Learning in a Mouse Model of Down Syndrome](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129126#sec002)

### Paper Description
- Might be too small
    - 7 
- Are they the *same mice*??
    - What is same here (how do we classify mice)?
        - Clearly the same **type** atleast (Trevor)
    - (Rhiannon) If they are the same, it might reduce the representative
- What does it mean to have a varying number of mice in the study
    - (Rhiannon) There may have been 7 in one class, 8 in another
    - (Trevor) The second article has 7 to 10 mice, and all male
    - (Riannon) The role of parents also varies the hormone levels
    - (Trevor) Ts65Dn is not a complete representation of Down's syndrome (paper abstract)

 - TODO Find out if they are the same mouse
     - What does it mean to be the same?
         -(Rhiannon) Ideally the mice will be identical in every area except the control variable.
     - What does this mean for the study conclusions?
 - TODO Is a Ts65Dn classification representative of populations considered in the study?
     - (Rhiannon)[Ts65Dn mice are described as "grossly normal", they are bred to have DS, carry Mmu1716 (1716)the translocation chromosome(/Wg_SbRYhT7S15inX3JXU_g), As they are bred specifically for these studies, I would say yesthey are representative.]
 - TODO What does it mean to have a varying number of mice in the study
     - Variability
 - TODO Is Down syndrome something we can describe with just these measures (see comment from Trevor, and something on sea slugs, [maybe this](https://www.science20.com/sarah_harrison/blog/what_do_sea_slugs_tell_us_about_learning-116786))
     - (Rhiannon) I do not believe that DS is something that can be described with these measures, as DS is a spectrum. And while begining the study at the level of genes themselves is a good start I think that studies into humans with DS could prove far more beneficial.

## Possible Study Plans
- Explore Data with Algorithms
    - ++ (do SOM) as well
- Explore the studies themselves

## Algorithms
- Self Organizing Maps
    - TODO Find out about them
- Why cluster data?
    - (Rhiannon) Clustering for visualization (after collecting data)
    - (Trevor) Helps see the bigger picture 
    - (Miles) Categorize them to help understand the data

# Team Tasks
## Project Mice Tasks

| Task                | Responsible | Due By |
| ------------------- | ----- | ------ |
|                     |       |        |
|                     |       |        |




## Site Visit Tasks+

| Done?Task | Due By |Responsible     |
| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------ | --- |
| Schedule Site Visit  [Here]( https://calendly.com/biotech_partners/site-visit)                           |        |     |
| Review site visit expectations                                                                                                                                                                                                                                                                                                                                          |        |     |
| 1) Review the Summer Internship Handbook and familiarize and prepare yourself for the questions that will be asked.                                                                                                                                                                                                                                                     |        |     |
| 2) Make sure your mentor has the timeslot for the meeting and knows where to login to the meeting online. (share the calendar invite link with them, and remind them with a polite email 30 minutes before the alloted time).                                                                                                                                           |        |     |
| 3) Intern will formally introduce their mentor and describe briefly ( 5 minutes max) what they do at their company. (Hint: Its a great place to use the information from your Brochure assignment)                                                                                                                                                                      |        |     |
| 4) Give a description of your day to day activity in the internship; describe any tools ( eg. software, instruments, research websites, etc) that you are using in your internship.( if you wish you may screenshare pictures, screenshots, coding demos you have written; MAKE SURE YOU HAVE APPROVAL FROM YOUR MENTOR BEFORE SHARING ANY DATA ON SCREEN. (15 min Max) |        |     |
| 5) The Site Visitor/Program Coordinator will then ask you the intern(s) the questions listed in the Handbook.                                                                                                                                                                                                                                                           |        |     |
| 6) Your Mentor will be asked to make a few comments.                                                                                                                                                                                                                                                                                                                    |        |     |
| 7) Interview Ends                                                                                                                                                                                                                                                                                                                                                       |        |     |
| Site Visit  Due Date  | 7/30   |     |