###### tags: `Estudiantes` `Organ-chips` `Tutoriales`

# Dearbhla

Since you will be staying with us for a year, you will join the projects we are carrying out, trying to combine lab work with training in bioinformatics and other things.

### Wet-lab:
- Set up qPCR for the identification of genes: MUC1, MUC4, TFF1, CLDN1, CLDN8, and OCLN (with SYBR green).

- Gather information

| GENE | Primer | Protocol | Controls | Reference |
| -------- | -------- | -------- | -------- | -------- |
| Text | Text | Text | Text | Text |

- Select necessary reagents
- Search for suppliers to order the reagents
:calendar: **Due date first part:** October 10th

- Run tests in the lab
:calendar: **Due date:** TBD when we have the material.

### Organ-chips (2026):
- Get training and see how the system works

### Dry-lab:
- R courses, starting with swirl.
- Practice with toy datasets, doing some simple analyses.
> When you arrive at this point I'll provide you datasets :smiley:

:::warning
Nice! You arrive at this point :wink:
Use this dataset: [toy.csv ](https://drive.google.com/file/d/1b8-JEERbx_7MyOO8LkmC1qMP_GCYqpC1/view?usp=sharing)
And also use the stawars dataset to practice in tydiverse.
You can create a [New Project](https://support.posit.co/hc/en-us/articles/200526207-Using-RStudio-Projects) in R to start everything a new directory and have all the date inthe same place.
:::

### :shrug: Toy dataset:

library(tidyverse)
toy <- read_csv("Downloads/toy.csv")
#Be careful with the route. 

- How many observations and variables are there?
- Are there missing values?
- Calculate the mean of: Peso, Altura, IMC, IAS, CCintura grouped by sex.
- Compute standard deviation, minimum, and maximum for the numeric variables. Which variable shows more variability?
- Filter only female patients. How many records meet this condition?
How many are classified as Overweight?
- Create scatter plots:
a. BMI vs Weight for all patients
b. BMI vs Weight for “Overweight” and “Obesity” patients only

### 🌌 Star Wars dataset

library(tidyverse) 
starwars <- starwars 

- How many rows and columns are there?
- Which variables have missing values?
- Calculate mean height and mass overall and by sex.
- Which group has the highest average height?
- Filter human characters only: How many humans are there? What is their average mass?
- Scatter plot of height vs mass. Color by species. Identify any outliers. Which species cluster together by body size?
- List the top 5 heaviest characters. Calculate the average number of films by species

### Other tasks:
- Literature search following PRISMA criteria on studies that contain microbiome data (public) before and after antimicrobial treatment. Only **human studies**, using **shotgun metagenomics** (WGS) data, including all diseases or health states. Anything that you can find :wink:

- The literature search must follow PRISMA steps [example](https://journals.asm.org/doi/epub/10.1128/msystems.00143-25): 

### Citizen science
- Doing a PRISMA research about using citizen science for nutritional/lifestyle studies. (**Keywords:** *citizen scince, diet, nutrition, lifestyle, habits*)
- The reserch question is: Can citizen science be an effective tool for changing lifestyle habits and behaviors through nutritional studies?
- For the review. https://blogs.ucl.ac.uk/open-access/2020/12/03/introduction-to-citizen-science/

### GutPlantHealth web & social media:
- Preparation of vFFQ invitations to participate.
- Some [info](https://docs.google.com/document/d/1rRTI52YybCak1IV5N8qkVxoPcF3iZ1HXE4AJkDg6z70/edit?usp=sharing) about vFFQ.
- Website