---
# System prepended metadata

title: 'Research stay: Dearbhla'
tags: [Honguitos, Estudiantes, WGS]

---

###### 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: 
```r=1
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 

```r=1
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): ![image](https://hackmd.io/_uploads/SyF4N3FXgx.png)

### 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



