# Essential Computational Skills for Biosciences at UCL

:::success
## :tada: Welcome!
### :calendar: Week 1 - 5

### :link: Links
- :page_facing_up: [Workshop website](https://ucl-biosciences.github.io/2025-11-03-Biosciences/)
- :page_facing_up: [Notes made during the workshop](#Notes)
- :female-teacher: :male-teacher: [Instructors and Helpers](#Staff)
- :+1:/:-1: [Feedback](#Feedback-and-Surveys)

### Contact and Help
**Slack**. Please join the [UCL Programming Slack](https://join.slack.com/t/ucl-programming-hub/shared_invite/zt-3gihwtght-Lpm681ywkfGrAT_nXBUxmw). Once there, join #ucl-biosciences and we will add you to #biosciences-comp-training.

**Email** [e-mail].

[**Book a meeting**](https://outlook.office.com/bookwithme/user/[e-mail]/meetingtype/GP1vEk6SdU6fTvgYLBKK8Q2?anonymous&ismsaljsauthenabled&ep=mlink).

Attend an ARC [drop-in session](https://www.ucl.ac.uk/advanced-research-computing/community-events/drop-sessions).

And last but certainly not least, ask us and each other!

### Lesson Material
Material will be available [here](https://github.com/UCL-Biosciences/2025_Biosciences_Computational_Training_Material).

#### Prerequisites (must download first!)
https://ucl-biosciences.github.io/2025-11-03-Biosciences/#setup

#### Datasets
Datasets will be available via github repository or downloaded during lessons. Nothing required in advance.

### Exercises

:::

---

# Staff

### Week 1:

Instructors: Mahmoud Abdelrazek
Helpers: David Pérez-Suárez, James Gilbert

### Week 2:

Instructors: Lakshithade Silva, Finley Bacon, Idil Ozdemir
Helpers: James Gilbert

### Week 3:

Instructors: Nicholas Owen, Angharad Green
Helpers: James Gilbert

### Week 4:

Instructors: Ryan Payton, Adam Lee, Laurence Blackhurst
Helpers: James Gilbert

### Week 5:

Instructors: Rob Vickerstaff
Helpers: Duncan Leggat, James Gilbert
Saadia [e-mail]

# Feedback and Surveys

Pre-workshop survey: [link here](https://forms.office.com/pages/responsepage.aspx?id=_oivH5ipW0yTySEKEdmlwg_hK73jbqFEhFXKM36BElNUMUtJS1NaWVFIUUlFVE9WVEJEWTlQN0dZUi4u&route=shorturl).
Post-workshop survey:

# Notes

# Sign In

## Week 1
Please write name and UCL email used to sign in to Slack (i.e. whether name or code e.g. ucsagil )

Mahum Shaikh [e-mail]
Giulia Casal [e-mail]
Paraskevi Boulasiki [e-mail]
Nicole Fu [e-mail]
Max Telford [e-mail]
Hana Cho [e-mail]
Emma Champneys [e-mail]
Veronika Lachina [e-mail]
Enric Urena [e-mail]
Julia Yige Li [e-mail]
saadia tabassum [e-mail]
Alice Balard [e-mail]
Xiaoya Wei [e-mail]
Zihe Geng [e-mail]
Andrea Ko [e-mail]
Alejandro Maeda-Obregón [e-mail]

## Week 2
Emma Champneys [e-mail]
Enric Urena [e-mail]
Xiaoya Wei [e-mail]
Nicole Fu [e-mail]
Giulia Casal [e-mail]
Paraskevi Boulasiki [e-mail]
Hana Cho [e-mail]
Max Telford [e-mail]
saadia tabasum [e-mail]
Julia Yige Li [e-mail]
Darren Wong [e-mail]
Alejandro Maeda-Obregón [e-mail]
Mahum Shaikh
Alice Balard [e-mail]
Veronika Lachina

## Week 3

Xiaoya Wei [e-mail]
Hana Cho [e-mail]
Paraskevi Boulasiki [e-mail]
Nicole Fu [e-mail]
Julia Yige Li [e-mail]
Elena Chan [e-mail]
Andrea Ko [e-mail]
Alejandro Maeda-Obregón [e-mail]
giulia casal [e-mail]
Alice Balard [e-mail]

## Week 4
Hana Cho [e-mail]
Emma Champneys [e-mail]
Darren Wong [e-mail]
Alejandro Maeda-Obregón [e-mail]
Mahum Shaikh

## Week 5
Hana Cho [e-mail]
Emma Champneys [e-mail]
Darren Wong [e-mail]
Alejandro Maeda-Obregón [e-mail]
Mahum Shaikh
giulia casal [e-mail]
saadia Tabasum [e-mail]
Max Telford
Leo Fordham

# Notes
## Week 1 - Python

### Setup
Download this [environment file](https://raw.githubusercontent.com/carpentries/workshop-template/refs/heads/gh-pages/data/carpentries_environment.yml)
On a console, run:

conda env create -f carpentries_environment.yml

### Data

Create a directory:

mkdir -p workshop-python/data
cd workshop-python/data

Download the data

curl -O https://raw.githubusercontent.com/UCL-Biosciences/2025_Biosciences_Computational_Training_Material/refs/heads/main/workshops/W1_intro_python/data/penguin_data.csv
curl -O https://raw.githubusercontent.com/UCL-Biosciences/2025_Biosciences_Computational_Training_Material/refs/heads/main/workshops/W1_intro_python/data/penguin_data_v2_final_v2_finalFINAL.csv
cd ..

### Setup notes
Conda needs more steps for some people. The steps seem to be different on every computer. Plus David is the pro of conda installation.

## Week 2 - GitHub & Environments

📦 [Repository](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop)
🌐 [website](https://ucl-biosciences.github.io/20251112-bioscigit-workshop/)

### Notes
When downloading content from github, what steps should we take to ensure we are downloading dangerous content?

### Exercise 1 - You and a city

Work on the city you've been assigned to:

- Alice - Wellington
- Andrea - Turku
- Emma - Suez
- Enric - Perth
- Giulia - Kolkata
- Hana - Denver
- Julia - Coimbra
- Mahum - Chengdu
- Max - Cape Town
- Nicole - Barranquilla
- Paraskevi - Ulaanbaatar
- Saadia - Zamboanga
- Veronika - Casablanca
- Xiaoya - Sao Paulo
- Zihe - Sendai
- Alejandro - Mazatlan
- Darren - Hiroshima
- ?? - Cordoba
- ?? - Cochabamba
- ?? - Berat
- ?? - Axum

Save the file, create a commit as shown by the instructor and open a pull-request.

Post your link below to get someone to review it

Link to the pull-request
- [Algiers](FIXME) 🔗
- [Auckland](FIXME) 🔗
- [Axum](FIXME) 🔗
- [Barranquilla](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/10)🔗 Nicole
- [Berat](FIXME) 🔗
- [Cape Town](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/6)🔗 Hana
- [Casablanca](FIXME) 🔗
- [Chengdu](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/8) 🔗 Alejandro
- [Cochabamba](FIXME) 🔗
- [Coimbra](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/15) 🔗 Mahum
- [Cordoba](FIXME) 🔗
- [Denver](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/13) 🔗 Darren
- [Hiroshima](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/5) 🔗Max
- [Kolkata](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/4) 🔗Evi
- [Mazatlan](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/9) 🔗 Julia
- [Perth]([FIXME](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/7)) 🔗 Xiaoya
- [Sendai](FIXME) 🔗
- [Suez](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/3) 🔗 giulia
- [Sao Paulo](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/14) 🔗 Alice
- [Turku](FIXME) 🔗
- [Ulaanbaatar](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/12) 🔗 Enric
- [Wellington](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/1) 🔗 Emma
- [Zamboanga](https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/11) 🔗 saadia

### Exercise 2 - Review contributions

Add name above as per the instructions

### Exercise 3 - Add a file: a new traveller

Add your Pull requests here for someone to review it.
Template

---
title: "FIXME - Name"
subtitle: "FIXME - characteristic"
image: FIXME - photo url
toc: false
about:
id: person-profile
template: jolla
---

    <nav aria-label="breadcrumb">
      <ol class="breadcrumb">
        <li class="breadcrumb-item"><a href="../travellers.html">Travellers</a></li>
        <li class="breadcrumb-item active" aria-current="page">{{< meta title >}}</li>
      </ol>
    </nav>

:::{#person-profile}
:::

## Biography

FIXME: add a one line description about the person

## Travelled cities

- FIXME - add cities visited.
- FIXME - city 2
- FIXME - city 3

- Alice https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/26 Hana
- Andrea
- Emma https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/31 Veronika
- Enric https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/21/files Nicole
- Giulia https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/17 Evi
- Hana https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/19 Mahum
- Julia https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/33 Giulia
- Mahum https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/22 Alice
- Max https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/23 Enric
- Nicole https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/27 Darren
- Saadia https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/28 Julia
- Veronika https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/32 Emma
- Xiaoya https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/30 Alejandro
- Zihe
- Evi https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/20 Giulia
- Darren https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/25 Max
- Alejandro https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/29 Xiaoya
- ??
- ??
- ??

As before, add your name next to the one you are reviewing.

### Exercise 4 - Making changes locally

#### Pre exercise

git config --list
git config --global user.name "Your Name"
git config --global user.email "[e-mail]"

#### Action

Add your Pull requests here for someone to review it.
Look the example in [quarto's documentation](https://quarto.org/docs/computations/python.html)

- Alice
- Andrea
- Emma
- Enric https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/36 Xiaoya
- Giulia https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/41 Evi
- Hana
- Julia
- Mahum
- Max https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/35 Nicole
- Nicole https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/43 Max
- Paraskevi https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/42 Giulia
- Saadia
- Veronika https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/44 giulia
- Xiaoya https://github.com/UCL-Biosciences/20251112-bioscigit-workshop/pull/45 Veronika
- Zihe
- Darren
- ??
- ??
- ??

### Exercise 5 - Create a repository from scratch

### Discussion - Environments
What do you think environments are? Why would we need them?

### Discussion - Conda environments

Why are so different?

### Exercise - VS Code and Python

Create a python project and select the environment

## Week 3

### Ice breaker
Make a brief note of data types you commonly work with
*initials - data1, data2 etc.*
Max Telford. DNA sequence data for phylogentics.
Veronika Lachina. In vivo data; simulations (many...) from my biomechanical model.
Mahum Shaikh - Brain and eye registrations
Nicole Fu Polyphosphate/phosphate levels via malachite green (colorimetric reading)
Evi Boulasiki
Xiaoya - omics data/RNAseq
Julia - Alphafold protein structure analysis
AK - Alphafold, DiffDock-L, Raman spectroscopy, light microscopy and EM images

### Data Horror Stories

### Data Archives and Plans
AK - https://spectrabase.com/
Alice Balard - [SRA](https://doi.org/10.25504/FAIRsharing.g7t2hv) & [EGA](https://doi.org/10.25504/FAIRsharing.mya1ff) for sequences; [Zenodo](https://fairsharing.org/FAIRsharing.wy4egf) for a specific code version

List of common archives by data type would be good?!

### Organising
File and folder structure!
Consistent across projects and across colleagues

Maybe we should have public guides or protocols for managing complicated projects.
- see slides :') - could put on Biosciences git?

For recording data about the plates:

Naming: DATE_DailyNumber_KeyExperimentalInfo
Metadata: Experiment (experiment type), condition or treatment, sample IDs, experimenter name, machine ID/model, where will files be saved,

Naming: Project_Date_DayNumber_PlateNumber

## Week 4
## Week 5