+ - 0:00:00
Notes for current slide
Notes for next slide

Collaborating on Open Data Science Projects

Dr. Batool Almarzouq- @batool664

A little bit about me!

  • A computational biologist affiliated with the University of Liverpool.
  • Founder of RLadies Chapter in Saudi Arabia (Dammam).
  • A curator in the R Weekly team.
  • Member of MiR accessibility committee.
  • Member in the turing way community.
  • Working to establish an Open Science community in Saudi Arabia.
  • I make R packages and review/evaluate packages in peer-reviewed journals.

Acknowledgment

  • The Carpentries
  • The Turing Way
  • Molecular Sciences Software Institute (MolSSI)
  • Alison Presmanes Hill (slides)

What are we going to learn?

What are we going to learn?

Introduction to Open Science

What are we going to learn?

Introduction to Open Science

Become a champion of open (data) science

What are we going to learn?

Introduction to Open Science

Become a champion of open (data) science

Intro to Version Control with Git

The classical way of data analysis is no longer useful?

What is the percentage of reproducible research?

Credit: Key results of the survey on reproducibility conducted by Nature in 2016

How can we overcome the reproducibility crisis?

How can you improve the reproducibility of your data science project?

How can you improve the reproducibility of your data science project?

OPEN SOURCE SOFTWARE

How can you improve the reproducibility of your data science project?

OPEN SOURCE SOFTWARE

SHARE CODE/ANALYSIS

How can you improve the reproducibility of your data science project?

OPEN SOURCE SOFTWARE

SHARE CODE/ANALYSIS

Share Computational ENVIRONMENT

How can you improve the reproducibility of your data science project?

OPEN SOURCE SOFTWARE

SHARE CODE/ANALYSIS

Share Computational ENVIRONMENT

VERSION CONTROL

How can you improve the reproducibility of your data science project?

OPEN SOURCE SOFTWARE

SHARE CODE/ANALYSIS

Share Computational ENVIRONMENT

VERSION CONTROL

TESTING

How can you improve the reproducibility of your data science project?

OPEN SOURCE SOFTWARE

SHARE CODE/ANALYSIS

Share Computational ENVIRONMENT

VERSION CONTROL

TESTING

DOCUMENTATION

How can you improve the reproducibility of your data science project?

OPEN SOURCE SOFTWARE

SHARE CODE/ANALYSIS

Share Computational ENVIRONMENT

VERSION CONTROL

TESTING

DOCUMENTATION

OPEN DATA/FAIR DATA

How can you improve the reproducibility of your data science project?

OPEN SOURCE SOFTWARE

SHARE CODE/ANALYSIS

Share Computational ENVIRONMENT

VERSION CONTROL

TESTING

DOCUMENTATION

OPEN DATA/FAIR DATA

LICENSE

This is called Open Science.

Open research aims to transform research by making it more reproducible, transparent, reusable, collaborative, accountable, and accessible to society. It pushes for change in the way that research is carried out and disseminated by digital tools.

Why do we use version control (git)?

Version Control in the Old Days ..

Real Version Control (including backup)

In this workshop, you'll learn:

In this workshop, you'll learn:

How vrsion control system can be leveraged as an electronic lab notebook for computational work.

In this workshop, you'll learn:

How vrsion control system can be leveraged as an electronic lab notebook for computational work.

Learn why adding licensing information to a repository is important, and how to choose a proper license.

In this workshop, you'll learn:

How vrsion control system can be leveraged as an electronic lab notebook for computational work.

Learn why adding licensing information to a repository is important, and how to choose a proper license.

Make your work easy to cite!

The 1st part: How to create a repo from your local machine

We will use the term repository which means your folder

The 1st part: How to create a repo from your local machine

We will use the term repository which means your folder

git init = initiate a repository

The 1st part: How to create a repo from your local machine

We will use the term repository which means your folder

git init = initiate a repository

git add = track this file

The 1st part: How to create a repo from your local machine

We will use the term repository which means your folder

git init = initiate a repository

git add = track this file

git commit = save these changes

The 1st part: How to create a repo from your local machine

We will use the term repository which means your folder

git init = initiate a repository

git add = track this file

git commit = save these changes

git push = transfer these changes to the remote

The 1st part: How to create a repo from your local machine

We will use the term repository which means your folder

git init = initiate a repository

git add = track this file

git commit = save these changes

git push = transfer these changes to the remote

git status = displays the state of the working directory and the staging area

Let's try, we'll use new project!

The 2nd part: How to use a public repo in Github

The 2nd part: How to use a public repo in Github

fork = Forking a repository allows you to freely experiment with changes without affecting the original project

The 2nd part: How to use a public repo in Github

fork = Forking a repository allows you to freely experiment with changes without affecting the original project

git clone = Make a local copy in my local machine

The 2nd part: How to use a public repo in Github

fork = Forking a repository allows you to freely experiment with changes without affecting the original project

git clone = Make a local copy in my local machine

git pull = Fetch and download content from a remote repository and immediately update the local repository to match that content

We will use glosario repo, ou can also use WiDS-ex repo in my account

The 3rd part: How to submit a PR?

The 3rd part: How to submit a PR?

git checkout -b BRANCH-NAME = Create a branch tp prevent conflict

The 3rd part: How to submit a PR?

git checkout -b BRANCH-NAME = Create a branch tp prevent conflict

git checkout master/main = Go back to the master branch

We will use glosario repo, ou can also use WiDS-ex repo in my account

The 4th part: How to solve any conflict?

The 4th part: How to solve any conflict?

git log = Shows all the commits

The 4th part: How to solve any conflict?

git log = Shows all the commits

git merge = Merge any changes from two branches unless there is a conflict

The 4th part: How to solve any conflict?

git log = Shows all the commits

git merge = Merge any changes from two branches unless there is a conflict

git checkout COMMIT_ID = Revert back in time

The 5th part: How to add a licensing information?

We will use WiDS-ex repo to add LICENSE

The 6th part: How to add a DOI and make your work citable?

We will use WiDS workshop repo and Zenodo

 What now?

 What now?

You can easily contributing to open-source, improve employability

 What now?

You can easily contributing to open-source, improve employability

You will learn programming and coding, have others review your code.

 What now?

You can easily contributing to open-source, improve employability

You will learn programming and coding, have others review your code.

You will not be (useless) data scientist

 What now?

You can easily contributing to open-source, improve employability

You will learn programming and coding, have others review your code.

You will not be (useless) data scientist

You will start build tools and packages

UNESCO is launching international consultations aimed at developing a Recommendation on Open Science for adoption by member states in 2021

UNESCO is launching international consultations aimed at developing a Recommendation on Open Science for adoption by member states in 2021

There is a network of Open Science Communities in Netherlands, Sweden, Germany, UK and others

In line with vision 2030, we are starting an Open Science Community in Saudi Arabia.

It's created and developed with the help of the "Open Life Sciences"

Open Life Sciences (OLS3) program helps individuals and stakeholders in research to become Open Science ambassadors.

We want to provide a place where newcomers and experienced peers interact, inspire each other to embed open science (research) practices and values in their workflows and provide feedback on policies, infrastructures and support services. Together working to make Open Science the norm. So we are calling out to researchers and colleagues in Saudi Arabia.

Batool Almarzouq The University of Liverpool

Founder and director of Talarify, Mentor OLS3

Paula Moraga, Assistant Professor in Statistics for Public Health (KAUST)

 Learn how to make packages, data viz, and more in RLadies

Thank you so much!

batool@liverpool.ac.uk

Twitter: @batool664

Join RLadiesDammam: @RLadiesDammam

A little bit about me!

  • A computational biologist affiliated with the University of Liverpool.
  • Founder of RLadies Chapter in Saudi Arabia (Dammam).
  • A curator in the R Weekly team.
  • Member of MiR accessibility committee.
  • Member in the turing way community.
  • Working to establish an Open Science community in Saudi Arabia.
  • I make R packages and review/evaluate packages in peer-reviewed journals.

Acknowledgment

  • The Carpentries
  • The Turing Way
  • Molecular Sciences Software Institute (MolSSI)
  • Alison Presmanes Hill (slides)
Paused

Help

Keyboard shortcuts

, , Pg Up, k Go to previous slide
, , Pg Dn, Space, j Go to next slide
Home Go to first slide
End Go to last slide
Number + Return Go to specific slide
b / m / f Toggle blackout / mirrored / fullscreen mode
c Clone slideshow
p Toggle presenter mode
t Restart the presentation timer
?, h Toggle this help
Esc Back to slideshow