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---
title: 'From research software engineering to data science: how technology will impact the way we research'
author:
- name: "Florencia D'Andrea, Ph.D."
affiliation: "Postdoctoral fellow at the Master of Data Science program"
institute: "University of British Columbia"
title-slide-attributes:
data-background-image: img/first-slide.png
data-background-size: contain
data-background-opacity: "0.5"
filters:
- roughnotation
format:
revealjs:
logo: img/wsu-logo.png
incremental: true # bullets one by one
smaller: true
scrollable: true
theme: custom.scss
slide-number: true
chalkboard: true
---
```{r}
library(tidyverse)
library(knitr)
library(kableExtra)
```
#### Slides
[https://www.flor14.github.io/wsu-dandrea/slides.html](https://flor14.github.io/wsu-dandrea/slides.html#/title-slide)
<br>
<br>
::: {.small-text}
<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
**Title slide illustration**: The Turing Way Community, & Scriberia. (2020, March 3). Illustrations from the Turing Way book dashes. Zenodo. http://doi.org/10.5281/zenodo.3695300
:::
:::footer
Click here! I can be a link!
:::
---
## Hello
#### Dr. Florencia D'Andrea
:::: {.columns}
:::{.column width="40%" #vcenter}
```{r foto, echo = FALSE, out.width=250, fig.align='center'}
knitr::include_graphics("https://res.cloudinary.com/flor/image/upload/w_1000,ar_1:1,c_fill,g_auto,e_art:hokusai/v1683580772/IMG_20220607_130734112_mu4fpd.jpg")
```
:::
:::{.column width="60%" #vcenter}
🐦 **Twitter**
[@cantoflor_87](http://twitter.com/cantoflor_87)<br>
📢 **Mastodon**
[@florencia@techhub.social](https://techhub.social/@florencia)
🌐 **Web**
[https://florenciadandrea.com](https://florenciadandrea.com)
:::
::::
---
:::: {.columns}
::: {.column width="50%" #vcenter}
lab
:::
::: {.column width="50%" #vcenter}
field work
:::
::::
# Do researchers develop [software]{.rn rn-type=circle rn-color=white}? {background-color="#E5E4E2"}
:::footer
Press R
:::
---
::: {.big-text}
*research software*
:::
Software that is used to generate, process or analyse results that you intend to appear in a publication
Research software can be anything [from a few lines of code written by yourself, to a professionally developed software package]{.rn rn-type=highlight rn-multiline=true}
:::footer
Press R
- [Hettrick *et al.* (2014) UK Research Software Survey 2014. Zenodo](https://doi.org/10.5281/zenodo.608046)
:::
# Do researchers develop [software]{.rn rn-type=circle rn-color=white}? {background-color="#E5E4E2"}
[Yes, they do!]{.rn rn-type=highlight rn-multiline=true}
:::footer
Press R
:::
---
## {background-image='img/back-question.png' background-size="1000px"}
::: {.fragment fragment-index=1}
**1.** Are Researchers Software Developers?
:::
::: {.fragment fragment-index=2}
**2.** Why is it important to write "good software" in research?
:::
::: {.fragment fragment-index=3}
**3.** What kind of practices and/or tools we need to apply for creating better research software?
- Examples
:::
---
## {background-image='img/back-question.png' background-size="1000px"}
::: {.fragment fragment-index=1}
**4.** We don't have training !
Where to find resources to learn?
:::
::: {.fragment fragment-index=2}
**5.** Where can I find other researchers interested in software?
:::
::: {.fragment fragment-index=3}
**6.** Career paths
- Survey results
:::
::: {.fragment fragment-index=4}
**Final comments**
:::
# Are Researchers Software Developers? {background-color="#67032F"}
Scientists can create software as part of their research
::: {.sectionhead}
1 [2 3 4 5 6]{style="opacity:0.25"}
:::
---
### Software quality can affect research results
:::: {.columns}
::: {.column width="60%" #vcenter}
:::
::: {.column width="40%" #vcenter}
What are the potential consequences of developing bad quality software?
:::
::::
:::footer
Logo: [https://www.software.ac.uk/about](https://www.software.ac.uk/about)
:::
---
## Reproducibility crisis
:::: {.columns}
::: {.column width="50%" #vcenter}
:::
::: {.column width="50%" #vcenter}
Code unavailable is **one** of the reasons why researchers can't reproduce their articles
:::
::::
:::footer
[Baker, M (2016) 1,500 scientists lift the lid on reproducibility - Nature](https://www.nature.com/articles/533452a)
:::
---
## Reproducibility
{width=50%}
::: footer
[Definitions - The Turing Way Handbook](https://the-turing-way.netlify.app/reproducible-research/overview/overview-definitions.html)
:::
---
A result is reproducible when the *same* analysis steps performed on the *same* dataset consistently produces the *same* answer
{fig-align='center'}
::: footer
[The Turing Way project illustration by Scriberia. Used under a CC-BY 4.0 licence.](DOI: 10.5281/zenodo.3332807)
:::
---
### Reproducibility
:::: {.columns}
::: {.column width="60%" #vcenter}
:::
::: {.column width="40%" #vcenter}
- **Empirical**
- **Statistical**
- [**Computational**]{.rn}
:::
::::
:::footer
Press R
- [Victoria Stodden (2014) What scientific idea is ready for retirement? - www.edge.org]( https://www.edge.org/response-detail/25340)
:::
---
::: {.big-text-long}
*Computational reproducibility*
:::
When detailed information is provided about code, software, hardware and implementation details.
{fig-align="center"}
:::footer
Victoria Stodden (2014) [What scientific idea is ready for retirement? - www.edge.org]( https://www.edge.org/response-detail/25340)
:::
# Why is it important to write "good software" in research? {background-color="#67032F"}
The more detailed information is provided about the software we create, the more likely it is to reproduce research results using it
::: {.sectionhead}
[1]{style="opacity:0.25"} 2 [3 4 5 6]{style="opacity:0.25"}
:::
---
## Example
:::: {.columns}
::: {.column width="40%" #vcenter}
**Situation 1**
Julia wants to share R code with her supervisor
:::
::: {.column width="60%" #vcenter}
:::
::::
---
#### Plot's code
Julia is running this code on her computer ✅
```{r plot}
#| echo: true
#| code-fold: true
#| code-summary: "Show the code"
library(readr)
library(tidyr)
library(ggplot2)
coffee_data <- read_csv("data/coffee_data.csv")
coffee_data |>
pivot_longer(cols=aroma:moisture,
names_to="caracteristicas_cafe",
values_to="value") |>
ggplot(aes(value, total_cup_points)) +
geom_smooth(method= "gam", span=0.3, color='purple') +
facet_wrap(~caracteristicas_cafe, scale="free_y")
```
---
## But!
### Her supervisor gets an error ❌
```r
Error in pivot_longer(.,
cols = aroma:moisture,
names_to = "types_coffe",
: could not find function "pivot_longer"
```
🤔 **What could be going on?**
---
## New package version
Code that is running in your computer now [**may not work** anymore if you upgrade the packages!]{.rn rn-type=underline rn-color=orange}
* `tidyr` package version `0.8.3` does not include `pivot_longer()`
* This functions was added in `tidyr` version `1.0.0`
:::footer
[`tidyr` package - releases](https://github.com/tidyverse/tidyr/releases?page=2)
:::
---
::: {.big-text}
*Computational environment*
:::
Characteristics of a 💻 that can affect the behavior of the work done on it, such as:
* your **operating system**
* what **software** do you have installed
* software **package versions** are installed
:::footer
[The Turing Way: A Handbook for Reproducible Data Science (2019)](https://the-turing-way.netlify.app/)
:::
---
## Computational environments
Important to capture them to avoid:
* [Problems when sharing your code]{.rn}
* That you code breaks with time
```{r error, echo = FALSE, out.width=600, fig.align='center'}
knitr::include_graphics("img/ErrorManagement.jpg")
```
:::footer
Press R - [The Turing Way Community, & Scriberia. (2020)](http://doi.org/10.5281/zenodo.3695300)]
:::
---
## The sleight-of-hand trick that can simplify scientific computing
:::: {.columns}
::: {.column width="50%" #vcenter}
Computational environments and the tools to manage them can help researchers to deliver code that is reproducible, documented and shareable.
:::
::: {.column width="50%"}
:::
::::
:::footer
[Perkel, J. (2023) The sleight-of-hand trick that can simplify scientific computing - Nature Article](https://www.nature.com/articles/d41586-023-01469-0)
:::
---
## Situation 1-bis
:::: {.columns}
::: {.column width="40%" #vcenter}
Julia wants to run the code 10 years later
:::
::: {.column width="60%" #vcenter}
:::
::::
---
## Challenge to scientists: does your ten-year-old code still run?
:::: {.columns}
::: {.column width="50%"}
:::
::: {.column width="50%"}
'Missing documentation and obsolete environments force participants in the Ten Years Reproducibility Challenge to get creative.'
:::
::::
:::footer
[Perkel, J. (2020) Challenge to scientists: does your ten-year-old code still run? - Nature Article](https://www.nature.com/articles/d41586-020-02462-7)
:::
---
## Computational environments
Important to capture them to avoid:
* Problems when sharing your code
* [That you code breaks with time]{.rn}
```{r error2, echo = FALSE, out.width=600, fig.align='center'}
knitr::include_graphics("img/ErrorManagement.jpg")
```
:::footer
Press R - [The Turing Way Community, & Scriberia. (2020)](http://doi.org/10.5281/zenodo.3695300)
:::
---
## How to avoid getting this error?
Minimum: Documentation
```{r session, echo=TRUE}
sessionInfo()
```
---
## Tools for reproducibility
We can use different tools to ensure the reproducibility of a project such as:
{fig-align='center'}
# Capturing the computational environment is needed to ensure code reproducibility {background-color="#E5E4E2"}
---
## Situation 2
:::: {.columns}
::: {.column width="60%" #vcenter}
Julia is writing code for an article. **What is the best way to share the code with other colleagues?**
:::
::: {.column width="40%" #vcenter}
:::
::::
---
:::: {.columns}
::: {.column width="50%" #vcenter}
**Git**
A version control system
{width=250}
:::
::: {.column width="50%" #vcenter}
**GitHub**
Repository hosting service
{width=300}
:::
::::
:::footer
[Git logo](https://git-scm.com/downloads/logos)
:::
---
```{r comic, echo = FALSE, out.width=500, fig.align='center'}
knitr::include_graphics("img/vc-final-comic.png")
```
::: footer
[“Piled Higher and Deeper” by Jorge Cham](http://www.phdcomics.com)
:::
---
## Why Git + GitHub is the best way to share code?
:::: {.columns}
::: {.column width="40%" #vcenter}
:::
::: {.column width="60%" #vcenter}
- It's possible to assign names to each **code version** and revisit specific points in its history.
- Your code is **backed up online** on GitHub.
- It is easy to track the **authorship** of each change made
:::
::::
:::footer
[The Turing Way Community, & Scriberia. (2020)](http://doi.org/10.5281/zenodo.3695300) - [Example repository](https://github.com/tidyverse/tidyr)
:::
---
## Why Git + GitHub is the best way to share code?
:::: {.columns}
::: {.column width="50%" #vcenter}
:::
::: {.column width="50%" #vcenter}
- You can share your code as an **open source project**
- Foster **collaboration**
- pull requests
- project boards
- github issues
:::
::::
:::footer
[The Turing Way Community, & Scriberia. (2020)](http://doi.org/10.5281/zenodo.3695300) - [Example 2](https://github.com/flor14/wsu-dandrea/issues/1)
:::
---
{fig-align="center"}
::: footer
[How to Run Your Open Source Software Project - The Turing Way Handbook](https://the-turing-way.netlify.app/reproducible-research/open/open-source.html#how-to-run-your-open-source-software-project) - [The Turing Way Community, & Scriberia. (2020)](http://doi.org/10.5281/zenodo.3695300)
:::
---
#### Many research groups have their GitHub organizations online
:::footer
https://github.com/dib-lab
:::
# Git + GitHub provide much more than just version control. They can also be used to foster collaboration and publish code. {background-color="#E5E4E2"}
---
## Situation 3
:::: {.columns}
::: {.column width="60%" #vcenter}
Julia wants to publish her first article. **How can she do it in a reproducible way?**
:::
::: {.column width="40%" #vcenter}
:::
::::
---
## Research Compendia
:::: {.columns}
::: {.column width="50%" #vcenter}
1. **Organize files** according to a prevailing convention.
2. Provide **separation between data, methods and results** expressing the relationship between the three.
3. Specify the **environment**
:::
::: {.column width="40%" #vcenter}
```{r rc3, echo = FALSE, out.width = 400}
knitr::include_graphics("img/ResearchCompendium.jpg")
```
:::
::::
:::footer
[`rrtools` package](https://github.com/benmarwick/rrtools) - [Research Compendia - The Turing Way: A Handbook for Reproducible Data Science (2019)](https://the-turing-way.netlify.app/reproducible-research/compendia.html?highlight=research%20compendium)
:::
---
## Documentation
Did you ever consider that your next scientific article **can have not only readers but also users**?
<br>
:::{.text-c}
[Readers]{.rn rn-type=crossed-off rn-color=purple}
[Users]{.rn rn-type=circle rn-color=green}
:::
:::footer
Press R
:::
# Project organization and documentation are also relevant to achieving computational reproducibility. {background-color="#E5E4E2"}
---
## Other practices
- Testing
- Continuous integration / development (ci - cd)
- Package development
- Code review
- Basic computational practices
- Automation / use of pipelines
---
## High reproducibility doesn't mean that things couldn't fail
#### What happens when the technology fails?
```{r notfound, echo = FALSE, out.width=600, fig.align='center'}
knitr::include_graphics("img/links.png")
```
---
## Some factors affecting **Reproducibility**
- The tools that ensure the reproducibility (Docker, Conda) could change with time
- The software/hardware we use change with time
---
## Some factors affecting **Reproducibility**
#### How the tools that ensure the reproducibility (Docker, Conda) change with time
**Example 1** - [Inactive Image Retention Policy (Nov 1, 2020)](https://github.com/docker/roadmap/issues/152): DockerHub removing Docker images in free accounts after 6 months
---
## Some factors affecting **Reproducibility**
#### The software/hardware we use change with time
**Example 2** - Mac M1 - Apple silicon chip (hardware) (Oct 2021)
Docker issues
{fig.align:'center'}
:::footer
[Image extracted from: Docker: comstrek/air doesn’t supported linux/arm64 in golang with Macbook M1](https://kecci.medium.com/docker-comstrek-air-not-supported-linux-arm64-in-golang-with-macbook-m1-solved-f7997bd54ee)
:::
---
## Software mantainance
Should our code have **maintainers**?
```{r FixingLinks, echo = FALSE, fig.align='center', out.width=600}
knitr::include_graphics("img/FixingLinks.jpg")
```
:::footer
[Maintainers and Reviewers on GitHub](https://the-turing-way.netlify.app/collaboration/maintain-review.html) - [The Turing Way Community, & Scriberia. (2020)](http://doi.org/10.5281/zenodo.3695300)
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# What kind of practices and/or tools we need to apply for creating better research software? {background-color="#67032F"}
- Capturing computational environments.
- Version controlling and publishing our code.
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# What kind of practices and/or tools we need to apply for creating better research software? {background-color="#67032F"}
- Document the code for your users.
- Software could need maintenance.
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---
### Ok, but I need a second career to learn all this!
{fig-align="center"}
:::footer
[Wilson *et al.* (2017) Good enough practices in scientific computing. PLOS Computational Biology 13(6): e1005510](https://doi.org/10.1371/journal.pcbi.1005510)
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---
"As researchers are under [immense pressure to maintain expertise in their research domains]{.rn rn-type=underline rn-color=orange}, they have little time to stay current with the latest software engineering practices (...) The lack of career incentives has occurred partially because the academic environment and culture have developed over hundreds of years, while [software has only recently become important, in some fields over the last 60+ years, but in many others, just in the last 20 or fewer years ]{.rn rn-type=highlight rn-multiline=true} (Foster, 2006)."
:::footer
Press R - [Carver *et al.* (2022) A survey of the state of the practice for research software in the United States](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9138129/)
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---
## There are many communities that can help to improve research software
- ReproHack
- The Turing Way
- `ROpenSci` / `pyOpenSci`
- The Carpentries
---
## 1. Reprohack
#### Reproducibility hackathons
:::: {.columns}
:::{.column width="70%"}
**Authors**: Send their papers with *publicly available associated code and data*
**Participants**: Attempt to *reproduce published research* of their choice from a list of proposed papers
At the end, the participants give *feedback* to the authors
:::
:::{.column width="30%"}
```{r circulo2, echo = FALSE, out.width=300, fig.align = "center"}
knitr::include_graphics("img/reprohack.png")
```
:::
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:::footer
[Reprohack website](https://www.reprohack.org/)
:::
---
## 2. The Turing Way project
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The TWP involve and support a diverse community of contributors to make data science accessible, comprehensible and effective for everyone.
**Book**
[The Turing Way Handbook (2022)](https://the-turing-way.netlify.app/index.html)
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:::footer
Image: [The Turing Way Community, & Scriberia. (2020)](http://doi.org/10.5281/zenodo.3695300)
:::
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## 3. rOpenSci / pyOpenSci
::::{.columns}
:::{.column width="70%"}
**Scientific package review process**
- [PyOpenSci webpage](https://www.pyopensci.org/about-peer-review/)
- [rOpenSci webpage](https://ropensci.org/software-review/)
- [rOpenSci Packages: Development, Maintenance, and Peer Review](https://devguide.ropensci.org/preface.html)
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## Software Carpentry
::::{.columns}
:::{.column width="50%" #vcenter}
:::
:::{.column width="50%" #vcenter}
**Lessons and infrastructure to teach them**
[The Carpentry lessons](https://software-carpentry.org/) in Unix, python, R and more
:::
::::
::: footer
[The Carpentries](https://carpentries.org)
:::
# We don't have training! Where to find resources to learn? {background-color="#67032F"}
There are many communities that can help researchers to learn how to improve their software
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## Why is there no career for software developers in academia?
- In 2012, the Software Sustainability Institute (SSI) organized the [Collaborations Workshop](http://software.ac.uk/cw12) that addressed this question.
- Foundation of the UK RSE association, and later to the **Society of Research Software Engineering**
---