Recognising research software in academia

Nicholas Tierney, Telethon Kids Institute

UNSW Seminar

Friday 29th October, 2021

https://njt-rse-unsw.netlify.app

nj_tierney

njt-rse-unsw.netlify.app • @nj_tierney
Your Turn: What software do people use in their research?2

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

I'll discuss why we need to consider software as academic output, what a research software engineer does, how I work in a team of researchers, and some of the practices I have put in place to maintain reproducibility.

njt-rse-unsw.netlify.app • @nj_tierney
Your Turn: Has anyone written software for their research and released it into the wild?3

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
Your Turn: Could you do your research without software?4

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

(R, Matlab, C, FORTRAN)

njt-rse-unsw.netlify.app • @nj_tierney
Do we need software to do our research?5

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Do we need software to do our research?

Yes

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Do we need software to do our research?

Yes

(if we want it to work)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Imaging a black hole

Congratulations to Dr. Katie Bouman to whom we owe the first photograph of a black hole ever. (from @TamyEmmaPepin

"...There are about 68,000 lines in the current software"

(ABC article

)

]

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

COVID19: Grattan Institute

(from Grattan institute report: "Australian governments can choose to slow the spread of coronavirus, but they would need to act immediately")

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

COVID19: Journalist @CaseyBriggs

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
Writing research software is a research contribution9

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
Functions help us manage complexity10

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Functions help us manage complexity

For example: R's model syntax

fit <- lm(y ~ x + factor(z))
coef(fit)

## (Intercept)           x  factor(z)2  factor(z)3 
##  0.15594165 -0.11102041 -0.17567974 -0.08798766

fit |> residuals() |> summary()

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
## -2.0688 -0.5884  0.0188  0.0000  0.5724  2.6394

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Functions help us manage complexity

Versus writing a model from scratch

X <- cbind(1, x, z == 2, z == 3)
fit <- solve(t(X) %*% X) %*% t(X) %*% y
residuals(fit)

## Error: $ operator is invalid for atomic vectors

# ugh, residuals...

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

(which is actually a syntactic algebra from a paper ... (heard via Emi Tanaka))

njt-rse-unsw.netlify.app • @nj_tierney
Functions help us manage complexityleaflet() %>%
  addTiles() %>%  
  addMarkers(
    lng = 174.768, 
    lat = -36.852, 
    popup = "R's birthplace"
  )

+−
Leaflet | © OpenStreetMap contributors, CC-BY-SA
12

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Functions allow you to abstract complexity so you can individually reason with them
Assembly --> C --> R --> ggplot

njt-rse-unsw.netlify.app • @nj_tierney
Abstraction of complexity: similarities between software and maths13

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Abstraction of complexity: similarities between software and maths

Users often remark on the ease of manipulating data with dplyr and it is natural to wonder if perhaps the task itself is trivial. We claim it is not. Many probability challenges become dramatically easier, once you strike upon the "right" notation. In both cases, what feels like a matter of notation or syntax is really more about exploiting the "right" abstraction.

-- Jenny Bryan & Hadley Wickham Data Science: A Three Ring Circus or a Big Tent?

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

This means that it is not just statistical models, but things like dplyr, ggplot

Abstraction of complexity: similarities between software and maths

Notation matters!

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Abstraction of complexity: similarities between software and maths

Notation matters!

\(1000000\) vs \(1,000,000\) vs \(10^6\)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Abstraction of complexity: similarities between software and maths

Notation matters!

\(1000000\) vs \(1,000,000\) vs \(10^6\)

\(1000000 * 10000 * 10000000 * 10000 = ?\)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Abstraction of complexity: similarities between software and maths

Notation matters!

\(1000000\) vs \(1,000,000\) vs \(10^6\)

\(1000000 * 10000 * 10000000 * 10000 = ?\)

\(10^6 * 10^4 * 10^7 * 10^4 = 10^{6 + 4 + 7 + 4}\)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Abstraction of complexity: similarities between software and maths

"Unmasking the theta method" (Rob Hyndman & Baki Billah)

The "Theta method" of forecasting performed particularly well in the M3- competition and is therefore of interest to forecast practitioners. The original description of the method given by Assimakopoulos and Nikolopoulos (2000) involves several pages of algebraic manipulation. We show that the method can be expressed much more simply and that the forecasts obtained are equivalent to simple exponential smoothing with drift.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
Research software is critically underfunded and not acknowledged16

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

We continue to lose people

Every great open source math library is built on the ashes of someone's academic career

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

William Stein

"The origins of SageMath - I am leaving academia to build a company"

1991-93: CS Undergrad
1997-99: Hecke + interpreter in C++
1998: Kohel: Introduced me to both "open source" and Magma, and said "too bad you have to write an interpreter"...
1999-2004: wrote a lot of Magma code (3 Sydney visits), and tried to convert everyone I met to using Magma.
2004: Problems: Magma is closed source, closed development model, expensive; authorship issues
2005: created SageMath
2016: Left academia to work full time on Sage

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Travis Oliphant

PhD 2001 from Mayo Clinic in Biomedical Engineering
MS/BS in Elec. Comp. Engineering
Creator of SciPy, Author of NumPy (The most imported machine learning projects on GitHub)
Founding chair of Numfocus / PyData
Professor at Brigham Young University (2001-2007)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Travis Oliphant

PhD 2001 from Mayo Clinic in Biomedical Engineering
MS/BS in Elec. Comp. Engineering
Creator of SciPy, Author of NumPy (The most imported machine learning projects on GitHub)
Founding chair of Numfocus / PyData
Professor at Brigham Young University (2001-2007)

Application for Tenure was denied. Software wasn't counted.

(Abbreviated from William Stein's talk)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Also worth noting that he has had a successful career from here, his company, Continuum Analytics received 24 million dollars in Seris A funding.

Jack Poulson

Hi William,

I am sitting on an offer from Google and am increasingly frustrated by continual evidence that it is more valuable to publish a litany of computational papers with no source code than to do the thankless task of developing a niche open source library. Deep mathematical software is not appreciated by either the mathematicians or the public. I had been on the fence about accepting the offer, and this conversation led to me making the difficult decision.

– Jack Poulson, Stanford

(Abbreviated from William Stein's talk)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

It should be noted that Jack appears to be doing well, had a successful career at Google and has his own company, HodgeStar

"The Astropy problem" (paper)

"[Astropy is] a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages."

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

"The Astropy problem" (paper)

"[Astropy is] a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages."

For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

"The Astropy problem" (paper)

"[Astropy is] a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages."

For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community.

Despite this, the project has always been and remains to this day effectively unfunded . Further, contributors receive little or no formal recognition for creating and supporting what is now critical software.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
Could grant bodies fund Astropy?22

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Could grant bodies fund Astropy?

..."the NSF hasn't funded software development for many years now, yet software continues to be written, so...?"

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Could grant bodies fund Astropy?

..."the NSF hasn't funded software development for many years now, yet software continues to be written, so...?"

"[The NSF] would consider funding software, but only once it has reached the point where it's very mature and has a large number of users."

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Could grant bodies fund Astropy?

..."the NSF hasn't funded software development for many years now, yet software continues to be written, so...?"

"[The NSF] would consider funding software, but only once it has reached the point where it's very mature and has a large number of users."

These opinions reflect a gross misunderstanding of the amount of time, effort, and expertise it takes to develop software, let alone specialized, scientific software.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
OK, but how important is astropy?23

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

OK, but how important is astropy?

... All NASA mission pipelines... [such as the]... venerable Hubble Space Telescope to the upcoming [Nancy Grace Roman Space Telescope], use Astropy.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

OK, but how important is astropy?

... All NASA mission pipelines... [such as the]... venerable Hubble Space Telescope to the upcoming [Nancy Grace Roman Space Telescope], use Astropy.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

'...Software just, "happens" ???'

For much of the community, software is something that just "happens" and is expected to be free.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

'...Software just, "happens" ???'

For much of the community, software is something that just "happens" and is expected to be free.

However, there is a cost and it is clear who is paying it.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

'...Software just, "happens" ???'

For much of the community, software is something that just "happens" and is expected to be free.

However, there is a cost and it is clear who is paying it.

The early career astronomers who contribute the lion's share of the effort do so at the expense of their research and publication output.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Who is funding scientific software?

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
What happens if you don't fund software26

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

What happens if you don't fund software

By 2014, two-thirds of all Web servers were using OpenSSL, enabling websites to securely pass credit card and other sensitive information over the Internet

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

What happens if you don't fund software

By 2014, two-thirds of all Web servers were using OpenSSL, enabling websites to securely pass credit card and other sensitive information over the Internet

...the project continued to be informally managed by a small handful of volunteers.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

What happens if you don't fund software

By 2014, two-thirds of all Web servers were using OpenSSL, enabling websites to securely pass credit card and other sensitive information over the Internet

...the project continued to be informally managed by a small handful of volunteers.

... a Google engineer named Neel Mehta stumbled upon a major flaw in OpenSSL's software...

(from "Roads and Bridges: The Unseen Labor Behind Our Digital Infrastructure)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

What happens if you don't fund software

That bug, nicknamed Heartbleed, had been included in a 2011 update. It had gone unnoticed for years. Heartbleed could allow any sophisticated hacker to capture secure information being passed to vulnerable web servers, including passwords, credit card information, and other sensitive data.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

What happens if you don't fund software

That bug, nicknamed Heartbleed, had been included in a 2011 update. It had gone unnoticed for years. Heartbleed could allow any sophisticated hacker to capture secure information being passed to vulnerable web servers, including passwords, credit card information, and other sensitive data.

The mystery is not that a few overworked volunteers missed this bug; the mystery is why it hasn't happened more often."

(from "Roads and Bridges: The Unseen Labor Behind Our Digital Infrastructure)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

What happens if you don't fund software: `elemental`

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

elemental C++ library for distributed-memory dense and sparse-direct linear algebra, conic optimization, and lattice reduction

njt-rse-unsw.netlify.app • @nj_tierney
Research: "done" vs Software: "Maintained"29

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Research: "done" vs Software: "Maintained"

Research:

3 year research plan
Survey population
Get + share data
Develop model, write about insights
Submit paper
reject/revise/publish
paper published
That component is done

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Research: "done" vs Software: "Maintained"

Research:

3 year research plan
Survey population
Get + share data
Develop model, write about insights
Submit paper
reject/revise/publish
paper published
That component is done

Software:

3 years of funding
Create software to perform modelling
Develop tests, documentation, examples
Extend to other niche use cases
Add features requested by community
Ongoing maintenance

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
Can we at least give software developers in academia a name?30

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
Can we at least give software developers in academia a name?A research software engineer!30

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

A not-so-brief history of Research Software Engineers (Abridged)

Many academics were aware of the importance of software to research; they could see that the people who created this software went largely unrecognised, and they were beginning to worry about the consequences of this oversight. What happens when something is so vital to research, yet overlooked and severely under-resourced?

(From the eponymous paper)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Define: Research Software Engineer

A Research Software Engineer (RSE) combines professional software engineering expertise with an intimate understanding of research.

-- (from https://society-rse.org/about/)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Define: Research Software Engineer

A Research Software Engineer (RSE) combines professional software engineering expertise with an intimate understanding of research.

-- (from https://society-rse.org/about/)

The Society of Research Software Engineering was founded on the belief that a world which relies on software must recognise the people who develop it.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Research software engineer vs Software Engineer

Researcher

Create statistical model of malaria for given region

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Research software engineer vs Software Engineer

Researcher

Create statistical model of malaria for given region

Software engineer:

Take existing code base, and productionise in containers to run on the web

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Research software engineer vs Software Engineer

Researcher

Create statistical model of malaria for given region

Software engineer:

Take existing code base, and productionise in containers to run on the web

Research software engineer:

Identify abstractions, create software that lets researchers write code focussing on the models

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Malaria modelling

yahtsee (Yet Another Hierarchical Time Series Extension + Expansion)

m <- fit_hts(
  formula = pr ~ avg_lower_age + 
  hts(who_region, 
      who_subregion,
      country),
  .data = malaria_africa_ts,
  family = "gaussian"
)

## # A tsibble: 1,046 x 15 [1D]
## # Key:       country [46]
##    who_region who_subregion country date       month_num positive examined
##    <fct>      <fct>         <fct>   <date>         <dbl>    <dbl>    <int>
##  1 AFRO       AFRO-W        Angola  1989-06-01       120     15.8       50
##  2 AFRO       AFRO-W        Angola  2005-11-01       372     82        111
##  3 AFRO       AFRO-W        Angola  2006-04-01       300    102        197
##  4 AFRO       AFRO-W        Angola  2006-11-01       384     41        347
##  5 AFRO       AFRO-W        Angola  2006-12-01       396    173        734
##  6 AFRO       AFRO-W        Angola  2007-01-01       276    216        828
##  7 AFRO       AFRO-W        Angola  2007-02-01       288     42         71
##  8 AFRO       AFRO-W        Angola  2007-03-01       300    119        448
##  9 AFRO       AFRO-W        Angola  2011-01-01       324      1        239
## 10 AFRO       AFRO-W        Angola  2011-02-01       336    148       1132
## # … with 1,036 more rows, and 8 more variables: pr <dbl>, avg_lower_age <dbl>,
## #   continent_id <fct>, country_id <fct>, year <int>, month <int>,
## #   avg_upper_age <dbl>, species <fct>

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Malaria modelling

cleaned_data <- data %>%
    as_tibble() %>%
    group_by(who_region) %>%
    transmute(.who_region_id = cur_group_id()) %>%
    ungroup(who_region) %>%
    select(-who_region) %>% 
    group_by(who_subregion) %>%
    transmute(.who_subregion_id = cur_group_id()) %>%
    ungroup(who_subregion) %>%
    select(-who_subregion) %>% 
    group_by(country) %>%
    transmute(.country_id = cur_group_id()) %>%
    ungroup(country) %>%
    select(-country)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Malaria modelling

model <- inlabru::bru(
formula = pr ~ avg_lower_age + Intercept + 
  who_region(month_num, 
             model = "ar1", 
             group = .who_region_id,
             constr = FALSE) + 
  who_subregion(month_num, 
                model = "ar1", 
                group = .who_subregion_id, 
                constr = FALSE) + 
  country(month_num, 
          model = "ar1", 
          group = .country_id, 
          constr = FALSE),
    family = "gaussian",
    data = malaria_africa_ts,
    options = list(control.compute = list(config = TRUE),
                   control.predictor = list(compute = TRUE, link = 1))
    )

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Malaria modelling

yahtsee (Yet Another Hierarchical Time Series Extension + Expansion)

m <- fit_hts(
  formula = pr ~ avg_lower_age + 
  hts(who_region, 
      who_subregion,
      country),
  .data = malaria_africa_ts,
  family = "gaussian"
)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

What sorts of things does an RSE do?

Create software to solve research problems
Develop tools that abstract the right components to facilitate research
Help researchers to find and learn good tools
Support researchers with (computational) reproducibility

(adapted from Heidi Seibold's UseR2021 Keynote talk)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

My journey into the RSE world

2008-2012: Undergraduate + honours in Psychology

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

My journey into the RSE world

2008-2012: Undergraduate + honours in Psychology

2013 - 2017: PhD Statistics

Exploratory Data Analysis (EDA)
Bayesian Statistics

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

My journey into the RSE world

2008-2012: Undergraduate + honours in Psychology

2013 - 2017: PhD Statistics

Exploratory Data Analysis (EDA)
Bayesian Statistics

2018 - 2020: Research Fellow / Lecturer at Monash

Design and improve tools for (exploratory) data analysis
Teach introduction to data analysis (ETC1010)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

EDA: Exploratory Data Analysis

...EDA is an approach to analyzing data sets to summarize their main characteristics, often with visual methods. (Wikipedia)

John Tukey, Frederick Mosteller, Bill Cleveland, Dianne Cook, Heike Hoffman, Rob Hyndman, Hadley Wickham

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

EDA: Why it's worth it

-- From "Same Stats, Different Graphs: Generating Datasets with Varied Appearance and Identical Statistics through Simulated Annealing"

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

`visdat::vis_dat(airquality)`

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

`naniar::gg_miss_var(airquality)`

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

`brolgar` - take spaghetti

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

`brolgar` - sample spaghetti

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

`brolgar` - spread spaghetti

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
What do I do as an RSE?47

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

{greta}: scalable statistical inference

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

{greta}: scalable statistical inference

Created by Professor Nick Golding

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

{greta}: scalable statistical inference

Created by Professor Nick Golding

greta

theta <- normal(0, 32, dim = 2)
mu <- alpha + beta * Z
X <- normal(mu, sigma)
p <- ilogit(theta[1] + theta[2] * X)
distribution(y) <- binomial(n, p)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

{greta}: scalable statistical inference

Created by Professor Nick Golding

greta

theta <- normal(0, 32, dim = 2)
mu <- alpha + beta * Z
X <- normal(mu, sigma)
p <- ilogit(theta[1] + theta[2] * X)
distribution(y) <- binomial(n, p)

BUGS

for(j in 1 : J) {
   y[j] ~ dbin(p[j], n[j])
   logit(p[j]) <- theta[1] + theta[2] * X[j]
   X[j] ~ dnorm(mu[j], tau)
   mu[j] <- alpha + beta * Z[j]
}
theta[1] ~ dnorm(0.0, 0.001)
theta[2] ~ dnorm(0.0, 0.001)

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Contact matrices - Prem et al

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Contact matrices

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Contact matrices

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Contact matrices

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Contact matrices

conmat (name in progress) package facilitates contact matrix analysis
Nick Golding contributed statistical modelling
I implemented package design, infrastructure, tests, documentation
absolutely critical in recent national covid19 modelling to prime ministers cabinet
package available on github

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
RSEs are everywhere!A lot of people have been doing this for a long time
It isn't necessarily new,
But providing a name gives us something to rally behind
The model "career" doesn't have a lot of evidence yet
We still need credit
54

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
Getting credit for software55

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Getting credit for software

Citations are one form of credit
Google scholar now picks up R packages on CRAN
Reference R monthly R package downloads with a badge:
From a university/grant writing/job application perspective:
- Papers (unfortunately) generally count for more beans more than software

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Getting credit for software

Citations are one form of credit
Google scholar now picks up R packages on CRAN
Reference R monthly R package downloads with a badge:
From a university/grant writing/job application perspective:
- Papers (unfortunately) generally count for more beans more than software

Monash University has recently started crediting statistical software!

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Publishing software as a paper

Statistical methods:

Create a new method
Write code to implement the new method
Ensure code is easy to use for other people
Write documentation for the software
Write tests to ensure the software works
Write a paper about the new method, which links the paper to the method, to the software
The reviewers review the paper
- They typically do not review the software or code

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Publishing software as a paper: some issues

You are writing many times:

Write the method
Write the code
Iterate on the code interface
Write the tests
Write Documentation
Write a paper

Not guaranteed your code is reviewed

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Publishing software as a paper: JOSS

Journal of Open Source Software

Write the code, tests, documentation
Provide a short 1-2 page abstract.
The code gets reviewed
Changes made
Paper gets accepted
DOI minted
Your software is now citable!
It is free!

The paper provides a link to the software. It means the person can write software and not need to write an entire large paper.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
60

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

JOSS Review process

Guided walk through

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

rOpenSci Software Review

More in depth software review backed by their developer guide
Details on how to review + more here
Guided walk through
Example package: ropenaq

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

rOpenSci Statistical Software Review

Expand the rOpenSci software review to statistics
Guide to statistical software peer review

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Getting credit: Awards / recognition

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
What can you do? How can we help sustain this?Research money for maintenance of existing software
Seed funding for new software ideas
Are you a reviewers? On grant committees? Heads of school?
Talk about the importance of software
Count software when reviewing applications and grants
cite software when you use it in your research!
Consider hiring RSEs!
65

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

it is valuable. I feel that I hear far too many people say, "oh yes, software is super valuable", and then that's it - show us that it is valuable in the same way that people at Monash do. As much as early career researchers like me can try and give talks like this, we can only impart so much change.

njt-rse-unsw.netlify.app • @nj_tierney
Take homesWe need software to do research
Writing research software is a research contribution
Research software is critically underfunded and now acknowledged. 
If we don't acknowledge and support it, we will lose people
We need to think about how we fund and support those who write software
RSEs are one path to helping enable and facilitate research impact
We all need to work together to acknowledge software
66

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

njt-rse-unsw.netlify.app • @nj_tierney
ThanksNick Golding
Tasmin Symons
Miles McBain

Di Cook
Rob Hyndman
Karthik Ram

67

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Resources

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Colophon

Slides made using xaringan
Extended with xaringanthemer
Colours taken + modified from lorikeet theme from ochRe
Header font is Josefin Sans
Body text font is Montserrat
Code font is Fira Mono
template available: njtierney/njt-talks

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

Learning more

talk link

nj_tierney

njtierney

nicholas.tierney@gmail.com

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

End.

Main arguments of the talk:

We need software to do research
Writing research software is a research contribution
Research software is critically under-funded and not acknowledged.
We will continue to lose software developers if they are not acknowledged.
We must fund and acknowledge software
What does a research software engineer do?
The history of research software in academia
What I do in a day to day role
What Academia, and you, can do to help

What does academia value?

The incentive structures of academic statistics still signal that mathematical statistics and the creation of new models and inferential procedures are more valuable than work related to data manipulation, visualisation, and programming. This is reflected in the content of for-credit courses, qualifying exams, and standards for funding and promotion.... It can be very difficult to present modern data scientific work as impactful scholarly activity, when the system still defines that primarily as theory and methodology papers.

-- Jenny Bryan & Hadley Wickham

The basic practices of modularity, testing, version control, packaging, and interface design are not mere niceties. They determine whether data scientific products can actually be trusted and built upon, like a proof in mathematics

-- Jenny Bryan & Hadley Wickham

It doesn't matter how good a theoretical solution is, unless there are practical tools that implement it. We must also recognise that humans are an essential part of the data science process and study how they can interact with the computer most effectively. Finding useful abstractions and exposing them through programming languages is an important part of this process

-- Jenny Bryan & Hadley Wickham

Data Science: A Three Ring Circus or a Big Tent?

Having RSEs in your team

Proactive vs Reactive research software
- Proactive: designs code that can be maintaed easily, for 10 years, is documented well, is tested, is maintainable
- Reactive: taking existing code and cleaning it up so it can be used for other use cases
More haste less speed: do it well so you can do it quickly
Examples of the types of RSE projects
- What sort of skillset they need, and how it contributes to reserach impacrt
How would having an RSE inprove the impact of the work?

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Recognising research software in academia

Nicholas Tierney, Telethon Kids Institute

UNSW Seminar Friday 29th October, 2021 https://njt-rse-unsw.netlify.app nj_tierney

Your Turn: What software do people use in their research?

Your Turn: Has anyone written software for their research and released it into the wild?

Your Turn: Could you do your research without software?

Do we need software to do our research?

Do we need software to do our research?

Do we need software to do our research?

Imaging a black hole

COVID19: Grattan Institute

COVID19: Journalist @CaseyBriggs

Writing research software is a research contribution

Functions help us manage complexity

Functions help us manage complexity

Functions help us manage complexity

Functions help us manage complexity

Abstraction of complexity: similarities between software and maths

Abstraction of complexity: similarities between software and maths

Abstraction of complexity: similarities between software and maths

Abstraction of complexity: similarities between software and maths

Abstraction of complexity: similarities between software and maths

Abstraction of complexity: similarities between software and maths

Abstraction of complexity: similarities between software and maths

Research software is critically underfunded and not acknowledged

We continue to lose people

William Stein

Travis Oliphant

Travis Oliphant

Jack Poulson

"The Astropy problem" (paper)

"The Astropy problem" (paper)

"The Astropy problem" (paper)

Could grant bodies fund Astropy?

Could grant bodies fund Astropy?

Could grant bodies fund Astropy?

Could grant bodies fund Astropy?

OK, but how important is astropy?

OK, but how important is astropy?

OK, but how important is astropy?

'...Software just, "happens" ???'

'...Software just, "happens" ???'

'...Software just, "happens" ???'

Who is funding scientific software?

What happens if you don't fund software

What happens if you don't fund software

What happens if you don't fund software

What happens if you don't fund software

What happens if you don't fund software

What happens if you don't fund software

What happens if you don't fund software: elemental

Research: "done" vs Software: "Maintained"

Research: "done" vs Software: "Maintained"

Research: "done" vs Software: "Maintained"

Can we at least give software developers in academia a name?

Can we at least give software developers in academia a name?

A research software engineer!

A not-so-brief history of Research Software Engineers (Abridged)

Define: Research Software Engineer

Define: Research Software Engineer

Research software engineer vs Software Engineer

Research software engineer vs Software Engineer

Research software engineer vs Software Engineer

Malaria modelling

Malaria modelling

Malaria modelling

Malaria modelling

What sorts of things does an RSE do?

My journey into the RSE world

My journey into the RSE world

My journey into the RSE world

EDA: Exploratory Data Analysis

EDA: Why it's worth it

visdat::vis_dat(airquality)

naniar::gg_miss_var(airquality)

brolgar - take spaghetti

brolgar - sample spaghetti

brolgar - spread spaghetti

What do I do as an RSE?

{greta}: scalable statistical inference

UNSW Seminar

Friday 29th October, 2021

https://njt-rse-unsw.netlify.app

nj_tierney

What happens if you don't fund software: `elemental`

`visdat::vis_dat(airquality)`

`naniar::gg_miss_var(airquality)`

`brolgar` - take spaghetti

`brolgar` - sample spaghetti

`brolgar` - spread spaghetti