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Software Sustainability Institute Collaborations Workshop 2018, Cardiff, 26-28 March 2018

Software Sustainability Institute Collaborations Workshop 2018, Cardiff, 26-28 March 2018

Live notes, so an incomplete, partial record of what actually happened.

Tags: collabw18


My asides in {}

Monday 26 March 2018 - day 1

10:00 - 10:05 Welcome to Collaborations Workshop 2018

Key links for the workshop

10:15 - 10:25 Introducing the Institute and getting the most out of a Collaborations Workshop 2018

Focus on what we can change in the here and now rather than lingering on the past.

3 unconference tips for #collabw18 (but they are relevant for most unconferences): be a participant rather than just listen; go off the beaten track rather than repeat old debates ; and not less than change the culture, change the world.

β€” Brigitta Sipocz (@AstroBrigi) March 26, 2018

#collabw18 - @npch encourages us to all be open, and cites the arrangement via social media of 15 #CollabW18 attendees at the same restaurant/bar last night as an open planning success 😎🍻

β€” yo yehudiπŸ³οΈβ€πŸŒˆπŸ‡ͺπŸ‡Ί (@yoyehudi) March 26, 2018

EU Copyright reform has an impact on open science: .. limits database work, poorly worded rather than bad intention

.@npch starting off the morning with an important message about EU Copyright Reform at #collabw18. Find out more. It's important! (cc @Senficon)

β€” M. H. Beⓐls (@mhbeals) March 26, 2018

First call to action at #collabw18 from @npch: find out about and check the wording of current copyright reform proposals in the EU - does it work for you and your work? #TDM

β€” Naomi Penfold (@npscience) March 26, 2018

10:25 - 11:00 Lightning Talks 1

  • Becky Arnold: (Sheffield) code review club for early career researchers. People get more out of informal settings.
  • Neil Chue Hong: what should we be doing for software sustainability - put code in a repo, ask for code/data with a paper, arrange training/support, tell someone senior about 1-3, +???

@npch 5 things to do to support s/w sustainability #collabW18

β€” Catherine Jones (@CM_J0nes) March 26, 2018
  • Eike Mueller: workshop on debugging (Bath)
  • Andrew Williams: Bristol has the EPSRC centre for doctoral training.
  • Melodee Beals: mathematicians taking pity on historians to make their database and visualisations better. CW collaborations are great!

I don't have time to tweet all the lightning talks (they're quick you know!) but I do want to shout out @mhbeals because it's AWESOME to have a historian at #collabw18 #NotOnlyForSTEM πŸ™ŒπŸ™ŒπŸ™Œ

β€” Kirstie Whitaker (@kirstie_j) March 26, 2018
  • Mark Woodbridge

Seven steps to ~heaven~ Sustainable Software
- Choose your weapon
- Git it
- Put it to the test
- Automate
- Write it down
- Open up
1! Shout about it#CollabW18

β€” DVD (@DVDGC13) March 26, 2018
  • Geraint Palmer: Welsh language resources for reproducible research
  • Nikoleta E Glynatsi: wrote a script to help her choose a reviewer for her work when asked

.@NikoletaGlyn shares her computational methods to determine which reviewers to request for a paper 😁 #collabw18

β€” yo yehudiπŸ³οΈβ€πŸŒˆπŸ‡ͺπŸ‡Ί (@yoyehudi) March 26, 2018
  • Joanna Leng: where should an RSE be in a university? what environment do they need?

Our first lightning survey at #collabw18! Joanna Leng asks β€œWhat environment does an #RSE need?”

β€” SSI - (@SoftwareSaved) March 26, 2018
  • Joseph Parker: Computational Science Centre for Research Communities (part of Science & Technology Facilities Council).
  • Razvan Telitoiu: Sage. Social research at scale.
  • Martin Donnelly: working on FOSTER open science project and with Digital Curation Centre

11:30 - 12:30 Culture Change Keynote - Kirstie Whitaker (Alan Turing Institute), How Far We'll Go

Up now is @kirstie_j on culture change here at #collabw18. Slides at

β€” M. H. Beⓐls (@mhbeals) March 26, 2018

Open science is no better than closed science if it takes with it existing ableism, transphobia, sexism, racism {Boom!} .. change - even to open science - requires taking a political stance ..

.@kirstie_j β€œwe will always outnumber them, together we can do more than they can alone in their closed institutions” #openscience #CollabW18

β€” Neil P Chue Hong (@npch) March 26, 2018

.@kirstie_j just quote @hjoseph at #collabw18: "you are not the leaders of tomorrow, you are the leaders of today". Anywhere! Including the picket line.

β€” Raniere Silva (@rgaiacs) March 26, 2018

Mozilla isn't just a software company, it is a foundation that aims to protect the open web .. Mozilla idea of open is that you structure work so that outsiders can become insiders .. Open Science Principles: Design for Participation, Share Decision-Making, Share Code and Content ..

Great take home from @kirstie_j: "it's easy to support passionate people. It's hard to turn an 800 years old ship." #CollabW18

β€” Raniere Silva (@rgaiacs) March 26, 2018

We have all had discussions like this... #collabw18

β€” Stuart Grieve (@GIStuart) March 26, 2018

.@kirstie_j says that even when you can’t make data *open* you can still make it FAIR (Findable, Accessible, Interoperable, Reusable) #CollabW18 #goFAIR

β€” Neil P Chue Hong (@npch) March 26, 2018

.. pledge to make open work at the Alan Turing Institute "too easy not to do" .. Turing Reproducibility Champions via RSE roles ..

Keeping these ants in line - - Is that how upper management is seeing us for #USSstrike - @kirstie_j at #CollabW18

β€” DVD (@DVDGC13) March 26, 2018

Everyone at CW18 #collabW18
Next on: @DrHammersley from @overleaf keynote talk on productivity. Stay tuned!

β€” SSI - (@SoftwareSaved) March 26, 2018
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13:30 - 14:15 Productivity Keynote - John Hammersley, Overleaf

Growth in multi-authored papers where authors from more than one country .. articles written by authors from more than one country more likely to be cited .. Overleaf came from starting out sticking latex documents into EtherPad .. WriteLatex came out of not wanting everyone to install latex on their machine to make things work .. 2 million authors in 5 years .. most the innovations in scholarly comms since 2005 have been cloud based or have core cloud based elements.

14:15 - 15:00 Panel Q&A on Culture Change and Productivity - Kirstie Whitaker (Alan Turing Institute), John Hammersley (Overleaf), Martin Donnelly (University of Edinburgh), Caroline Jay (University of Manchester), James Baker (University of Sussex) and Neil Chue Hong (Software Sustainability Institute) as Panel Chair.

Panel Q&A: @j_w_baker @kirstie_j @mkdDCC Caroline Jay & @DrHammersley share their experiences and thoughts on #culturechange #Productivity #collabw18

β€” SSI - (@SoftwareSaved) March 26, 2018

{I'm on the panel, so no notes}

17:15 - 17:50 Mini-workshops & demos 1

  • M/0.40 - Using Overleaf for Collaboration by Vincent Knight, Cardiff University.
  • M/0.34 - Making research software easily citable with the Citation File Format by Stephan Druskat, Humboldt-UniversitΓ€t zu Berlin.
  • M/03.3 - JupyterLab play session

Tuesday 27 March 2018 - day 2

10:05 - 10:45 Lightning Talks 2

  • Robin Long: how can we make Python and R speak with the same C code.
  • Alexander Konovalov: GAP maths package .. dream for every mathematician to use version control

Very nice slide and ⚑️talk describing @gap_system packages by @CIRCA_StAndrews's Alexander #collabw18.

"My dream is that all mathematicians learn version control" :)

β€” Vince Knight (@drvinceknight) March 27, 2018
  • Andrew Washbrook: code review and continuous integration can become 'nice to have' very quickly is we are busy .. goal for CI infrastructure in Azure.

#collabw18 Andrew Washbrook: "Do you want code review and continuous integration practices to be an integral part of your software development workflow?"
Anyone??? πŸ™‹πŸ»πŸ˜

β€” π•‹π•’π•Ÿπ•šπ•’ πŸ’€πŸ‘©β€πŸ’»πŸ‡¬πŸ‡§ (@ixek) March 27, 2018
  • Adam Jackson: 'if computers can drive a car, they should be able to use chemistry'
  • James Baker: {me!} Enron email archive, email cultures, finding and teasing out visual code/cues

Aaaaah! This is SUCH A FASCINATING PROJECT trying to understand how people experience their email - how they respond to them and how they flag important points. Faaaaascinating @j_w_baker #collabw18 Get in touch w him if you want to work on the corpus!!

β€” Kirstie Whitaker (@kirstie_j) March 27, 2018
  • Shoaib Sufi

Shoaib Sufi shares integrations between #cwl common workflow language and Research Objects at #CollabW18

β€” yo yehudiπŸ³οΈβ€πŸŒˆπŸ‡ͺπŸ‡Ί (@yoyehudi) March 27, 2018
  • Daniel S. Katz

β€˜Parsl’, a Python-based Parallel Scripting Library
Environment independent (HPC, Local Machine, etc.).
Quite interesting :D#CollabW18

β€” Thibault Clerice (@PonteIneptique) March 27, 2018
<script async src="" charset="utf-8"></script>
  • Rinku Gupta: work on being productive without undermining quality of science. Focus on user stories.
  • Yo Yehudi: code is science

Come later today to @yoyehudi’s workshop to help to work on the Code Is Science manifesto! #CollabW18

β€” CIRCA St Andrews (@CIRCA_StAndrews) March 27, 2018
  • Diana Suleimenova: 67m displaced people globally .. simulating/predicting refugee movements and visualising them .. consequences of closing borders

#collabw18 πŸ‘πŸΌπŸ‘πŸΌπŸ‘πŸΌ "Simulating refugee movements" because refugee lives matter. Great work from Diana Suleimenova

β€” π•‹π•’π•Ÿπ•šπ•’ πŸ’€πŸ‘©β€πŸ’»πŸ‡¬πŸ‡§ (@ixek) March 27, 2018
  • Sam Cox: survey of RSE users at Leicester .. very popular is not using version control at all

10:45 - 11:05 Sponsored talk: Are we interoperable yet? - Adrian-Tudor Panescu, figshare

Discussion of interoperability often leads to a discussion of whether we need a new standard.. (which of course we don't want)

Far, far too many meta data standards, and yet, they never have the field I need most (at any given moment) #collabw18

β€” M. H. Beⓐls (@mhbeals) March 27, 2018

Let's create a new standard @adrop That reminds me πŸ‘‡#CollabW18

β€” DVD (@DVDGC13) March 27, 2018

Brain exploded: gives you a super short link to your DOI! Great for adding to slides etc so people can find your work easily! #CollabW18 Here's the short one from my slides yesterday:

β€” Kirstie Whitaker (@kirstie_j) March 27, 2018

.@adrop Asking suppliers whether they support a non-proprietary standard/interface helps interoperability by making them think about it #Collabw18

β€” Neil P Chue Hong (@npch) March 27, 2018

Interoperability is not nice to have it needs to be there at the start ..

13:45 - 14:30 Sustainability Perspectives: talks by Daniel S. Katz (University of Illinois Urbana-Champaign), Naomi Penfold (eLife) and Matthew Upson.

Daniel Katz

Loving @danielskatz's image of mapping the @WSSSPE working groups on to his digram of home research software engineering works! #collabw18 - I think it's all covered! πŸ˜†

β€” yo yehudiπŸ³οΈβ€πŸŒˆπŸ‡ͺπŸ‡Ί (@yoyehudi) March 27, 2018

How to make the case for a US SSI when the pot from which researchers draw will be (a little) smaller as a result .. ethnographic studies + survey to figure out what people need .. Developing a pathway to research software sustainability

Naomi Penfold - Sustainability in Research Publishing

Eek, how to squeeze too many thoughts into 10 minutes for today's #collabw18 panel on sustainability @softwaresaved... talk fast or skip a section? Probably the latter.

Slides CC-BY
View speaker notes at

β€” Naomi Penfold (@npscience) March 27, 2018

Way to validate datasets

.@npscience: 3/4 of data tables provided by researchers will have errors when they are validated by a machine - e.g. missing rows, bad column headers. How can we make things human readable AND machine readable without forcing people to data-wrangle too much? #CollabW18

β€” yo yehudiπŸ³οΈβ€πŸŒˆπŸ‡ͺπŸ‡Ί (@yoyehudi) March 27, 2018

Pumped to hear about @npscience 's vision re sustainable research. A human readable spreadsheet is not the same as a machine readable spreadsheet! #CollabW18

β€” Alexander Morley (@alex__morley) March 27, 2018

Including code and data in article XML .. forking GitHub repos as a snapshot of code at time of publication ..

.@npscience "How do we archive research code right now?" @eLife manages this by forking repos at time of publication. This doesn't fix everything but is a great start! People want to download, re-use, and discover software via papers. Many requirements here! #CollabW18

β€” yo yehudiπŸ³οΈβ€πŸŒˆπŸ‡ͺπŸ‡Ί (@yoyehudi) March 27, 2018

####Β Matthew Upson

Sustainability is social! Reproducibility is technical.

@m_a_upson hits the nail on the head at #collabw18:

β€œ#reproducibility is technical. Sustainability is social. We need the right people who can enact the principles.”

β€” eLife Innovation (@eLifeInnovation) March 27, 2018

14:40 - 15:15 Mini-workshops & demos 2

  • M/0.40 - Code is Science - open source scientific code manifesto by Yo Yehudi, University of Cambridge.
  • M/0.34 - Python testing with pytest by Matt Williams, University of Bristol.
  • M/0.33 - The Software Engineering Initiative of the German Aerospace Center by Carina Haupt, German Aerospace Center and Tobias Schlauch, German Aerospace Center.

15:15 - 15:50 Mini-workshops & demos 3

  • M/0.40 - A Registry for Research Software Repositories by Alexander Struck, Humboldt-Universitaet zu Berlin. 0 M/0.33 - Building Effective, Sustainable, Research Software Communities by Jeremy Cohent, Imperial College London.

16:10 - 16:55 Panel Q&A on sustainable software practice - Daniel S. Katz (University of Illinois Urbana-Champaign), Alys Brett (Culham Centre for Fusion Energy), Carina Haupt (German Aerospace Center), Louise Brown (University of Nottingham), Joseph Parker (Science and Technology Facilities Council) and Neil Chue Hong (Software Sustainability Institute) as Panel Chair.

Modernisation process: how do you get people from methods that worked once to best practice now .. doing things well is about the little things not going for the holy grail .. software citation, customise the guidance for domains ..

Panel discussion! Really happy with how diverse #collabw18 is, especially for a software engineering conference

β€” Toaster (@T2Toaster) March 27, 2018

@danielskatz has great suggestion for improving software practises: go to domain specific conferences and engage directly #CollabW18

β€” Naomi Penfold (@npscience) March 27, 2018

.. strategic choice of adoption platforms that RSEs support can ensure good practice is instigated and deepened ..

Thanks @npch for asking the tough questions: how do we measure success when we attempt to improve practises? #collabw18

β€” Naomi Penfold (@npscience) March 27, 2018

.. encouraging version control can be a good way of removing fear some people have of changing their code ..

Even if people are reluctant to learn things like version control, once people _do_ use it, they'll usually say they feel safer modifying things without fearing they'd lose it. #collabw18

β€” yo yehudiπŸ³οΈβ€πŸŒˆπŸ‡ͺπŸ‡Ί (@yoyehudi) March 27, 2018

.. who enforces sustainability? who persuades the recalcitrant? .. only help someone fix their code by putting it in Git/GitHub, adding in tests, then giving it back to them via a GitHub link ..

"Actually talk to your users" - @danielskatz πŸ˜† #CollabW18

β€” yo yehudiπŸ³οΈβ€πŸŒˆπŸ‡ͺπŸ‡Ί (@yoyehudi) March 27, 2018

@npch @SoftwareSaved trying to summarise two days of great work #CollabW18 New themes: interoperability & human-centre. People are important

β€” Catherine Jones (@CM_J0nes) March 27, 2018

Some admin...

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