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Week 4

tags: OLS-2 cohort calls project-leads

Before this meeting:

  • Look up two other projects and comment on their GitHub issues with feedback on their open canvas.
  • Rework on your vision statement
    • Write your vision in the Up-Goer 5 editor
    • Refine it with the editor's help
    • Paste it in your GitHub issue
    • Read it to the Breakout room friends during the next call and hear their feedback :)
    • Other possibility: Hemingway Editor

Resources : Opening Your Project

Table of contents

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Cohort call

Call time:24 September 2020, 16:30 - 18:00 UTC

Hosts: Malvika, Bérénice, Yo

Syllabus: OLS-2 Week-4

Video recording of this call

  • Please note that this call will be recorded
  • The video will be available on the YouTube channel in the next few days
  • Turn on your webcam if you don't mind being in the video (or off if you do!)

This week

During our second cohort call, we will:

  • Look at project structure as we build open projects
  • Go over the standard files in open projects: README, LICENSE, CODE_OF_CONDUCT.md, CONTRIBUTING.md The exact project structure and files used may look different on your project.

Roll call

  • Name / Project / social handles (twitter, GitHub, etc.) / emoji mood
  • Malvika / OLS Team / t+gh: malvikasharan
  • Yo / OLS Team / t: yoyehudi g: yochannah
  • Danny Garside / Registered Reports in Primate Neurophysiology / t+gh: da5nsy
  • Bailey Harrington / Chronic Learning / baileythegreen
  • Sangram Keshari Sahu / Reproducibility in Bioinformatics / @sk-sahu @sangram_ksahu
  • Karega Pauline/ The Hub Portal / Twitter: @KaregaP Github:@karegapauline
  • Emma Karoune/ open science in phytolith research
  • Sophia Batchelor / The Turing Way - Ethical Research / @brainonsilicon
  • Samuel Burke / OSUM / twitter: @kernow_qc
  • David Beavan / The Alan Turing Institute / @DavidBeavan
  • Emmy Tsang / OLS friend + fan
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    / t: emmy_ft g: emmyft /
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  • Georgia Aitkenhead / Autistica-Turing Citizen Science /GeorgiaHCA/ 🌻
  • Holger Dinkel / OLS mentor / / aaaaaaaaaaaaaaaaaa
  • Andréanne Proulx/ OSUM/ University of Montreal / Twitter :@AndreanneProulx, Github : anproulx
  • Neha Moopen / Utrecht University Library / Twitter: @NehaMoopen, GitHub: @nehamoopen
  • Mateusz Kuzak / will talk about READMEs / t:@matkuzak
  • Paul Owoicho / The Turing Way Project / Github @paulowoicho
  • Ismael Kherroubi Garcia / The Turing Way - Ethical Research / @IsmaelKherGar
  • Kendra Oudyk / Open Science Office Hours / Twitter: @koudyk_ Github: koudyk / -Ekeoma festus ⛈️
  • Joyce Kao / Open Innovation in Life Sciences/ Twitter: @joyceykao, @openlifescience
  • (Chris)Tina Ambrosi / Open Innovation in Life Sciences / twitter @openlifescience / ⛈️
  • Pradeep Eranti / @pradeeperanti / ⛈️
  • jjd
  • Dave Clements / Galaxy Project
  • Laura Carter / The Turing Way - Ethical Research / tw: @LauraC_rter gh: LauraCarter /
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  • Ekeoma Festus/open life sciences/mentee
  • Lilly Winfree / Open Knowledge Foundation + Frictionless Data / @lilscientista 😶
  • Teresa Laguna / Science4All / twitter: @teresa__laguna / github: @tlaguna /
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  • Stephen Klusza/Public Domain SynBio Chassis/@codebiologist/🧟
  • Piv Gopalasingam / EMBL-EBI / mentor / github: @PivG / Twitter: Cascade21
  • Markus Löning / sktime project / twitter: @mloning_, GitHub: @mloning /
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  • Kate Simpson/ Retrofit / t: @Dr_KateSimpson g: @KateSimpson 🙂
  • Jez Cope / OLS Mentor / The British Library / @jezcope /
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  • Camila Rangel Smith / Turing Data Stories / The Alan Turing Institutes/ T: @camilarangels
  • Muhammet Celik/ Metagenomic Classification/ Master's student/ i.g: a.muhammetcelik
  • Jelioth Muthoni/OLS mentee/twitter @jelioth
  • Brenda Muthoni / OLS mentee / GitHub @sonibk
  • Harriet Natabona/ OLS mentee/ github: @natty2012
  • Kevin Xu / Turing Data Stories / The Alan Turing Insitute / T: @kevinxufs
  • Eva Herbst / FE (Finite Element Zurich) / Github: @evaherbst / Twitter: @EvaCHerbst

Icebreaker question

How have your first few weeks in OLS-2 been? - share a picture, a word, a gif to express how you are feeling about your role as a project lead and/or team member

Name / answer

  • Malvika Sharan
  • Danny Garside / I've been unwell and so I'm behind and playing catch up!
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  • Bailey – in the middle of running graduate student trainings, so constantly busy
  • Emma 🤓 - learning a lot!
  • Sophia
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    my brain is full and my knowledge is low (which is a good thing because it means I'm learning how much there is to learn)
  • David B 🏖️ <- I've been on two weeks leave, now the hard work starts
  • Samuel Burke / Really good. Helped structure a project which feld chaotic and unclear. Our mentor @renato_alvs has helped puts thing into context.
  • Yo - 👩‍💻👨‍💻💻👨‍💻💻👨‍💻💻👨‍💻💻👨‍💻💻👨‍💻<3
  • Joyce / I'm exhausted, but ready to go. How do you put in a link?!
    • It's square brackets followed by circular brackets, like this: link to website
  • Tina - overwhelmed but getting there
  • Neha - omg what even is happening + omg super duper excited
  • Paul - Very excited :D
  • Laura - excited, but also worried about keeping up as we head into a new uni term…
  • Pauline - joyfully overwhelmed
  • Sangram
  • Pradeep -
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    between graduate responsibilities and
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    recovering! … Excited to catch up on the work and learn from you all
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  • Ismael Really pleased I'm in a group and not trying to do this on my own!
  • Teresa Incredibly busy but glad to progress even with small steps
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  • Kate Inspired and reassured by the friendly community, though struggling a little with time.
  • Stephen Overwhelmed but happy to be working on projects that will bring positive change to the world 🙀
  • Piv Getting into the swing of it, learning a little every week! I'm not in the UK this week, dialing in from France!
  • Georgia Learning fun new things!
  • Kendra. My thoughts on being a 'leader' and starting something new…
  • Harriet. making slow steady steps; very excited about this :-)
  • Eva. A bit overwhelmed juggling this with my research but also energized to learn so many new things.
  • Jelioth. exited and looking forward to be an OLS ambassador
  • Tainá: too much things at same time

👋 Welcome!

Host (⏰ 2 min)

⚡️Introductions

Moderated by Host: (⏰ 8 min) 10

Anyone new in this week? What's your name, location & project name (30 seconds)

Name / Location / Project name

  • Danny / Washington DC / Registered Reports in Primate Neurophysiology
  • Neha / Utrecht / Embedding Accessibility in the Turing Way Open Source Community Guidance
  • Paul / Glasgow / Embedding Accessibility in the Turing Way Open Source Community Guidance
  • David B / London / The Alan Turing Institute / Research Engineering / Turing Data Stories project, with others here, Camila, Kevin and Sam VS-
  • Joyce / Zurich / Open Innovation in Life Sciences (OILS)
  • Christina / Zurich / OILS
  • Samuel Burke / Montreal / OSUM [Open Science UMontreal]
  • Stephen Klusza/Atlanta Georgia/A Synthetic Biology Chassis for Public Domain Use
  • Andréanne Proulx/ Montreal / OSUM
  • Kendra Oudyk / Montreal / open science office hours
  • Bakary N'tiji Diallo / South Africa/Mali / medical record system
  • Eva Herbst / Zurich / online workflow for mode
  • Ekeoma Festus / South Africa / H3BioNet - precision medicine
  • Taina / Rio de Jeneiro / Biodiversity related tools

🏗 Building for Open

Host: (⏰ 10 min) 20

👥 Break-out room (10 minutes, ~3 ppl per room)

  • Think of a time you were collaborating or working on an open project and it was a complete trainwreck. What happened? What made it chaotic?
  • Think of a time you were collaborating or working on an open project and everything was perfect. What happened? What made it sublime?

✏️ Any insights/thoughts/comments to share from your breakout room?

Breakout room 1 (Boi, Christina, Ismael, Piv)

  • Discussed culture change within teams and organizations relating to open science.
    • Taking the temperature of your team/organization's values before/while imposing values from the top-down.

Breakout room 2 (Mateusz, Camila, Teresa)

Keys to succeed in collaboration:

  • Communication
  • Documentation

Breakout room 5 (Neha, Brenda, Sangram)

  • Many contributors work on a voluntary basis, so this means people come and go depending on their availability. This can create some ambiguity in the project.
  • Considering the above, it's good to think about how you can ensure your project remains sustainable with contributors coming and going.
  • Another thing to keep in mind is lowering the threshold for people to make contributions. For example, the Collaboration Cafes or sprints. The community should be involved in deciding what works best for them to work together.

Break out room 3 (Kate and Harriet)

Nega

  • Public wiki – lots of challenges with bringing together data. Solved with lost of meetings
  • Project with people in a new area and social challenges – people not sharing information

Positive:

  • Outreach – social relations were co-operative, school was receptive
  • The Turing Way collaboration cafe was truly welcoming!

Break out room 6(?) (Ekeoma, Bakary, Joyce)

  • common misconception of OS is that it is a binary state (either you have to be completely open or closed), which can prevent people from doing OS

Break out room 8(?) (Emma Karoune, Laura Carter and Danny Garside)

Where open projects have gone poorly:

  • when people don't do stuff
  • when people don't do stuff and don't tell you about it
  • when projects stagnate

Where things have gone well ('perfectly'):

  • example of Turing Way - spending so much time on meta-project management.
  • having a good mentor

Break out room 11 (non-verbal)

  • Markus: I've not worked on too many open projects so far and luckily none of them has been a complete train wreck. One issue has been to correclty identify what the problem is in some situations. I think we have sometimes spent some time trying to solve a problem through lots of technical discussion when we needed to agree and make a more principled decision as a group.
  • Bailey – Most projects I've worked on have been as part of a degree, so not exactly open or closed…
  • nice, what exactly do you do in forensics? - nothing; I'm in genetics now, but kind of drifting more into the programming/computer science side - yes, but what is forensics about :) ? Just our of curiosity, I always hear that word anever really know what it involves
  • Ah. Forensic science is the application of science to law, or the crossover between the two. So, you can have forensic any science, if that science relates to a legal matter, but some fields come up more or have actual established forensic practices. - alright thanks :) we're beeing zoomed back

Breakout Room 12 (non-verbal)

  • -ves: no co-ordination, bad communications, not listening to collaborators, no clear instructions for new peoplennnnn
  • +ves: responsibilities, skills matching, 'reading' the community and being flexible as a leader
  • interesting point that came out: Is it possible to be 'too open'? If there's no clear leadership, then the project can go in too many directions and become chaotic. But having a leader making decisions makes the project less open.

Breakout Room 13 (no-verbal)

Complete trainwreck stories

  • Georgia I had a really difficult time reconciling corporate workflows with open source. I had lots of (what I thought were) great ideas, but I didn't do enough to communicate them properly or bring them on board. 😑 It was sooo sloooow.
  • Sometimes it's important to accept not everyone in the community will want to use the same platforms as you, e.g. GitHub puts lots of people off.
  • Tainá: Many times I worked with colaborators in article text and without any version control editor (because they don't know how to use this). So everytime the text was very confuse… and we got lost, it was chaotic.
  • Paul I have not collaborated a lot on open source projects but from my experience working with others, I find that the most successful projects I have worked on are the ones with a clearly defined goal and enthusiastic team members. Without a clear goal, projects can last "forever". Without enthusiastic team members, few things would get done.

Perfection stories

  • Georgia I've worked with people from a foundation who specialise in data agency and transparency. It makes such a difference working with people who are value aligned!
  • Georgia When GitHub angels appear and debug, fix links, and just help!
  • Tainá: I don't have this experience
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  • Paul The biggest thing for me is having a clear goal to work towards, with defined ways of making contributions. Oh and enthusiastic team members.
  • Jelioth, setting goals and deligations of duties, have hepled in building perfect stories

💡 Project Structure

Open projects are never completely a trainwreck or completely sublime. We'll be going over best practices to structure your project to help set it up to be more sublime.

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Host(⏰ 2 min) 20

Here are four standard files in open projects:

  1. LICENSE
  2. README.md
  3. CONTRIBUTING.md
  4. CODE_OF_CONDUCT.md

We will go over each of these files and best practices for putting them together. Your project may not have this exact structure but should include this information.

🖥 LICENSE

Host:
Christine Rogers (⏰ 10 min) 30

Notes

  • Christine works on LORIS data base: reach her on twitter :)
  • Licensing - it gives you the power to govern how others can reuse your work!
    • copyleft: others need to share derivatives with compatible licenses
    • patent clause:clause preventing peoepl from using patent laws to take away opensource rights
  • how to apply a license: LICENSE, LICENSE.txt (or.md) can be created on GitHub that will prompt you to choose license from a set of predefined ones:
    • For example, use MIT for open source software and codes and CC-BY (and its equivalent) for text resources
    • choosealicense.com to help pick your software license!

Questions / Comments / your own tips for picking a license? (silent GDoc-ing and +1ing)

  • What is the difference between non-copyleft and copyright? (M)
    • copyright generally isn'y open, whereas non-copyleft is still open, but unlike copyleft, allows proprietry (Closed) use. So Copyright = closed, copyleft = must be open and stay open, non copyleft (aka permissive) starts open but can be taken closed if wished. non-copyleft is the most flexible.
  • Is there a technical difference between open source and public domain? Is Public domain synonymous with non-copyleft?
    • Yo: I think there are technical differences although I don't know them offhand - I do know that CC0 is public domain and isn't considered open source. It might simply be that the open source definition is strict and public domain doesn't comply.
  • If a commercial project uses a copyleft toolbox (for example) do they then need to make their entire project open? (presumably not). Presumably if they build on that toolbox then they would need to release that part back into the wild, right?
    • usually they do - this is why people can be reluctant to use copyleft licences, and is why copyleft are sometimes unkindly known as "viral" licences. It's complicated
  • if we're doing a survey to assess the need for our project, do we need ethics approval? would we be able to openly share results from that data without ethics approval?
    • Yo - if it's research, and if you're based at a university, we'd strongly advice approaching your ethics board and checking if you need to run something through ethics. For small surveys, it might be fine, especially if things are anonymous. Whether or not at a university, be thoughtful about how you gather, share, and use data - and make sure people know how their data will be used before you gather the data - e.g. add a notice "this will be shared publicly" or a checkbox to allow people to opt out of shating.

🖥 README

Expert: Mateusz Kuzak (⏰ 10min)

Notes

  • It's a great reminder that this is a common place to find all the major resource links for the project
  • Use badges (CI, DOI, etc)
  • Make it easy to navigate so people can identify what they are looking for
  • Link your license and Code of Conduct

Questions / Comments?

✏️ What are your License and README related reflections and tips? (silent GDoc-ing and +1ing)

  • README: emojis. use them.
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    +1

👥 Breakout Rooms

Host:
(⏰ 5 minutes, 2 ppl per room)

  • Share your vision statement after modification with upgoer 5
  • What do you think about this exercise?

Any insights/thoughts/comments to share from your breakout room?

  • We were discussing in room 2 that Upgoer5 is not ideal to reflect a good vision statement, but it's good to have an idea wether you can simplify it a little bit.
  • -We were also discussing this in room 7, that even words we thought could replace our jargon were not allowed (e.g. shape, model). I like the concept but I think a bit of a wider range would be more helpful for making our vision statements contain less jargon but still be project specific.

Break out room 5 (Neha, Brenda)

Neha:

Make the book written by so many people more easy to read and also easy add more things to.

Break out room 11

Markus:

UH OH! YOU HAVE USED NON-PERMITTED WORDS (ENABLE, UNDERSTANDABLE, ACCESSIBLE, MACHINE, SERIES, PROVIDING, INSTRUCTIVE, DOCUMENTATION, FRIENDLY, COLLABORATIVE, INCLUSIVE, COMMUNITY, AIM, UNIFY, SERIES, ANALYSIS, PROVIDING, COMMON, FRAMEWORK, MULTIPLE, TASKS, CONTRIBUTORS, ACADEMIA, DATA, SCIENCE, COMMUNITY, JOINT, FRAMEWORK, EMBEDDING, PRACTICES, SERIES, ANALYSIS)

So I basically need to rewrite everything

Bailey

Original version:

I'm working to create a repository of open, accessible educational resources for academics and individuals trying to teach or learn something new, so that the learning curve for new ideas is a manageable one.

Result:

UH OH! YOU HAVE USED NON-PERMITTED WORDS (CREATE, REPOSITORY, ACCESSIBLE, EDUCATIONAL, RESOURCES, ACADEMICS, INDIVIDUALS, TEACH, CURVE, MANAGEABLE)

Modified version:

I'm working to build a database of open, accessible learning materials to make learning something new, easier.

This still has three words that are not in the ten-hundred-most-common words (database, accessible, and materials), and I feel it loses a lot of the information.

  • database -> collection? or just … collect?
    • collection is also not allowed
    • oh dear and simply "I'm working to collect"
  • materials -> resources (probably even rarer than materials …)
    • resources was the original word. materials was the attempt to fix it
    • mh …
    • :sigh: (which is apparently not an emoji)

Andréanne

Original version: Build an inclusive and global community, lowering existing barrier of accessibility by making open and reproducible-related knowledge accessible in French.

UH OH! YOU HAVE USED NON-PERMITTED WORDS (INCLUSIVE, GLOBAL, COMMUNITY, LOWERING, EXISTING, BARRIER, ACCESSIBILITY, REPRODUCIBLE, RELATED, KNOWLEDGE, ACCESSIBLE, FRENCH)

Interesting exercice : the inclusivness of a community also lies in its ability to be understood and reach people. More difficult than expected…lots of words are specific to science jargon

Modified verison: Build a group of people open to all, that helps understand ways of doing open science by building french content (still 3 words - science, french and content)

  • I think this illustrates pretty well that it's not going to be possible to explain many visions in the super-basic terminology allowed by Up Goer Five rules. The language component is key to your project, but I don't think any language would pass this test – English does not.

Break out room 13

  • Tainá:Vision statment after Hemingway editor: There are several Land-use Land-cover (LULC) datasets available for ecological studies. There is large gap of LULC data covering periods along past (older than 1970). Projections of LULC changes into the future is other significant gap. Land-Use Harmonized project (https://luh.umd.edu/) provides LULC data from 850 to 2300. This data is available in NetCDF format, that is not friendly for most ecologists that need this data. I will convert this data and make it available to make it useful.

    • About the Hemingway editor: it seems really good in the first time. But when I used more I noticed that every long sentence is a problem. So I was split all long sentences with a dot and after this everything was ok. But I don't think every long sentence it's a problem. In other kinds of text, if I put just short phrases it sounds strange (for me).

  • Georgia: I came out with this using the restrictive vocabulary editor: "We're working with people who sense the world in different ways to make a place where they can share their stories. This will help us learn and build a better world for everyone." I found it useful, especially because the word "autistic" was forbidden so I had to think carefully about why that was an important category. Also it weeds out overly technical terms quickly

  • Paul I am contributing to a project that already has a vision statement which is along the lines of 'Our vision is to collaborate with members of the data science community to create a handbook that ensures that reproducible data science is "too easy to not do"'. This does not make it through the Up-Goer editor however. This has helped me realise how hard it could be to simplify ideas. After some thiniking, I came up with this 'Our work is to make a book that helps people do work that can be repeated by others.'

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🖥 Contributing Guidelines and Code of Conduct

Host:
Lilly Winfree, connect with her in twitter, info in slide

Notes:

  • Ideally you want to create a community

    • make conscious decision in creating a culture you want to develop in your project - if not it will develop on its not, without matching your project vision
    • How can you build your projects culture?
      • Clear guideline for contribution
      • understand why people are in your community and create a process for them to collaborate with you
    • What is a contribution? Who is a contributor in my project?
      • Contribution can be any support you receive from individuals from within the project team and from community like developing a feature, raising a bug, fixing an errors, sharing ideas, helping others who are new etc.

  • How to create a contribution file:

    • in github, create CONTRIBUTING.md
      • look up example projects and develop on other open access/source contribution guideline
    • You can use CoC in your website

  • Why is it important to have CoC?

    • You project requires you to have diverse community
    • but what if something happens that is not acceptable - CoC can help you set a common norm and tone for your community
      • do we need it? Yes
      • why? it lets people know that they feel safe in your community

  • how to write it?

    • in GitHub you will call is CODE_OF_CONDUCT.md
    • on websites it should be clearly listed
    • it should have acceptable behavior, unaccepted bahviours, what happens if something happens, how can someone report it, who will receive those reports, how will they enforce it?
      • no need to write a CoC from scratch, reuse and adapt existing

  • Questions / Comments?

    • Balancing Thorough with Readable / Likely to be read. (Dave C)

✏️What are your reflections on Contributing Guidelines and Code of Conduct? (silent GDoc-ing and +1ing)

🗣️Closing

Host:

✏️ Assignments for the next weeks:

  • Create a GitHub repository for your project
    • Join us for a GitHub lesson in the week-5 if you are new to GitHub: Details below
  • Add the link to your repository in your OLS-2 issue
  • Use your open canvas from this week to start writing a README, or landing page, for your project
  • Link your README in a comment on your GitHub issue.
  • Choose an open license to add to your repository as a file called LICENSE.md
  • Select a code of conduct and adapt for your project
    • When ready, please add it to your repository as a file called CODE_OF_CONDUCT.md

🗓 Next weeks

Open Q & A time

Is there anything OLS team can support you with? Any questions related to your participation and role you want to mention

  • Teresa How can we adapt a not purely computational project to the Github structure? Especially about Licensing and Readme

🔙 Feedback

What worked?

What didn't work?

  • I personally didn't like the no-talking break-out rooms, for 2 main reasons:
    • The linear Zoom chat isn't ideal for conversations with multiple people; maybe we could use Slack instead.
    • It takes longer to type than to talk, so we didn't have time to cover all the discussion points; it might work better if we had more time or fewer points to cover.

What would you change?

What surprised you?

Reference: Open leadership Framework, Mozilla Open Leaders 6 & 7, Open Life Science 1 License: CC BY 4.0, Open Life Science (OLS-2), 2020

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