# Week 16: Group 3 ###### tags: `OLS-2` `cohort calls` `project-leads` :earth_asia: Cohort call --- **Syllabus** : [https://openlifesci.org/ols-2/schedule/#week-16](https://openlifesci.org/ols-2/schedule/#week-16) **Looking for other Graduation notes? see here:** https://hackmd.io/@ols-2/week-16 * Slot 1: 15 December, Tuesday - 09:00 - 10:00 AM UTC * [Notes](https://hackmd.io/@ols-2/week-16-gr1) * [In your timezone](https://hackmd.io/iBhjjBnxTzGTqqzMws6-gg?both) * Slot 2: 16 December, Wednesday - 14:00 - 15:00 UTC * [Notes](https://hackmd.io/@ols-2/week-16-gr2) * [In your timezone](https://arewemeetingyet.com/London/2020-12-16/14:00/week-16-ols-2-grad2) ## **Project Leads: Register by adding your name below** _Name / Project / social handles (twitter, GitHub, etc.) /_[ _emoji mood _](https://emojipedia.org/) 1. Stephen Klusza/Synthetic Biology Chassis for Public Domain Use/t: @codebiologist/ 🐟 2. Pradeep Eranti (he/him)/ Open platform for Indian Bioinformatics community / t: @pradeeperanti 3. Georgia Aitkenhead (she/her) with James Scott/ Autistica/Turing citizen science project/GeorgiaHCA 4. Beatriz Serrano-Solano (she/her) / Growing the Galaxy Community / t: @Birthae gh: beatrizserrano 5. Karega Pauline / The-Hub-Portal/ t:@KaregaP /gh: @karegapauline 6. Neha Moopen + Paul Owoicho / Embedding Accessibility in The Turing Way Open Source Community Guidance / NM t: @NehaMoopen, gh: @nehamoopen + PO t: @ogbonokopaul, gh: paulowoicho 7. Sangram Keshari Sahu / Practical Guide to Reproducibility in Bioinformatics / gh: @sk-sahu 8. The OSUM team / Open Science UMontreal / @OSUMontreal /[ openscience](https://openscience.ca/) 9. TainĂĄ Rocha / Global land-use and land-cover (LULC) data under historical, current, and future climatic conditions for ecologists /github (Tai-Rocha) twitter (@Tai_Rocha_). 10. Sebastian Eggert /[ OpenWorkstation](https://github.com/SebastianEggert/OpenWorkstation) - Empowering Bench Scientists to Develop Customizable and Accessible Lab Automation ### **Guests, colleagues, and friends of OLS** _Name / Project / social handles (twitter, GitHub, etc.) /_[ _emoji mood _](https://emojipedia.org/) * Sarah Gibson / The Alan Turing Institute / t: @drsarahlgibson, gh: @sgibson91 / :D * Lena Karvovskaya @langdata 👏 * Yvan Le Bras / French museum of natural history / PNDB french biodiversity e-infrastructure / @Yvan2935 * Samuel Guay * Renato Alves / EMBL Bio-IT / t:@renato_alvs gh:@unode * Hans-Rudolf Hotz / Friedrich Miescher Institute / @hrhotz * Piv Gopalasingam / EMBL-EBI / t:@cascade21, gh:@PivG * Jez Cope / The British Library / @jezcope * Stephen Klusza/Synthetic Biology Chassis for Open Domain Use/t: @codebiologist * David Opoku / Growing Gold Farms / @sdopoku * Meag Doherty / _AllofUs_ Research Program / t: @emdohh :wave: Welcome --- **Hosts**: BĂ©rĂ©nice, Malvika, Yo, Emmy * Please note that this call will be streamed on the OLS[ YouTube channel](https://www.youtube.com/openlifesci) * Turn on your webcam if you don’t mind sharing your face (or off if you do!) **Icebreaker question**: What was your favourite pastime when you were 1o, and is it something you still do? * _Name / answer_ * Yo / reading / and YES, READING 4 EVA 📚📚📚📚📚 +1 * +1000000 * yesss! * Malvika / sketching I still do it sometimes! * Lena/reading books - I still do it but much much less :-( * Renato / doing weird ramps to then jump over with a MTX bike * Georgia / making up weird languages with my sister usually involving animal symbols - yep, still do it! 🐑 * Ahh! That’s true! * Paul / Playing video games + watching cartoons. I still do it! +1(piv) * Stephen / read lots of fiction books/now I read pseudoscience papers for fiction * Neha / probably just reading :) I struggle to keep up with books nowadays, but generally reading is <3 +1(lena) +1(piv) * Sebastian / skiing * Piv / building stuff with lego. I don’t do it anymore, but hopefully this holiday I’ll be able to pick it up again. * Martina / reading / yes! ## **đŸ–„ Project Presentations** Emmy (⏰ 3 min) Presenters will add their info in the following format 1. Stephen Klusza/Synthetic Biology Chassis for Public Domain Use/t: @codebiologist/ 🐟 * Links * Slides - [https://docs.google.com/presentation/d/1Q-NmuDVi6RindwwTCWmLhhQPPE4JEuZ1sBvxOQvKekk/edit?usp=sharing](https://docs.google.com/presentation/d/1Q-NmuDVi6RindwwTCWmLhhQPPE4JEuZ1sBvxOQvKekk/edit?usp=sharing) * Where can others help? * Questions / Comments from the audience? * Wow, what a well-explained intro! I feel like I genuinely understand synthetic biology better as the intro was so approachable. * Stephen - Thank you for the kind words! * love the analogy between smart phones and bacteria * Very happy that this analogy resonated for you! * I love that synbio and plasmid repositories have a possibility of involving more people (particularly non-traditional “scientists”) into research - but there are also concerns that they may be used for malicious intent
. I wonder what your thoughts are on this? * Stephen: Excellent question. The work in this project will be place with Open MTA license which makes these reagents freely available with underlying conditions including using only for the benefit for humanity. That in itself is not enough but fortunately if you want to build new parts, you need to clone the gene or get it synthesized. Any sequences sent to reputable companies are screened to ensure that the products will not create harmful reagents. It’s still not 100% effective, but it makes it very difficult to do so under the present circumstances. I hope this helps answer your question! * Thank you Stephen - yes! It’s good to know that there are some screening steps in place. I guess every coin has two sides, it’s better to open it up and learn and adjust - great work! * Questions / Comment 2. Pradeep Eranti (he/him)/ Open platform for Indian Bioinformatics community / t: [@pradeeperanti](https://twitter.com/pradeeperanti) * Links: * Until January’21, please follow the updates here: [https://github.com/open-life-science/ols-2/issues/86](https://github.com/open-life-science/ols-2/issues/86) or DM me on Twitter [@pradeeperanti](https://twitter.com/pradeeperanti) * Where can others help? * Questions / Comments from the audience? * I love that you rose to the challenge when faced with the difficulties from covid, and that you created a community survey to really understand stakeholders! 70 respondents is AMAZING too! * Pradeep: Thank you! * Great idea, I love seeing these kinds of initiatives! Have you connected with APBioNet? They may have contacts you can link with. * Pradeep: I am planning to connect with them soon as soon as the website is ready. * This is such a valuable dataset! Esp that you have respondents from different regions of India too +1+1 * Can’t wait to see the website in 2021!!!! 🙌🙌🙌 * Thanks for the interest, I shall update the community once it is ready. 3. Georgia Aitkenhead (she/her)/ Autistica/Turing citizen science project/GeorgiaHCA * Links * Slides: [https://doi.org/10.5281/zenodo.4339655](https://doi.org/10.5281/zenodo.4339655) * Repo: [https://bit.ly/AutisticaTuringCitSciForm](https://bit.ly/AutisticaTuringCitSciForm) * Email me: gaitkenhead@turing.ac.uk * Where can others help? * All kind of ways (tech skills or non-tech) - follow this link: https://github.com/alan-turing-institute/AutisticaCitizenScience/tree/master/get-involved * Questions / Comments from the audience? * Hearing about all of the hands-on citizen involvement is amazing * Yay hidden REF! * Such clever collab w/ hidden REF - and “Lived experience” is such an important, under-acknowledged category of contributors * Questions / Comment * SO HAPPY to hear you onboarded a contributor!! * Thank you! There were actually a few new contributors who had different interests, it was good to have a clear visual. * I would LOVE to learn how you build such a participatory project in terms of processes, managing group dynamics and expectations. +1(piv) * Thanks! There’s a whole lot of complexity to this - but definitely being prepared to listen is important, and respect difference. Actually there’s a lot of info about this on the repository as all the study protocols are openly available there, 4. Beatriz Serrano-Solano (she/her) / Growing the Galaxy Community / t: @Birthae gh: beatrizserrano * Links * [Slides](https://docs.google.com/presentation/d/19NOEKTW7Z6XslPlGKzjzToZvtuyu01GM_r0XDsUvSFE/edit#slide=id.g9f278485e2_1_20) * [Galaxy Community Hub](https://galaxyproject.org/) * [Galaxy Project EU](https://galaxyproject.eu/) * Where can others help? * [Join our events!](https://galaxyproject.org/events/) * Questions / Comments from the audience? * Really happy to see the Galaxy community evolving and growing and super glad to see it’s in great hands, Bea * It’s great to see how you went in as a new community manager and take the existing initiatives further and with your own spin :) +1 * “Paper cuts” is such a great clear name!+1(piv) * 5. Karega Pauline / The-Hub-Portal/ t:@KaregaP /gh: @karegapauline * Links: [bioinformatics-hub-ke/The-Hub-Portal: A collaboration and data sharing platform for Universities in Kenya (github.com)](https://github.com/bioinformatics-hub-ke/The-Hub-Portal) * Where can others help? Contribute as much resources as they can, interactive coding platforms, books for beginners to advanced programmers (all languages) * Questions / Comments from the audience? * SUPER happy to see extensions of OLS-1 projects!!! 😍😍😍😍 * Great to hear about the hands-on skills and links you’ve assembled, and SO happy to hear about your experiences with GitHub :) * The hub portal sounds so useful, this is great!! * +1 sounds amazing! 6. Neha Moopen + Paul Owoicho / Embedding Accessibility in The Turing Way Open Source Community Guidance / NM t: @NehaMoopen, gh: @nehamoopen + PO t: @ogbonokopaul, gh: paulowoicho * Links: * A detailed report of the work we did can be found here: [https://github.com/alan-turing-institute/the-turing-way/blob/master/communications/GSOD-applications/GSoD-2020-Project-Report.md](https://github.com/alan-turing-institute/the-turing-way/blob/master/communications/GSOD-applications/GSoD-2020-Project-Report.md) * Our slides live on Canva: [https://www.canva.com/design/DAEJBw2dyKE/68IaWGeVTSxUd_CfysJR_Q/view?utm_content=DAEJBw2dyKE&utm_campaign=designshare&utm_medium=link&utm_source=sharebutton](https://www.canva.com/design/DAEJBw2dyKE/68IaWGeVTSxUd_CfysJR_Q/view?utm_content=DAEJBw2dyKE&utm_campaign=designshare&utm_medium=link&utm_source=sharebutton) * Where can others help? * Please come contribute chapters, personal stories, case studies or just fix bugs! There are lots of good first issues as well if you are looking make your first (or just an ‘easy’) PR. * Project Repository: [https://github.com/alan-turing-institute/the-turing-way](https://github.com/alan-turing-institute/the-turing-way) * Questions / Comments from the audience? * 💜💜💜 Enhancing accessibility, so important, so often ignored. LOVE IT! +1 * Thanks for highlighting the importance of consistency and link with accessibility +1 * Love the lessons learned slides. Really nice tips to bear in mind for similar endeavours, thank you for sharing! +1 * Loving to hear about the challenges keeping up with different time commitments - it’s good to know that these can be a challenge but that it can be worked around. * 7. Sangram Keshari Sahu / Practical Guide to Reproducibility in Bioinformatics / gh: @sk-sahu * Links [https://github.com/sk-sahu/PGRB](https://github.com/sk-sahu/PGRB) * Where can others help? [https://github.com/sk-sahu/PGRB](https://github.com/sk-sahu/PGRB) * Questions / Comments from the audience? * I was telling my mum about the reproducibility crisis in biology, i’m DEFINITELY going to tell her there are projects like yours trying to fix it!! * Great progress!! Also lovely to see that you’ll be cross-referencing existing material - but still build this for your local community * Questions / Comment 8. The OSUM team / Open Science UMontreal / @OSUMontreal /[ openscience](https://osumontreal.github.io) * [https://osumontreal.github.io/](https://osumontreal.github.io/) soon-to be [https://openscience.ca/](https://openscience.ca/) * Where can others help? * Get in touch [info@openscience.ca](mailto:info@openscience.ca) or join us on matrix [https://chat.openscience.ca](https://chat.openscience.ca) * Questions / Comments from the audience? * Making resources available in many languages is so important and French is such a huge one - so happy to see this! +1 * It just struck my how many open science terminology (at least to my small sphere of knowledge) are English based - e.g. FAIR, how would that look in French? 1. Facilement trouvable - Accessible - InteropĂ©rable - RĂ©utilisable ;) 1. We mostly try to match acronym most of the time. 2. But tbh, many words are hard to define and often add another layer of abstraction... * Maybe someone can launch OLS-francophone one day (and portuguese and spanish?!) +1+1 2. Let’s launch the MOLS, Multilingual OLS. 3. MultilinguOLS +1 * Questions / Comment 9. TainĂĄ Rocha / Global land-use and land-cover (LULC) data under historical, current, and future climatic conditions for ecologists /github (Tai-Rocha) twitter (@Tai_Rocha_). * Links * Where can others help? * Questions / Comments from the audience? * This looks like incredibly important work! I would love to see more non-specialists access and make use of this work! * Optimising scripts: it’s one of those tasks I think you can always do more and is hard to say “it’s done” - good luck! +100 * This is incredibly important for everyone to see and access this data. Excellent job! * Such impressive and important work for the world, you’ve amazed me with how much one person can achieve * 10. Sebastian Eggert /[ OpenWorkstation](https://github.com/SebastianEggert/OpenWorkstation) - Empowering Bench Scientists to Develop Customizable and Accessible Lab Automation * Links * Where can others help? * Questions / Comments from the audience? * Who’d have thought that science can be boring hands-on labour ;) yay for high throughput machines! * I kind of missed the hands-on manual downtime
. But rather irreproducible ): I love how you’ve taken the problem on your own hands! * Questions / Comment * Science wasn’t doing what I needed
 so I built my own platform YESSSSSSSSSS đŸ’ȘđŸ’ȘđŸ’Ș * So cool, the stuff of sci-fi! * “Democratize access to laboratory automation”!!! +100 * Just looked at your GH repo- WOW the clarity of that documentation, thank youuuu for building and sharing all this knowledge * Users are not devs - important realisation but I bet it can take time! * This looks like an amazing resource - def useful to me to check out your GitHub :) ## **đŸ—Łïž Closing** **Feedback** _What worked?_ * * _What didn’t work?_ * * _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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Lens Protocol Subgraph - Manual Testing (SG HACKATHON)

Resources: Hosted Service: https://thegraph.com/hosted-service/subgraph/mike-data-nexus/lens-sg-hack This covers contract that emit events for the Lens Protocol Tests Test 1 ✅ User Account

4/28/2023
TU-Delft celebrates a year of Open Science Course: Share your research with the world

Project background The Delft University of Technology (TU Delft) in the Netherlands runs once a year a Massive Online Open Course (MOOC) on Open Science on the edX platform => Open Science: Share your research with the world. Our primary target is PhD candidates but the MOOC is meant also for MSc students, researchers, support staff, policy makers that want to learn the basic principles of and motivations behind Open Science. The OSMOOC has been running for multiple years with a decreasing number of enrollments and varying levels of engagement. We have high dropout rates and we do not know if the participants practice Open Science later on. Our project goal was to improve the engagement by creating a community around the MOOC participants. _Figure1: _Logo of the Open Science MOOC and titles of the six modules contained in the course. Image by TU Delft and licensed under CC-BY-NC-SA 4.0 International License. Expectations from this program Since we had both just started in our jobs as open science teachers, the first thing we hoped to learn was more about the different themes within Open Science. We also hoped that through our participation in the OLS program, we would learn more ways to engage our MOOC’s participants and build a solid community, as well as workflows and processes to make our own work more open.

7/18/2022
Speed Blog: Project name, team members

THIS PAGE IS OBSOLETE. NOTES MOVED TO: https://github.com/open-life-science/policies-procedures-and-docs/blob/main/cohort-procedures-and-templates/speedblog.md ==This document provides guidance for you to summarize your OLS journey so far and the project you worked on during the entire period of OLS-2 in a speedblog. Please draft your speedblog in your 'mentor-mentee hackMD notes' and share with the OLS team.== Ideally your speed blog will be a written piece with a picture (max 2) and contain some links and references. In terms of word count you are aiming for between 500 and 1200 words. We will post your speedblog on OLS website: openlifesci.org/posts See this post for guidance on speed blogging: https://software.ac.uk/speed-blogging-and-tips-writing-speed-blog-post Example you can draw from: https://openlifesci.org/posts/2019/10/21/culture-track Here are a few questions to help you generate ideas and content for your speedblog:

6/1/2022
Week 10

:earth_asia: Cohort call Schedule: Open Science III: Next steps - applying FAIR research principles Date and time: 05 November 2020, 09:00 - 10:30 LONDON, Duration: 90 minutes Video on YouTube :house: Before this meeting After this meeting: Think about and plan to apply FAIR principles to your project in your own time. Resources for more information have been linked in the notes.

3/9/2021
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