# Week 8 ###### tags: `OLS-2` `cohort calls` `project-leads` - Schedule: [**Open Science II: Sharing your open project: Knowledge Dissemination**](https://openlifesci.org/ols-2/schedule#week-08) - Date and time: [22 October 2020, 17:30 - 19:00 LONDON](https://arewemeetingyet.com/London/2020-10-22/17:30/week-8-cohort-call), Duration: 90 minutes - Link to the shared notes: https://hackmd.io/@ols-2/week-08 - Zoom call joining link: https://us02web.zoom.us/j/82819983583?pwd=Wk1MZVRKbkV5eW5WSjVnd29aTXpBQT09 Meeting ID: 828 1998 3583 Passcode: 993801 Find your local number: https://us02web.zoom.us/u/kvD0asfWm 👩‍🔬 Before this meeting --- - Create a project development plan for your project - [Assignment to help you use Agile methods](https://docs.google.com/document/d/1bn4qR9b3XmAYXT8GZK9yI1xI3GE71GBMQ0ySkXtba4o/edit?usp=sharing) to breakdown your milestones into smaller tasks and define a timeline for your milestones - You can transfer your tasks to a project management or kanban tools such as GitHub projects ([short intro](https://unito.io/blog/github-projects-agile/)), [Trello](https://trello.com/templates/project-management), [Asana](https://asana.com/uses/kanban-boards?msclkid=c0e51366148511fc77394d30727faada&utm_source=bing&utm_medium=cpc&utm_campaign=NB%7CUK%7CEN%7CBoards%7CEX&utm_term=kanban%20board&utm_content=Kanban%20Board), [Zenhub in GitHub](https://www.zenhub.com/) - Make sure that by now you have added a license, contribution guideline and a Code of Conduct in your GitHub repository. If you feel stuck and don't know where you start, take a look at [this repo](https://github.com/malvikasharan/developing_collaborative_document) - Look up two other projects and comment on [their issues](https://github.com/open-life-science/ols-2/issues) with feedback on their project **Table of contents** [TOC] :earth_asia: Cohort call --- **Call time**: 22 October 2020, 17:30 - 19:00 LONDON time, [see in your time zone](https://arewemeetingyet.com/London/2020-10-22/17:30/week-8-cohort-call) [see in your time zone](https://arewemeetingyet.com/London/2020-10-08/09:00/week-6-cohort-call) **Hosts**: Emmy, Malvika, Yo **Syllabus**: [OLS-2 Week-8](https://openlifesci.org/ols-2/schedule/#week-08) **This week** During this week's cohort call, we will learn about: - Open Education & Training - Citizen Science - Preprint publications, DOI and citation - Open protocols (protocols.io) :wave: Roll call --- **Breakout room preference:** please edit your Zoom name (click on the three dots on the top right of your video) and add one of the following letters in front of your name. This will help us assign you to the breakout room with format of your choice (Read more about [why we run different format of breakout rooms](https://hackmd.io/Rxv59dqAQ1C7gnHz5P-5PQ)): - **W** for *Written Discussion Breakout Room* - **S** for *Spoken Discussion Breakout Room* - **B** for *both* if you are happy to be assigned to any breakout room. **Name (pronouns - optional) / Project / social handles (twitter - t, GitHub - gh, etc.) / [emoji mood](https://emojipedia.org/)** - B / Yo Yehudi (they/them) / OLS / t: yoyehudi / :hibiscus: Flower emojis 4eva - Malvika Sharan (she/her) / OLS / t+gh: malvikasharan / 😅 (happy but rushed!) - Emmy Tsang (she/her) / TU Delft, OLS-host / t: emmy_ft / 💐 (colours brighten up days, and i agree with Yo) - Ismael Kherroubi Garcia (he/him) / The Turing Way Ethical Research / t: @IsmaelKherGar, gh: Ismael-KG / :sunrise: - Peter van Heusden (he/him) / RSSE Africa / t: pvanheus gh: pvanheus / :| (recovering from sinusitis) - Arielle Bennett-Lovell (she/her) / Mentor / @biotechchat / :fallen_leaf:beautiful leaves today! - David Beavan (he/him) / The Alan Turing Institute / @DavidBeavan / :sunglasses: - Bailey Harrington / Chronic Learning / t: @ChronicLearning; gh: @baileythegreen - Pradeep Eranti/ Open platform for Indian Bioinformatics community / t: [@pradeeperanti](https://twitter.com/pradeeperanti) / - B / Danny Garside (he/him) / Registered Reports in Primate Neurophysiology / t: da5nsy / :zzz: - Georgia Aitkenhead (she/her)/The Alab Turing Institute/GeorgiaHCA - B / Dave Clements (he) / Galaxy / tnabtaf / Wee bit stressed - B Ekeoma/open life science - Kevin Xu (he/him) / Civil Service / @kevinxufs - Sam Van Stroud (he/him) / UCL / @samvanstroud - Beatriz Serrano-Solano (she/her) / Growing the Galaxy community / gh: beatrizserrano, t:Birthae - Laura Carter (she/her) / Ethicsbook, The Turing Way / :right_anger_bubble: (it's been...a day) - Camila Rangel Smith (she/her) / The Alan Turing Institute / t: @CamilaRangelS gh: @crangelsmith - Paul Owoicho / Embedding Accessibility in The Turing Way Open Source Guidance / g: @paulowoicho, t: @ogbonokopaul - Sangram keshari Sahu / Practical Guide to Reproducibility in Bioinformatics - Laura Acion (she/her) / MetaDocencia - University of Buenos Aires - CONICET, Argentina / t: @\_lacion_ - Markus Löning (he/him) / sktime / t: @mloning_, gh: @mloning :turtle: - S / Kendra Oudyk (she/her) / Open Science Office Hours / t: @_koudyk g:koudyk / 🌦️ - Emma Ganley (she/her) / Director of Strategic Initiatives, protocols.io / @GanleyEmma / emma@protocols.io - Eva Herbst (she/her) / FEZ / T: @EvaCHerbst / G: @evaherbst 🥱 - Neha Moopen (she/her) / Utrecht University Library / G:nehamoopen + T -Stephen Klusza (he/him) / SynBioChassis For Public Domain Use/ T : @codebiologist/ - **S**/ Joyce Kao (she/her) / Open Innovation in Life Sciences/ Twitter and Github: @joyceykao / 😰 - Hilya (she/her) / APBioNetTalks / G: @hzahroh / :cat: - Jelioth Muthoni (she/her)/g:Jelioth: **Icebreaker question** *What music/artist/audiobook have you been listening to these days?* - _Name / answer_ -g to Malvika / [Punisher album by Phoebe Bridgers](https://www.youtube.com/watch?v=ncSf8Nk3aq4) - Yo - [Unchained Melody](https://www.youtube.com/watch?v=qiiyq2xrSI0) - I can't stop listening!! - Peter - TWIV (new one out today! - looking forward to the next TWIP too) - Ismael K.G.: any classic rock playlist on Spotify! - Dave C / My "turn it up" playlist because I need the boost - Bailey – Okkervil River, super indie/folk music which was recommended to me a few months ago - Arielle - I am obssessed with the Old Gods of Appalachia podcast, perfect for anyone who is feeling spooky this month :jack_o_lantern: - Georgia - Sachiko M! https://www.youtube.com/watch?v=qetxNwezkcg&t=604s - David B - Sibelius, coz I need to chill 🇫🇮 :+1: (violin conerto :heart:) - Sam VS - New Sufjan Stevens - Danny G - The new Sylvan Esso album ('Free Love') - Paul O - I just discovered Florence d - Camila RS - This week I discovered a podcast called "You are wrong about", insighful and entreteining. - Kendra O - [nightingale song](https://www.youtube.com/watch?v=NK2_bcQcoD4&t=2913s) - Eva - podcast "How to save a planet" - Neha - _Three Bows_ from the Chef's Table soundtrack - Stephen - Te/DIS (Tempted Dissident) Transparent Subsistence - Joyce - Rupaul...💋 - Hilya - all wonder woman 1984 OS -Ekeoma B- open life science 🗣️ Welcome! --- Malvika: (4 mins) [⏰ 4] **Call recording reminder:** - Please note that this call will be recorded - The video will be available on the [YouTube channel](https://www.youtube.com/c/OpenLifeSci) in the next few days - Turn on your webcam if you don't mind being in the video (or off if you do!) **Participation reminder:** - [Code of conduct & community participation guidelines ](https://openlifesci.org/code-of-conduct) - If you experience or witness unacceptable behaviour, or have any other concerns, please report it by contacting the organisers - Bérénice, Malvika and Yo. ([team@openlifesci.org](mailto:team@openlifesci.org)). - To report an issue involving one of the organisers, please email one of the members individually ([berenice@openlifesci.org](mailto:berenice@openlifesci.org), [malvika@openlifesci.org](mailto:malvika@openlifesci.org), [yo@openlifesci.org](mailto:yo@openlifesci.org)). ✏️ Open Science II: Sharing your open project: Knowledge Dissemination --- **Quiet reflection exercise**: *Planning and preparing what outcomes of your project should be shared with the wider community.* Yo (⏰ 10 minutes) 15 **Questions to reflect upon** 1. **Practicing Open Science:** What sorts of things can be shared? Why? - [name / comment] - [name=Georgia] Share code, resources, rough working, inspiration; - [name=Ismael] Methodology, possibly metadata, anonymised data, ethical and philosophical assumptions baked into the research - [name=Sam] "anonymised" data is a real can of worms sometimes, there can be ways to deanonymise... - [name=Danny] Project vision, roadmap, drafts of papers (potentially, hot topic...), raw data, pre-processed data, analysis (code and results). Radical approach would be the [open notebook science](https://en.wikipedia.org/wiki/Open-notebook_science) approach. - [name=Bailey] Aggregated data - [name=Peter] Share reference data, code, parameters used, documentation!! & method/protocol descriptions, grant applications (after the grant closes), when sharing data: share as raw as possible (e.g. sequencing reads not just consensi, multiple sequence alignments, not just phylogenies) - [name=DavidB] ways of working, expectations, the team, readings, papers, outputs, data, context of the data, context of the archive, document your assumptions, ambiguities, uncertianties, transformations, pipelines, methods to reproduce, ways to validate data and code (e.g. hashing - there's a nice project on this... checks that data and jupyter notebooks and outputs are what the author expected... someone help with the project plz?) - [name=Sangram] code with documentation, references, raw and processed data, at least examples. - [name=Bea] all kind of activities and information relevant to the Galaxy community. - [name=Paul] it is useful to share code and aggregated data so that experiments and analyses can be reproduced - [name=Pradeep] Research plan, Code, progress, results, data respecting the individual privacy, - [name=Emma G] Any thoughts about clinical data/information? Endangered species locations - [name=Neha] Typically it's a manuscript which includes your writing, your main findings incl. tables/figures, and references. But there are many more resources produced during the research process - protocols, code, notebooks, presentations etc. It could be made available as well. Not to mention the data (where possible) and the full results, not just the values your insert into your text. 2. **Is it a little too open?**: Are there things in science we shouldn't share, or that we should be thoughtful about sharing? Why? - [name / comment] - [name=Sam] If the science has been done using personal information, and the information people who the information is about have not explicitly given their permission, then the data (and perhaps conclusions / analysis on the data?) should not be shared. - [name= Arielle] Genetic data is an interesting one - how much should be shared of an individual sequence if you can theoretically identify someone by seuqencing their DNA? - [name=Kendra] I think we need to be thoughtful about sharing any identifiable information. - [name=Bailey] Any data that could allow identification of individuals participating (whether this is a single data field, or several in combination) - [name=Ismael] "Sensitive information" (as per Equality Act in the UK, GDPR) that is not anonymised (even if anonymised, take care we cannot triangulate individuals' identities with publicly available data) - [name=Peter] Photographs (without consent of all involved), data associated with vulnerable communities (without permission & clear benefit sharing agreement in place) - [name=Camila] When working with sensitive data we must be careful of also sharing models that might leak information (the modelling might reflect an outlier). - [name=Georgia] don't share sensitive information, private data, data from research participants which is not consented to be shared; anything which violates code of conduct - [name= Kevin] Sometimes you don't want to share all source code because there may be security vulnerabilities. - [name=Ekeoma] - [name=hilya] Data that are tied to individuals, such as medical records and images/videos, can only be shared with consent - [name=Neha] I've seem some researchers are concerned about open peer review and of course, data sharing. 🖥 Open Education --- Yo (⏰ 8 minutes) - Speaker: Laura Acion - [Link to the presentation](https://docs.google.com/presentation/d/1Pw8w5EYw_N2hhrGQaFBXnsK5Qg5ID84tCNzCTpNbYyA/edit?usp=sharing) - Contact information: - Email: lacion@gmail.com - Other social media: :bird: - personal twitter: @\_lacion_ - MetaDocencia: @metadocencia - [personal website](https://lacion.rbind.io) - [MetaDocencia website in English](https://www.metadocencia.org/en/) - Notes: - Open Educational Resources shoold be Findable, Accessible and Reusable! - Metadocencia:  Meta teaching, teaches to teach in Spanish - everything is licensed CC BY - mission: nurture a community of Spanish-speaking educators - heavily inspired by [the Carpentries](https://carpentries.org) - Most resources are available in English but that's not the language that is used everywhere - Considerations around tooling and internet accessibility, communities thinking and their benefits are helpful in the pandemic - The team of 8 collaborate remotely - they reached 1200+ spanish speaking educators - Actively communicating resources through social media - Building community: LatinR, Carpentries, ROpenSci, Early career researchers - Supporting people to reuse materials - Supporting other communities to reuse resources - - Questions / comments? - Name / Question - [name=Emmy] I'm very curious to know what you find most different between the MetaDocencia community and English-speaking communities in general, beyond the language? - the initial platforms that are used are quite different, loads of people rely heavily on cell phones! - [name=Stephen] for programming like Python and R, what kind of language support is there? Is there a big push to include as many languages in programming as possible, whether it is African languages or Latin-American languages? - Everything metadocencia does is in Spanish. So far we are doing train the trainer to people who are teaching programming and also school teachers. - [name=Open LifeSci] How will you support a new member start an open education project? What advice will you give? - First advice: do not start from scratch. There is a lot of brilliant communities out there (e.g., The Carpentries, RStudio Education) that can help you providing previous lessons learned. - Having a strong network that can help you spread the word of your open education project is also key. Our network in other communities of practice in Latin America has been essential to help us spread the word. Locally, formal institutions do not understand quite well what our model is and how we work, it is too unusual, and we have found not much support yet. - We are also hoping to write about our experience and help others get their own MetaDocencia started in other regions, adapting to other regional needs. So far, among our blog posts we also wrote about how to add a license and a doi to your materials. 🖥 Pre-print and open review --- Emmy (⏰ 10 minutes) - Speaker: Umar Ahmed - https://bit.ly/OLS-AfricArXiv - Contact information: - Email: babasaraki@yahoo.co.uk - Joined the call with Jo Havermann, co-founder of AfricArXiv (jo@africarxiv.org) - Notes: - AfricArXiv: https://info.africarxiv.org/ - There are a variety of preprint servers for different areas of research, e.g. BioRXiv, medRXiv, chemRXiv - Regional archives like AfricArxiv help bring visibility to regional research, e.g. research in specific regional languages - Preprints: full draft/complete scientific manuscripts *before* peer review - the research is freely available, with DOI and citable, before journal submission! - Preprint allows people to find collaborator, share research ideas early on, attract funding and receive complementary support - https://v2.sherpa.ac.uk/romeo/ - journal policy on preprint submission before/during submission process - AfricArXiV allows submission of multiple publication formats, and promotes the use of African languages; ultimately to bridge language barriers and encourage collaborations - - Questions / comments? - Name / Question - Can people submit papers to more than one preprint repo? e.g., to both bioarxiv and africarxiv? - It depends of individual arxiv policy, some may not allow to submit to two different arxivs (you want to maintain a single unique DOI, adding to multiple archives may give two different DOI and will reduce you to assess the impact) - What's your view on the compromise between preprint accepting low impact factor journals and not accepting high-impact factor journals? How to make the decision? - I don't see impact factor for ranking journal, we shoukd really look for the quality of work - at the same time who can read and make use of them. - A close access paper can not make impact because it won't reach everyone. - [name=Arielle] Have you experienced any resistance to preprints and Africarxiv? What type of concerns do people express? - We have not received resistance from the community. There is a bit lack of awareness on what preprints are, but we keep promoting and keep recieving article submission everyday. - Concern: they worry if they may not get accepted for peer review journals - but we try to help. 👥 Breakout session --- Malvika (⏰ 15 minutes) Sharing in science isn't always straightforward. _INSTRUCTIONS: Every group has a set of questions._ 1. _Assign a note taker in your group_ 2. _Pick_ __one__ _of the questions assigned to your group and discuss the issues._ 3. _Make sure to take notes under each question you discuss so others can read later on!_ **Breakout room reminder:** if you need assistance in your breakout room, please click the '**Ask for Help**' button at the bottom of your screen ⏰ **Shared breakout room time:** https://cuckoo.team/ols-2 👥 Break-out room (10 minutes, ~3-4 rooms): **Group 1: Written Discussion** - Khadijat, Georgia, Markus, Emma, Jo, Danny, Camila 1. If I share my work with other researchers, they might try to claim my work as their own. 2. **I'm nervous that others will find faults with my research results if my code is open.** +1 +1 3. I'm fine with my personal data being used for important or groundbreaking scientific research as long as it's anonymized. **Notes** #### We picked question 2. - [name=Georgia] I think that this is difficult without significant culture - [name=Danny] Everyone has the fear that their work is not good enough to share (but I realise now that the question is actually about something slightly different...) - [name=Emma Karoune] Maybe we have to accept that we are all humans and so there will always be faults? - [name=Georgia] I think it requires really careful community building and a supportive environment to encourage people to feel safe - [name=Camila] +1 - [name=Georgia] Norm-setting and a code of conduct is super important I think - [name=Emma Karoune] I think there is often a culture of having to always get the right results in science and you can't fail in anyway or have negative results. - [name=Khadijat] Mistake can be identified and corrected by other people who might be better in coding - [name=Emma] There is a new journal that only accepts negative results. https://www.jtrialerror.com/ - journal of trial and error - I really like the idea of it as you learn a lot from failure - [name=Georgia] That journal sounds like such a good idea! - [name=Georgia] For sure, it corresponds to a wider issue which is part of the reproducibility crisis we think of peer scrutiny. Which seems scary and competitive in a way whereas peer support to get to the turn is more what science feels like it should be about. - [name=Camila] Because scrutiny in science is not always pleasant - [name=Camila] definitely! - [name=Khadijat] Surely, errors could be good in research - [name=Danny] I think we should actively *want* people to find problems in our work (if there are any!). Have you folks heard of [red teams](https://en.wikipedia.org/wiki/Red_team)? And specifically [in academia](https://daniellakens.blogspot.com/2020/05/red-team-challenge.html). - [name=Emma] do we have time to do another question? Has anyone got anything to say about no 1? I want to know if anyone has actually every had their data stolen?I suspect it is very rare? - [name=Danny] My understanding is that that would be *exceptionally* rare - [name=Camila] Last week I found myself trying to convince some researchers that has exactly those reservations from 1. - [name=Danny] Having data "stolen"? Or being scooped?
 - [name=Camilla]They don’t want their idea to be scooped, and is understandable. - [name=Georgia] I think that having it out in the open especially if data is also published must make it attributable to you in most cases? - [name=Camila] So we concluded that we would open the repo after we have a first prototype developed. - [name=Georgia] +1 - [name=Danny] + 1 (esp if it gets a doi) - [name=Emma] +1 - [name=Camila] Being confortable with this means a change on the scientific culture, where making mistakes is something that can happen and it's ok. **Group 2: Spoken Discussion** - Kendra Oudyk, Ismael Kherroubi Garcia, Muhammet A. Celik, Peter van Heusden, Jelioth Muthoni, Priscilla Mensah, Harriet Natabona, David Beavan ** 1. I don't want to invest a lot of time helping others who might end up taking all the credit.** 2. I spent hours debugging and troubleshooting my code, so I'm not going to give it away for free. 3. My collaborators don't seem to care about protecting personal data. **Notes** - Q1 - Scenario: funding call wherein somebody is asked for advice but their advice is not considered relevant for authorship - Supervisor asking for co-authorship despite not writing a word; this can differ from field to field - People can feel undermined if their work is *not* properly acknowledged - Publish or perish culture - In acknowledging contributions, where do we draw the line? Does fixing a few typos count? - Credit places long-term value on publishing - Is there a fine line between acknowledgement and credit? Maybe the first can suffice for those who have "enough of" the latter? - Makes it feel like not wanting to collaborate with others - [Fair Cite](https://faircite.wordpress.com/) <- bit old now - [CRediT – Contributor Roles Taxonomy](https://casrai.org/credit/) - [All Contributors](https://github.com/all-contributors/all-contributors) **Group 3: Spoken Discussion** - Arielle, Bailey, Laura, Beatriz, Joyce, Yupita, Gokcen 1. If I choose to collaborate with other researchers on a project, I don't understand who will be the first author of the publication. 2. I use open source software but to be honest I don't know how to contribute. 3. **My research is so specific. Nobody else would be interested in or be able to understand my data.** **Notes** - Q.3 - Niche area with complex data anaylsis - true of a lot of people in research! - Lots of academic research is a bit esoteric - PhD projects are tiny and it sometimes feels that no-one cares about them - but there's wider implications and areas of interest - People might be interested in how you're using a big dataset, or your methods, even if its not directly applicable to a disease phenotype - in some political contexts open research can help with visibility and safety, especially where there is less freedom for researchers to work - if there is international attention on your work, it can mean you can work more freely - maybe you'll write something that starts a whole new field of research! **Group 4: Written Discussion** - Sam VS, Pradeep, Eva, Neha, Emmy 1. Contributing to collaborative projects has helped improve my productivity. 2. In research projects, we should set aside part of the budget to spend on making the results openly available. 3. I'm worried that other researchers will make use of my data and get better results. 4. How does one attract collaborators apart from gitHub page? **Notes** - Q.1: [name=Sam] I find that my productivity is improved if I'm not stuck doing one thing for a long time, so having smaller side projects that you can contribute to every so often makes me feel like I'm being more productive. About a collaborative project specifically, having other people availible who can answer questions when you get stuck means you end up spending less time ramming your head against a wall (hopefully!). - [name=Neha] I can relate to the first part especially :) I've been guilty of using side-projects as a productive procrastination route but the small wins are great and so is chance for help or feedback. - Q.1: [name=Neha] Yes & No. Sometimes I'm more productive when I'm part of a group and either there's some accountability or more structured tasks / delegation. On the other hand, some projects are not so clearly structured and you feel motivated sometimes, but other times it's like you're being strung along. In general, I like being part of collaborative projects, they're rewarding and cool. It helps in your day job too (if it wasn't part of your job already) - [name=Sam] Your "on the other hand" I definitely agree with actually, didn't thinka about it first time. Sometimes when you have a lot on in your "main work" and the side projects feel like they are taking up time, without producing meaningful results, it can be frustrating - [name=Emmy] I wonder how we can make everyone understand how structures can really help facilitate collaboration... sometimes i still have to "fight" with people to put together an agenda for a meeting ): - Q.1: [name=Pradeep] Whenever I am stuck in main project, I work on the collaborative projects with my colleagues. It helps me come back with clear mind to approach my problem in the main project. - [name=Sam] Definitely feel the same way! :) - [name=Neha] +1 :) - [name=Pradeep] Moreover, finding the projects with different background participants helps. - At the same time, there were instances when these collaborative projects brought headache while waiting over a long period to hear back from the other participants. - [name=Emmy] This! +100 - Q1: [name=Emmy] I find this particularly useful when we have problems to solve, usually more people with diverse perspectives we have, the better the solution we find! - [name=karegapauline]This is true Emmy. Everyone sees things differently so this works if everyone is open minded. - [name=Neha] For sure, people with different perspectives add to the solution and you learn a lot along the way. - Q1: [name=Paul] With collaborative projects, I can approach problems from different perspectives. THis helps unblock me whenever I get stuck on a challenging task. There's also accountability with collaborative projects ensuring that work is completed on time and to a high standard -[name=Karega] hi Paul. Open accountability does give that extra kick coz you knw you have a responsibility not just to you. Agree 100% - [name=Neha] Hiya Paul! We've to catch up soon :) - +1 to the first part of your comment, waiting for you to finish.. - [name=Paul] Hi Neha! - - Q1: [name=Eva] I also agree with the points above, as long as the work is clearly divided up in the beginning I find that collaborative projects get me more excited about my work and also are really good for sanity checking (e.g. deciding when something is good enough to move on to the next part) - [name=Neha] +1, the planning/communication/structure helps a lot. The admin part takes some effort and can be dreary to set up, but it makes things smoother in the long run. -Q1: I have got stuck with developing goals for my project because am wondering how much of it should be open. The interest in the project is in offshoot from what i am presently working on in my masters. Some i get stuck because i am rationalizing what information i shouldnt be giving out until i finish my masters. _I have starting considering a community based open learning project. But I am lacki - Q1- collaborative projects open up your mind to staff you hadn't seen and you get creative solutions for something you are working on too. - **Wrap up and shared insights: share few important points below and +1 what you agree with**: (5 minutes) - - - - - - - 🖥 Open Protocols --- Emmy (⏰ 10 minutes) - Speaker: Emma Ganley - https://docs.google.com/presentation/d/1_8Fp5DKh_XXwj34DwR-dzTvUCk1c0ynhy7MvmaHFFoA/edit?usp=sharing - Contact information: - Email: emma@protocols.io - Other social media: @GanleyEmma - Notes: - The amount of information regarding experimental methods and protocols is liimted to what's in the methods section of the paper, that has impact on reproducibility - Protocols.io is a platform for publishing more detailed protocols, and you can also collaborate on protocol development! - they are amazing at reproducibility - there's also a "this work for me button" which indicates that someone has replicated the study - it allows a single paper to reference multiple protocls, and the other way round - all protocols in a paper can also be put in a collection - Protocols over materials & methods? just a much better experience specifically built around protocols and how they're used! - Open protocols allow much faster and more feedback, and ultimately enhanes the value of research, also helps with the stewardship of research output - your future self will thank your present self! - Questions / comments? - Name / Question - [name=Yo Yehudi] I loved your point that "crisis" isn't a great choice of wording - what would you suggest instead? +1 - I'd go with challenge as something that we can address (with existing tools and better research practice) rather than something that is out of control - [name=Yo] it strikes me how much the "lack of recipes" is true for research code as well as lab recipes :) - Absolutely and there have been initiatives pushing for open code. A lot of journals already have policies specifically about code sharing and what their expectations are for whether authors are required to share code or not. - [name=Stephen] are published protocols in protocols.io peer-reviewed before publication? - Great question! No, they're not peer reviewed. In this regard they are more like a preprint. They can be included in a research manuscript so a reviewer could access the protocol and review it at the same time as an article if the author/journal/reviewer wants. Review of a protocol itself happens more via the dynamic commenting/discussions that take place after publication. And of course the ultimate positive review is if someone else clicks the works for me button. - [name=Laura] you mentioned protocols.io is for profit, but it is free to use. Could you please tell a bit more on where the profit part comes from? +1 - Of course. And I'll note that we are a start-up so still working towards sustainability, but the key to the model is charging for private use. Anyone can publish as much as they like for free, but users want to have lots of private collaboration for method development then this is paid for. We sell workspaces for groups to pharma, some universities, and have support from some funders who want the researchers they fund to use protocols.io and make their methods/protocols open. - [name=Jo] - Can we integrate protocols.io to AfircArXiv via Zenodo, OSF, Figshare, PubPub or ScienceOpen? - We have a great API and welcome integrations with others. Take a look at https://www.protocols.io/developers for more information. - [name=Neha] In research data management, we have similar tools to prepare data management plans (like DMPonline). Am I right in understanding that protocols.io is really just about the methods/procedure/materials? If yes, protocols.io and a DMP tool would be very complementary. Pre-registration / Regstered Reports can address the analysis planning part... cool stuff! - Yes, this sounds right. protocols.io can absolutely be used for pre-registering a research project plan. And Wellcome even suggests protocols.io as one location for clinical trial registration. - [name=Danny] Having DOIs point to something that changes scares me. Does it actually go to the original and then tell you that there's a new version? (like on preprint servers?) - Yes, the DOI always points to the same version (a DOI corresponds to a static protocol, or research paper, that cannot change). But if you follow the DOI link and there is a newer version on protocols.io you'll always be alerted to the newer versions. Every version will have its own DOI and date-stamp, and you can compare the versions really easily to see what changed. This really allows for simply edits/clarifications as needed when/if someone tries to repeat an experiment but realises some info is missing or not clear. - [name=Emma] does it have versioning to show the changes? as surely if you change the method, your future work is not comparable to previous work? - Yes, you can compare any version to any other version and see the changes. I'd normally have shown this but didn't have time. For a great example, take a look at this protocol: https://www.protocols.io/view/bench-top-cut-amp-tag-bcuhiwt6 - if you click the black triangle to the right of the protocol title, you'll see the option 'Compare' - have a play around! - [name=Emmy] Not a question- I just had an "aha" moment about how actually user journeys and expectations around each section of the paper (or even finer divisions) are really different - hence it's a complete pity that we've chosen to just dump most things into a PDF/render as a static html page... - YES! Static, non-dynamic html or PDF is the biggest tragedy of the current internet era. I have high hopes for new developments coming to research dissemination in the future! - [name=Danny] Does this mean that I finally have a way to not have to rephrase the method section every paper?? - YES!!!! You can cite your protocol in more than one paper so get past the need to try and rewrite a method time and again using different phrasing. Even better if you publish a protocol, it will appear on your ORCiD profile, so counts as a standalone research output. If you developed the method but weren't the main results generator so aren't a key author on the paper, you can get recognition for the method development as a hugely important research output in and of itself. - More seriously, is there an export option so that we could export something for a paper (and then we have to broach the question of publishing things that are verbatim coopies) - Also yes, all published content on protocols.io can be exported as PDF or JSON. But if published you don't need to paste the text into a paper, you can just cite the protocol in the materials and methods. >500 journals support their authors doing this (some encourage more than others) so generally they won't mind if you take this approach and you can simply state 'We performed PCR as described here and cite the protocol' - [name=Danny] Are there templates for different fields (I'm a visual neuroscientist and I would love if there was a simple way to reproduce figures such as this one: [top left](https://iiif.elifesciences.org/lax:50340%2Felife-50340-fig1-v1.tif/full/1500,/0/default.jpg) (but normally with timing also) which I would love if there was a 'stadard' format for.) - There probably isn't a template for this exactly, but any available protocol can be 'forked' so you can create your own new version (the forking means attribution is already taken care of as you can track the original protocols). You can then modify your version to do whatever you want. We are working on more templates but this is in progress. If you want to try out protocols.io for something like this, we'd welcome your input if you can see ways we might improve to serve a particular community. **More ways to share other research outputs (getting a DOI - making your content citable).** - Figshare / Zenodo - Code: - JOSS - JORS - Connecting GitHub with Zenodo - CodeOcean - Data - Dryad - Add your own? - - - - 🖥 Citizen Science --- **Offline** - Speaker: ~~Anne Clinio~~ Bastian Greshake - https://youtu.be/HaQyv48sMPY?t=860 - Contact information: - Email: bgreshake@googlemail.com - Other social media: https://twitter.com/gedankenstuecke 🗣️ Closing --- **Open Q&A time** - - **Assignments** - Any remaining assignments? - catch up on your project - Need help? Invite experts. - Feel stuck and need help, invite an OLS team members in your meeting - Complete the midterm survey: https://forms.gle/wSxAxcX2uhit5fDJA - Next calls - Week 9 - Self Care and Ally Skills, Schedule: https://openlifesci.org/ols-2/schedule/#week-09 - Week 10 - Cohort call, Schedule: https://openlifesci.org/ols-2/schedule/#week-10 **Feedback** _What worked?_ - [name=Danny] Just for the ratio - I :heart: hackmd and it works well for me almost all the time. - <3 Thanks Danny - That OLS session was so useful @Malvika @Yo Yehudi :star::star::star: thank you :slightly_smiling_face: I especially hearing about protocol.io useful because I tend to use GitHub for putting my study frameworks and methods, but it's hard to find and this looks like a great additional option. - I loved hearing about initiatives that aren't centered around Western, English-speaking academia! _What didn't work?_ - [name=Danny] Having to pick between the questions for the breakout room took a disproportionate amount of time (esp for a writing room). It might have been better to just have a single predetermined question. - [name=Danny] Several people weren't on the hackmd, which made being a written room quite difficult - [name=Danny] It meant that they didn't know we were a written room, and so people defaulted to talking. - [name=Danny] It meant that we had our discussion in zoom chat and then copy/pasted, which introduced a lot of unexpected formatting issues. - [name=Georgia] I think making it clearer that the writing rooms should involve no talking would help. It's fine for me, but I can see how it might be troubling to others if they don't expect it. _What would you change?_ - [name=Danny] I wanted to hear more about open peer review! - [name=Georgia] I would have had a few more breakout rooms between talks - Maybe have more breakout rooms with fewer people - it was hard to hear from 8 people in 10 minutes _What surprised you?_ - [name=Georgia] The range of responses to questions about what people were worried about in terms of openly sharing work. This seemed really broad and it was helpful to get that perspective. - - - *Reference*: Open leadership Framework, Mozilla Open Leaders 6 & 7, Open Life Science 1 *License*: CC BY 4.0, Open Life Science (OLS-2), 2020