Slides Carnival template Open Neuroscience: Challenging scientific barriers with Open Source & Open Science tools SONA & TReND in Africa Webinar Series 12/05/2020 Seminar recording https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://www.youtube.com/watch?v=bsPmLF65r3k Hello! Research Bioengineer @Sussex Neuroscience Open Source coordinator @Trend in Africa Founder @Open Neuroscience Consulting @Prometheus Science 2 Slides Carnival template http://www.sussex.ac.uk/sussexneuroscience/ https://trendinafrica.org/ https://open-neuroscience.com https://prometheus-science.com https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Open Neuroscience ▪ Academic barriers & practical issues ▪ Open Solutions ▪ Open Solutions @ TReND in Africa ▪ Q&A 3 Slides Carnival template https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Academic Barriers Cost For tools/literature shuts many people out of research. Lack of access Even with necessary funds, supply chains do not reach labs/schools globally Irreproducibility Even when costs and access are taken care of, we are still facing a reproducibility crisis. 4 Slides Carnival template https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Cost - Publications 5 Slides Carnival template https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Cost - Publications 6 Slides Carnival template Lariviere et al 2015 https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127502 Cost - Publications - Software 7 Slides Carnival template From MATLAB website 10/05/2020 https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://uk.mathworks.com/pricing-licensing.html?prodcode=ML Cost - Publications - Software 8 Slides Carnival template https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Cost / Lack of access - Publications - Software - Equipment 9 Slides Carnival template By Zephyris at the English language Wikipedia, CC BY-SA 3.0By Chad Anderson, CC BY-SA 2.0 5000£ microscope https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://commons.wikimedia.org/w/index.php?curid=13320450 https://commons.wikimedia.org/w/index.php?curid=13320450 https://commons.wikimedia.org/w/index.php?curid=45625745 Irreproducibility 10 Slides Carnival template https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 11 Slides Carnival template 100 studies Irreproducibility https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Academic Barriers Cost for tools/literature shuts many people out of research. Lack of access Even with necessary funds, supply chains do not reach labs/schools globally Irreproducibility Even when costs and access are taken care of, we are still facing a reproducibility crisis. 12 Slides Carnival template LACK OF TRANSPARENCY “Nothing good ever came from secrecy (except surprise parties...)” https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Everything (code, hardware design, protocols, cake recipes) created is shared freely via licenses (GNU, Creative Commons, OSHWA, and many other), using any means at hand (Internet, usb sticks, recipe notebook) 13 Slides Carnival template OPEN SOURCE https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 source 14 Slides Carnival template https://www.zdnet.com/article/its-an-open-source-world-78-percent-of-companies-run-open-source-software/ https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Open Source Cost All code/designs are freely available, users can know exactly what each part costs. Lack of access All code/designs are freely available, users can download/copy them free of charge Irreproducibility All code/designs are freely available, users can reproduce tools to the smallest details 15 Slides Carnival template TOTAL TRANSPARENCY “Given enough eyeballs all problems become trivial” https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Open Solutions - Publications 16 Slides Carnival template https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 - Publications - Software 17 Slides Carnival template Lopes et al 2015 Open Solutions https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://www.frontiersin.org/articles/10.3389/fninf.2015.00007/full#F3 - Publications - Software 18 Slides Carnival template Mathis et al 2018 Open Solutions https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://www.nature.com/articles/s41593-018-0209-y - Publications - Software 19 Slides Carnival template + Open Solutions https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 - Publications - Software 20 Slides Carnival template Open Solutions Jupyter https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://jupyter.org/index.html - Publications - Software 21 Slides Carnival template Open Solutions mybinder https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://mybinder.org/ - Publications - Software 22 Slides Carnival template Open Solutions https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 General purpose language Jacknife of packages: - Hardware control - Web development - User interfaces - Data analysis - and much more! Open Solutions Statistics and plotting language: - High quality plots - Integrated environment - Easily extendable - Effective data handling - and Much more! 23 Slides Carnival template https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 - Publications - Software - Equipment 24 Slides Carnival template Open Solutions https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Open Solutions http://bit.ly/flypipos 25 Slides Carnival template https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Open Solutions http://bit.ly/flypipos 26 Slides Carnival template http://bit.ly/flypipos https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Deployments 27 Slides Carnival template https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Open Solutions http://bit.ly/flypipos 28 Slides Carnival template FlyPi inspired: PiSpy - A cross-disciplinary Bucknell collaboration Images by Greg Pask http://bit.ly/flypipos https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://twitter.com/G_Pask - Publications - Software - Equipment 29 Slides Carnival template Rendering by Maxime Zimmermann Open Solutions https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://twitter.com/MJY_Zimmermann - Publications - Software - Equipment 30 Slides Carnival template Open Solutions Repository Preprint https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://github.com/bionanoimaging/UC2-GIT https://www.biorxiv.org/content/10.1101/2020.03.02.973073v1 Open solutions @ 31 Slides Carnival template From Baden et al 2015 https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002086&utm_source=web&utm_medium=pdf&utm_campaign=ppu15 - Publications - Software - Equipment 32 Slides Carnival template Open Solutions https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 - Publications - Software - Equipment 33 Slides Carnival template Open Solutions https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 - Publications - Software - Equipment 34 Slides Carnival template Chagas et al in prep Open Solutions https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://github.com/amchagas/open-hardware-supply - Publications - Software - Equipment - Rapid Response 35 Slides Carnival template Open Solutions https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Reach out! 36 Slides Carnival template Lab on the cheap Neuromethods Slack LEARN DISCOVER COLLABORATE https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://www.labonthecheap.com/ https://neuromethods.slack.com/#/ Reach out! 37 Slides Carnival template Form to upload projects to the website: https://bit.ly/2LkTd2a Contact to contribute with the project itself: openeuroscience@gmail.com https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 https://bit.ly/2LkTd2a mailto:openeuroscience@gmail.com Open Source / Open Science tools Open Source Software Computer programs where all code is freely available for people to check, modify, improve and redistribute: Python, R, Deep Lab Cut, Open Source Hardware Scientific equipment where all designs/blueprints are freely available so people can learn, build, modify & redistribute: Miniscopes, UC2, Arduino Open Access Journals/Pre-prints Journals and manuscripts before peer review freely available to read: PLoS, ELife, BiorXiv, AfricArXiv, PrePrints Communities Groups tackling specific issues. Welcoming to newcomers and with a lot knowledge on a specific topic: Open Science MOOC, GOSH, Africa OSH, Software carpentry Repositories Portal and webpages which curate content, so it is easier for the community to find what they need: Open Neuroscience, Open Source toolkit, Open Behavior 38 Slides Carnival template https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929 Thanks! Time for your questions Find me at: ▪ Twitter @chagas_am ▪ a.maia-chagas@sussex.ac.uk 39 Euler lab Slides Carnival template https://twitter.com/chagas_am https://www.slidescarnival.com/jacquenetta-free-presentation-template/1929