Niklas Morberg (CC BY-NC 2.0)
Purpose: Training for early stage researchers and young leaders interested in furthering their Open Science skills
Outcome: Ambassadors for Open Science practice, training and education across multiple European and international bioinformatics communities.
Process: A 16-week mentoring & training program, based on the Mozilla Open Leader program, helping participants in becoming Open Science ambassadors by using three principles:
The vision of Open Life Science program is to strengthen Open Science skills for early stage researchers and young leaders in life science.
At the end of the program, our participants will be able to:
OLS’s second cohort (OLS-2) will be conducted from September 2020 until December 2020.
May 20, 2020 : Opening of the applications on Easychair
We have templates you can download to use when preparing your application.
June 12, 2020 : Application webinar( Talk + Q&A) - Notes with Zoom call link
June 23, 2020 : Application webinar( Recording + Q&A) - Notes with Zoom call link
June 30, 2020 : Closing of the applications on Easychair for main cohort applications
July 15, 2020 : Closing of the applications on Easychair for the collaborating organisations - The Turing Way
July 24, 2020 : Call for applications closed
July 24, 2020 : Successful applicants announced
August 31, 2020: Start of the program
December 14, 2020: End of the program
During the program,
Organizers will inform participants of the week schedule by email.
Week | Call | Date | Topic | Agenda |
---|---|---|---|---|
Week 01 (start. August 31, 2020) | Mentor-Mentee | Meet your mentor! | Meet each other and discuss your personal motivation, expectations, working practices and project goals | |
Mentor | September 1, 2020 (16:00 Universal Time) | Mentor training | ||
Mentor | September 4, 2020 (11:30 Universal Time) | Mentor training | ||
Week 02 (start. September 07, 2020) | Mentor | September 8, 2020 (09:00 Universal Time) | Mentoring workshop | |
Mentor | September 8, 2020 (16:00 Universal Time) | Mentoring workshop | ||
Cohort | September 10, 2020 (08:00 Universal Time) | Welcome to Open Life Science! | Meet other members of your cohort, Share project vision, Intro to working openly (open canvas) | |
Week 03 (start. September 14, 2020) | Mentor-Mentee | Meet your mentor! | Discuss assignments from the cohort call & concrete implementations | |
Coworking | September 17, 2020 (15:00 Universal Time) | Coworking on assignments, knowledge exchange and networking | ||
Week 04 (start. September 21, 2020) | Cohort | September 24, 2020 (16:30 Universal Time) | Tooling and roadmapping for Open projects | Working with GitHub as a community hub: Markdown as a tool to make websites, Licence, Goals and Roadmap, Contributors, Code of Conduct |
Week 05 (start. September 28, 2020) | Mentor-Mentee | Meet your mentor! | ||
Coworking | October 01, 2020 (15:00 Universal Time) | Coworking on assignments, knowledge exchange and networking | ||
Cohort | October 01, 2020 (11:30 Universal Time) | Skill-up: GitHub tutorial for beginners | ||
Skill-up | October 01, 2020 (11:30 Universal Time) | GitHub tutorial for beginners | ||
Week 06 (start. October 05, 2020) | Cohort | October 08, 2020 (08:00 Universal Time) | Open Science I: Project Development | Developing Open Projects: Iterative and agile project management, Open- Source, Software, Hardware, Data |
Week 07 (start. October 12, 2020) | Mentor-Mentee | Meet your mentor! | ||
Coworking | October 12, 2020 (10:00 Universal Time) | Coworking on assignments, knowledge exchange and networking | ||
Mentor | Mentor training | |||
Week 08 (start. October 19, 2020) | Cohort | October 22, 2020 (16:30 Universal Time) | Open Science II: Knowledge Dissemination | Sharing Open Project: Preprint publications, DOI and citation, Open protocols, Open Education & Training |
Week 09 (start. October 26, 2020) | Mentor-Mentee | Meet your mentor! | ||
Coworking | October 29, 2020 | Coworking on assignments, knowledge exchange and networking | ||
Skill-up | October 29, 2020 (15:00 Universal Time) | Personal Ecology and Ally Skills | ||
Week 10 (start. November 02, 2020) | Cohort | November 05, 2020 (09:00 Universal Time) | Open Science III: Next steps - applying FAIR research principles | FAIRification of existing or mature projects, etc |
Week 11 (start. November 09, 2020) | Mentor-Mentee | Meet your mentor! | ||
Week 12 (start. November 16, 2020) | Cohort | November 19, 2020 (17:30 Universal Time) | Open Leadership: Academia, industry and beyond! | |
Week 13 (start. November 23, 2020) | Mentor-Mentee | Meet your mentor! | ||
Cohort | November 26, 2020 (14:00 Universal Time) | Pub Quiz! | ||
Skill-up | October 26, 2020 (14:00 Universal Time) | Pub Quiz! | ||
Week 14 (start. November 30, 2020) | Cohort | December 03, 2020 (09:00 Universal Time) | Designing & Empowering for inclusivity | |
Week 15 (start. December 07, 2020) | Mentor-Mentee | Meet your mentor! | Preparation for the final demos | |
Cohort | December 10, 2020 (09:00 Universal Time) | Final presentation rehearsal - Group 1 | ||
Cohort | December 10, 2020 (17:30 Universal Time) | Final presentation rehearsal - Group 2 | ||
Week 16 (start. December 14, 2020) | Cohort | December 15, 2020 (09:00 Universal Time) | Final presentations & Graduation! - Group 1 | 5-minute demos of projects (Audience: entire community & public, Open and recorded call) |
Cohort | December 16, 2020 (14:00 Universal Time) | Final presentations & Graduation! - Group 2 | 5-minute demos of projects (Audience: entire community & public, Open and recorded call) | |
Cohort | December 17, 2020 (17:30 Universal Time) | Final presentations & Graduation! - Group 3 | 5-minute demos of projects (Audience: entire community & public, Open and recorded call) |
Participants join this program with a project that they either are already working on or want to develop during this program. More details about the role of a project lead (mentee) can be found here.
For the second round of the Open Life Science program, we welcome 52 participants with 32 projects.
Our project leads are supported in this program by our mentor-community who are paired based on the compatibility of expertise, interests and requirements of their projects. Our mentors are Open Science practitioners and champions with previous experiences in training and mentoring. They are currently working in different professions in data science, publishing, community building, software development, clinical studies, industries, scientific training and IT services.
Mentors advise and inspire
PhD with twenty years working around bioinformatics research, project-management, and training. Currently working as a leadership trainer for postdocs and PIs. For fun I enjoy painting, playing Dungeons and Dragons, and walking my dog.
I am an Experimental Psychologist and Fellow of the SSI at the University of Manchester interested in data visualisations, open science, and reproducible research. I am the University of Manchester Open and Reproducible Research Institutional Lead.
Anelda is the founder of Talarify, a South Africa-based consultancy working with researchers and postgraduates to help grow digital, computational, and open science literacy. She has a formal background in bioinformatics, but spend most of her time working in interdisciplinary teams these days. Main projects currently: 1) afrimapr, funded by Wellcome Open Research, where the team is working with data science communities in Africa and beyond to help make African data more accessible via the development of R building blocks; and 2) ESCALATOR - growing an inclusive and active community of practice in Digital Humanities and Computational Social Sciences in South Africa.
Anita Bröllochs is the Head of Outreach at protocols.io. She studied Life Science Engineering at the Friedrich-Alexander University in Erlangen, Germany and her background is on optical clearing of skeletal muscle for multiphoton microscopy. Anita has a passion for open science and is also the host of a science podcast called ‘Minor Tweak, Major Impact’ which is aiming to shine a spotlight on method development.
Anjali is the Thematic Lead on AI, Justice and Human Rights at the Alan Turing Institute for Data Science and Artificial Intelligence (UK), including projects on data science/AI to combat modern slavery and other exploitative crimes (and co-organiser of Code 8.7), statistics and the law, and bias measures/fairness methods in algorithms in justice. She is also an Assistant Research Professor in the Department of Statistics & Data Science and faculty affiliate in the Block Centre for Technology and Society at Carnegie Mellon University.
Arielle has spent her career to date working in research-adjacent fields, starting with a stint at open access publisher PLOS, where she learnt the importance (and challenges) of open science, code, and data. Currently the Research Project Manager on the Tools, Practices & Systems programme at The Alan Turing Institute, she was a CSCCE Community Engagement Fellow in 2019 and continues to be actively involved in the community. She is a contributor to the Turing Way project.
Bruno is a Brazilian ecologist working on a more collaborative and open science.
I am an Assistant Professor at Penn State University and I have been part of the Galaxy team for 5 years. I work on genomics and epigenetic and develop workflows and tutorials.
Holger is the head of Core IT team at the Max Planck Institute for Biolological Cybernetics. He enjoys the technical aspects of science - be it programming (Python), version control (git), web services (REST), or generally (self) organization and anti-procrastination. His mission is to support scientists in all aspects IT.
Hans-Rudolf is a Molecular Biologist turned Bioinformatician who is working in the Computational Biology facility at the Friedrich Miescher Institute in Basel Switzerland. Before, he was leading the Bioinformatics Core group at the Sanger Institute in Cambridge UK.
Research Scientist at UC Santa Cruz, Incubator Fellow at the UC Santa Cruz Center for Research on Open Source Software (CROSS); Adjunct Professor at University of Sonora (Mexico). Interested in large-scale distributed data management systems, applied aspects of data science, and reproducibility. I am currently working on Popper (https://getpopper.io), as part of the CROSS Incubator Program.
Jez is Data Services Lead in The British Library’s Research Infrastructure Services team. He has over 10 years of experience developing and delivering research data management services and strategies at research-intensive higher education institutions in the UK, as part of a long-term goal to help communicate and collaborate more effectively using technology. He is an experienced teacher and is involved with The Carpentries as a Certified Instructor and early contributor to Library Carpentry. He is particularly interested in elevating the status of research software alongside research data in the scholarly record, and helping researchers develop the skills to make the most of this. He is a Fellow of the Software Sustainability Institute, 2020 intake.
I am Community Manager RDM and Open Science at VU Amsterdam. My background is in theoretical linguistics. My goal is to help colleagues connect and learn from each other and with each other
Caleb is a 19/20 Mozilla Fellow and a Bioinformatician, interested in teaching, open science, reproducibility, machine learning, FAIR Genomics, and community building.
PhD in medical sciences with expertise in infectious diseases and vaccines with expansive knowledge of the data driven life science industry. Proven ability to present and write clearly and persuasively, complex scientific and technical content, tailored to different audiences. Experience in inspiring, enthusing and influencing stakeholders and leading teams while navigating different cultural contexts. Extensive experience in developing strategies for national and international projects covering public-private partnerships, communication, and outreach as well as scientific programmes.
Computational biologist focused on genomic regulation and data integration. 12 years of experience in biological data analysis using the most well-established tools and contributing to novel algorithms to improve the quantification and visualization of genomic data. She approaches scientific challenges with passion and believes that a collaboration and not an individual alone can successfully conquer them.
I am the principal investigator of the Big Data Biology Lab at Fudan University (Shanghai) since September 2018. Our group works in computational biology, with a focus on the very large-scale. See https://luispedro.org/
Mallory is Coordinator for the EMBL-EBI European Genome-phenome Archive supporting archiving and sharing of personally identifiable genetic and phenotypic human data. Her academic background is in bioinformatics specifically to study post-transcriptional gene regulation. She has worked with Open Science projects including the Galaxy Project and the Human Cell Atlas, and is passionate about promoting metadata standards and best practices.
Role in OLS:
Director of Partnerships and Strategy
Malvika Sharan is a Senior Researcher at The Alan Turing Institute, where she leads a team of community managers and co-leads The Turing Way, a community-led handbook on data science. She is a co-founder of Open Life Science, and an active contributor of several open source/science projects. Connect with her on topics such as community building, open science, strategic collaboration and representation of marginalised members in leadership.
Martina is currently working at the Max-Planck-Institute AE, doing cognitive neuroscience research using computational modeling techniques. She is an open-science advocate who enjoys programming and contributing to open-source projects and communities. She provides infrastructure support for The Turing Way project as a core contributor.
A designer and open source advocate with experience building on and offline communities in open government and health and life sciences
Mesfin Diro is a faculity at Addis Ababa University, Ethiopia. Currently, He’’s a PhD student at his home institute on Redox Flow Batteries in the area of nanotechnology. He has high enthusiasm in expanding comutatational and data science skills for better research outputs. He is also passionate and advocate of open source, open access and open scientific.
Markus is a PhD student at UCL and he is one of the core developers of sktime, a toolbox for machine learning with time series.
I’ve wandered through science (neuroscience), access to science communication (open access, preprints) and community building. I currently find myself thinking more about how the money flows, who has power and how to dismantle inequitable power structures. I also watch the numbers as treasurer for Dryad (open data).
Role in OLS:
Fellowship and Finance Manager
Patricia is currently a Research Data Specialist working at the Digital Curation Centre at the University of Edinburgh. Before joining the DCC, she was the Research Repository Advisor at the University of Birmingham and have previously worked as a data librarian at CERN’’s Scientific Information Service working closely with software developers to deliver data and code sharing solutions. She loves collaborating openly and making projects welcoming to new comers.
I am a scientific training officer at the European Bioinformatics Institute (EMBL-EBI) where I mainly coordinate and support training in Latin America via the CABANA project (https://cabana.online/). My background lies in structural biology and biomedical sciences, and I am passionate about science communication, equity and inclusion.
Raniere is a PhD student at Department of Infectious Diseases and Public Health, City University of Hong Kong. He worked with the Software Sustainability Institute in the UK as community officer.
While completing his PhD in cognitive neuroscience at the Université de Montréal, Samuel organizes training events to equip his peers to make science more robust, accessible, and inclusive to all. He is the cofounder of Open Science UMontreal, an initiative that aims to facilitate the transition to a more open and transparent way of doing science.
David is a “self-designated” Data Plumber from Ghana working to build technical and data capacity for low-income individuals, organisations and communities. His background is in Biology and Computer Science and has worked with journalists, advocacy organisations, research institutions, government officials and private businesses in over 30 countries across 5 continents. Currently, he leads data research at Growing Gold Farms, a food startup in Tema, Ghana.
Sarah Gibson is a Research Software Engineer at the Alan Turing Institute where she helps solve real-world problems with cutting-edge techniques across academia, industry and the public sector. She is also a passionate open source contributor, primarily working with Project Binder to serve reproducible computational environments in the cloud around the world. On top of all that, she also promotes software best practices and reproducible workflows through her Fellowship with the Software Sustainability Institute.
Dave coordinates training and outreach for the Galaxy Project. He has been a community person in life sciences for 13 years. Before that he worked in biological databases for 7 years. His training is in Computer Science, with an emphasis on databases.
Sonika has a Ph.D. in Bioinformatics and over 15 y of work experience in academia & industry. She is currently Bioinformatics senior lecturer and research group head at Monash University Melbourne, Australia. Her expertise is in developing novel Bioinformatics and machine learning methods and applying them to solve biological research questions. In the past, she has worked in collaboration with the Australian bioinformatics network and EMBL-EBI on developing and delivering bioinformatics workshops for biologists and bioinformaticians.
Renato is a computational biologist with a background in evolution, genomics and the microbiome. Currently project and community manager of the EMBL Bio-IT project, supporting the local bio-computational community through training, consulting and core resources. Open-source and scientific reproducibility advocate. When not tanning in front of a screen you may find him wandering the green and blue in Nature.
Role in OLS:
Executive Director, Business and Development Lead
Yo is the executive director and a co-founder of OLS. As an EngD student at the University of Manchester, Yo is studying pathogen-related data sharing and sustainability of open source software.Yo is a founder of Code is Science, and previously, they were editor for the PLOS Open Source Toolkit, editor emeritus at the Journal of Open Source Software, board member of the Open Bioinformatics Foundation, and a software developer at the University of Cambridge, working on an open source biological data warehouse called InterMine.
Yvan is data management and analysis lover, for life science, health and environment
Mentorship roles can sound like a big personal responsibility and can be overwhelming for new mentors. To support our mentors in this program, we will offer training, topic-based guided discussions and opportunity for social interaction over 4 calls during the mentorship round:
In the mentor training, our mentors will then gain mentoring skills (active listening, effective questioning, giving feedback), learn to celebrate successes and gain confidence on navigating challenges in mentoring.
A dedicated slack channel will facilitate open discussions among mentors to help them discuss their experiences, challenges and tips and tricks (contact the team if you are not yet on this channel).
Experts are invited to join cohort calls or individual mentorship calls to share their experience and expertise during the program.
Athina is a neuroscientist, with a background in electrical and computer engineering. Her research combines computational and electrophysiological techniques to study human cognition.
Alejandra is the Software Engineering Group Leader at the Science and Technology Facilities Council (STFC). STFC is part of UK Research and Innovation. Her focus is around software management, which includes supporting the software developmnt process, and data management projects, which include the development of bespoke software systems to manage the experimental data produced by the large scale scientific facilities at STFC. Before joining STFC she was a Research Lecturer at the University of Oxford. Her research interests are around developing models, methods, and software tools for data science and innovative scholarly communication with the aim of enabling Findable, Accessible, Interoperable and Reusable (FAIR) data, research reproducibility and aggregation of research results.
PhD with twenty years working around bioinformatics research, project-management, and training. Currently working as a leadership trainer for postdocs and PIs. For fun I enjoy painting, playing Dungeons and Dragons, and walking my dog.
I am an Experimental Psychologist and Fellow of the SSI at the University of Manchester interested in data visualisations, open science, and reproducible research. I am the University of Manchester Open and Reproducible Research Institutional Lead.
Software Sustainability Institute’s training lead. Over the past 5 years committed to ongoing improvement of research software practice through training and community engagement work. Driving the trends in training for researchers and scientists in computational and data analysis skills forward and helping develop new training curricula.
Anita Bröllochs is the Head of Outreach at protocols.io. She studied Life Science Engineering at the Friedrich-Alexander University in Erlangen, Germany and her background is on optical clearing of skeletal muscle for multiphoton microscopy. Anita has a passion for open science and is also the host of a science podcast called ‘Minor Tweak, Major Impact’ which is aiming to shine a spotlight on method development.
Arielle has spent her career to date working in research-adjacent fields, starting with a stint at open access publisher PLOS, where she learnt the importance (and challenges) of open science, code, and data. Currently the Research Project Manager on the Tools, Practices & Systems programme at The Alan Turing Institute, she was a CSCCE Community Engagement Fellow in 2019 and continues to be actively involved in the community. She is a contributor to the Turing Way project.
I’m a research consultant and social scientist and I support researchers in developing mixed methods and qualitative research skills. I also run a peer support group called Open Post Academics (OPA) where we encourage those with a PhD to share their skills and knowledge outside of the academy.
Role in OLS:
Director of Learning and Technology
Bérénice is a bioinformatician (post-doc in the Freiburg Galaxy Team), analyzing biological data and developing tools for data analysis, mainly via Galaxy. In her current role, she also serves as a deputy training coordinator for ELIXIR Germany (de.NBI). Bérénice is passionate about training and education. She founded and co-leads the Galaxy Training Material project, and regularly giving talks and workshops on topics like data analysis, and tool development. She is also a founder of Street Science Community, a citizen science and outreach program.
Björn is working in the European Galaxy team and tries to help make science open wherever he can. He is an expert in the topics related to Container, Conda, Galaxy, Python, reproducible research, and training.
Melissa is the Training and Communications Officer with Australian BioCommons. She previously worked at EMBL-EBI and has extensive experience in developing, organising, delivering and running face-to-face and online workshops and webinars. She has a PhD in Molecular Parasitology and has worked as a Scientific Curator through which first became interested in open science practices. Some of the open-science related projects that she has been involved in include applying FAIR principles to training materials and showing researchers how they can get the most out of their data by teaching best practice in data management and the FAIR principles.
I’ve been promoting open science since 2018 (formalised with OLS-1!), and in 2020 I moved to a research support role to implement behaviour change towards the adoption of open science and reproducibility practices at our Centre (https://www.win.ox.ac.uk). I care a lot about inclusivity and being a positive role model in my interactions and leadership.
Project Officer and Technical lead in neuroscience software and infrastructure to accelerate and open neuroinformatics research workflows, based at the Montreal Neurological Institute. Mentor for Google Summer of Code and Season of Docs, and past participant in OLS program.
Daniela is a Neuroscientist with a passion for open, equitable, and transparent scholarship. She is a former Mozilla Fellow, and she now leads a project called PREreview to empower researchers to engage with each other and review preprints.
Demitra Ellina is the Editorial Community Manager at F1000Research. She is a strong advocate of Open Research and engages with the research community to raise awareness of the F1000Research publishing platforms.
Role in OLS:
Director of Finance and Operations
Emmy is the Director of Finance and Operations at Open Life Science and Engagement Lead at Invest in Open Infrastructure. She is passionate and curious about open, research culture and knowledge equity. Her expertise is in community design, and open research and scholarly communication.
Doing Bioinformatics and ML @ CERTH, Thessaloníki, GR, fan of training, Open Science and e-infras.
Bastian is a long-term research fellow at the Center for Research & Interdisciplinarity in Paris, where he studies how bottom-up communities in citizen science can peer-produce knowledge. He’s also the Director of Research for the Open Humans Foundation, an online platform & community around empowering individuals to learn from their personal data. He started his academic career in evolutionary biology & genomics and has a PhD in Bioinformatics.
Theoretical & Quantitative Ecology freak. SciComm & Open Science leader. Catalyst of movements.
Hao is the Reproducibility Librarian at the University of Florida Health Science Center Libraries. He is passionate about empowering others, whether through training in open science and reproducible research practices or promoting equity and inclusion by dismantling gatekeeping in academia.
Holger is the head of Core IT team at the Max Planck Institute for Biolological Cybernetics. He enjoys the technical aspects of science - be it programming (Python), version control (git), web services (REST), or generally (self) organization and anti-procrastination. His mission is to support scientists in all aspects IT.
Jason is a life scientist who spends most of his time working to help researchers adopt computational practices in research and education
Former neuro-geneticist (10 year of research on fruit fly memory and behavior), I have been more recently interested in data analysis and management, as a specialisation for my interests in open science (open research). I am presently working on ways (technical and social) to implement the principles of FAIR and open data in the lab workflow and ways to foster collaboration between researchers via the SmartFigure Gallery project.
Jez is Data Services Lead in The British Library’s Research Infrastructure Services team. He has over 10 years of experience developing and delivering research data management services and strategies at research-intensive higher education institutions in the UK, as part of a long-term goal to help communicate and collaborate more effectively using technology. He is an experienced teacher and is involved with The Carpentries as a Certified Instructor and early contributor to Library Carpentry. He is particularly interested in elevating the status of research software alongside research data in the scholarly record, and helping researchers develop the skills to make the most of this. He is a Fellow of the Software Sustainability Institute, 2020 intake.
Kari is the Senior Director of Equity and Assessment for The Carpentries, Executive Director of the Engineer Like a Girl after-school program, and a Zumba Fitness Instructor! Kari’s background is mechanical engineering, and she earned a PhD in Engineering Education from The Ohio State University. Her doctoral research explored self-efficacy of underrepresented engineering students. After completing a post-doc in the Engineering Fundamentals Department at Embry-Riddle Aeronautical University, she was hired to lead The Carpentries assessment efforts. In her current role, her focus is developing programs through the lens of equity, and setting strategic efforts around assessment that inform The Carpentries curriculum and other initiatives.
PhD in medical sciences with expertise in infectious diseases and vaccines with expansive knowledge of the data driven life science industry. Proven ability to present and write clearly and persuasively, complex scientific and technical content, tailored to different audiences. Experience in inspiring, enthusing and influencing stakeholders and leading teams while navigating different cultural contexts. Extensive experience in developing strategies for national and international projects covering public-private partnerships, communication, and outreach as well as scientific programmes.
Caleb is a 19/20 Mozilla Fellow and a Bioinformatician, interested in teaching, open science, reproducibility, machine learning, FAIR Genomics, and community building.
Kirstie is a lead of the Tools, Practices and Systems research programme at the Alan Turing Institute (London, UK) and senior research associate in the Department of Psychiatry at the University of Cambridge. Her work covers a broad range of interests and methods, but the driving principle is to improve the lives of neurodivergent people and people with mental health conditions. Dr Whitaker uses magnetic resonance imaging to study child and adolescent brain development and participatory citizen science to educate non-autistic people about how they can better support autistic friends and colleagues. She is the lead developer of The Turing Way, an openly developed educational resource to enable more reproducible data science. Kirstie is a passionate advocate for making science ‘‘open for all’’ by promoting equity and inclusion for people from diverse backgrounds, and by changing the academic incentive structure to reward collaborative working. She is the chair of the Turing Institute’’s Ethics Advisory Group, a Fulbright scholarship alumna and was a 2016/17 Mozilla Fellow for Science. Kirstie was named, with her collaborator Petra Vertes, as a 2016 Global Thinker by Foreign Policy magazine.
I am Community Manager RDM and Open Science at VU Amsterdam. My background is in theoretical linguistics. My goal is to help colleagues connect and learn from each other and with each other
I am a tenured researcher leading a collaborative health data science research group. I also work to improve data analysis teaching and practice. I co-founded MetaDocencia, an open, collaborative, and Spanish-speaking education community. One of the roles I enjoy most is mentoring and teaching others.
I am the principal investigator of the Big Data Biology Lab at Fudan University (Shanghai) since September 2018. Our group works in computational biology, with a focus on the very large-scale. See https://luispedro.org/
Lilly works on open source software for open science as the product manager for the Frictionless Data for Reproducible Research project at Open Knowledge Foundation. Lilly has her PhD in neuroscience from Oregon Health and Science University, where she researched brain injury in fruit flies and became an advocate for open science and open data.
Role in OLS:
Director of Partnerships and Strategy
Malvika Sharan is a Senior Researcher at The Alan Turing Institute, where she leads a team of community managers and co-leads The Turing Way, a community-led handbook on data science. She is a co-founder of Open Life Science, and an active contributor of several open source/science projects. Connect with her on topics such as community building, open science, strategic collaboration and representation of marginalised members in leadership.
Martin is a computer fellow with an interest to help scientists tackle heaps of data. Spent last 7 years working on Galaxy project core codebases.
Martina is currently working at the Max-Planck-Institute AE, doing cognitive neuroscience research using computational modeling techniques. She is an open-science advocate who enjoys programming and contributing to open-source projects and communities. She provides infrastructure support for The Turing Way project as a core contributor.
Maria is the Application and Training Specialist for Research Computing at the Peter MacCallum Cancer Centre in Melbourne, Australia. She specialises in bioinformatics and data science education and training. She is passionate about supporting researchers, reproducible research, knowledge sharing and working collaboratively.
A designer and open source advocate with experience building on and offline communities in open government and health and life sciences
Mateusz is Research Software Community Manager at the Netherlands eScience Center. He has background in life sciences and have been working with bioinformatics data analysis and research software engineering. Past few years he has been involved in the Carpentries as an instructor, trainer and mentor (both in the mentoring subcommittee and mentoring teams).
Physicist, Teacher, Mozillian
Nicolás se unió a MetaDocencia desde sus inicios en marzo de 2020 y actualmente comparte la coordinación general y es chair del comité asesor. Además es Investigador Adjunto del CONICET y miembro del Grupo de Bioinformática Estructural de la Universidad Nacional de Quilmes en Argentina. Vive con su esposa y su hijo en Buenos Aires.
I’ve wandered through science (neuroscience), access to science communication (open access, preprints) and community building. I currently find myself thinking more about how the money flows, who has power and how to dismantle inequitable power structures. I also watch the numbers as treasurer for Dryad (open data).
Paula is an Open Science advocate her passions are data management, data analytics, research, and diversity. She is a computer scientist who has worked on data intensive bioinformatics and data management. She has also collaborated on community projects such as The Carpentries, rOpenSci, RLadies. Currently she works for the National Imaging Facility in Australia.
Paul is group Leader in Machine Leader and Developmental Biology at the Turing Center for Living Systems in Marseille (France). He is leading the open science project “the digital embryo atlas” and was several times mentor in Mozilla Open Leadership’’s program.
Role in OLS:
Fellowship and Finance Manager
Patricia is currently a Research Data Specialist working at the Digital Curation Centre at the University of Edinburgh. Before joining the DCC, she was the Research Repository Advisor at the University of Birmingham and have previously worked as a data librarian at CERN’’s Scientific Information Service working closely with software developers to deliver data and code sharing solutions. She loves collaborating openly and making projects welcoming to new comers.
Former university professor and researcher. IT specialist for R&D in bioinformatics. Wikipedian and open culture enthusiast.
Rachael is the Research Software Community Manager for the Software Sustainability Institute and Open Research advocate at the University of Manchester. She is passionate about openness, transparency, reproducibility, wellbeing and inclusion in research. She was a project lead in Round 4 and Mentor and Cohort Host in Round 5 of Mozilla Open Leaders, and organises a women in data meetup group in Manchester called HER+Data MCR.
Raniere is a PhD student at Department of Infectious Diseases and Public Health, City University of Hong Kong. He worked with the Software Sustainability Institute in the UK as community officer.
A biodiversity scientist who wants to liberate research from the constraints imposed by paywalls & PDFs. Also a Lubuntu user and Software Sustainability Fellow (2016 Inauguration).
I am biologist. I worked with fungal genomics during my master and doctorate projects. Over my career, I organized several workshops for teaching programming skills to bioscientists, including the Brazilian Python Workshop for Biological Data. This year (2022), I will be an Ambassador in the eLife Community Ambassadors program.
David is a “self-designated” Data Plumber from Ghana working to build technical and data capacity for low-income individuals, organisations and communities. His background is in Biology and Computer Science and has worked with journalists, advocacy organisations, research institutions, government officials and private businesses in over 30 countries across 5 continents. Currently, he leads data research at Growing Gold Farms, a food startup in Tema, Ghana.
Sarah Gibson is a Research Software Engineer at the Alan Turing Institute where she helps solve real-world problems with cutting-edge techniques across academia, industry and the public sector. She is also a passionate open source contributor, primarily working with Project Binder to serve reproducible computational environments in the cloud around the world. On top of all that, she also promotes software best practices and reproducible workflows through her Fellowship with the Software Sustainability Institute.
Swedish-born computational biologist, since 2018 heading systems medicine (host-microbiome focus, ‘association hunting’) lab in Berlin, interested in too many things. AMR, metabolic/inflammatory/cardiovascular diseases, drug-microbiome interactions, confounder analysis, gene family evolution. Queer, transgender woman and intersectional feminist.
Julieta Arancio is a postdoctoral researcher at Drexel University (US) & the University of Bath (UK), and an associate researcher at CENIT-UNSAM in Argentina. Her research focuses on social studies of open hardware, in particular for democratization of the production of science and technology. She is a co-organizer at reGOSH, the Latin America open science hardware network, and 1/3 of the mentorship program Open Hardware Makers.
Biotechnician turned bioinformatician turned animal scientist trying to standardise workflows using Galaxy
Dave coordinates training and outreach for the Galaxy Project. He has been a community person in life sciences for 13 years. Before that he worked in biological databases for 7 years. His training is in Computer Science, with an emphasis on databases.
Toby is Director of Curriculum at The Carpentries, a community of practice building global capacity in essential data and computational skills for conducting efficient, open, and reproducible research. Before that, he was a CSCCE CEFP2019 Fellow and community manager for EMBL Bio-IT, a community of bioinformaticians/computational biologists at the European Molecular Biology Laboratory.
Sonika has a Ph.D. in Bioinformatics and over 15 y of work experience in academia & industry. She is currently Bioinformatics senior lecturer and research group head at Monash University Melbourne, Australia. Her expertise is in developing novel Bioinformatics and machine learning methods and applying them to solve biological research questions. In the past, she has worked in collaboration with the Australian bioinformatics network and EMBL-EBI on developing and delivering bioinformatics workshops for biologists and bioinformaticians.
Renato is a computational biologist with a background in evolution, genomics and the microbiome. Currently project and community manager of the EMBL Bio-IT project, supporting the local bio-computational community through training, consulting and core resources. Open-source and scientific reproducibility advocate. When not tanning in front of a screen you may find him wandering the green and blue in Nature.
Veronika’’s research area is machine learning in medical imaging. She is an now assistant professor but will be leaving her position soon. She is blogging about this and other academia-related topics on her website veronikach.com
Vicky has a PhD in Bioinformatics and an MPhil in Monitoring and Evaluation. Her research experience (qualitative and quantitative) spans Genomics and Public Health. She is currently a Project Coordinator for the Sickle Africa Data Coordinating Center at the University of Cape Town. She also coordinates several other groups and projects including the African Genomic Medicine Training Initiative (AGMT), Sickle Cell Disease Ontology Working Group (SCDO) and mGenAfrica. She is the current secretary of the African Society of Human Genetics (AfSHG). She is passionate about building research capacity, mentoring young investigators and translational research.
Role in OLS:
Executive Director, Business and Development Lead
Yo is the executive director and a co-founder of OLS. As an EngD student at the University of Manchester, Yo is studying pathogen-related data sharing and sustainability of open source software.Yo is a founder of Code is Science, and previously, they were editor for the PLOS Open Source Toolkit, editor emeritus at the Journal of Open Source Software, board member of the Open Bioinformatics Foundation, and a software developer at the University of Cambridge, working on an open source biological data warehouse called InterMine.
Yvan is data management and analysis lover, for life science, health and environment
A mentor for many previous waves of open leaders, who is currently studying for their PhD at UCL.
A dedicated slack channel will facilitate open discussions among experts and other participants in OLS-2 to help them expand their network while discussing relevant topics (contact the team if you are not yet on this channel).
Role in OLS:
Director of Learning and Technology
Bérénice is a bioinformatician (post-doc in the Freiburg Galaxy Team), analyzing biological data and developing tools for data analysis, mainly via Galaxy. In her current role, she also serves as a deputy training coordinator for ELIXIR Germany (de.NBI). Bérénice is passionate about training and education. She founded and co-leads the Galaxy Training Material project, and regularly giving talks and workshops on topics like data analysis, and tool development. She is also a founder of Street Science Community, a citizen science and outreach program.
Role in OLS:
Director of Partnerships and Strategy
Malvika Sharan is a Senior Researcher at The Alan Turing Institute, where she leads a team of community managers and co-leads The Turing Way, a community-led handbook on data science. She is a co-founder of Open Life Science, and an active contributor of several open source/science projects. Connect with her on topics such as community building, open science, strategic collaboration and representation of marginalised members in leadership.
Role in OLS:
Executive Director, Business and Development Lead
Yo is the executive director and a co-founder of OLS. As an EngD student at the University of Manchester, Yo is studying pathogen-related data sharing and sustainability of open source software.Yo is a founder of Code is Science, and previously, they were editor for the PLOS Open Source Toolkit, editor emeritus at the Journal of Open Source Software, board member of the Open Bioinformatics Foundation, and a software developer at the University of Cambridge, working on an open source biological data warehouse called InterMine.
OLS team have established the following collaborations to support organisation specific projects within the OLS-2 cohort:
Under the collaboration name OLS-2 for Turing, Open Life Science has partnered with The Turing Way, a project within the Tools, Practices and Systems Research Program in The Alan Turing Institute.
This partnership will offer training and mentoring to interested members from Turing and The Turing Way communities to join the second cohort (OLS-2) individually or in teams. They will have an opportunity to develop Open Science aspects in the projects that they either already have been working on, or want to develop in the near future. Mentors will be preferably selected from The Alan Turing Institute but there will be a possibility to match projects with the right mentor from the broader cohort. The roles and benefits for the participants and the eligibility of proposed projects will be as described for our main program.
Since this partnership was announced close to the deadline of the OLS-2 application call, we will welcome applications for OLS-2 for Turing projects until 15 July 2020 via EasyChair. This extension in deadline will ensure that the interested participants have sufficient time to discuss their plans with their supervisors within the organisation.
To share this announcement with the potential mentors, experts and project leads from the Turing and The Turing Way, please use our promotion pack.
The resources available to the OLS-2 cohort members will facilitate their communication, training, mentoring and learning process during their participation in the program.
The full cohort meetings take place every 2 weeks (unless mentioned otherwise) and last for 90 minutes.
During these calls:
The calls will be hosted online using the Zoom web-conferencing option. A link for the calls will be shared for each meeting separately.
Look up the shared notes for each call linked to the schedule in this website. You will also be updated via email each week by the organisers with additional details to aid your participation.
If you can’t make it to a call:
The call will be recorded and available on the OLS YouTube channel after the call.
If you can not attend most calls during the program due to the time zone incompatibility or other personal obligation, please let the organisers know. If you are unable to communicate with your mentor regularly or do not engage in the program as planned, we may need to evaluate if you are able to finish the program.
The Mentor-mentee calls take place every 2 weeks (unless mentioned otherwise) and last for 30 minutes.
During these calls:
Coordinate with your mentor how you manage the notes and assignments for your 1:1 calls.
The online communication options can be agreed upon by the mentor-mentee pairs. A few options to explore are the following:
If a mentor has to miss a mentee-mentor meeting, please discuss it with your mentee and reschedule your call. If you are unable to make it to any slot together, please find other ways (asynchronous documentation) to interact with your mentee.
If a mentor has to step back from the program for any reason, please communicate with the organisers to identify an alternative for their mentees.
In some weeks during which there is not cohort call, we will offer some optional skill-up calls.
The calls will be hosted online using the Zoom web-conferencing option. A link for the calls will be shared for each meeting separately.
Look up the shared notes for each call linked to the schedule in this website. You will also be updated via email each week by the organisers with additional details to aid your participation.
The coworking sessions take place in weeks during which there is not cohort call. These calls are optional but highly valuable for enhancing your understanding of the materials discussed in OLS-2 with the help of other participants.
During these calls,
The calls will be hosted online using the Zoom web-conferencing option. A link for the calls will be shared for each meeting separately.
4 mentor calls will take place during the program.
The calls will be hosted online using the Zoom web-conferencing option. A link for the calls will be shared for each meeting separately.
We have a short guide for invited speakers.
A dedicated Slack channel has been setup to facilitate real-time as well as asynchronous communication among the all members of the OLS-2 cohort. A personal invitation link will be shared with the participants via an email.
Organizers inform participants of the week schedule by email. An archive of all emails can be found on the private OLS-2 Google group.
An invitation is sent to all participants (mentees, mentors, etc) at the beginning of the program. If it is not the case, please contact the team
General updates from the program such as new posts, collaborations and relevant retweets will be shared via our official Twitter channel.
We have a public Gitter channel that can be used by members of the public contact the OLS team and community.
Updates regarding new calls for applications, announcements, and final project presentations are posted on the OLS public Google group
This project, as part of the Open Life Science community, is committed to providing a welcoming, friendly, and harassment-free environment for everyone to learn and grow by contributing. As a result, we require participants to follow our code of conduct.
This code of conduct outlines our expectations for participants within the community, as well as steps to reporting unacceptable behavior. We are committed to providing a welcoming and inspiring community for all and expect our code of conduct to be honored. Anyone who violates this code of conduct may be banned from the community.
Our open source community strives to:
Be friendly and patient.
Be welcoming: We strive to be a community that welcomes and supports people of all backgrounds and identities. This includes, but is not limited to members of any race, ethnicity, culture, national origin, colour, immigration status, social and economic class, educational level, sex, sexual orientation, gender identity and expression, age, size, family status, political belief, religion, and mental and physical ability.
Be considerate: Your work will be used by other people, and you in turn will depend on the work of others. Any decision you take will affect users and colleagues, and you should take those consequences into account when making decisions. Remember that we’re a world-wide community, so you might not be communicating in someone else’s primary language.
Be respectful: Not all of us will agree all the time, but disagreement is no excuse for poor behavior and poor manners. We might all experience some frustration now and then, but we cannot allow that frustration to turn into a personal attack. It’s important to remember that a community where people feel uncomfortable or threatened is not a productive one.
Be careful in the words that we choose: We are a community of professionals, and we conduct ourselves professionally. Be kind to others. Do not insult or put down other participants. Harassment and other exclusionary behavior aren’t acceptable. This includes, but is not limited to: Violent threats or language directed against another person, Discriminatory jokes and language, Posting sexually explicit or violent material, Posting (or threatening to post) other people’s personally identifying information (“doxing”), Personal insults, especially those using racist or sexist terms, Unwelcome sexual attention, Advocating for, or encouraging, any of the above behavior, Repeated harassment of others. In general, if someone asks you to stop, then stop.
Try to understand why we disagree: Disagreements, both social and technical, happen all the time. It is important that we resolve disagreements and differing views constructively. Remember that we’re different. Diversity contributes to the strength of our community, which is composed of people from a wide range of backgrounds. Different people have different perspectives on issues. Being unable to understand why someone holds a viewpoint doesn’t mean that they’re wrong. Don’t forget that it is human to err and blaming each other doesn’t get us anywhere. Instead, focus on helping to resolve issues and learning from mistakes.
We encourage everyone to participate and are committed to building a community for all. Although we will fail at times, we seek to treat everyone both as fairly and equally as possible. Whenever a participant has made a mistake, we expect them to take responsibility for it. If someone has been harmed or offended, it is our responsibility to listen carefully and respectfully, and do our best to right the wrong.
Although this list cannot be exhaustive, we explicitly honor diversity in age, gender, gender identity or expression, culture, ethnicity, language, national origin, political beliefs, profession, race, religion, sexual orientation, socioeconomic status, and technical ability. We will not tolerate discrimination based on any of the protected characteristics above, including participants with disabilities.
If you experience or witness unacceptable behavior, or have any other concerns, please report it by contacting the organisers - Bérénice, Malvika and Yo. (team@we-are-ols.org).
To report an issue involving one of the members, please email one of the members individually (berenice@we-are-ols.org, malvika@we-are-ols.org, yo@we-are-ols.org).
All reports will be handled with discretion. In your report please include:
Your contact information.
Names (real, nicknames, or pseudonyms) of any individuals involved. If there are additional witnesses, please include them as well. Your account of what occurred, and if you believe the incident is ongoing. If there is a publicly available record (e.g. a mailing list archive or a public IRC logger), please include a link.
Any additional information that may be helpful.
After filing a report, a representative will contact you personally, review the incident, follow up with any additional questions, and make a decision as to how to respond. If the person who is harassing you is part of the response team, they will recuse themselves from handling your incident. If the complaint originates from a member of the response team, it will be handled by a different member of the response team. We will respect confidentiality requests for the purpose of protecting victims of abuse.
This code of conduct is based on the Open Code of Conduct from the TODOGroup.