Welcome to the 2nd cohort of Open Life Science program!

Niklas Morberg (CC BY-NC 2.0)

The OLS-2 program

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:

  1. Sharing essential knowledge required to create, lead, and sustain an Open Science project.
  2. Connecting members across different communities, backgrounds, and identities by creating space in this program for them to share their experiences and expertise.
  3. Empowering them to become effective Open Science ambassadors in their communities.

Table of content

  1. Goals and Learning Objectives
  2. Timeline
  3. Schedule
  4. Role Descriptions
    1. Project leads (aka Mentees)
    2. Mentors
      1. Mentoring training
    3. Experts
    4. Organizers
  5. Collaborators
    1. OLS-2 for Turing
  6. Resources
  7. Calls
    1. Cohort calls
    2. Mentor-mentee calls
    3. Coworking calls
    4. Mentors calls
    5. Communication channels
      1. Communication within the cohort members
        1. OLS-2 Slack Channel
        2. OLS-2 private Google group
      2. Communication with members not in the cohort
        1. Twitter
        2. Gitter
        3. OLS Google group
  8. Community Participation Guidelines
    1. Diversity Statement
    2. Reporting Issues
    3. Attribution & Acknowledgements

Goals and Learning Objectives

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:

  • Describe and define the terms openness, open science, open leadership, community interactions, value exchanges, inclusivity, accessibility, open Science practices in developing resources and training
  • Learn how to apply those principles to open leadership and working open in their projects and communities . Learn how to collect, invite, and tell stories that demonstrate how and why openness benefits the communities they serve
  • Give original examples for the types of openness in science
  • Design
    • Illustrate the need for a project, its vision, and its goals
    • Embrace and communicate the benefits of Open Science and how to strategically apply different open practices to their work
    • Identify the public resources to share their data
    • Identify the different type of Open Access and associated journals
  • Build
    • Start any project with openness in mind from day one
    • Setup a project repository on GitHub using best practices for enabling collaboration
    • Choose and apply open licenses appropriately
  • Empower
    • Create and enforce a safe working environment
    • Promote the values of Open Science to empower others to lead and collaborate
    • Include a broad range of contributors in their work
    • Communicate their work and vision in a 2min demo of elevator pitch
  • Lead an open project in science

Timeline

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 (17:00 European Time): Application webinar ( Talk + Q&A) - Notes
  • June 23, 2020 (11:00 European Time): Application webinar ( Recording + Q&A) - Notes
  • 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: Successful applicants announced
  • September, 2020: Start of the 16-week program
  • December 2020: Conclusion of the 16-week program

Schedule

During the program,

Organizers will inform participants of the week schedule by email.

Subscribe to the OLS calendar

Week Call Date Topic Agenda
Week 01: Mentor-Mentee   Meet your mentor! Meet each other and discuss your personal motivation, expectations, working practices and project goals
  Mentors   Mentor training  
Week 02: Cohort   Welcome to Open Life Science! Meet other members of your cohort, Share project vision, Intro to working openly (open canvas)
Week 03: Mentor-Mentee   Meet your mentor! Discuss assignments from the cohort call & concrete implementations
  Cohort   Social Call & Coworking session  
  Mentors   Mentor training  
Week 04: Cohort   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: Mentor-Mentee   Meet your mentor!  
  Cohort   GitHub Tutorial  
Week 06: Cohort   Open Science I: Project Development Developing Open Projects: Iterative and agile project management, Open- Source, Software, Hardware, Data
Week 07: Mentor-Mentee   Meet your mentor!  
  Coworking   Coworking session  
  Mentors   Mentor training  
Week 08: Cohort   Open Science II: Knowledge Dissemination Sharing Open Project: Preprint publications, DOI and citation, Open protocols, Open Education & Training
Week 09: Mentor-Mentee   Meet your mentor!  
  Coworking   Coworking session  
Week 10: Cohort   Open Science III: Next steps FAIRification of existing or mature projects, etc
Week 11: Mentor-Mentee   Meet your mentor!  
  Coworking   Coworking session  
  Mentors   Mentor training  
Week 12: Cohort   Mental health care, Ally skills and Career Guidance Call  
Week 13: Mentor-Mentee   Meet your mentor!  
  Cohort   Open Agenda - Social Call  
Week 14: Cohort   Designing & Empowering for inclusivity Personas and pathways for contributors, Implicit bias & mental health care, Community interactions & Ally-skill
Week 15: Mentor-Mentee   Meet your mentor! Preparation for the final demos
  Cohort   Final presentation rehearsal  
Week 16: Cohort   Final presentations & Graduation! 5-minute demos of projects (Audience: entire community & public, Open and recorded call)
  Mentors   Mentor wrap up  

Role Descriptions

Project leads (aka Mentees)

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.

Mentors

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 advice and inspire

  • Connect: to people, programs, companies
  • Recommend: resources, readings, classes, experiences
  • Feedback: for the project leads to consider

Pool of mentors for OLS-2

The GitHub avatar of

Aidan Budd

@AidanBudd

Expertise:
Community building, Communications, Inclusion and diversity, Delivering events, Leadership training, Previous research, event organisation and planning, in bioinformatics

More about Aidan

The GitHub avatar of

Andrew Stewart

@ajstewart_lang

Expertise:
Experimental Psychology, Research Methods, Data Science, R (teaching and research), Cognitive (Neuro)science

More about Andrew

The GitHub avatar of

Anelda van der Walt

Pronouns: she/her
@aneldavdw

South Africa

Expertise:
Open science, Capacity development, Community building, Following the road less travelled, Working with academia as non-academic, Setting up project websites (as non-developer), Women in tech, Used to work in NGS

More about Anelda

The GitHub avatar of

Anita Bröllochs

Pronouns: she/her
@AnitaBroellochs

Expertise:
Open method sharing, Best practices for writing protocols, Reproducibility, Podcasting, Social media, Webinars, protocols.io which covers a large diversity of life science topics

More about Anita

The GitHub avatar of

Anjali Mazumder

Pronouns: she/her

Alan Turing Institute , UK

Expertise:
Data Science, Ethics, Human Right, Statistics, Law, Data science informed decision-making in policy

More about Anjali

The GitHub avatar of

Arielle Bennett

Pronouns: she/her
@biotechchat

Expertise:
Road mapping and strategy planning, Community consultation, Culture change, Code of conducts, Community goals, Drug discovery, Computational biology, Neuroscience.

More about Arielle

The GitHub avatar of

Bérénice Batut

Pronouns: she/her
@bebatut

University of Freiburg , Germany

Expertise:
OLS co-lead, Galaxy and Galaxy training, Citizen science, Bioinformatics, High-throughput sequencing, Metagenomics

More about Bérénice

The GitHub avatar of

Björn Grüning

@bjoerngruening

Expertise:
Containers, Conda, Galaxy, Python, Training, Reproducible research, Cheminformatics, Genome annotation, High-Throughput-Screening, Epigenetics

More about Björn

The GitHub avatar of

Bruno Eleres Soares

Pronouns: he/him
@Bruno_E_Soares

Universidade Federal do Rio de Janeiro , Brazil

Expertise:
OLS-1 project lead, SciComm, Community building, Open Data, Biodiversity

More about Bruno

The GitHub avatar of

Melissa Burke

Pronouns: she/her
@burkemlou

Australia

Expertise:
Training, Functional genomics, Data management basics, E-learning, Infectious diseases, Molecular biology, Bioinformatics, Parasitology, Microbiology, Host-pathogen interactions

More about Melissa

The GitHub avatar of

Christine Rogers

Pronouns: she/her
@xtinerogers

Montreal Neurological Institute, McGill University , Canada

Expertise:
OLS-1 project lead, Data sharing, Open science, Software development, Open source, Neuroscience, Interoperability, Neuroinformatics

More about Christine

The GitHub avatar of

Delphine Lariviere

@ddlariviere

Penn State University , USA

Expertise:
Organization of open-source/collaborative projects, Github, Zenodo, Publishing tools in Galaxy, Writing documentation, Construction of analysis workflow, Handling data format, Quality control, Genomics analyses, Statistical analyses

More about Delphine

The GitHub avatar of

Emmy Tsang

@emmy_ft

Expertise:
Community strategies, Publishing and scholarly communication, Neuroscience

More about Emmy

The GitHub avatar of

Festus Nyasimi

Pronouns: he/him
@Festus_nyasimi

International Centre of Insect Physiology and Ecology (ICIPE) , Kenya

Expertise:
OLS-1 project lead, Bioinformatics, Biomedical Research

More about Festus

The GitHub avatar of

Fotis Psomopoulos

@fopsom

Expertise:
Open Software, Software Management, Reproducible workflows, E-Infrastructures (ELIXIR, EOSC), RDA, Machine Learning, Algorithm design and implementation, Bioinformatics (NGS data analysis, Data Integration)

More about Fotis

The GitHub avatar of

Holger Dinkel

Expertise:
Programming (Python), Version control (git), Web services (REST), Anti-procrastination, Protein biology, Bioinformatics, Disorder motifs

More about Holger

The GitHub avatar of

Hans-Rudolf Hotz

Pronouns: he/him
@hrhotz

Friedrich Miescher Institute , Switzerland

Expertise:
Galaxy, Bioconductor, Perl, Python, PostgreSQL, Bioinformatics, Next Generation Sequencing

More about Hans-Rudolf

The GitHub avatar of

Ivo Jimenez

Pronouns: he/him
@ivotron

UC Santa Cruz , US

Expertise:
Reproducibility, Open science, Open data, Working open, Automation, Large-scale data management, General aspects of applying ML, Kubernetes, DevOps in scientific projects, Genomics, and bioinformatics in general

More about Ivo

The GitHub avatar of

Jez Cope

Pronouns: he/him
@jezcope

The British Library , UK

Expertise:
Research data management, Open access publishing, Research software sharing, Learning & teaching, Libraries

More about Jez

The GitHub avatar of

Kari L. Jordan

@drkariljordan

Expertise:
Equity and Inclusion, Assessment, Strategic Planning, Project Planning, Public speaking, Leadership

More about Kari

The GitHub avatar of

Katharina Lauer

Pronouns: she/her

Expertise:
Stakeholder engagement, Entrepreneurship, Open data resources, Strategy and business development, Public-private partnerships, Data driven life sciences, Virology

More about Katharina

The GitHub avatar of

Michael Kofia Landi

@CofiaLandy

International Livestock Research Institute , Kenya

Expertise:
OLS-1 project lead

The GitHub avatar of

Lena Karvovskaya

Pronouns: she/her
@LangData

Free University of Amsterdam , Netherlands

Expertise:
Research data management, Data stewardship, FAIR principles, Community building, Life sciences, Community of research supporterss

More about Lena

The GitHub avatar of

Lilian Juma

Pronouns: she/her

Information Training and Outreach Centre for Africa , Kenya

Expertise:
OLS-1 project lead

The GitHub avatar of

Lorena Pantano

Pronouns: she/her
@lopantano

CRG, Barcelona , Spain

Expertise:
Genomic, Transcriptomic, Python, Visualization, Gene editing, Xenotransplantation, Health science

More about Lorena

The GitHub avatar of

Luis Pedro Coelho

@luispedrocoelho

Expertise:
Computational biology, Group leadership, Microbiome

More about Luis Pedro

The GitHub avatar of

Mallory Freeberg

Pronouns: she/her
@MalloryFreeberg

EMBL/EBI , UK

Expertise:
Metadata, FAIR principles, Single cell sequencing, RNA/small RNA biology, Post-transcriptional gene regulation, Ontologies, Project management, Data management, Bioinformatics, Galaxy, Python, R, SQL, Unix, GitHub, Human genomics and phenomics

More about Mallory

The GitHub avatar of

Malvika Sharan

@MalvikaSharan

Expertise:
OLS co-lead, Community building, Mentorship, Data Science best practices, Inclusive and collaborative practices, Python, Git, Unix, Bioinformatics, Algorithm design

More about Malvika

The GitHub avatar of

Martina Vilas

Pronouns: she/her
@martinagvilas

Expertise:
Open-source, Open-source documentation, Open-infrastructure, Open-science communities, Version control, Machine learning, Neuroimaging, Neuroscience

More about Martina

The GitHub avatar of

Maria Doyle


Peter MacCallum Cancer Centre , Australia

Expertise:
Training material, Documentation, Cancer research

More about Maria

The GitHub avatar of

Meag Doherty

Pronouns: she/her
@emdohh

Expertise:
User research, Product strategy, Experience analytics, open research tools (https://www.researchallofus.org/)

More about Meag

The GitHub avatar of

Margaret Wanjiku

@meg_wanjiku

International Livestock Research Institute , Kenya

Expertise:
OLS-1 project lead

The GitHub avatar of

Mesfin Diro

Pronouns: he/him
@mesfindiro

Addis Ababa University , Ethiopia

Expertise:
Data science, Machine Learning, HPC, Nanotechnology, Bioinformatics

More about Mesfin

The GitHub avatar of

Mateusz Kuzak

@matkuzak

Expertise:
Training, Open research software, Community building

More about Mateusz

The GitHub avatar of

Markus Löning

Pronouns: he/him
@mm_loening

University College London , UK

Expertise:
Git, GitHub, Software development, Python, Continuous integration, Unit testing, Machine learning, Packaging/distribution, Applied machine learning projects in biochemical engineering, health and agricultural research

More about Markus

The GitHub avatar of

Naomi Penfold

Pronouns: she/her/they/them
@npscience

Expertise:
Designing participatory events (online and in-person), Community management (including codes of conduct, programming and content), The importance of self-care!, Community engagement across life and biomedical sciences

More about Naomi

The GitHub avatar of

Patricia Herterich

@pherterich

Expertise:
Data management, Collaboration, Library and archiving skills, Open Science and community

More about Patricia Herterich

The GitHub avatar of

Piv Gopalasingam

Pronouns: he/him
@cascade21

EMBL-EBI , UK

Expertise:
Education and training, Course design and delivery, Science communication, Structural biology, Biomedical sciences

More about Piv

The GitHub avatar of

Raniere Silva

Pronouns: he/him
@rgaiacs

Expertise:
GitHub/GitLab, License, Community, Teaching, Machine Learning, X-rays

More about Raniere

The GitHub avatar of

Radhika Khetani

Pronouns: she/her
@rs_khetani

Harvard T.H. Chan School of Public Health , USA

Expertise:
Training, Consulting in the genomics area, Next Generation Sequencing in general, Transcriptomics

More about Radhika

The GitHub avatar of

Samuel Guay

Pronouns: he/him
@SamGuay_

Université de Montréal , Canada

Expertise:
OLS-1 project lead, Open Science, Building website with Hugo, Reproducible reports, Clinical neuroscience

More about Samuel

The GitHub avatar of

David Selassie Opoku

Pronouns: he/him
@sdopoku

Ghana

Expertise:
Open data, Low-income/low-tech data skills and resource design, Accessible data skills and resources in low-income contexts.

More about David

The GitHub avatar of

Sarah Gibson

Pronouns: she/her
@drsarahlgibson

Alan Turing Institute , UK

Expertise:
reproducibility, cloud infrastructure, Project Binder, Effective and transparent communication of scientific analyses across a range of domain, Digital Humanities research into the Industrial Revolution

More about Sarah

The GitHub avatar of

Dave Clements

Pronouns: he/him
@tnabtaf

Galaxy Project, Johns Hopkins University , USA

Expertise:
Community outreach, Training, Imposter Syndrome, Data analysis and integration

More about Dave

The GitHub avatar of

Sonika Tyagi

Pronouns: she/her
@tsonika

Monash University Melbourne , Australia

Expertise:
Genomics, Machine Learning, Data Science, Computational Epigenomics, Transcriptomics

More about Sonika

The GitHub avatar of

Renato Alves

Pronouns: he/him
@renato_alvs

European Molecular Biology Laboratory (EMBL) , Germany

Expertise:
Full-stack developer, Computational Training, Reproducibility, OLS-1 project lead, Computational biology, Metagenomics, Meta-transcriptomics

More about Renato

The GitHub avatar of

Yo Yehudi

@yoyehudi

Expertise:
OLS co-lead, Software development, Community building, Mentoring

More about Yo

The GitHub avatar of

Yvan Le Bras

Pronouns: he/him
@Yvan2935

Muséum national d'Histoire naturelle , France

Expertise:
Galaxy power user, Life science data analysis, Ecology

More about Yvan

The GitHub avatar of

Harry Smith

@Zebetus

Expertise:
Community Organisation, Event organising, Communication, Physics (Quantum Nanowires)

More about Harry

Mentoring training

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:

  • 2 training calls in the beginning of the cohort to get participants trained and prepared for their role as mentors
  • 1 catch-up call in the middle of the cohort to discuss new topics and challenges that might have occurred and address them
  • 1 call at the end to capture experiences of mentors and assess their interest in future cohorts
  • Social and co-working calls schedule will be agreed among the mentors as per their needs and interests

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

Experts are invited to join cohort calls or individual mentorship calls to share their experience and expertise during the program.

The GitHub avatar of

Athina Tzovara

@aath0

Expertise:
Machine Learning, Statistics, Python programming, Neuroscience

More about Athina

The GitHub avatar of

Aidan Budd

@AidanBudd

Expertise:
Community building, Communications, Inclusion and diversity, Delivering events, Leadership training, Previous research, event organisation and planning, in bioinformatics

More about Aidan

The GitHub avatar of

Andrew Stewart

@ajstewart_lang

Expertise:
Experimental Psychology, Research Methods, Data Science, R (teaching and research), Cognitive (Neuro)science

More about Andrew

The GitHub avatar of

Alex Chan

Pronouns: they/them
@alexwlchan

Wellcome Trust , UK

The GitHub avatar of

Aleksandra Nenadic

@aleks_nenadic

Expertise:
Teaching pedagogy and instructor training, Programming, GitHub, Version control, Website and Frameworks, Carpentry community, Event hosting and organisation.

More about Aleksandra

The GitHub avatar of

Anita Bröllochs

Pronouns: she/her
@AnitaBroellochs

Expertise:
Open method sharing, Best practices for writing protocols, Reproducibility, Podcasting, Social media, Webinars, protocols.io which covers a large diversity of life science topics

More about Anita

The GitHub avatar of

Arielle Bennett

Pronouns: she/her
@biotechchat

Expertise:
Road mapping and strategy planning, Community consultation, Culture change, Code of conducts, Community goals, Drug discovery, Computational biology, Neuroscience.

More about Arielle

The GitHub avatar of

Beth Duckles

@bduckles

US

The GitHub avatar of

Bérénice Batut

Pronouns: she/her
@bebatut

University of Freiburg , Germany

Expertise:
OLS co-lead, Galaxy and Galaxy training, Citizen science, Bioinformatics, High-throughput sequencing, Metagenomics

More about Bérénice

The GitHub avatar of

Björn Grüning

@bjoerngruening

Expertise:
Containers, Conda, Galaxy, Python, Training, Reproducible research, Cheminformatics, Genome annotation, High-Throughput-Screening, Epigenetics

More about Björn

The GitHub avatar of

Melissa Burke

Pronouns: she/her
@burkemlou

Australia

Expertise:
Training, Functional genomics, Data management basics, E-learning, Infectious diseases, Molecular biology, Bioinformatics, Parasitology, Microbiology, Host-pathogen interactions

More about Melissa

The GitHub avatar of

Cassandra Gould van Praag

Pronouns: she/her
@cassgvp

University of Oxford , UK

Expertise:
OLS-1 project lead, Online conferences, Behaviour change, Community engagement, Open science practices, Neuroimaging

More about Cassandra

The GitHub avatar of

Chiara Bertipaglia

Pronouns: she/her
@ChiaBertipaglia

Columbia University’s Zuckerman Institute , USA

Expertise:
OLS-1 project lead, Neuroscience

The GitHub avatar of

Christine Rogers

Pronouns: she/her
@xtinerogers

Montreal Neurological Institute, McGill University , Canada

Expertise:
OLS-1 project lead, Data sharing, Open science, Software development, Open source, Neuroscience, Interoperability, Neuroinformatics

More about Christine

The GitHub avatar of

Daniela Saderi

@Neurosarda

Expertise:
Open scholarship, Community organizing, Research, leadership, Neuroscience

More about Daniela

The GitHub avatar of

Demitra Ellina

@j_ellina

Expertise:
Open Research practises, Open data, Open peer review models, Open access publishing

More about Demitra

The GitHub avatar of

Emmy Tsang

@emmy_ft

Expertise:
Community strategies, Publishing and scholarly communication, Neuroscience

More about Emmy

The GitHub avatar of

Fotis Psomopoulos

@fopsom

Expertise:
Open Software, Software Management, Reproducible workflows, E-Infrastructures (ELIXIR, EOSC), RDA, Machine Learning, Algorithm design and implementation, Bioinformatics (NGS data analysis, Data Integration)

More about Fotis

The GitHub avatar of

Bastian Greshake Tzovaras

@gedankenstuecke

Expertise:
Citizen science, Open source, Genomics, Bioinformatics

More about Bastian

The GitHub avatar of

Gracielle Higino

Expertise:
Project management, Outreach and communication, Creativity, Research, Version control

More about Gracielle

The GitHub avatar of

Hao Ye

Pronouns: he/him
@Hao_and_Y

University of Florida Health Science Center Libraries , USA

Expertise:
R, Git and Github, Version control, Time series analysis, Research reproducibility, Community management, Ally skill training, Ecology, Health Sciences

More about Hao

The GitHub avatar of

Holger Dinkel

Expertise:
Programming (Python), Version control (git), Web services (REST), Anti-procrastination, Protein biology, Bioinformatics, Disorder motifs

More about Holger

The GitHub avatar of

Jason Williams

@JasonWilliamsNY

Expertise:
Education and training, Life Science Education, Management and leadership, Bioinformatics, Molecular biology

More about Jason

The GitHub avatar of

Julien Colomb

Pronouns: he/him

Germany

Expertise:
Research data management, Software, Communtiy building, Neurobiology

More about Julien

The GitHub avatar of

Jez Cope

Pronouns: he/him
@jezcope

The British Library , UK

Expertise:
Research data management, Open access publishing, Research software sharing, Learning & teaching, Libraries

More about Jez

The GitHub avatar of

Kari L. Jordan

@drkariljordan

Expertise:
Equity and Inclusion, Assessment, Strategic Planning, Project Planning, Public speaking, Leadership

More about Kari

The GitHub avatar of

Katharina Lauer

Pronouns: she/her

Expertise:
Stakeholder engagement, Entrepreneurship, Open data resources, Strategy and business development, Public-private partnerships, Data driven life sciences, Virology

More about Katharina

The GitHub avatar of

Caleb Kibet

@calkibet

Expertise:
Community building, Reproducibility, Computational Biology, Regulatory Genomics

More about Caleb

The GitHub avatar of

Kirstie Whitaker

@kirstie_j

Expertise:
Open research, Reproducibility, Community building, Citizen science, Equity and inclusion, Human brain imaging (neuroscience)

More about Kirstie

The GitHub avatar of

Lena Karvovskaya

Pronouns: she/her
@LangData

Free University of Amsterdam , Netherlands

Expertise:
Research data management, Data stewardship, FAIR principles, Community building, Life sciences, Community of research supporterss

More about Lena

The GitHub avatar of

Laura Ación

Pronouns: she/her
@_lacion_

University of Buenos Aires-CONICET , Argentina

Expertise:
Health data science and artificial intelligence/Biostatistics, Addiction research, Open education, Community building

More about Laura

The GitHub avatar of

Luis Pedro Coelho

@luispedrocoelho

Expertise:
Computational biology, Group leadership, Microbiome

More about Luis Pedro

The GitHub avatar of

Lilly Winfree

Pronouns: she/her
@lilscientista

Open Knowledge Foundation , USA

Expertise:
Project management, Open source, Open data, Open science, Data management, Project communications, Giving presentations, Writing documentation, Working with a distributed team, Working with oceanographers, neuroscientists, geneticists, bioinformaticians, ecologists to name a few, Cellular neuroscience

More about Lilly

The GitHub avatar of

Malvika Sharan

@MalvikaSharan

Expertise:
OLS co-lead, Community building, Mentorship, Data Science best practices, Inclusive and collaborative practices, Python, Git, Unix, Bioinformatics, Algorithm design

More about Malvika

The GitHub avatar of

Martin Čech

Pronouns: he/him

Czech Republic

Expertise:
Galaxy project, Software development, Reproducibility, Computational infrastructure, Computer science, DNA sequencing, Multi-omics, Frameworks behind the software aspects of the science.

More about Martin

The GitHub avatar of

Martina Vilas

Pronouns: she/her
@martinagvilas

Expertise:
Open-source, Open-source documentation, Open-infrastructure, Open-science communities, Version control, Machine learning, Neuroimaging, Neuroscience

More about Martina

The GitHub avatar of

Maria Doyle


Peter MacCallum Cancer Centre , Australia

Expertise:
Training material, Documentation, Cancer research

More about Maria

The GitHub avatar of

Meag Doherty

Pronouns: she/her
@emdohh

Expertise:
User research, Product strategy, Experience analytics, open research tools (https://www.researchallofus.org/)

More about Meag

The GitHub avatar of

Mateusz Kuzak

@matkuzak

Expertise:
Training, Open research software, Community building

More about Mateusz

The GitHub avatar of

Nikolaos Nerantzis

@nerantzis

Expertise:
Inclusion, Accessibility, Teaching and education

More about Nikolaos

The GitHub avatar of

Nicolas Palopoli

Pronouns: he/him
@npalopoli

Universidad Nacional de Quilmes & CONICET , Argentina

Expertise:
Bioinformatics and Computational Biology, Molecular Biology, Protein sequence, structure, evolution and interactions, Molecular interactions, Molecular evolution

More about Nicolas

The GitHub avatar of

Naomi Penfold

Pronouns: she/her/they/them
@npscience

Expertise:
Designing participatory events (online and in-person), Community management (including codes of conduct, programming and content), The importance of self-care!, Community engagement across life and biomedical sciences

More about Naomi

The GitHub avatar of

Paula Andrea Martinez

Expertise:
Biomedical, Bioinformatics, Training and skill-building, Open Science

More about Paula

The GitHub avatar of

Paul Villoutreix

Pronouns: he/him
@paulvilloutreix

Expertise:
Machine learning, Microscopy, Transcriptomics, Applied mathematics, Graph based modelling, Developmental biology, Transcriptomics, Microscopy imaging data analysis

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Patricia Herterich

@pherterich

Expertise:
Data management, Collaboration, Library and archiving skills, Open Science and community

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Giuseppe Profiti

Pronouns: he/him

Expertise:
Devops - Continuous Integration/Deployment, Reproducible environments, Best practices in research software, Wikidata, Wikipedia, Reproducible science, Git, Automation, Open and public databases and sources, Bioinformatics, Computational biology

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Rachael Ainsworth

@rachaelevelyn

Expertise:
Open Science/Research, Reproducibility, Organising events, Community building, GitHub

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Raniere Silva

Pronouns: he/him
@rgaiacs

Expertise:
GitHub/GitLab, License, Community, Teaching, Machine Learning, X-rays

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Ross Mounce

Pronouns: he/him

Expertise:
Policy, Legal aspects of text and data mining, Taxonomy & Nomenclature, Systematics & Palaeontology

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Renato Augusto Corrêa dos Santos

@CorreaSantosRA

Expertise:
Bioinformatics, Introduction to programming skills (Python or Perl), Fungal Biology

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David Selassie Opoku

Pronouns: he/him
@sdopoku

Ghana

Expertise:
Open data, Low-income/low-tech data skills and resource design, Accessible data skills and resources in low-income contexts.

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Sarah Gibson

Pronouns: she/her
@drsarahlgibson

Alan Turing Institute , UK

Expertise:
reproducibility, cloud infrastructure, Project Binder, Effective and transparent communication of scientific analyses across a range of domain, Digital Humanities research into the Industrial Revolution

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Sofia Kirke Forslund

Pronouns: she/her
@inanna_nalytica

Berlin

Expertise:
Computational biology, Leadership, Bioinformatics, Multi-omics, Microbiome, Systems medicine, Host-microbiome health associations, Drug mediation/effects, Antibiotic resistance, Microbiome-immune interactions, Disease biomarkers...

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Julieta Arancio

@cassandreces

Argentina

Expertise:
Hardware prototypes, Contributing and using open science hardware, Inclusive citizen/community science projects, Wikidata and other linked data tools, Open science in Latin America, Science and knowledge democratization, Open science hardware inside/outside the lab

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Tomas Klingström


Swedish University of Agricultural Sciences , Sweden

Expertise:
Bioinformatics, Figuring out the social aspects of collaborations, Thinking about stakeholder needs, Bioinformatics, Biobanking, Ethics, Cattle genomics

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Dave Clements

Pronouns: he/him
@tnabtaf

Galaxy Project, Johns Hopkins University , USA

Expertise:
Community outreach, Training, Imposter Syndrome, Data analysis and integration

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Toby Hodges

Pronouns: he/him
@tbyhdgs

Expertise:
Designing training material, Collaborating with Git & GitHub/GitLab, Publishing web content, either with GitHub/GitLab Pages or Wordpress, Community engagement, Teaching and organising workshops, Resources for learning bioinformatics, Supporting computational biology across a wide range of fields, Taxonomic classification of high-throughput DNA/RNA sequencing data

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Sonika Tyagi

Pronouns: she/her
@tsonika

Monash University Melbourne , Australia

Expertise:
Genomics, Machine Learning, Data Science, Computational Epigenomics, Transcriptomics

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Renato Alves

Pronouns: he/him
@renato_alvs

European Molecular Biology Laboratory (EMBL) , Germany

Expertise:
Full-stack developer, Computational Training, Reproducibility, OLS-1 project lead, Computational biology, Metagenomics, Meta-transcriptomics

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Veronika Cheplygina

Pronouns: she/her
@DrVeronikaCH

Expertise:
Machine learning, Medical imaging (classification / segmentation), Productivity/organization, Medical imaging

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Vicky Nembaware

@VickyNembaware

Expertise:
Bioinformatics, Genomics and Genomic Medicine, Training, Public Engagement, Sickle Cell Disease, Bioinformatics

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Yo Yehudi

@yoyehudi

Expertise:
OLS co-lead, Software development, Community building, Mentoring

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Yvan Le Bras

Pronouns: he/him
@Yvan2935

Muséum national d'Histoire naturelle , France

Expertise:
Galaxy power user, Life science data analysis, Ecology

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Harry Smith

@Zebetus

Expertise:
Community Organisation, Event organising, Communication, Physics (Quantum Nanowires)

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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).

Organizers

The GitHub avatar of

Bérénice Batut

Pronouns: she/her
@bebatut

University of Freiburg , Germany

Expertise:
OLS co-lead, Galaxy and Galaxy training, Citizen science, Bioinformatics, High-throughput sequencing, Metagenomics

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The GitHub avatar of

Malvika Sharan

@MalvikaSharan

Expertise:
OLS co-lead, Community building, Mentorship, Data Science best practices, Inclusive and collaborative practices, Python, Git, Unix, Bioinformatics, Algorithm design

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The GitHub avatar of

Yo Yehudi

@yoyehudi

Expertise:
OLS co-lead, Software development, Community building, Mentoring

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Collaborators

OLS team have established the following collaborations to support organisation specific projects within the OLS-2 cohort:

OLS-2 for Turing

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.

Resources

The resources available to the OLS-2 cohort members will facilitate their communication, training, mentoring and learning process during their participation in the program.

Calls

Cohort calls

The full cohort meetings take place every 2 weeks (unless mentioned otherwise) and last for 90 minutes.

During these calls:

  • Organisers/hosts will introduce new topic of the week
  • Speakers will present their work related to the topic of the week
  • Participants will be given group discussion exercises
  • An open Q&A will be run and notes will be co-developed
  • Exercises will be given for the week to be completed before the mentee-mentor meeting

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.

Mentor-mentee calls

The Mentor-mentee calls take place every 2 weeks (unless mentioned otherwise) and last for 30 minutes.

During these calls:

  • Mentors help their mentees evaluate their understanding of the new topics
  • Mentees will complete their task assigned at the cohort calls using new skills learned that week
  • Mentors and mentee will review progress together where mentees provide constructive feedback
  • Mentors will connect mentees with other experts and get consulted on their project when needed

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:

  • Zoom: 40 mins limit for each call
  • Google hangout: Free for members with google account
  • Skype: Free, download the app
  • Whereby.com: Free option, valid upto 4 participants
  • Jitsi: Free, open source web-based call is possible
  • Whatsapp or other phone-based calls: Only if both mentor and mentee are comfortable with exchanging numbers

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.

Coworking calls

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,

  • Participants can work together on the assignments
  • Participants connect and talk about their projects

The calls will be hosted online using the Zoom web-conferencing option. A link for the calls will be shared for each meeting separately.

Mentors calls

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.

Communication channels

Communication within the cohort members

OLS-2 Slack Channel

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.

OLS-2 private Google group

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

Communication with members not in the cohort

Twitter

General updates from the program such as new posts, collaborations and relevant retweets will be shared via our official Twitter channel.

Gitter

We have a public Gitter channel that can be used by members of the public contact the OLS team and community.

OLS Google group

Updates regarding new calls for applications, announcements, and final project presentations are posted on the OLS public Google group

Community Participation Guidelines

As a community we welcome everyone, and encourage a friendly and positive environment.

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.

Diversity Statement

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.

Reporting Issues

If you experience or witness unacceptable behavior, or have any other concerns, please report it by contacting the organisers - Bérénice, Malvika and Yo. (team@openlifesci.org).

To report an issue involving one of the members, please email one of the members individually (berenice@openlifesci.org, malvika@openlifesci.org, yo@openlifesci.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.

Attribution & Acknowledgements

This code of conduct is based on the Open Code of Conduct from the TODOGroup.