Table of content
Timeline
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September 16, 2024: Start of the program
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January 20, 2025: End of the program
Schedule
During the program,
- Mentors and mentees meet every 2 weeks for a 30 minutes call
- Mentees participate every ~2 weeks to 90-minutes cohort calls during which the program leaders introduce new topics and resources, facilitate break-out discussions, and invite experts from the field to give talks
- Mentees can participate to skill-up, Q&A or coworking sessions in the weeks without cohort calls
- Mentors take part in mentoring workshop and calls
Organizers will inform participants of the week schedule by email.
Role Descriptions
Project leads (aka Mentees)
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 advise and inspire
- Connect: to people, programs, companies
- Recommend: resources, readings, classes, experiences
- Feedback: for the project leads to consider
We thank the 11 mentors this round.
Esther works as a Data Steward at Delft University of Technology (Faculty of Applied Sciences) in the Netherlands. As a Data Steward she supports researchers with their data/code management and with sharing their research. Before this, Esther did a PhD in bioanthropology, studying the isotopic composition of human teeth to determine where they grew up.
I’m the co-founder and CEO of Ersilia, a tech non-profit focused on developing open source AI/ML tools for infectious disease research. I am excited about making open source research software accessible to everyone, building communities and supporting neglected areas of scientific research
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.
Caleb is a 19/20 Mozilla Fellow and a Bioinformatician, interested in teaching, open science, reproducibility, machine learning, FAIR Genomics, and community building.
A bioinformatician + biochemist passionate about drug discovery and finding solutions for Africa’s most burdensome diseases.
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.
Biologist turned developer, I did my PhD studying the microtubule cytoskeleton using yeast genetics, microscopy and simulations. I got interested on FAIR data and Open Science and I worked as biocurator in PomBase, the model organism database for fission yeast. Nowadays I work on ShareYourCloning, a web application to plan and document cloning strategies and genetic engineering.
Systems administrator and PhD student specializing in Workflows, Open Science and data management. I manage research platforms that enhance collaboration and reproducibility, combining technical expertise with advanced research skills.
I am a young researcher and freelance data scientist with a diverse background in Bioinformatics and Cheminformatics. Being passionate about open science, I contribute to various research and software development communities, advocating for open-source practices and fostering collaboration across different fields.
Role in OLS:
Programme Manager & Catalyst (contract)
Experts
Experts are invited to join cohort calls or individual mentorship calls to share their experience and expertise during the program.
We thank the 9 persons who registered to be experts in this round.
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.
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.
Systems administrator and PhD student specializing in Workflows, Open Science and data management. I manage research platforms that enhance collaboration and reproducibility, combining technical expertise with advanced research skills.
I am an enthusiast for using tech to make processes more efficient and reproducible. Currently, I am the Co-Executive Director of the Digital Research Academy that provides bespoke training in Open Science, Research Software Engineering, and Data Literacy through an international network of expert trainers. Things that make me happy right now are sunshine and spending time with my school-aged kid discovering the world.
Role in OLS:
Developer (contract)
I am a spirited human who specialises in breaking stereotypes and exceeding expectation. A student nurse by day, and techie by night. I enjoy podcasts, horror flicks and Jack Reacher novels.
I have a genetic engineer background and i work now as a data steward. Helping to write data management guidelines for researchers.
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.
A dedicated slack channel will facilitate open discussions among experts and other participants in OLS-9 to help them expand their network while discussing relevant topics (contact the team if you are not yet on this channel).
Facilitators
Facilitators work closely with the OLS organisers to manage and run cohort calls. They lead efforts in preparing cohort call notes, co-hosting cohort calls and ensuring the sharing of call recordings and resources through OLS channelss
We thank the 9 persons who facilitated in this round.
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.
Umar Ahmad is currently the Head, Department of Anatomy at Bauchi State University, Nigeria. He is also a founder and CEO of BioSeq, a bioinformatics company that translates omics data into informative knowledge by providing quality high-throughput sequencing (NGS) data analysis. His work in basic and translational research is focused on developing targeted therapy for human bladder cancer, colon and lung cancers with primary focus on genomics (WGS, WES) and transcriptomics (RNA-Seq, scRNA-Seq, Microarray) data integration to investigate the regulatory pathways that drive tumour recurrence and progression. Additionally, Umar works in an international team of scholarly professionals at AfricArXiv - the pan-African Open Access portal – towards increased discoverability of African research output. His role involves facilitating manuscript submission moderation and quality assurance as well as representing AfricArXiv at international meetings, events and webinars. At the Science Communication Hub Nigeria, he supports a team that provides mentorship, implements training and community building for the next generation of Nigerian scientists. Umar is a fellow of Accelerating Science and Publication in Biology (ASAPbio), a mentee and a member in The Carpentries community and a member of Open Bioinformatics Foundation. He is also the current Regional Coordinator (North East) of the Nigerian Bioinformatics and Genomics Network (NBGN). Moreover, Umar maintains a community of scientists who are passionate about bioinformatics in a slack workspace called Bioinformatics Hub to facilitate sharing of bioinformatics knowledge in Nigeria. (Link: https://docs.google.com/document/d/14ayo1wHRpDvF-L5yHaBHyEqXW29EqEApfCtf3F3xiq4/edit?usp=sharing)
Emmanuel Adamolekun is a Research fellow with Helix Biogen Institute, Ogbomosho, Nigeria ,a research organization focused on accelerating research in life through in-depth technical skills, training and capacity building in Bioinformatics and Genomics. Emmanuel graduated with a Bachelor’s degree in Medical Laboratory Science from the prestigious Ladoke Akintola University of Technology, Ogbomosho, Oyo State, Nigeria. He is currently a member of the Education and Internship committee of the International Society for Computational Biology-Student Council (ISCB-SB). He is a fellow of the Open Life Science (OLS) Mentorship programme where he is designing a Bioinformatics outreach for universit
open life science ambassador and bioinformatician interested with infectious disease research
Michael is a PhD bioinformatics student with a keen interest in epigenetics and genomics. A co-founder of Bioinformatics Hub of Kenya (BHKI). He is a certified Software Carpentries instructor, an Open Life Science (OLS) graduate and a mentor. He is passionate about capacity building!
A bioinformatician + biochemist passionate about drug discovery and finding solutions for Africa’s most burdensome diseases.
Fabrice LESSA is a young seed technologist who graduated from the University of Yaounde 1-Cameroon and has over 5 years of experience in project management in the domains of sustainable agriculture, waste management, and climate change. He has worked as a research trainee at RASA Life Science Informatics and BIOCLUES, where he researched Genome-Wide Analysis, NGS data analysis, RNA-seq/Transcriptome analysis and articles review.
I am an Early Stage Researcher focused on developing and applying novel statistical and machine learning methods for studying human health and disease. I prefer to invest my time in science communication, open science, reproducibility, and community building.
Organizers
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.
Role in OLS:
Programme Manager & Catalyst (contract)
Collaborators
This cohort is a joined effort between OLS and 3 international organisations and communities:
- Africa-OLS with Bioinformatics Hub of Kenya initiative (BHKi) amd the South African Center for Digital Language Resources (SADiLaR) via the ESCALATOR programme
- VU Amsterdam
- MetaDocencia
Resources
The resources available to the OLS-9 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.
Skill-up calls
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.
Q&A calls
The Q&A 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-4 with the help of other participants.
The calls will be hosted online using the Zoom web-conferencing option. A link for the calls will be shared for each meeting separately.
Mentor 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.
Speaker Guide
We have a short guide for invited speakers.
Community Participation Guidelines
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:
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Be friendly and patient.
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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.
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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.
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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.
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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.
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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@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:
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Your contact information.
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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.
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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.