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Open Science at EMBL

For a positive culture change in life science research

Renato Alves: Open-source practices and community building power reproducible and collaborative science

Quick take summary

Open science thrives through a blend of open-source tools, robust infrastructure, and most importantly, strong, inclusive communities.

Renato Alves shares his journey from biology to bioinformatics and community management, highlighting how collaboration, mentorship, and kindness lower barriers, improve reproducibility, and connect lab work with data and code.

The key takeaway is that sustaining open science requires investing not just in technology, but in people, communication spaces, and roles that empower others to participate openly and confidently.

Challenge 1

Life science research can suffer from fragmentation between wet-lab scientists, data scientists, and software developers, making collaboration and knowledge exchange difficult.

Solution 1

Community management and shared communication spaces (such as chat platforms and training initiatives) help bridge these gaps by creating accessible environments where people can ask questions, share knowledge, and collaborate across disciplines.

Challenge 2

Many researchers face practical barriers to open and reproducible science, such as complex tools, poor documentation, and high technical overhead.

Solution 2

Introducing tools progressively, using clear storytelling, simple language, and beginner-friendly workflows lowers friction and helps researchers focus on solving scientific problems rather than technical obstacles.

Challenge 3

Researchers often navigate concerns about recognition, accuracy, and priority, which can influence how comfortably they participate in open and collaborative practices.

Solution 3

Fostering a culture of kindness, mentorship, and generosity, modeled after open-source communities, encourages researchers to ask questions, share early work, and participate confidently in open science.

Helpful Resources

Helpful Resources

  • Open-source software and communities, including Linux and the broader open-source ecosystem
  • Python (and its community), highlighted as an accessible and well-supported programming language
  • IRC (Internet Relay Chat) as an early, low-barrier platform for open, global technical learning and collaboration
  • Google Summer of Code, as an example of structured open-source mentorship and contribution
  • Open Life Science (OLS), supporting training and mentoring around open science practices
  • Stack Overflow and Q&A-style forums, referenced as part of the evolving support ecosystem for developers and scientists
  • Workflow management systems to improve reproducibility and scalability of data analysis

EMBL Resources

  • EMBL GitLab for code sharing, version control, and issue tracking
  • EMBL chat and coding clubs at EMBL, used to lower barriers, connect experts, and support community learning
  • BioIT and training infrastructure at EMBL, providing coordinated support for data, software, and open science culture

Transcript

About Renato Alves

Dr. Renato Alves is the Senior Bioinformatics Community Manager at EMBL, where he supports training, infrastructure, communities, and building collaborations as a member of EMBL’s Data Science Center. Renato is a trained biologist and bioinformatician whose career spans open-source software development, computational biology, and community building within life sciences.

Interested in speaking on The Knowledge Catalyst?

Please contact Victoria Yan: osim@embl.de

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Credits

Production: Victoria Yan, Anandhi Iyappan

Audio Technician and Editing: Sergio Alcaide, Felix Fischer

Original music: Sergio Alcaide, Felix Fischer

Graphics: Holly Joynes

Web Design: Victoria Yan, Szymon Kasprzyk

Photography: Kinga Lubowiecka

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