Nextflow and nf-core mentorship program to train scientists in under-represented regions to use open-source tools for reproducible research

Christopher Hakkaart

Funding Area: Capacity building / Construcción de capacidad

Problem Statement: Mentorships have proven themselves time and again to be one of the best forms of teaching. In 2022-23 the Nextflow / nf-core community ran three rounds of mentorships, pairing 30 mentees with experienced mentors. Mentees were selected from under-represented countries with scarce bioinformatics training resources. Mentors have been paid for their time using money from Chan Zuckerberg Initiative “Essential Open Source Software for Science” (CZI EOSS) grants. The results and feedback from these rounds have been fantastic. As we come to the end of the final round, the CZI funding has now expired and no new rounds are open for application. We have had many requests for additional rounds of mentorships; the mentee positions have been oversubscribed by 20x on each round. However, the program demands a significant time commitment from mentors and we do not believe that we will be able to attract sufficient volunteers without new funding. Although the Nextflow and nf-core communities have a broad international reach it is currently predominantly composed of individuals in Europe and North America. As the community grows, we continue to strive towards being a diverse global community and are motivated to promote inclusion in our projects. In particular, we intend to increase support for new members from outside of the main centers that experience greater entry barriers, including time-zone differences, language, and lack of access to local expertise.

Proposed Activities: We propose a two-year continuation of our very successful Nextflow and nf-core mentorship program, focused on leveling the playing field of entry of new nf-core pipeline developers and tool contributors and empowering them to be integrated into the active developer community. We would specifically like to continue bolstering the participation of women, LGBTQ+, underrepresented minority groups, and those from low and middle-income economies. The program will be split into two rounds per year, running from December to March and June to September, respectively. Mentors and mentees will apply to be a part of the program during an application window. Ten mentor-mentee pairs will be established each year and will work on a Nextflow or nf-core programming project, such as improving core tool functionality, adding specific features to existing pipelines, or reviewing new pipeline code. Each experienced mentor will work with a mentee to guide them through a project of their choice. Mentor-mentee pairs will work together for a minimum of 2 hours per week for 4 months. Regular check-in and networking events will be organized during the program to foster the integration of the mentees into the wider community. Mentors will provide more than 40 hours of contact time during the program. The contact time will often be at irregular and unsocial hours as many mentors will be in different time zones to mentees and will have other work commitments. As a small token of appreciation, mentors will be compensated with a $500 USD gift voucher for their commitment to the program.

Openness: Open science and open development are at the heart of Nextflow and nf-core. All nf-core code, be it nf-core components, pipelines, or tooling, is governed by the MIT license and accessible to all. All community members abide by a code of conduct and discussion happens in the open, via GitHub and Slack. Mentors will support mentees as they learn best practices for using and developing Nextflow pipelines and contributing to the nf-core project. Mentees are encouraged to use code management tools such as git and open code repositories such as GitHub. Mentees are also encouraged to attend other Nextflow and nf-core virtual events and, if possible, contribute their code to the nf-core GitHub repository. A significant part of the mentee selection criteria is based on their intentions for onward outreach during and after the program. Selection of mentees already involved with other initiatives to promote and share knowledge (e.g., local bioinformatics groups) will be favored. Mentees are encouraged to share their new knowledge with others in their local, regional, and national communities. The successes of each round of participants are celebrated and shared in a Nextflow blog post (e.g., https://www.nextflow.io/blog/2023/czi-mentorship-round-2.html) and promoted on community social media channels. Program participants are also given the opportunity to share their experiences in our weekly nf-core / bytesize seminar series (e.g., https://nf-co.re/events/2023/bytesize_mentoring).

Challenges: Attracting applications from global communities with low engagement, such as low and middle-income economies, is challenging. However, we are encouraged by the hundreds of diverse applications received during the previous rounds of the program. We also note an increase in the diversity of applications as the program builds momentum and receives recommendations from previous program participants.

Neglectedness: The first three rounds of the Nextflow and nf-core mentorship program was funded as a part of a Chan Zuckerberg Initiative EOSS Diversity and Inclusion grant (https://chanzuckerberg.com/eoss/proposals/nextflow-and-nf-core/). The third and final round of the program funded by this grant is scheduled to conclude at the end of September 2023. At present, there are no open rounds of applications to apply for continued support for this program. We are unaware of other sources of funding that would be able to support the mentorship program.

Success: We are working towards a “train the trainer” approach, whereby we hope that the mentorship program will lead to a diverse global network of skilled individuals that will support local communities and create a knock-on effect that lasts well beyond the duration of the grant. The program's success will be measured by tracking the growth and engagement of new community members. Measures, such as the number of questions asked and answered on the community Slack channels and contributions made to the organization's code base, will help us determine the program's reach. Additional measures such as attending community events, such as the bi-annual nf-core hackathons, will show us if new members actively engage with the wider community. We will also utilize the annual Seqera Labs “State of the Workflow” surveys to help track the growth of our community. The ultimate success of the program will be measured by the number of local events occurring in the mentee's communities. In time, we anticipate that mentees will take active roles in their own communities and become Nextflow and nf-core leaders, supporting others in their own leadership roles.

Total Budget: $10,000

Affiliations: Seqera Labs

LMIE Carveout: The Nextflow and nf-core communities are highly decentralized, operating in online spaces. The previous rounds of the mentorship program have been very positive for us, providing opportunities to improve our outreach to underrepresented groups. Despite this, we recognize there are still gaps in our reach and are committed to bridging these as we continue to grow. We will prioritize outreach to minority groups, such as those from LMIEs, when selecting candidates. By enabling more diverse communities we aim to continue impacting both the local communities and the broader nf-core community itself. By making connections between those who are new to the community and those who are already established implement new ideas and initiatives to further diversify our projects.

Team Skills: Seqera Labs employs a global team of three dedicated developer advocates who are focused on building the open-source Nextflow / nf-core community. They are passionate about Nextflow and nf-core and organize and oversee community initiatives, including the Nextflow and nf-core mentorship program. They have successfully run the three rounds of the program and have demonstrated the skills and knowledge that will ensure that future rounds are a success.

How Did You Hear About This Call: Word of mouth (e.g. conversations and emails from IOI staff, friends, colleagues, etc.) / Boca a boca (por ejemplo, conversaciones y correos electrónicos del personal del IOI, amigos, colegas, etc.)

Submission Number: 27