Building a local bioinformatics community

A lightning talk that I had created for CarpentryCon 2018, and modified for SciPy.

Transcript

1. Malvika Sharan SciPy 2018 Building a Local Bioinformatics Community: Challenges and Efforts
2. What facilitates Bioinformatics discoveries? 11.07.18 2 Data & Database Compute Infrastructure Tools & Resources Experts & Trainers Maintenance & Distribution Development & Optimization 11.07.18 2
3. At Which organizational level to support them? Research Group Independent developers Institution Level Redundancy reduction Regional Level Connecting different groups National Level Gaining funding and visibility International Level Standardization and more resources 11.07.18 4 Community Exchanging experiences - Training, mentoring, supporting other communities
4. 11 July 2018 5 I’ll Talk About… • Work from direct or indirect collaboration in European Molecular Biology Laboratory (EMBL), Germany • Collective efforts of several people • Some challenges and lessons learned
5. 11 July 2018 6 Bioinformatics Communities Heidelberg Center for Human Bioinformatics ELIXIR coordinates, integrates & sustains bioinfo. resources in European member states. de.NBI is the German bioinformatics Infrastructure. EMBL is Europe’s flagship laboratory for the life sciences with more than 80 independent research groups Communities of researchers to informally exchange knowledge on different topics: training, coding, resources EMBL Bio-IT
6. 11.07.18 7 Supporting Bioinformatics Community: EMBL Bio-IT & Beyond
7. 11.07.18 8 Contributing to building other local communities • Hosted event series for local researchers Supporting Bioinformatics Community: Beyond EMBL Local Outreach Activities
8. 11.07.18 9 Volunteer Activities Contributing to building other local communities • Hosting event series for local researchers Contributing to international communities: The Carpentries • Co-organized the 1st conference in Dublin Image: Berenice Batut Local Outreach Activities Supporting Bioinformatics Community: Beyond EMBL
9. Efforts: Promoting Interaction 11/07/2018 10 Bio-IT lunches, coding club, TaskForce Meetings, Beer/pizza/BBQs events for face-to-face meetup Informal meet-up sessions to interact with local researchers and exchange ideas Online channels: remote participation to the courses, Chat system, Twitter, The Carpentries Zoom calls
10. Combining Resources: Collaborative Training Activities • Creating opportunities by combine the best resources from different communities • EMBL’s training capacity and infrastructure • de.NBI’s cloud compute and Europe-wide audience • Software and Data Carpentry courses 11.07.18 11 As of June 13, Bio-IT has offered 50 courses 0 5 10 15 20 25 2012 2013 2014 2015 2016 2017 2018 Training activities: Bio-IT and de.NBI Bio-IT Collaboration de.NBI
11. Challenges (=Aims!) 11/07/2018 12 Promote an inclusive culture & normalizing diversity and equality Make our efforts more visible and attract volunteers Enhance capacity, knowledge transfer & collaborations
12. Lessons Learned: Things Don’t Always Work! Promote communication, Encourage volunteering. Acknowledge their work 11/07/2018 13 Be open to a wider audience Identify interests & develop active groups Be consistent persistent when organizing *events. Engage Positively Diversity must exist in the core of a community. Give everyone a fair chance
13. Acknowledgement • All past and present trainers, volunteers & contributors of Bio-IT • The Carpentries (Software & Data Carpentry) Community • All past and current members 11.07.18 14 EMBL Bio-IT Few Mentions: Aidan Budd, Marc Gouw, Jean-Karim Heriche, Florian Huber, Charles Girodot, Jelle Scholtalbers, Grischa Toedt, Bernd Klaus, Matt Rogon, Eva-Maria Geissen, Mike Smith, Michael Wahlers, Jure Pecar, Markus Fritz, Thomas Hoffmann, Jonas Hartmann, Holger Dinkel, Frank Thommen, IT-Services, Wolfgang Huber, Members of Gibson, Zeller & Bork groups, HUB members Toby Hodges (Bio-IT Project co-coordinator) Toby Gibson (EMBL Group Leader)
14. Acknowledgement • All past and present trainers, volunteers & contributors of Bio-IT • The Carpentries (Software & Data Carpentry) Community • All past and current members 11.07.18 15 EMBL Bio-IT Few Mentions: Aidan Budd, Marc Gouw, Jean-Karim Heriche, Florian Huber, Charles Girodot, Jelle Scholtalbers, Grischa Toedt, Bernd Klaus, Matt Rogon, Eva-Maria Geissen, Mike Smith, Michael Wahlers, Jure Pecar, Markus Fritz, Thomas Hoffmann, Jonas Hartmann, Holger Dinkel, Frank Thommen, IT-Services, Wolfgang Huber, Members of Gibson, Zeller & Bork groups, HUB members Toby Hodges (Bio-IT Project co-coordinator) Toby Gibson (EMBL Group Leader) Travel Support from Two Sigma & NumFocus