IBG hosted one of a kind EMBO course on “Research to service: Planning and running a bioinformatics core facility”

IBG hosted one of a kind EMBO course on “Research to service: Planning and running a bioinformatics core facility”

The EMBO practical course organized during 8-12 April 2019 at the IBG.

The course provided an opportunity for established and aspiring new managers of core facilities to learn from experienced core facilities managers how to develop a framework for the future development, resourcing, operation and impact assessment of their core services.

Our EMBO course was distributed over five days, each focused on discussing different challenges faced when managing a bioinformatics core facility. The unique aspect of the course was having each lecture/practical updated according to the discussions held in the previous day(s). Establishing such a dynamic content was achieved by keeping both the trainers and trainees involved in each course/practical. This stimulated lively discussions, and helped everyone to learn from each other’s experience.


Trainers and trainees all together, in front of the IBG’s entrance

Here are some highlights from each course day.

Day 1: Introduction, opportunities and challenges in managing bioinformatics core facilities

Day 1 started with an introduction given by Ezgi Karaca (IBG) on how this course was nucleated. Ezgi's presentation was followed by the keynote talk from Alexandre Bonvin (Utrecht University). Alexandre has long-standing experience in running research and service (especially EU eInfrastructure) activities concurrently. Alexandre's examples in balancing these activities provided new perspectives to the participants.


Alexandre Bonvin’s talk on Juggling research and services in bioinformatics

After the keynote, Revathi Nathaniel (EMBL-EBI) guided everyone in defining their bottlenecks/challenges. The depicted problems set five major "Challenge Themes". The breakout of each theme was summarised on boards which stayed in the training room during the entire course and were referred to at the end of each day to check which challenges we had addressed.


Five themes defined to be discussed during the course

Day 2: Designing and creating your bioinformatics service - user needs

Day 2 started with George Bell's (Whitehead Institute) refined experience in running a bioinformatics core facility. George introduced how he has been leading the Whitehead's bioinformatics core team, of which task he defines to "empowering researchers". George’s session ended with a practical covering 25 questions, guiding the participants to think and discuss the role and future of their facilities.


George Bell introduces everyone his team in Whitehead

Following George’s session, Revathi and Vera ran a dynamic and fun practical where the group was divided into teams aiming to design a "toast-making service". Observing each team approach the same task from a different angle made everyone comprehend the complexity of service design. Day 2 ended with Cath's interactive session, stimulating the trainers to think about the impact of their facilities.

Day 3: Operating your bioinformatics core facility

Day 3 started with a focus on the technical aspects of two distinct bioinformatics facilities, a small-scale compute example from IBG (by Serap Erkek), and a large-scale compute model from FMI (by Michael Stadler). Presenting these cases addressed the background heterogeneity of the trainees. Serap and Michael also led a breakout session to guide different use-case teams in defining their data, workflow, and compute needs.


Serap Erkek and Micheal Stadler introducing their bioinformatics facilities

After this session, Yasemin Turkyilmaz provided participants with handy tips and tricks in sustainably managing bio-data. Expanding on his extensive experience, Brent Richter (Partners HealthCare) then discussed how to work with sensitive data. In his talk, Brent specifically focused on data privacy and security. He underscored the importance of data encryption and data sharing/storing protocols. Brent also presented the global Bioinfo-Core interest group, which could serve as a platform in future knowledge exchange activities.


Brent Richter discusses the global Bioinfo-Core interest group

Upon Brent’s talk, Emre Karakoc (Wellcome Sanger Institute) discussed how sensitive data were handled in an Africa-wide genome association study. Emre’s talk nicely introduced how blockchain can be utilized in controlling patient/customer data. Day 3 ended with a discussion on defining/building competencies in one’s group (Cath) and what to consider when hiring staff (Brent).

Day 4: Financial and business management aspects of running a bioinformatics core facility

Sarah Butcher (EMBL-EBI) shared her diverse experience in what she calls the f-words (funding & finance). She comprehensively explained how to cost up staff, compute and service. The introduced concepts were reinforced through case studies. Finally, Vera gave an introductory training on project management, which she defines to be the path between where you are and where you want to be. She solidified her lecture by running a practical on the theory of change (where the expected outcome of the project should be updated continuously through the course of the project). The day ended in the ancient Ionian library, the Celsus Library, which became the major scientific highlight of the day.


We are at the Celsus Library, Ephesus!

Day 5: Supporting your users

Cath and Vera extended service design and competency concepts to training core facility users. Participants learned the characteristics of effective training and A how to gather user feedback and quantify the impact of a training program. In the end, the “untouched” challenges (IT management, Time management) were revisited. These topics were chosen by voting on the highest priority challenges captured on day 1 that had not yet been covered. This session was with each participant writing a ready-to-implement action plan to be followed up on their return.


Cath Brooksbank explaining her IT-decision-tree

The course ended with feedback (Revathi), wrap-up (Ezgi) sessions, and a big applause!

For more pictures and highlights, please search for #EMBObioinfocore on Twitter. Alternatively, visit our course website at http://meetings.embo.org/event/19-bioinformatics-core.


Final bus ride all together: it’s time to say good bye!

Authors: Ezgi Karaca, Cath Brooksbank