The BioNT consortium is dedicated to providing a comprehensive training program and fostering a community for digital skills relevant to the biotechnology industry and biomedical sector. With a curriculum tailored for both beginners and advanced professionals, BioNT aims to equip individuals with the necessary expertise in handling, processing, and visualising biological data, as well as utilising computational biology tools. Leveraging the consortium's strong background in digital literacy training and extensive network of collaborations, BioNT is poised to professionalise life sciences data management, processing, and analysis skills.

BioNT delivered its first training workshop, a Bioinformatics Introduction workshop from 4th to 8th of September, 2023. It was fully online and free of costs.

Within this practical introduction to bioinformatics, key concepts of sequencing data analysis were explained and a broader overview on bioinformatics data analysis was given. The focus was on RNA-sequencing. Indeed, RNA-sequencing revolutionised genomics and health care research, by being a high-throughput and comparatively low-cost method. Together with the development of computational tools to enable their analysis, it has fundamentally improved our understanding of RNA biology.

The Galaxy platform was selected as the training infrastructure to support this workshop. Galaxy is a worldwide open source project. The European Galaxy server is the biggest instance in Europe with more than 70,000 users. It offers free access to databases and more than 3,200 bioinformatics tools which can be used through a graphical user interface.

Within this workshop, the 30+ participants learnt how to use Galaxy and how to perform a full RNA-seq data analysis. In bioinformatics, RNA-seq data is one of the most commonly performed data analyses. However, there are many different kinds of data and potential ways to analyse them. Therefore, the last workshop day provided an overview of the wide range of bioinformatics databases and data formats.

Organisation of the workshop

The workshop "A practical introduction to bioinformatics and RNA-seq using Galaxy" ran for 5 days, from 4th to 8th of September 8, 2023. It was fully online and free of costs. Each day, a 4-hour session was delivered from 9:00 to 13:00 CEST.

Webpage and registrations

The CECAM event management platform, provided by the EPFL, was used to create a dedicated webpage (accessible at https://www.cecam.org/workshop-details/1260) for the workshop, which included the workshop description, learning objectives, requirements, program, and any further information relevant to potential participants.

For registration, the CECAM platform was used to manage the applicant's information and communication. In parallel, the EMBL servers were used to collect pre- and post-workshop information through pseudo-anonymised surveys. The survey data was linked to the applicant's data only via a unique identifier, provided in the CECAM registration process, as well as in the EMBL-based survey. This ensures that only the workshop organisers access the applicants' personal data while still collecting information relevant to the workshop separately. To register, applicants had to:

1. register on the CECAM platform,
2. complete and submit the pre-workshop survey,
3. complete the application on the CECAM platform using the unique identifier generated at the end of the pre-workshop survey.

Infrastructure for the workshop

The workshop was delivered in a Zoom webinar format, with participants' visibility disabled to preserve their privacy. Participants were able to see and learn from the trainers. However, direct interactions (e.g. chat or voice) were not possible within Zoom during the sessions. All direct interaction took place in written form via a collaborative document, where anonymous participation was ensured. To serve the collaborative documents, a HedgeDoc collaborative space was set up by BIOBYTE, and is hosted on their server.

A Main collaborative document, setup by the instructors and organisers, was shared with the participants before the session. Each section of the workshop had dedicated Hands-on boxes to report on the task status, ask questions, or raise issues. Helpers engaged and helped participants by answering the questions and issues directly in this document. This Main document was filled in live during the workshop. Separate boxes to answer questions were used to improve participant engagement and as an indirect learning assessment.

To help with the organisation, four HedgeDoc documents were used:

1. a Template with all instructions and boxes for hands-on, questions, etc;
2. the Main document with the information for the participants during the workshop, filled with boxes related to the section covered by the instructor to help with the navigation and cleaned during each break to avoid an overcrowded document;
3. a History document with everything that needed to be kept and shared with participants after the workshop
4. a document for Helpers & Instructors was created providing the workshop setup, interactions and explaining tasks of the helpers and instructors.

Galaxy, an open source platform for accessible, reproducible, and transparent computational research, via the European Galaxy server, was used during the workshop because it enables participants to access 3,000+ tools, high-performance compute resources, through a standard web browser, without requiring informatics expertise. To support this workshop, a dedicated job queue and resources was provided via the Training Infrastructure as a Service (TIaaS - https://usegalaxy.eu/tiaas/). This service also provided instructors with a dashboard, enabling them to monitor the progress of the participants.

The training material used during this workshop, i.e. slides and tutorials, are all stored and publicly available on the Galaxy Training Network website. For the first four days, existing tutorials and slides were used. For the last day, dedicated tutorials and slides were developed specifically for this workshop and contributed to the Galaxy Training Network.

Certificates

Certificates were provided to those participants who explicitly required them after checking for their participation using two criteria:

1. they joined at least one session on Zoom or notified that they could not attend live and
2. they provided links to their Galaxy histories corresponding to the taught tutorials.

Outcomes of the workshop

Applications and pre-workshop survey

73 applicants completed the pre-workshop survey and 60 submitted their application form via the CECAM platform. The pre-workshop survey consisted of 13 questions covering skills, demographics, and miscellaneous topics. The majority of questions were not mandatory for the successful completion and submission of the survey.

General information

The 73 applicants, almost at a balanced gender representation with 43.84% female and 46.58% male, were from and were working in 35 countries: 16 countries in Europe, 10 in Asia, 5 in Africa, 3 in South America, and 1 in North America. 38.36% described themselves as White, 27.4% as Asian, 9.59% as Black or African American, 8.22% Hispanic or Latino(a).

Most applicants (63%) were academic employees as graduate students (31%) or research staff (27%), from the Genetics, Genomics, or Bioinformatics field.

Related to the original target audience of this workshop, 6 applicants were industry employees and 21 were job seekers (with 12 in Academia and 3 in Industry). Regarding the connections with SMEs, 13 mentioned working in an SME, 12 collaborating with SME(s) and 22 aiming at working in an SME.

63% of the applicants planned to use Windows for the workshop, 20% macOS and 12% Linux. Finally, two applicants had visual accessibility requirements. These two participants were contacted in advance to enquire about their accessibility requirements. The organisers afterwards provided the full learning materials and an offer for further assistance, if needed.

Background information

The aim of this workshop was to give an introduction to bioinformatics and RNA-seq using Galaxy. When asked about their knowledge and use of Galaxy, the answers are quite diverse, from "never" to "daily".

There was an interest in learning how to analyse sequencing data, given the frequency with which they analyse data: 68% analyse sequencing data at least several times per year (A), but the vast majority never builds bioinformatics workflows (B). They use programming languages and/or command line tools for that (C-D).

Most applicants (85%) agree with the importance of having access to the original, raw data to be able to repeat an analysis (data not shown). The majority agree that using a programming language can make their analyses easier to reproduce, but 37% of applicants were satisfied with their current data management and analysis workflow.

Expectations

The expectations of the applicants regarding the workshop were quite diverse. They were mostly interested in learning: How to perform basic analyses, in particular RNA-seq; how to build pipelines and workflows; how to use Galaxy and cloud based bioinformatics infrastructure without complex coding; new tools; how to process (massive) biological data.

Participation

All applicants that submitted their complete application were selected to participate in the workshop, but not all of them joined for the complete workshop.

After the workshop, 18 participants requested a certificate. The certificate was provided to those 16 participants that completed the post-workshop survey and submitted their Galaxy history.

Daily feedback

At the end of each day, participants were asked for feedback on the following three points:

• Please share one thing that was good about today
• Please share one thing that that could be improved about today
• Do you have any other comments?

The daily feedback is summarised in the following Table:

Postworkshop survey

At the end of the workshop, participants were asked to fill a post-workshop survey consisting of 20 questions. In total, 28 participants completed this survey.

Regarding the workshop environment, the answers were overall positive. Participants felt comfortable learning in this workshop environment and interacting with the instructors (A-B). They felt that the instructors were enthusiastic about the workshop and knowledgeable about the material being taught (C-D). Participants could get clear answers to their questions from the instructors (E) and felt they could immediately apply what they learned at the workshop (F).

Only one accessibility issue was reported: Unstable internet connection on Wednesday that affected their ability to participate in this workshop.

Participants also shared examples of how an instructor or helper affected their learning experience. One participant liked that the instructors motivated participants to self-explore the additional available training material, as well as to finish parts of the tutorial by themselves after the course. Participants felt that it gives them a boost of inspiration and motivation to continue learning on their own, specially with the excellently prepared tutorials. Participants appreciated that instructors and helpers answered detailed questions about all the aspects of tutorials, but were also able to answer general questions that helped them improve their work even more. They appreciated the help when experiencing problems by sharing their history with helpers. Finally, it was appreciated that instructors made mistakes on their own and showed afterwards how to solve the problem.

Participants were also asked about strengths and ways to improve the workshop. All answers are summarised in the following Table:

The feedback on the post-workshop survey was positive and participants were likely to recommend this workshop to a friend or colleague.

Conclusion

The first BioNT workshop, a Bioinformatics Introduction workshop, was successfully held from 4th to 8th of September, 2023.

As it was the first workshop in this format, the infrastructure for communication, registration, collecting surveys, and teaching had to be developed and implemented. Everything has been documented and will be reused for the second workshop that will be run in November 2023.

60 persons applied for this workshop and were accepted, 41 participated and 28 filled the post-workshop survey. The feedback was positive. Some of the proposed improvements, like sharing the history document and the video directly after each workshop day, could be implemented for the second workshop. But overall, we can conclude that the workshop successfully achieved its goals.