BioNT - BIO Network for Training - is an international consortium of academic entities and small and medium-sized enterprises (SMEs). BioNT 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.

This practical introduction to bioinformatics will explain key concepts of sequencing data analysis as well as provide a broader overview on bioinformatics data analysis.

Data analysis is a job in high demand. As early as 2012, a Harvard Business Review article declared data science the “sexiest job of the 21st century”[1,2], and it remains an excellent career choice in “2022 and beyond” [3]. Furthermore, a study of the healthcare job market during COVID-19 clearly showed a shift towards analytical skills as a requirement in new job offers [4].

RNA-seq has revolutionised genomics and health care research by being a high-throughput and comparatively low-cost method. Along with the development of computational tools for its analysis, RNA-seq has fundamentally improved our understanding of RNA biology [5].

Galaxy is a global open-source project with the European Galaxy server being the largest instance in Europe, serving more than 70,000 users. The Freiburg Galaxy Team hosts this server out of Freiburg. Through Galaxy as a gateway, we offer free access to databases and more than 3,200 bioinformatics tools which can be used through a graphical user interface.

In this workshop, you will learn how to use Galaxy and how to perform a complete RNA-seq data analysis. However, RNA-seq data is just one of many different kinds of data analysed in bioinformatics. 

To provide an outlook on what is possible in the field of bioinformatics beyond RNA-seq data analysis, this course includes additional training materials that will be linked at the end of the course. You are encouraged to review this material on your own during the week following  the course. To address your questions about the additional materials and other course content, we will provide an open question document where you can submit any course related questions during this week.

Join this workshop if you are:

• Working in the field of Bioinformatics or biological data analysis or if you aspire to do so
• Interested in learning how to analyse transcriptomic data
• Interested in learning how to use Galaxy for data analysis

Learning Outcomes

By the end of this workshop, you will be able to:

• Interact with the data analysis platform Galaxy
• Get data from external sources into Galaxy
• Run tools on Galaxy and create a workflow
• Perform and interpret quality control of sequencing data
• Map reads on a reference genome and evaluate the mapping quality
• Explain the principle and specificity of mapping of RNA-seq data to an eukaryotic reference genome
• Select and run a state-of-the-art mapping tool for RNA-seq data
• Estimate the number of reads per gene
• Explain the count normalisation to perform before sample comparison
• Construct and run a differential gene expression analysis
• Analyse the DESeq2 output to identify, annotate, and visualise differentially expressed genes
• Understanding different bioinformatic data formats

Requirements:

• No formal training in bioinformatics or genetics is needed. Only basic knowledge of genetics is required, like: What is DNA, RNA? or What is a gene?
• Knowledge about sequencing techniques is a plus
• There is no need for programming or informatics skills 
• PC/Laptop with an up-to-date browser. Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer, may not be)
• Register a Galaxy EU account before the workshop
  • European Galaxy Server (https://usegalaxy.eu)
    • Verify the confirmation email!
    • If you have any problem please contact: contact@usegalaxy.eu
• Install the genome browser IGV if you would like you would like to inspect your data outside Galaxy

Recommendations for your setup and interaction during the workshop:

• To follow the workshop more efficiently, we recommend having a TWO-SCREEN SETUP setup. 
• To actively communicate during the workshop, please familiarise yourself with Markdown formatting by reviewing the HedgeDoc features document.

Useful links and videos

• European Galaxy Server
• Galaxy Training Material
• Meet & Join the Galaxy Community!
• Welcome to the Galaxy Training Network! 
• Galaxy UI
• History Introduction
• Code of Conduct

Interaction between participants, trainers and helpers

The workshop will be delivered in a Zoom webinar format, with participants’ visibility disabled to preserve their privacy. As a participant, you will be able to see and learn from the trainers, but a direct interaction (e.g., chat or voice) will not be possible during the sessions. Instead, a collaborative document, previously set up by the trainers, will be shared with you before the session. You will be expected to engage and interact anonymously with other participants as well as with the workshop helpers and trainers directly in this document.

Trainer Hubs

All BioNT workshops are offered at no cost, but there are a limited number of seats available. To make workshops more accessible for members of the same company we highly recommend organising what we refer to as "Training Hubs." In this arrangement, one person is formally registered for the workshop, but the knowledge sharing can be expanded to numerous colleagues within their company or SME through live-streaming the session.

Topics

How to register

The workshop is free of charge. To participate, please follow these steps:

To participate, please follow these steps:

1. Click on the window “Participate” at the top of this page
2. You will be redirected to the members.cecam.org page. If you already have an account on our platform, please proceed to Step 5
3. On the top-right corner click "Register" and complete the provided form. As indicated, completing this form does not register you for the workshop. Within 72 hours you will receive an email confirming your account has been activated. Due to this processing time, we advise you to register a few days before the registration deadline
4. After receiving the account activation confirmation, visit the workshop page again and follow instructions starting from step 1
5. You should now have an active account. After login in with your login details, you should be redirected to the workshop registration page
6. In order to start your registration please follow the instructions of the linked pre-workshop survey until you get your unique identifier
7. To finalise your registration please use the unique identifier in the CECAM platform in the corresponding section and press “Send mail” 
8. Your application is now submitted for evaluation. If selected, you will be contacted later to confirm your attendance and provide instructions for installing the required software and participating in the online workshop.

Literature

[1] Davenport, Thomas H. & Patil, DJ. “Data Scientist: The Sexiest Job of the 21st Century” Harvard Business School Publishing, October 2012, https://hbr.org/2012/10/data-scientist-the-sexiest-job-of-the-21st-century.

[2] Berinato, Scott. “Data Science and the Art of Persuasion” Harvard Business School Publishing, January-February 2019, https://hbr.org/2019/01/data-science-and-the-art-of-persuasion.

[3] UniKaksha. “Is Data Science a Good Career Choice in 2022 & Beyond?” LinkedIn, 10. März 2022, https://www.linkedin.com/pulse/data-science-good-career-choice-2022-beyond-unikaksha/.

[4]Upadhyay, H., Simsekler, M. C. E., Maalouf, M., Anwar, S., & Omar, M. COVID-19, jobs and skills—Exploratory analysis of the job postings in the US and UK healthcare job market. PloS one, 18(1), (2023). https://doi.org/10.1371/journal.pone.0278237

[5] Stark, R., Grzelak, M. & Hadfield, J. RNA sequencing: the teenage years. Nat Rev Genet 20, 631–656 (2019). https://doi.org/10.1038/s41576-019-0150-2