Streamline your research through the development of reproducible analysis pipelines
May 27-29, 2024
9 am - 5 pm (CEST UTC+2)
The purpose of the workshop is to introduce the concepts of bioinformatic pipeline development through the context of the open source Workflow Management System (WMS) Nextflow. The participants will be trained in the scripting, configuration and execution of example analysis pipelines based on current industry best-practices, and learn how to share them with other users. Finally, the participants will apply everything they have learned by implementing their own analysis pipelines from the ground up.
By the end of the workshop all attendees will be enabled to build their own scalable, reproducible bioinformatic pipelines which can be run locally, on high-performance computing clusters or even in the cloud. The course layout has been adapted to the needs of beginners in the field of computational biology and allows scientists with little or no background in software development to get a first hands-on experience in this new and fast-evolving area of expertise. This instructor-led live online workshop has been newly designed for an engaging, interactive online learning experience.
Our trainers have a proven record of academic and/or industrial experience in NGS data analysis. Because up-to-date expert knowledge is needed to answer your questions and know what is important in the field.
We only use open source tools that are free to use for academia and industry.
For an optimal learning experience we carefully prepare our learning materials and example data.
This workshop has been adapted to the needs of beginners in the field of (biological) data analysis and comprises these three course modules:
Dr. Adam Nunn (ecSeq Bioinformatics GmbH)
is a PhD student at the Marie Skłodowska-Curie Innovative Training Network 'Epidiverse'. He developed several bioinformatics pipelines using Nextflow for this European network.
Dr. Mario Fasold (ecSeq Bioinformatics GmbH)
Mario works in the analysis of microarray data since 2007 and developed several bioinformatics tools such as the Bioconductor package AffyRNADegradation and the Larpack program package. Since 2011 he specialized in the field of NGS data analysis and helped analysing sequencing data of several large consortium projects.
The target audience are biologists or data analysts with no or little experience in developing computational pipelines for data analysis. A superficial understanding of molecular biology (DNA, RNA, gene expression, PCR, ...) is assumed, as examples will be given in the context of this field.
Some familiarity with a command line interface (e.g. Linux, Mac OS X) and a minimal understanding of object-oriented programming (with e.g. Python or Java) is recommended but not required.
A current desktop computer / laptop with an up-to-date browser (Firefox or Chrome) is required.
Available Seats: 20 (first-come, first-served)
Registration Fee: 989 EUR (excluding VAT)
Opening Date of Registration: Dec 13, 2023
Closing Date of Registration: May 17, 2024
Workshop: May 27-29, 2024 from 9 am to 5 pm (CEST UTC+2)
Find out what time it is at your location: Time Difference
"Well, to be honest, I didn't know what to expect. I've gained a lot of experience in programming pipelines in Perl and Bash or Python over the last few years, I know the common bioinformatics tools, ... and yet I spent three full days learning so many new things that I now feel like a beginner again. And that's a, uhmm, good feeling :-) Adam led the workshop fantastically, with calm and patience. Even at 4:30 pm you still felt like listening and continuing. Always happy to do it again!" Sven Klages, Max Planck Institute for Molecular Genetics, Germany
"This hands-on nextflow workshop was very useful to get a better understanding of the language, from programming details to the larger picture of how to design and implement a new workflow. I liked that the transition to the DSL2-version of nextflow was also given attention. The presentation of the course material in the form of lectures was outstanding, while questions were welcomed any time and resolved quickly. The instructors were very helpful and patient whenever I ran into problems working on the exercises. All in all I learned a lot and feel lucky to have met the other participants, a group of very nice and friendly people from all over the world." Thorsten Köchling, MVZ Dr. Eberhard & Partner Dortmund, Germany
"The workshop exceeded my expectations. It was well designed and well laid out for 4 days. Apart from theory, there were excercises at each stage which worked well for basic as well as advanced users. The instructors were competent and their excellent communication helped us to absorb this advanced course. They also provided opportunity to discuss our custom problems." Aashish Srivastava, Haukeland University Hospital, Bergen, Norway
When you register for this workshop you are agreeing with our Workshop Terms and Conditions. Please read them before you register.
What you need:
The course cannot be run on phones, tablets and similar handheld devices.
We will start every morning at 9am sharp and work together until 5pm in the afternoon. There will be regular short breaks and a longer break at lunchtime.
As this is a live broadcast, you cannot pause the course and continue later. The individual exercises build on each other, so you should not leave in between.
No, you do not have to install any software to follow the course. You will get access to a high performance computer in the cloud, which you can easily log into using an in-browser console. All necessary programs are already installed on this computer. This way, we can start right away.
Of course we'll help you. If such a case should occur, we have assistants in the virtual room whom you can contact via chat. They can discuss your issue in a separate room/chat. They can also dial into your in-browser console and see exactly the same as what you see. This way they can help you directly and without much detour.
Note: The assistent can only see your in-browser terminal window but nothing else and also do not have any access to your computer.
A few days before the course we will send you the manuscript by mail. After the course, you will get the environment to continue analysis and/or practice all the tasks of the course.
ecSeq Bioinformatics GmbH