Streamline your research through the development of reproducible analysis pipelines
May 3-6, 2021
9 am - 5 pm (CEST)
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:
Adam Nunn (ecSeq Bioinformatics GmbH & University of Leipzig)
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: 30 (first-come, first-served)
Registration Fee: 989 EUR (excluding VAT)
Opening Date of Registration: January 5, 2021
Closing Date of Registration: May 1, 2021
Workshop: May 3 - 6, 2021 from 9 am to 5 pm (CEST UTC+2)
Find out what time it is at your location: Time Difference
"Excellently structured and polished workshop! The material was challenging but the way it was presented made it easy to follow and fun to engage with. The tutors made the learning environment really friendly and safe, and I got much more out of this workshop than I initially expected. Thank you!" Antonina Karakostova, University of Copenhagen, DK
"It is a very condensed course, covering really practical tricks for beginners on coding in Linux, and basically all the primary steps dealing with NGS data. Really worths the contribution of the fee and the time spent :)" Tianhao Zhao, University of Groningen, Netherlands
"This was an excellent course and I highly recommend it for anyone beginning to learn NGS data analysis. All of the topics were explained very well and it was the right amount of information for my first time taking a course on NGS data and using the Linux command line." Lynsey W., USA
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 receive a download link for our Live-Linux system with pre-installed NGS tools. When you start this with a virtualization tool (such as the free VirtualBox), a live version of Linux will be running on your computer where you can repeat and/or practice all the tasks of the course.
ecSeq Bioinformatics GmbH