René Rahn (SeqAn), Hannes Hauswedell (SeqAn), Svenja Mehringer (SeqAn), Jeanette Prinz (KNIME) (CIBI)
19.09. – 21.09.2018
Berlin, Freie Universität Berlin
We are delighted to announce this year’s SeqAn User Meeting 2018 from 19th to 21st of September in Berlin. For the second time we will host it as a common User Meeting of the de.NBI Center for Integrative Bioinformatics (CIBI) and cordially invite researchers in the fields of genomics, proteomics, metabolomics, data mining and bioimage analysis to come together and share their knowledge.
We are excited to demonstrate for the first time the brand-new design of SeqAn3. In this context, we have a dedicated training day for beginners and advanced users on implementing applications with SeqAn3. With the help of your feedback and our experiences from past years we are convinced that SeqAn3 will make it genuinely easier to write applications with our library, while still providing the familiar performance of our algorithms and data structures.
Furthermore, we will have a training course for data scientists to learn how to process genomics data within KNIME using SeqAn and external NGS tools and the KNIME REST Web service functionality to query information from online web services such as ENSEMBL.
In addition, we will setup bring-you-own-data (BYOD) sessions, where you can bring your data and meet the developers and other scientists to discuss and implement solutions for analysing your own data.
The program will be complemented with key notes and talks from researchers in the field that give you new insights in the most recent development of our tools and show you demonstrations of current projects using multi-omics analysis.
- What SeqAn 3 is and is capable of
- How to write tools with SeqAn 3
- What KNIME is and is capable of
- How to incorporate and share existing tools within KNIME
- Practical experience with KNIME through an exercise on sequence analysis
The tutorials are suited for beginners and intermediate programmers and users in the domain of sequence analysis (read mapping, variant detection, metagenomics, RNseq, assembly, etc.). Prior knowledge of SeqAn or KNIME is not required, albeit it can be very helpful.
For the programming part a basic knowledge in C++ is required. Also, the following compilers and command line tools for the programming part are required:
- MacOS (g++-7 or higher) or Linux or BSD (g++-7 or higher)
- Cmake-3.0 or higher
For the KNIME part the latest version 3.6 will be used.
We will provide an ubuntu virtual machine with preinstalled software ready to use (requires virtual box installation and at least 40 GB of free disk space.)
Please register here: https://sites.google.com/view/cibi-user-meeting-2018/home/registration
SeqAn, KNIME, Sequence Analysis
KNIME 3.6, SeqAn 3, [optional] VirtualBox (We will provide a fully integrated Ubuntu VM with all necessary software preinstalled)