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  • OpenMS Developer Meeting

    3 - 7 August 2020

    OpenMS Developer Meeting Educators: Julianus Pfeuffer (CIBI), Timo Sachsenberg (CIBI) Date: 3 - 7 August 2020 Location: Online Contents: The OpenMS developer meeting brings bioinformaticians working in computational mass spectrometry together to shape the future development of OpenMS. It is targeted to core developers, new developers, and potential future contributors. Short talks, developer tutorials, and code sprints will be intertwined. Participants will have the opportunity to design custom tools and workflows together with instructors. External users are welcome to bring their own ideas and will receive detailed feedback as well as help getting started in OpenMS development. Progress will be tracked on our GitHub page with a resume of each day. Prerequisites: • Target audience: This developer retreat is targeted to core, new and potential future developers of the OpenMS library and its tools. • Software requirements: For the retreat we require a working installation of any supported compiler, cmake, git, doxygen and OpenMS’ contrib libraries. Basic knowledge in C++ is highly beneficial. The participants should bring their own laptop computers. Learning goals: • Developing algorithms and tools with the OpenMS library • Working with OpenMS, its build system and its datastructures • Documenting code with Doxygen. • Deeper insights into new and established algorithms of the library • Learning the GitHub workflow of OpenMS • Designing and implementing tools or kernel classes in OpenMS Keywords: LC-MS-based proteomics and metabolomics, OpenMS, C++, algorithms for mass spectrometry, software engineering/design Tools: OpenMS, git, cmake, C++ gcc / clang toolchain 2020-08-03 09:00:00 UTC 2020-08-07 17:00:00 UTC de.NBI Korinth, Korinth, Greece Korinth Korinth Greece [] [] [] workshops_and_courses [] []
  • BioC++ - solving daily bioinformatic tasks with C++ efficiently - GCB2020

    14 September 2020

    BioC++ - solving daily bioinformatic tasks with C++ efficiently - GCB2020 Educators: René Rahn, Marcel Ehrhardt, Svenja Mehringer (CIBI) Date: 14.09.2020 9:00 - 17:00 (CEST) Location: Online - GCB Conference Contents: In this half-day tutorial we are going to teach how to use modern C++ and utilise modern C++ libraries to rapidly develop tools and scripts for operating on and manipulating large-scale sequencing data. The high variability and heterogeneity often observed within various genomic data is challenging for many standard tools, for example for read alignment and variant calling. Often, these tools are wrapped in complicated pre- and postprocessing data curation steps in order to obtain results with higher quality. However, these additional steps incur a high maintenance and performance burden to the established work process and often do not scale with larger data sets. Seldomly, C++ is considered as the language of choice for these small processes, although it is the main language used in high-performance computing. We are going to show that implementing modern C++ can be as easy as using other modern high-level languages. Learning goals: Students will develop - skills in developing an application using the C++ programming language - skills in using modern C++ libraries to query large sequence databases (e.g. SeqAn, SDSL, etc.) - knowledge and understanding of modern C++ features, such as ranges and concepts - knowledge and understanding about modern and efficient data structures as well as algorithms crucial for large-scale genomic sequence analysis - knowledge and understanding about how to develop and sustain high-quality software Prerequisites: This tutorial is mostly suited for computational biologist and bioinformaticians with research focus on sequence analysis (e.g., genomics, metagenomics, proteomics, read alignment, variant detection, etc.). A fundamental knowledge about sequencing experiments and the involved data is required. We expect that attendees have an intermediate knowledge in programming with any high-level programming language, e.g. Python, Java or C++. Some basic C++-knowledge is helpful but not mandatory to successfully complete the course. This tutorial is targeting beginners and intermediate C++ developers that want to learn more about modern C++ features like ranges and concepts. Keywords: BioC++, modern C++, bioinformatics, SeqAn, FileIO Tools: - A simple text editor - g++ >= 7 - cmake >= 3.12 - git 2020-09-14 09:00:00 UTC 2020-09-14 17:00:00 UTC de.NBI Frankfurt am Main, Frankfurt am Main, Germany Frankfurt am Main Frankfurt am Main Darmstadt Germany [] [] [] meetings_and_conferences [] []
  • ProteinsPlus at the German Conference for Bioinformatics (GCB)

    14 September 2020

    ProteinsPlus at the German Conference for Bioinformatics (GCB) Educators: Matthias Rarey & Katrin Schöning-Stierand (BioData) Date: 14.09.2020 13:00-18:00 Location: Online - GCB 2020 Contents: Three-dimensional protein structures are a fundamental basis for understanding, modulating, and manipulating protein functionality. With over 155,000 structures, the Protein Data Bank (PDB) is one of the most important bioinformatics resources for life science. In this workshop, we present the ProteinsPlus server enriching structural knowledge from the PDB by additional computed information required for common biological research questions. ProteinsPlus enables easy access to this information for all researchers in the fields of molecular life sciences. The provided computational services comprise various tools for the assessment, representation, preprocessing, and interconnection of structural data. Many of the provided tools focus on protein binding pockets and molecular interactions to small molecules due to their relevance for various research questions. Participants will get to know a combination of tools and web services for searching and analyzing protein structure data. The focus will be on protein function and related interactions to small molecules. We will work with the ProteinsPlus web service that contains a diverse range of software solutions for the analysis of protein structures and its application in molecular modeling approaches. Learning goals: This course is designed for life and computer scientists with interest in protein structures, but only very basic experience in 3D modeling. Topics include: Finding and selecting protein structure data, evaluating the quality of experimental data, preprocessing structure data for modeling, first modeling steps like the analysis of binding site properties and conformational flexibility. Usage of ProteinsPlus is free and open to all users. Prerequisites: General knowledge of proteins and their role in life sciences Keywords: Protein structures, protein-ligand interactions, molecular modeling, structure-to-function relationships, cheminformatics, ProteinsPlus, BRENDA, EnzymeStructures, KNIME Tools: ProteinsPlus, 2020-09-14 13:00:00 UTC 2020-09-14 18:00:00 UTC de.NBI Frankfurt am Main, Frankfurt am Main, Germany Frankfurt am Main Frankfurt am Main Darmstadt Germany [] [] [] meetings_and_conferences [] []

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