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9 events found

Organizer: SIB Swiss Institute of Bioi...  or de.NBI 

  • OpenMS Developer Meeting

    3 - 7 August 2020

    OpenMS Developer Meeting https://tess.elixir-europe.org/events/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 [] []
  • Software Carpentry 1.2020

    31 August - 1 September 2020

    Software Carpentry 1.2020 https://tess.elixir-europe.org/events/software-carpentry-1-2020 Educators: Rabea Müller, Konrad Förstner, Till Sauerwein (ZB MED/Associated Partner) Date August 31 - September 01 2020 Location: Online Contents: Data, Shell, Git and GitHub, Python: Day 1 Before Pre-workshop survey 09:00 Data Intro 10:30 Morning break 12:00 Lunch break 13:00 Shell Lessons 14:15 Afternoon break 15:30 Wrap-up 16:00 END Day 2 09:00 Python Intro 10:30 Morning break 12:00 Lunch break 13:00 Git Intro 14:15 Afternoon break 15:30 Wrap-up 15:45 Post-workshop Survey 16:00 END Learning goals: Get basic knowledge of the programming language python, the unix-shell, automating tasks, the version control software git and the cloud service GitHub, Prerequisites: Attendees must use their own laptop with the following software already installed: Gitbash (Windows) / Shell (Linux) / Terminal (MAC OS) , Anaconda3 and Git. Every attendee also needs a GitHub account. Keywords: programming, automation, version control, reproducible science Tools: Shell, Git and GitHub, 2020-08-31 09:00:00 UTC 2020-09-01 17:00:00 UTC de.NBI Köln, Köln, Germany Köln Köln Köln Germany [] [] [] workshops_and_courses [] []
  • OpenMS at the German Conference for Bioinformatics (GCB)

    14 September 2020

    Frankfurt am Main, Germany

    OpenMS at the German Conference for Bioinformatics (GCB) https://tess.elixir-europe.org/events/openms-at-the-german-conference-for-bioinformatics-gcb TBA 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 [] []
  • SeqAn at the German Conference for Bioinformatics (GCB)

    14 September 2020

    Frankfurt am Main, Germany

    SeqAn at the German Conference for Bioinformatics (GCB) https://tess.elixir-europe.org/events/seqan-at-the-german-conference-for-bioinformatics-gcb TBA 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

    Frankfurt am Main, Germany

    ProteinsPlus at the German Conference for Bioinformatics (GCB) https://tess.elixir-europe.org/events/proteinsplus-at-the-german-conference-for-bioinformatics-gcb TBA 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 [] []
  • Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2020

    21 - 23 September 2020

    Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2020 https://tess.elixir-europe.org/events/hdhd Educators: Axel von Kamp, Steffen Klamt, Sven Thiele (MPI Magdeburg), Frank T. Bergmann, Ursula Kummer (University of Heidelberg), Wolfgang Müller, Maja Rey, Andreas Weidemann, Ulrike Wittig (HITS) (de.NBI-SysBio) Date: 21. - 23 September 2020 Location: MPI Magdeburg Sandtorstrasse 1 39106 Magdeburg or online Contents: Key concepts of stoichiometric and kinetic modeling of biochemical networks: - stoichiometric matrix and stoichiometric networks - steady state flux distributions - principles of constraint-based modeling - metabolic flux analysis and flux optimization (flux balance analysis) - metabolic pathway analysis with elementary flux modes - metabolic network design via minimal cut sets - simulation of dynamic (kinetic) models - sensitivity analysis - carrying out parameter estimation tasks - model exchange using SBML Data and model management: - manual/programmatic access to reaction kinetics data from SABIO-RK - storage and exchange of data and models using FAIRDOMHub/SEEK - modeling specific functionalities in FAIRDOMHub/SEEK Learning goals: During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day SABIO-RK is used as a resource for kinetic data and FAIRDOMHub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists. The second day introduces principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The third day continues with kinetic modeling techniques which will be illustrated and exercised with COPASI The hands on exercises throughout the three days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks. Prerequisites: Some knowledge of mathematical modeling will be advantageous. The participants should bring their own laptop with MATLAB installed (if you do not have MATLAB please let us know during registration). Download and preinstallation of COPASI and CellNetAnalyzer is recommended but not mandatory. Keywords: CellNetAnalyzer (CNA), COPASI, SBML, FAIR, modeling, kinetic data access, database, data and model management Tools: CellNetAnalyzer, COPASI, Matlab, SABIO-RK, FAIRDOMHub/SEEK 2020-09-21 09:00:00 UTC 2020-09-23 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • Computational genomics course for hands-on data analysis 2020

    23 - 25 September 2020

    Computational genomics course for hands-on data analysis 2020 https://tess.elixir-europe.org/events/computational-genomics-course-for-hands-on-data-analysis-2020 Educators: Altuna Alkalin, Verdan Franke, Bora Uyar (RBC/deNBI-epi Scientists from Berlin) Date: 23-25 September 2020 Location: Online Contents: The general aim of the course is to equip participants with practical and technical knowledge to analyze single cell RNA-seq data. With this aim in mind, we will go through unsupervised machine learning methods to analyze high-dimensional data sets, and move on to statistical methods developed to analyze bulk RNA-seq. Lastly, we will introduce analysis techniques used for single cell RNA-seq. There will be theoretical lectures followed by practical sessions where students directly apply what they have learned. The programming will be mainly done in R. Day 1: Intro to machine learning & data visualization for genomics Day 2: Bulk RNA-seq analysis Day 3: Single cell RNA-seq analysis Learning goals: The course will be beneficial for first year computational biology PhD students, and experimental biologists and medical scientists who want to begin data analysis or are seeking a better understanding of computational genomics and analysis of popular sequencing methods.r Prerequisites: Some statistics and R programming experience will be good to keep up with the course. Practicals will be done in R. Keywords: Computational genomics, RNA-seq, Machine learing, Tools: R/Bioconductor 2020-09-23 09:00:00 UTC 2020-09-25 17:00:00 UTC de.NBI Berlin, Berlin, Germany Berlin Berlin Germany [] [] [] workshops_and_courses [] []
  • 3rd de.NBI Cloud Usermeeting

    8 - 14 October 2020

    3rd de.NBI Cloud Usermeeting https://tess.elixir-europe.org/events/3rd-de-nbi-cloud-usermeeting 3rd de.NBI Cloud Usermeeting Online Educators: de.NBI cloud group including Peter Belmann, Daniel Hübschmann, Peter Ebert, Martin Zurowietz, Kay Schallert, Sven Olaf Twardziok, Jan Krüger, Maximillian Hanussek, Martin Braun, Marius Dieckmann, Björn Grüning etc. Date: 8.10.2020 – 14.10.2020 Location: Online Contents: We are pleased to announce the third de.NBI Cloud User Meeting. In comparison to preceding meetings, this year`s meeting will be organized as an online conference. Over five days users can watch talks of already experienced users and long running projects and thereby learn about best practices in cloud computing. Same as the last years we will try to cover topics for beginners such as virtualization but also topics for software engineers and administrators such as orchestration with Kubernetes. Participants will learn how to scale up their analysis to handle growing input data and how to use workflow managers such as Snakemake in a cloud environment. As every year we are also going to demonstrate the usage of bioinformatics software in the de.NBI Cloud using Docker images or Bioconda packages. Planned Courses: - Running Snakemake Workflows in the de.NBI Cloud - OpenStack Introduction - BioConda and BioContainers - Kubernetes Introduction - Deploying Web Services in the de.NBI Cloud - Extensible Cluster Setup in the Cloud with BibiGrid and Ansible - Using Terraform to define infrastructure as code Learning goals: Working with the de.NBI cloud Prerequisites: We welcome people from all background, no matter if you are new to the de.NBI Cloud or considering to submit a project application, to learn and network in our growing community. Keywords: de.NBI cloud Tools: de.NBI cloud Webpage: https://cloud.denbi.de/3rd-de-nbi-cloud-user-meeting/ 2020-10-08 09:00:00 UTC 2020-10-14 17:00:00 UTC de.NBI [] [] [] meetings_and_conferences [] []
  • Computing Skills for Reproducible Research: Software Carpentry Course 2020

    20 - 22 October 2020

    Heidelberg, Germany

    Computing Skills for Reproducible Research: Software Carpentry Course 2020 https://tess.elixir-europe.org/events/computing-skills-for-reproducible-research-software-carpentry-course-2020 2020-10-20 09:00:00 UTC 2020-10-22 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []

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