OpenMS Developer Meeting
3 - 7 August 2020OpenMS Developer Meeting https://www.denbi.de/training/749-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  
Computational genomics course for hands-on data analysis 2020
23 - 25 September 2020Computational genomics course for hands-on data analysis 2020 https://www.denbi.de/training/806-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  
Computing Skills for Reproducible Research: Software Carpentry Course 2020
19 - 23 October 2020Computing Skills for Reproducible Research: Software Carpentry Course 2020 https://www.denbi.de/training/789-software-carpentry-course-2020 https://tess.elixir-europe.org/events/computing-skills-for-reproducible-research-software-carpentry-course-2020 Educators: Renato Alves (HD-HuB) Date: 19-10-2020 - 23-10-2020 09:00-18:00 Location: Online Contents: Computation is an integral part of today's research as data has grown too large or too complex to be analysed by hand. An ever-growing fraction of science is performed computationally and many wet-lab biologists spend part of their time on the computer. Many scientists struggle with this aspect of research as they have not been properly trained in the necessary set of skills. The result is that too much time is spent using inefficient tools when progress could be faster. This course provides training in several key tools, with a focus on good development practices that encourage efficient and reproducible research computing. Topics covered include: Introduction to Python scripting Introduction to the Unix shell and usage of cluster resources Version control with Git and Github Analysis pipeline management Scientific Python & working with biological data Literate programming with Jupyter notebooks Learning goals: This course aims to teach software writing skills and best practices to researchers in biology who wish to analyse data, and to introduce a toolset that can help them in their work. The goal is to enable them to be more productive and to make their science better and more reproducible. Prerequisites: This is a course for researchers in the life sciences who are using computers for their analyses, even if not full time. The target student will be familiar with some command line/programmatic computer usage, will want to become more confident using these tools efficiently and reproducibly. A target student will have written a for loop in some language before, but will not know what git is (or at least not be very comfortable using git). Keywords: Programming; Command Line; Version Control; Bioinformatics; Data Analysis; Cluster Computing Tools: Python; Bash; Unix/Linux; Git; GitHub; SnakeMake; Biopython; Pandas; Numpy; SciPy; Matplotlib 2020-10-19 09:00:00 UTC 2020-10-23 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany    workshops_and_courses  
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