Content provider: de.NBI
Software Carpentry 1.2020
31 August - 1 September 2020Software Carpentry 1.2020 https://www.denbi.de/training/821-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  
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  
Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2022
9 - 11 August 2022
Heidelberg, GermanyTools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2022 https://www.denbi.de/training/1409-tools-for-systems-biology-modeling-and-data-exchange-copasi-cellnetanalyzer-sabio-rk-fairdomhub-seek-2022 https://tess.elixir-europe.org/events/tools-for-systems-biology-modeling-and-data-exchange-copasi-cellnetanalyzer-sabio-rk-fairdomhub-seek-2022 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 introduces kinetic modeling techniques which will be illustrated and exercised with COPASI. The second day continues with principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer and a demonstration of CNApy. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOM Hub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists. 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. 2022-08-09 09:00:00 UTC 2022-08-11 17:00:00 UTC de.NBI /ELIXIR-DE BioQUANT, Heidelberg, Germany BioQUANT Heidelberg Germany 69120 University of Heidelberg, BioQUANT Frank T. Bergmann (email@example.com)  ResearcherModellerStudents workshops_and_courses  
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