Event types: Workshops and courses
Computational genomics course for hands-on data analysis 2021 - Machine Learning for Genomics
2 - 6 August 2021Computational genomics course for hands-on data analysis 2021 - Machine Learning for Genomics https://www.denbi.de/training/1227-computational-genomics-course-for-hands-on-data-analysis-2020 https://tess.elixir-europe.org/events/computational-genomics-course-for-hands-on-data-analysis-2021-machine-learning-for-genomics Educators: Altuna Alkalin, Verdan Franke, Bora Uyar, Jan Dohmen, Artem Baranovsky (RBC/deNBI-epi Scientists from Berlin) Date: August - September 2021 Location: Online Contents: The general aim of the course is to equip participants with practical and technical knowledge to deploy machine learning methods on genomic data sets. With this aim in mind, we will go through certain statistical concepts and move on to unsupervised and supervised machine learning methods to analyze high-dimensional data sets. This will be an online training event which will be mostly asynchronous. A typical module would comprise of lectures followed by hands-on exercises and a quiz. The participants will have a week to complete the lectures and exercises for each module at their own pace and at the time of their choosing within that week. Only the participants who complete the exercises and a quiz in a timely manner and have at least 50% of the tasks in the exercises will be invited to the capstone project. The capstone project tasks are designed using data from a real world problem. The participants who provide the best reports for the capstone projects will be invited to co-author a manuscript with the Akalin lab. Most tasks can be done on a regular laptop. A recent version of R and Rmarkdown is necessary to complete the hands-on exercises. Module 1: Statistics for genomics Module 2: Unsupervised learning and applications in genomics Module 3: Supervised learning and applications in genomics Module 4: Capstone project: Drug response prediction using genomic data 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 Application Deadline: 30th of June 2021-08-02 09:00:00 UTC 2021-08-06 17:00:00 UTC de.NBI    workshops_and_courses  
5th BioInfra.Prot Tool-Training for Proteomics & Community Meeting
23 August 20215th BioInfra.Prot Tool-Training for Proteomics & Community Meeting https://www.denbi.de/training/1149-5th-bioinfra-prot-tool-training https://tess.elixir-europe.org/events/5th-bioinfra-prot-tool-training-for-proteomics-community-meeting Educators: Anika Frericks-Zipper, Markus Stepath, Michael Turewicz and Julian Uszkoreit (BioInfra.Prot) Date: Monday, 2021-08-23 Location: online Contents: In this one-day event we will show some of BioInfra.Prot's tools provided by de.NBI and have a community meeting in the afternoon. The focus of the tool part will be protein inference and boosting of identification performance. In order to do this we will use the tool PIA (Protein Inference Algorithms). PIA allows inspecting and combining the results of proteomics search engines. The focus lays on the integrated inference algorithms for identification and quantification purposes. Besides the tool-based session, we offer a session where we show advantages of cloud based bioinformatics and give a tutorial how to access the de.NBI cloud. In addition, attendees will get to know the data science platform KNIME. As a novelty, there will be an optional community meeting on the same day (“Current and future use cases for BioInfra.Prot services mentioned by the user community”), where the focus will be on social networking and a relaxed exchange of ideas. In addition, selected use cases for data analysis from the proteomics area with BioInfra.Prot tools or services will be presented in short flash talks. Is your interest sparked? Then simply register with a few clicks via the registration form listed below. Learning goals: Tool-Training (in the morning): Attendees of the course will learn how to use the tools PIA effectively for their daily proteomics tasks. Additionally they will learn how to use the de.NBI cloud and the data science platform KNIME. Community Meeting (optional in the afternoon): Networking and sharing of ideas in the field of proteomics data analysis and especially the user-oriented development of BioInfra.Prot tools and services. Learning and discussion based on presented use cases for data analysis from the proteomics area with BioInfra.Prot tools or services Prerequisites: This course is for all researches in the field of proteomics. The attendees should have basic knowledge of LC-MS proteomics, but no prior bioinformatics skills are required. Basic knowledge of how to analyse LC- MS data are sufficient. Attendees are required to have a computer, headset, camera, and a stable internet connection. Keywords: Proteomics; Data Analysis; de.NBI Cloud; Community Meeting Tools: PIA; KNIME; 2021-08-23 09:00:00 UTC 2021-08-23 17:00:00 UTC de.NBI    workshops_and_courses  
The Linux Command Line: From Basic Commands to Shell Scripting 2-2021
24 - 26 August 2021The Linux Command Line: From Basic Commands to Shell Scripting 2-2021 https://www.denbi.de/training/1265-the-linux-command-line-from-basic-commands-to-shell-scripting-2 https://tess.elixir-europe.org/events/the-linux-command-line-from-basic-commands-to-shell-scripting-2-2021 Educators: Malik Alawi, Ceren Saygi (UKE Bioinformatics Core) (External Training Partner) Date: 24th - 26th June 2021 (14:00-17:00) Location: Online Contents: Nearly all Bioinformatics analyses are best performed using the Linux command line. Many researchers consider this a drawback and choose to learn only the bare minimums required for a certain task or even try to circumvent Linux completely. A common misunderstanding is, that working on the command line is archaic or performed because it is a cheaper alternative to often costly proprietary solutions. However, it is neither antiquated views nor avarice which makes nearly all Bioinformaticians use the command line, but rather its unmatched efficiency and overwhelming power. Topics: - Basic file operations - Working with (large) text files - Using the shell efficiently - Data compression - Working with tables - Regular expressions - Variables and loops - Bash scripting - Common application scenarios of command line usage in a bioinformatics context Learning goals: This three-day course will introduce the Linux command line from scratch. Participants will learn to work efficiently with its tools and they will also learn to automate tasks and write first bash scripts. The focus is on processing (large) texts and tables. Examples will be from the field of genome informatics, but methods taught will be universally applicable. Prerequisites: Participants will join remotely using their personal computers (mobile phones and tablets are not suitable). Installing Linux locally is not required, other recent operating system should also be fine. We will use the conferencing solution Zoom and work in a virtual Linux environment (de.NBI cloud). Keywords: Linux, Bash, Shell, Scripting, Command line Tools: Linux, Command line 2021-08-24 14:00:00 UTC 2021-08-26 17:00:00 UTC de.NBI    workshops_and_courses  
de.NBI Summer School 2021 Part 1 - Analysis and integration of Mass Spectrometry based omics data in Proteomics, Metabolomics and Lipidomics
27 - 30 September 2021de.NBI Summer School 2021 Part 1 - Analysis and integration of Mass Spectrometry based omics data in Proteomics, Metabolomics and Lipidomics https://www.denbi.de/training/1150-de-nbi-summer-school-2021-proteomics-lipidomics https://tess.elixir-europe.org/events/de-nbi-summer-school-2021-proteomics-lipidomics TBA 2021-09-27 09:00:00 UTC 2021-09-30 17:00:00 UTC de.NBI    workshops_and_courses  
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