Citation: U. Scholz (2017-10-01): GCBN de.NBI User Training - PLANT 2030 Summer School - Basis Bioinformatics Training for Biologists. DOI:10.5447/ipk/2017/17
Abstract: The 4th German Crop BioGreenformatics Network (GCBN, https://www.denbi.de/gcbn) user training provided a hands-on introduction to useful bioinformatics tools for biologists with little or no previous knowledge. The training enabled biologists to process their own small and large datasets using R and Linux based methods and is entirely computer-based with interspersed lectures. The first part started with an introduction into the use and basic administration (software installation) of the Linux distribution Ubuntu and demonstrated the first steps into the use the R software (trainer Andrea Bräutigam, folder AB). In part two the use of Blast+ in the command line version, of simple Linux commands like 'cut', of Perl scripts and the graphical user interface of the phylogeny tool 'seaview' were demonstrated (trainer Uwe Scholz, folder US). The third session introduced basic concepts and practical tools for processing biological datasets in Linux. In particular, 'awk' and 'sed' were used. Moreover, 'SAMtools' and 'BEDTools' were applied (trainer Martin Mascher, folder MM). In the fourth part 'Introduction to Databases' a quick start guide to use relational databases was presented. By providing easy examples, this lesson set the fundamentals to motivate to use relational database systems as daily bioinformatics tool to store, retrieve and even analyze -omics data in the big data age (trainer Matthias Lange, folder ML). The last part introduced basic statistics to biologist, teach some commonly used statistical methods and demonstrated the creation of graphical visualizations with software R (trainer Yusheng Zhao, folder YZ).
License: CC BY-SA 4.0 (Creative Commons Attribution-ShareAlike)
Content: 6 Directories 22 Files (2 GB)
Andrea Bräutigam, Martin Mascher, Matthias Lange, Yusheng Zhao [Show full information]
Uwe Scholz [Show full information]
|PUBLISHER:||e!DAL - Plant Genomics and Phenomics Research Data Repository (PGP), IPK Gatersleben, Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany|
|SUBJECT:||de.NBI, GCBN, training course, linux, R, databases, SQL, PLANT 2030|