31 augustus 2021
Group assignment Design of Experiments (DoE)
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Tutor/group assignment for students with (some) theoretical knowledge on DoE (e.g. theory lesson) Students present scientific research, in which DoE is used, by means of a presentation. This is based on an article, that students can pick from a list.
HBO
Document
Nardy Kip
14 december 2021
Genome Assembly of MRSA using Illumina MiSeq Data
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In this training you’re going to make an assembly of data produced by “Complete Genome Sequences of Eight Methicillin-Resistant Staphylococcus aureus Strains Isolated from Patients in Japan” from Hikichi et al. 2019 which describes: Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen causing nosocomial infections, and the clinical manifestations of MRSA range from asymptomatic colonization of the nasal mucosa to soft tissue infection to fulminant invasive disease. Here, we report the complete genome sequences of eight MRSA strains isolated from patients in Japan. In this tutorial you learn to use Galaxy to assemble and analyze the sequencing data from these strains.
HBO
Document
Bazante Sanders, Saskia Hiltemann, Helena Rasche
2 februari 2022
16s rRNA Primer design tutorial
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The bacterial ribosome consists of 3 rRNA molecules and 54 proteins and plays a crucial role in translating mRNA-encoded information into proteins. Because of the structural complexity of the ribosome, it is believed that each ribosomal component coevolves to maintain function. In particular, because the 16S and 23S rRNAs form the structural core of the ribosome, they are believed to be least likely to experience horizontal gene transfer between species. On the basis of the species-specific nature of rRNA and their omnipresence in all bacteria, the rRNA genes, especially those for 16S rRNA, have long been used as an “ultimate chronometer” 16S ribosomal RNA (or 16S rRNA) is the component of the 30S small subunit of a prokaryotic ribosome that binds to the Shine-Dalgarno sequence. The 16S rRNA gene is used for phylogenetic studies as it is highly conserved between different species of bacteria and archaea. It is suggested that 16S rRNA gene can be used as a reliable molecular clock because 16S rRNA sequences from distantly related bacterial lineages are shown to have similar functionalities. In this tutorial, you will learn to use online tools to design universal and species specific primers for 16rRNA primers. The products can be used for PCR or Sequencing experiments.
HBO
Document
Miaomiao Zhou
1 september 2020
Workshop Metabolomics
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After completing this workshop, the student: • understands and recognizes the relevance of metabolomics research for society, • knows and understands the basic concepts and workflow of metabolomics, • knows how to pretreat metabolomics data prior to data analysis using Microsoft Excel • knows how to apply multivariate analysis on experimental data using MetaboAnalyst, • and knows how to transform the output of the multivariate analysis into biological information using the Human Metabolite Database. Required software: Microsoft Excel Time investment: 3 hours.
HBO
Document
Andre van Roon, Peter Lindenburg, Sonja Kaal
12 november 2019
Tissue Culture : Passing suspension cells
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Instructional video on “Tissue Culture: Passing suspension cells”. This instruction is used in the practical “Cell Cultivation and Purification”. Video: 8:45 min
HBO
Video
Milou Timmer
31 augustus 2021
Group assignment Biotechnological process Poster presentation
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Tutor/ group assignment for which students should have some biotechnological process knowledge. Students will present a biotechnological process based on a scientific article. Presentation is done in the form of a poster.
HBO
Document
Nardy Kip
26 januari 2021
COVID-19 data analysis using a parameterized R Markdown and Shiny
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This repo is a demo on how to use parameters and an embedded Shiny app in R Markdown
HBO
Website
Marc Teunis
14 december 2021
Genome Assembly of MRSA using Oxford Nanopore MinION Data
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In this training you’re going to make an assembly of data produced by “Complete Genome Sequences of Eight Methicillin-Resistant Staphylococcus aureus Strains Isolated from Patients in Japan” from Hikichi et al. 2019 which describes: Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen causing nosocomial infections, and the clinical manifestations of MRSA range from asymptomatic colonization of the nasal mucosa to soft tissue infection to fulminant invasive disease. Here, we report the complete genome sequences of eight MRSA strains isolated from patients in Japan. In this tutorial you will learn how to make a genome assembly by using Galaxy on ONT long read data.
HBO
Document
Bazante Sanders, Saskia Hiltemann, Helena Rasche
24 maart 2022
Kennisclip: Atmospheric pressure chemical ionization (APCI)
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Een kennisclip over APCI in LCMS analyse. Dit is een onderdeel uit een analytische chemie module in het derde leerjaar. Lengte 8 min
HBO
Video
15 september 2022
Kennisclip: Aantoonbaarheidsgrens
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Een kennisclip over de aantoonbaarheidsgrens. Het doel is inzicht te krijgen in de betekenis van dit prestatiekenmerk. Lengte 10 min
HBO
Video