Teaching

Target enrichment for plant systematics - HybSeq course 2022

Submitted by vojta on Fri, 06/03/2022 - 11:42

Practical course of phylogenomic methods focused on Hyb-Seq NGS method. The Hyb-Seq method combines target enrichment and genome skimming of the genome. The course covers the theory, discussion of the newest papers from the field, probe design, laboratory and computer part. Several methodological approaches to data analysis, from raw data to species tree analysis, are demonstrated within the course. The lab part includes NGS library preparation (using sonicator) and enrichment.

Virtual machine for my courses

Submitted by vojta on Tue, 01/11/2022 - 16:37

For my courses ofwork in Linux command line not only for MetaCentrum and with molecular data in R I provide VirtualBox image, which allows to run complete desktop Linux (in this case openSUSE Leap) with all preinstalled applications needed for both courses. It's easy way how to get fully working Linux to play with. It requires at least bit powerful notebook, e.g. at least quad-core with at least 8 GB RAM, but more is better.

Getting VirtualBox image

Course of work with molecular data in R 2022

Submitted by vojta on Thu, 11/11/2021 - 12:55

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Their representative selection will be introduced during the course.

The course contains theory of used methods, tutorials with test data, tasks for individual work of participants, and more. The aim is to teach students how to analyze molecular data in R programming language, introduce available packages for their analysis and practical trying out to work with own or provided data.

Course of work in Linux command line not only for MetaCentrum 2022

Submitted by vojta on Thu, 11/11/2021 - 11:51

Don’t be afraid of command line! It is friendly and powerful tool allowing to process large data and automate tasks. Practically identical is command line also in Apple macOS, BSD and another UNIX-based systems, not only in Linux. The course is designed for total beginners as well as intermediate advanced students. The only requirement is an interest (or need) to work in command line, typically on Linux computing server.

Course of work with molecular data in R 2021

Submitted by vojta on Tue, 10/06/2020 - 17:08

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course.

The course contains theory of used methods, tutorials with test data, tasks for individual work of participants, and more.

Previous knowledge of R is useful, but not necessary. At least basic knowledge of molecular biology is required, previous knowledge about any methods how to analyse DNA data is recommended.

Course of work in Linux command line not only for MetaCentrum 2021

Submitted by vojta on Tue, 10/06/2020 - 16:49

Don’t be afraid of command line! It is friendly and powerful tool allowing to process large data and automate tasks. Practically identical is command line also in Apple macOS, BSD and another UNIX-based systems, not only in Linux. The course is designed for total beginners as well as intermediate advanced students. The only requirement is an interest (or need) to work in command line, typically on Linux computing server.

Course will be taught in Linux, but most of the point are applicable also for another UNIX systems like macOS.

Course of work with molecular data in R 2020 in České Budějovice

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course. The course will be taught from October 19th to Friday 23rd (see below). The course will be exclusively on-line, there will be no personal meeting.

vojta Fri, 03/06/2020 - 22:39

HybSeq course 2020

Submitted by vojta on Thu, 12/19/2019 - 21:25

Intensive 4-days (5th day is not compulsory, but is open for any discussion, if there would be interest) course to learn all theory about HybSeq and practically learn how to analyze HybSeq data, how to solve all problems, and how to evaluate differences among gene trees. Important part is enough time to discuss everything, including practical problems and projects of individual participants.

Course of work in Linux command line not only for MetaCentrum 2020

Submitted by vojta on Mon, 10/07/2019 - 16:56

Don’t be afraid of command line! It is friendly and powerful tool allowing to process large data and automate tasks. Practically identical is command line also in Apple osX, BSD and another UNIX-based systems, not only in Linux. The course is designed for total beginners as well as intermediate advanced students. The only requirement is an interest (or need) to work in command line, typically on Linux computing server.

Course will be taught in Linux, but most of the point are applicable also for another UNIX systems like osX.

Course of work with molecular data in R 2020

Submitted by vojta on Mon, 10/07/2019 - 16:28

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course.

The course contains theory of used methods, tutorials with test data, tasks for individual work of participants, and more.

Previous knowledge of R is useful, but not necessary. At least basic knowledge of molecular biology is required, previous knowledge about any methods how to analyse DNA data is recommended.