Fish Workshop (8 persons)
The fish workshop will be held at the Řimov Reservoir, and will be comprised by three sessions: i) presentation of various standard techniques for sampling of fish in large standing waters (gillnets, beach seine nets, trawls, fyke nets, electrofishing); ii) introduction of a new high-tech method for observation of fish behavior - positioning of the telemetry system; and iii) practical demonstration of the use of gillnets and beach seine nets.
Milan Říha (Fish Ecology group at IHB)
Data management and food web modelling (15 persons)
- Part I – Organization and manipulation of lymnological data (Vilem Ded)
This part will focus on general data organization and manipulation in scientific (limnology) fields. First part will be a lecture covering various aspects of data (data types, space, time, organization, software). Common mistakes and pitfalls will be emphasized and real (anonymous) limnology data collected in different projects on IHB will be used for demonstration. Advanced big volume database designs (relational databases) will be mentioned with brief description of basic features (integrity, security, consistency, indexing). Data organization is dependent on personal preferences, for example on favourite software, optimal work-flows, rigorousness, etc… Therefore, any inputs, questions, discussions and ideas from attendants will be more than welcomed.
Next, a fictional project will be presented with all its data inflows (devices, observations, samplings, etc...). Each participant will create its own data design covering all levels of organization (folders -> files -> tables -> columns -> data types). Some of the datasets will be then used in Part II of the workshop.
If you don't know what following terms mean, please come :)
UTC, latlon, UTM, long/wide format of data, merging tables, raster, integer, POSIX time, primary/foreign key, special character, header, NA value, UTF-8...
- Part II – Introduction to Food web modelling (Samuel Dijoux)
The workshop aims to present some basics of food web modelling. Applicants will learn simple tips i) to read & understand the use of mathematical equations applied to ecological purposes, ii) and to build simple population dynamic models.
A practical activity will enable applicants to discover some of R packages used for population dynamic (deSolve and PSPM packages). This will also be a good opportunity to discuss openly and share your interest in this topic according to your respective research field.
Vilém Děd (Database management and scientific IT support at IHB)
Samuel Dijoux (Biological system modelling at University of South Bohemia)
Single filament isolation method, a precious tool in genome sequencing (5 persons)
Many cyanobacteria form nuisance water blooms producing harmful metabolites, so called cyanotoxins, posing a risk to the human and animal healt. Establishment of reliable and rapid methods are crucial in detecting potential toxic species. This interactive workshop will provide an insight on how to perform genome sequencing of monoclonal strain culture applying single filament isolation combined with MDA. Investigation of genes responsible for cyanobacteria toxic potential and specific primer design can be used for both easy toxic potential detection method and for future estimation of target-gene expression with help of real time quantitative PCR.
Andreja Kust (Aquatic Microbial Ecology group at IHB)
In the footsteps of heterotrophic nanoflagellates, small but powerful predators (5 persons)
Heterotrophic nanoflagellates (HNF) are important members of the food chain in most aquatic environments. These protists are often selectively controlling bacterial populations, and play a role in carbon flow to higher trophic levels. Despite this, only small amount of microbial ecologists is working with HNF. In our workshop, we will present simple but informative methods, which can help you to learn more about HNF population from environment of your interest: (1) We will estimate the grazing rate of HNF community using fluorescently labelled bacteria (FLB). (2) We will provide examples of catalyzed reporter deposition fluorescent in situ hybridization (CARD-FISH) of flagellates groups with explanation of methodology, as well as examples of combined CARD-FISH of flagellates and bacterial populations in the same sample.
Tatiana Shabarova & Vesna Grujčić (Aquatic Microbial Ecology group at IHB)
Preliminary reservation on Doodle