DEB2025 final preparations

This page explains preparations to perform before coming to Heraklion
  • Read about your fellow participants in the DEB2023 course document: AmP project species, Discussion Topics, Participant list. We will skip introduction rounds when in Heraklion!
  • Look at TOPICS 1 and 2 under discussiong groups in the course document.
  • Check that the software works (see section below), and if not get help to make it work before coming. Email questions to deb2025.school.
  • Assemble your data, ask how to best formulate the data. Email questions to deb2025.school. The more you can compile data before coming the better.

Software testing before coming to Heraklion

Before working make sure all packages are up to date. They change frequently. If you like, you can clone DEBtool_M and AmPtool directly with GitHub for desktop, and synchronize before use to make sure you are up to date with the latest versions. You need to download and overwrite AmPdata each time.

Phylogeny and Ecology related packages

Make sure you have latest version of AmPdata and AmPtool, with paths set to both directories.

Test that AmPtool works on your PC: 

	
    % outputs a table with selected properties of selected species to html format
 	prt_tab({select('Daphniidae'),read_stat(select('Daphniidae'),{'p_M','R_i'})},{'species','[p_M]','R_i'}) 
	
	
    get_n(list_taxa('Carnivora',4))	
	
	
    treeview_taxa('Crustacea')
	gallery_png(select('Daphniidae'))
	
	
   [~, taxon] = clade('Lemmus_trimucronatus'); pedigree(taxon,'p_M')
If you like, feel free to use the lineage, pedigree and treeview_taxa functions to see which species are in AmP that are most closely related to your study organisms.

Advanced data analysis

There are multiple ways to visualize and plot data for which parameters are estimated, as well as some advanced reporting which can be useful.
  1. Download MikTex. The production of the report runs BibTex (under Matlab), which can be downloaded freely, to produce an html with references; if not available, the bib-file is shown. (in short, if you don't have this you can still work, but it is free and easy to install and then references in the report look amazing!).
  2. If you like to visualize data in 4 dimensions, with time the 4th dimension, make sure to dowload the "animated png assembler" apngasm64.exe. Unzip, put folder somewhere like in C drive. Set path in the "Environment Variables" (PC users).
  3. Download the AmPtox GitHub repository and save it in a directory outside of everything else. AmPtox manual is on AmP website Use> AmPtox
  4. In matlab, navigate to OECD202_dichromate, open run_OECD202_dichromate, and run that. If it works, and generates all files. Stop and we pick it up at the course. If not, and you cannot fix the problem, write to Starrlight