DEB2023 final preparations

This page explains preparations to perform before coming to Baton Rouge
  • Read about your fellow participants in the DEB2023 course document: AmP project species, Discussion Topics, Participant list. We will skip introduction rounds when in Baton Rouge!
  • 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. PC users contact Starrlight, mac users contact Dina.
  • Assemble your data, ask how to best formulate the data. Email questions to Starrlight. The more you can compile data before coming the better.

Software testing before coming to Baton Rouge

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.

Populations

We will not have in-depth technical lectures on population and ecosystem modelling, however this theme is included and depending on skills and interests you have the opportunity to explore this. Please read the DEB-in-Practice page on Population Dynamics, and note that we will only be working with the last section "IBMs".

Set path to MinGW for the GNU Compiler Collection for Windows, and see YouTube for installation instructions (basically how to set the path via editing the system Environment Variables). Matlab needs to be restarted after setting a windows path to MinGW.

Next go to your Matlab console and type:

	
[txNL23W, info] = EBT('Daphnia_magna', [], [], [], [], [], 80);
	
You should obtain a set of graphs. If you get warnings of the type that 'gcc' is not recognized as an internal or external command... and no figures are generated, that means something went wrong with the MinGW set-up. This is best to trouble shoot and fix before coming, to make the most out of the population work. (Download NetLogo v 6.2.0 and set system path to the folder with NetLogo.exe as you did with the MinGW. YOu may also need to set the system path to Java if you encounter issues with Java).

Next, lets make sure Netlogo is running:

	
    [txNL23W, info] = IBM('Daphnia_magna', [], [], [], [], [], [], 80, 1);
	
Check that 7 figures are plotted, and that two html reports are generated. Then stop and we pick it back up at the course. It is fine if there are warnings in the console.

Last step, type:

	
    [txNL23W, info] = IBM('Daphnia_magna', [], [], [], [], [], [], 80, 1,0);
	
3 txt files, 3 html pages and netlogo software will open. If that happens, stop and we pick this back up at Baton Rouge.

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

Trouble shooting

PC

You need to set paths to MinGW for the GNU Compiler Collection for Windows, netlogo, miktex, java via the "Edit the system environment variables" in windows. An example how put a new path into the system variables is in the YouTube for installation instructions for MinGW.

MAC

If you run the zsh put in the file .zprofile (or if you run the bash shell in .bash_profile) the following lines
	
export JAVA_HOME=/Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home
export EBTPATH=/Applications/EBTtool.app/Contents/Resources
export PATH=${JAVA_HOME}/bin:/Applications/NetLogo\ 6.2.0/app:/Applications/EBTtool.app/Contents/MacOs:$PATH