Purpose of this website

The simuPOP cookbook is an online collection of simuPOP examples, extensions, and evolutionary scenarios contributed by simuPOP users. It is also a repository of documents and examples that are complementary to the simuPOP user’s guide and reference manual.

If you are teaching a population genetics course, the simuPOP cookbook might have some examples to demonstrate basic population genetics models. If you would like to simulate a particular genetic effect such as a selective sweep but have no idea where to start, the simuPOP cookbook might have a few existing examples. To make this possible, please consider contributing to this cookbook if you have written some scripts that might benefit others.

Why is this cookbook password-protected?

The simuPOP cookbook is based on a wiki system so that everyone can contribute to it. However, allowing anyone to freely write to a wiki site has given wiki-spammers some business opportunities and wiki-administrators a lot of headaches. Because of these, the simuPOP cookbook is password-protected.

If you are not a spammer and have enough patience to read this paragraph, the password is written in this section in white. I guess you know how to see it. :-) This password might change from time to time so please visit this page again if your password does not work. The cookbook edit password is cookbook.

How do I create/modify a recipe (wiki page)?

The simuPOP cookbook is based on pmwiki. Some basic editing rules will be given below the edit box when you edit a page. It is recommended that you first read the basic editing rules for pmwiki though.

  1. Login to this website.
  2. Add a page
    • Using the side panel, navigate to an appropriate category. Press Edit.
    • Start a new item with a new page name such as [[Cookbook/HowToDoBlah]] . This will be your new page. Add some description to your item afterward.
    • Save the summary page. You will see a question mark after [[Cookbook/HowToBlah]] if this page does not exist.
    • Click on [[Cookbook/HowToBlah]] will create a new page with this name. In case that you would like to rename this page later, add ?action=rename to the page to be renamed and set a new name for it.
  3. Set a more informative title using the (:title:) directive. For example, (:title A more informative title:).
  4. Add you example for download. It is strongly recommended that you only list the core parts of the code and add the whole script (or a zip file of several files) for download. What you need to do is
    • Save the page if you have unsaved modifications. Click Attach and upload you file.
    • Go back to the Edit page, add 
      %rfloat text-align=center margin-top=5px margin-right=25px
 margin-bottom=15px margin-left=25px % [[Attach:XXXXX.py | 
http://simupop.sourceforge.net/images/download.jpg]]|XXXXX.py
    where XXXXX.py is the file you uploaded.
  5. Edit your page using the basic editing rules. The website uses a beautifier to beautifier Python and C/C++ code. To use it, simply quote your example in 
    =python [=
=]
'=cpp' can be used for C++ code.