• strict warning: Non-static method view::load() should not be called statically in /home/peco/webapps/dp6_peter/sites/default/modules/views/views.module on line 906.
  • strict warning: Declaration of views_handler_argument::init() should be compatible with views_handler::init(&$view, $options) in /home/peco/webapps/dp6_peter/sites/default/modules/views/handlers/views_handler_argument.inc on line 744.
  • strict warning: Declaration of views_handler_filter::options_validate() should be compatible with views_handler::options_validate($form, &$form_state) in /home/peco/webapps/dp6_peter/sites/default/modules/views/handlers/views_handler_filter.inc on line 607.
  • strict warning: Declaration of views_handler_filter::options_submit() should be compatible with views_handler::options_submit($form, &$form_state) in /home/peco/webapps/dp6_peter/sites/default/modules/views/handlers/views_handler_filter.inc on line 607.
  • strict warning: Declaration of views_plugin_style_default::options() should be compatible with views_object::options() in /home/peco/webapps/dp6_peter/sites/default/modules/views/plugins/views_plugin_style_default.inc on line 24.
  • strict warning: Declaration of views_plugin_row::options_validate() should be compatible with views_plugin::options_validate(&$form, &$form_state) in /home/peco/webapps/dp6_peter/sites/default/modules/views/plugins/views_plugin_row.inc on line 134.
  • strict warning: Declaration of views_plugin_row::options_submit() should be compatible with views_plugin::options_submit(&$form, &$form_state) in /home/peco/webapps/dp6_peter/sites/default/modules/views/plugins/views_plugin_row.inc on line 134.

Simulating a protein gel

The blue bar is protein shortly after the gel run is started

I have started a simulation of a protein gel. As it runs, a blue bar of protein moves down the gel, getting increasingly diffuse - a little too diffuse at the moment. And the bar eventually disappears, which is annoying. Still, it's a start, and the program is all nice and object oriented. I just need to work out a better equation for simulating the movement of proteins in a gel. After that: more proteins in more lanes with different percentage gels and different colours (makes it less realistic, but more fun). Also, some lateral diffusion might be nice, but could make things unnecessarily computationally complex.

I have also started to reread Barbieri's The Organic Codes: An Introduction to Semantic BiologyI seem to recall that it has a lot of interesting ideas, even if they are presented as being more revolutionary than I think they are. Maybe I just haven't seen their full implications. Nonetheless, I think it will be useful to read while I try to simulate life.

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