Biogenesis Files

Welcome to this modern microbiology laboratory called Biogenesis!
It's quite easy here to experiment with a huge variety of our organisms
and study their life and behavior. Just take a seat, prepare your microscope
and test tubes and enjoy the colorful evolution of life.

Study your favorite beings and clone them. Check the ecosystem stability
by stimulating the growth of a concrete species or eradicating another one.
Be the first one to discover a new life pathway or freeze an interesting
organism to share it with your colleagues. Be fascinated by the different
ways evolution can take and play with different parameters to see how
organisms mutate to adapt to the environment.

Biogenesis simulates in a visual fashion the processes involved in the evolution
of unicellular organisms at nature. It tries to be a didactic approximation to
the ideas of mutation or evolution and can be enjoyed also as an entertainment.
It's intended to serve as a support to show students some basic biological
facts.

In order to execute this program it is necessary to have a Java Virtual
Machine installed in your computer. This version will only work with a 6 or
later version, such as the official Sun machine, which can be downloaded from
http://java.com/en/. Once the virtual machine is installed you only need to
double click on the biogenesis.jar file in order to execute it. It is not
necessary to do any program installation. Alternatively, you can right-click on
the file and select Open with Java Runtime, or run it from the command line with
the command:

java -jar biogenesis.jar

See the performance section in the user manual to know how to improve program's
performance for your computer.

In version 0.8 there are a few improvement, such as better file management, keys
to start and pause the game without using the menu, and the possibility to import
genetic codes directly into the laboratory. Moreover, in this release, and thanks
to Florian Haag, we have now the missing icons we needed to complete the toolbar.



In version 0.9 there are performance improvements and bug fixes, 
and the download also includes the Color Mod and the X Mod.

Changelog: 

biogenesis (0.9) by MarcoDBAA (0.8 and earlier by Joan Queralt);

   0.9 v2:
  * Fixed a bug, where the web link to the game manuals was not working.
  * Fixed a bug, where organisms could be "born" with 0 segments
    and disappear immediately. Therefore:
  * Through mutation organisms can have between 1 and 100 genes (was 1- 840 segments) 
  
  0.9 v1:
  * STRtrees (by Vivid Solutions) implemented by Richard David Williams
    to make the simulation run much faster.
  * Better function to create random organisms, independent from symmetry.
  * Through mutation organisms can have between 1 and 840 segments (was 4-64)
  * Fixed a bug where organisms disappeared from the world after a collision, 
    or immediately at birth (if they were very small).
  * Fixed a bug, where you couldn´t change the value for the parameter 
    "Energy lost by dead organisms".
  * Fixed a bug, where the statistics window didn´t work in empty worlds.
  * German translation by MarcoDBAA
  * Portuguese translation by Mauricio Leonardi
  * Russian translation by Alexey Loginov
  
  P.S: 
  * These are just small changes and bug fixes for Joan Queralts 0.8 version,
    limited like that, so that the user manual is still up to date.
  * Check out my "Color Mod" or AdaMs "X Mod" (both included in extra folders), 
    if you want to have new content (there is much) for biogenesis.

biogenesis (0.8);

  * Added import button in the laboratory, to import genetic code files.
  * File dialogs now remember last directory.
  * File extensions automatically added if not specified.
  * New parameter to control corpses decomposition speed.
  * Energy to reproduce is now visible from the info toolbar.
  * Info toolbar now automatically updates its label when changing locale.
  * Mutate every treat (length, degree or color) independently.
  * Accelerator keys for pause and save actions.
  * Added command line argument to set random seed.
  * Show biogenesis icon in all windows.
  * Use only one main window.
  * New icons by Florian Haag.
  * Let's save world when quitting.
  * Localized option dialogs.
  * Fixed bug: CO2 were consumed when using yellow segments, even if the child
    couldn't be placed into the world. (thanks to marcodbaa)
  * Updated documentation.

biogenesis (0.7);

  * Organisms can have any symmetry from 1 to 8.
  * Gene segments use now polar coordinates.
  * Many more possible organisms.
  * Slightly better drawing performance.
  * Easier edition in genetic laboratory.
  * Improved genetic code visualization in the laboratory.
  * Fixed bug: now really preserve window size.
  * Fixed bug: better coordinate rounding when drawing organisms.
  * Fixed bug: avoid shrinking organisms if haven't space.

biogenesis (0.6);

  * Organisms shrink when have little energy.
  * New info panel. Removed old info window.
  * Removed old genetic code window.
  * Improved genetic code visualization.
  * Improved laboratory window visualization.
  * Preserve main window position and size.
  * Updated documentation.

biogenesis (0.5);

  * Network: added connections between different world.
  * Network: added corridors to send organisms through connections.
  * Network: added a dialog to manage connections.
  * Network: added a dialog to configure network settings.
  * New parameters to activate OpenGL.
  * Added an uninstaller.
  * Added an option to kill all organisms.
  * Added killed and infected counters to the organism's state window.
  * Added toolbars with the main options in each circumstance.
  * Added mnemonics in menu options.
  * Added number of kills and number of infected in the information window.
  * Now the program dynamically adapts its speed to the computer performance.
  * Show current and last version in a better format.
  * Show some information messages in the status bar.
  * Changed default parameters to have a smaller and faster world.
  * Remove Vectors and convert them to Lists.
  * Added comments in many files.
  * Some speed optimization.
  * Fixed a bug that prevented some corpses to disappear.
  * Fixed a bug that prevented the initial organisms number from being saved
  between sessions.
  * Fixed a bug that let the user to kill a dead organism if the context menu
  was showed before the organism died.
  * Updated documentation.
  * Other minor details.

biogenesis (0.4);

  * Added Spanish translation (program and documentation).
  * Added a genetic code editor (genetic laboratory).
  * Now the application can act as an applet as well.
  * Added an option to save a JPG image of an organism.
  * Added status bar with basic world statistics.
  * Added an option to launch the web browser at the manual page.
  * Added an option to check the last released version.
  * Added new parameters to control the probability of a color appearing in a
  segment and the energy cost that using each color implies.
  * Added a tab in the parameters window to configure these parameters.
  * Added options to increase or decrease the carbon dioxide in a running world.
  * Added an option to disperse all corpses back into the environment.
  * Adapted to Java 5 and compiled for this version. This makes execution faster.
  * Changed the mutation rate parameter to allow values lesser than 1%.
  * Changed the way genetic codes are saved and restored. Now exported files are
  in XML.
  * Fixed a bug that makes organisms with more than 64 segments appear when the
  symmetry mutates.
  * Fixed a bug that makes the visible world to be bigger than the world when world
  size changed.
  * Increased the unit increment of scroll bars to facilitate navigation.
  * Updated about window to give some more information.
  * Updated documentation.
  * Other minor details.

biogenesis (0.3);

  * Started internationalization process.
  * Added English translation (program and documentation).
  * Menu bar instead of buttons.
  * Added a lot of user interaction.
  * Changed organism's metabolisms: processes are more realistic now.
  * Added oxygen and carbon dioxide instead of abstract substances.
  * Changed the meaning of some segment colors.
  * Now corpses remain in the world while they have energy.
  * Since carbon is constant in the world, population stabilizes and doesn't keep growing for ever.
  * Better parameters window.
  * Now delay can be changed without restarting.
  * Don't ask file name if already has one.
  * Added scroll bars to move through worlds bigger than the window.
  * Changed class names to conform standards.
  * Updated documentation.
  * Other minor details.

biogenesis (0.2.1);

  * Fixed parameters window visualization problems.
  * Better draw process: only draw organisms that move.
  * Better exception handling when loading files.
  * Information frames now appear always on top.
  * Other minor details.

biogenesis (0.2);

  * Now organisms collide in a more realistic way.
  * Fixed organisms growth.
  * Colors are calculated only once now.
  * Ask for confirmation when overriding a file.
  * Added a dialog to configure parameters.
  * Now parameters are stored outside the source.
  * Deactivate antialiasing if there are a lot of organisms.
  * Updated documentation.
  * Other minor details.

biogenesis (0.1);

  * Initial release.