<EM>This blueprint is nearly identical to the Gleba Iron Ore blueprint I have. If you've read that you've pretty much read this.</EM>
Inputs: <BR>Jellynuts <BR>Yumako
Returns: <BR>Jellynut/Yumako Seeds <BR>Jellynuts and Yumako (when ore/bacteria backup)
Outputs: <BR>Copper Ore/Bacteria 30/sec <BR>Spoilage x2 (rate varies)
Short Version
To start the system, add nutrients to the top four biochambers and provide inputs. Alternatively, add about half a stack of spoilage to each assembler. Production system will slowly turn on as biochambers get nutrients and ingredients.
This blueprint does have circuits. This is to return inputs when copper ore/bacteria back up (better to use them elsewhere). Other circuits help restart bacteria production and nutrient product in the event of issues.
Spoilage outputs can be burned or used elsewhere. Seed returns should be sent back to your agricultural towers.
Long Version
There are circuits, but no combinators to keep things simple. (room for minor improvements if you're inclined to add combinators)
Tested in sandbox for a long time on x64 speed. Spoilage is emptied from every building and belt as it occurs. The bioflux to nutrient biochamber empties its spoilage onto the center nutrient belt where it is later filtered. All other places will filter it's spoilage directly into spoilage belts.
Copper bacteria cultivation biochambers are jumpstarted (an re-jumpstarted) by the yumako mash->copper bacteria biochamber. Circuits check the main output to see if there are zero copper ore/bacteria. If there are, then it will turn on the biochamber and its jelly input inserter.
Copper bacteria cultivation feed themselves. It takes the first six rows of cultivators to get just under the 30 ore/bacteria per second. It take the bottom two rows to make sure the red belt rate stays maxed out. Either there is some diminishing returns for more cultivators or perhaps there's a better way to self feed bacteria.
The top crop processors will feed the wood boxes above them. They DELIBRATELY spoil. These will feed the assemblers in the event of a nutrient outage. It checks to see if the crop on it's side is there (to ensure replenishment) and if the nutrient belt has zero nutrients. If these two requirements are met it will create nutrients from spoilage to jump start the system.
In the event of an ore/bacteria backup (expected if you inevitably use less ore than you produce), the jellynuts and yumako are released to the return to be place back in whatever your main line is and the input belt halts to prevent more crops from entering (they would just spoil for no reason). This helps keep inputs fresh for when they actually needed and not waste inputs in the system. If you'd rather not use the crop return feature, you can remove those return belts.