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I'm glad someone asked lol. There's a buffer inventory inside the bioreactor that you can place materials in by hand as many stacks of whatever type you want, and then theres the inventory it uses which you cant directly place items in, but it will use one item of each different type you have in the buffer inventory. When connecting with buildcraft pipes the buffer inventory is super buggy, even with insertion pipes it accepts or doesn't accept items randomly, a lot of times not accepting an item even when it's completely out. The best way to hook it up with buildcraft pipes is make a stop back from your farm and lead insertion pipes into hoppers into the bioreactor. This will require a bit of babysitting though.

The absolute best way is to just use AE and use one precision export cable, and one basic export cable. With AE the buffer inventory works as intended and will only accept one of each stack so just set it to fill er up and use all the different types of items you have. You will literally never have to look at them again.

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