2. Cases which contain the Borer prohibition:

A. Making cheese on Shabbos:[1]

Making the curd:[2] One who curds [milk], in which he takes milk and places a stomach [or other enzyme] into it in order to curd[3] it, is liable for separating because he has separated the curd from the milk.

Placing the curd into a strainer: Similarly, if one places the curd into an elastic vessel[4] and the whey drips from inside it then this is an offshoot of separating food from waste through using a sieve and sifter and one is thus liable.

The reason: Now, although the curd and the milk are both a single species of food and there is [thus] no waste [here] at all, nevertheless since they are liquid substances which mix well which he is [now] separating, therefore this contains the separating [prohibition] just like one who is separating food from waste.

Making hard cheese:[5] If one solidified [curd] and turned it into cheese he is liable for building.

The reason for this is:[6] because anyone who gathers parts [of an item] to each other and bonds them together until they become a single substance has [transgressed] an offshoot of [the] building [prohibition]. 

B. Removing seeds and nuts from honey:[9]

One may place sesame and nuts into honey, although he may not [press them[10] and thus] separate them [from the honey] with his hands [as doing so is considered separating.[11] Accordingly, it may be done for immediate use.[12] Alternatively, doing so is considered Kneading and is forbidden to be done even for right away use.[13] However, according to all to simply remove a seed or nut from the honey would be permitted for right away use.]

C. Catalyzing beverages on Shabbos:[14]

It is forbidden to place dregs into beverages in order to catalyze it even though [the liquid] is already fit to be drunk on Shabbos being that through doing so one causes the dregs of the liquid itself to sink to the bottom of the vessel and it is an offshoot of separating similar to one who curds milk.

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[1] Admur 319:25; Michaber 319:17

[2] Admur ibid; M”A 39:18; M”B 319:62

^[3] Cheese is made by separating the milk into solid curds and liquid whey. Usually this is done by acidifying (souring) the milk and adding rennet. The acidification can be accomplished directly by the addition of an acid like vinegar  These starter bacteria convert milk sugars into lactic acid. Most cheeses are made with starter bacteria from the Lactococci, Lactobacilli, or Streptococci families. 

^[4] This refers to a vessel made of material that can be stretched out do to having tiny holes in it, and thus allows the milk to drip out. Similar to a plastic bag.

[5] Admur 319:26; M”A 319:18; M”B 319:63; Shabbos 95b; Vetzaruch Iyun if making Tofu or Halva into a block also transgresses the Boneh prohibition

[6] Admur 319:26

[7] Shabbos Kehalacha Vol. 2 p. 176

[8] M”B 319:60; Shabbos Kehalacha Vol. 2 p. 176

[9] Admur 319:27; Michaber 319:17; 340:11

^[10] Mishneh Berurah on 319:66; 340:39; Literally “Michabeitz”

^[11] Mishneh Berurah on 340:39

[12] M”B 319:64

[13] M”B ibid based on M”A from Tosefta

[14] Admur 319:29; M”A 319:28