What kind of data do simulation packages like PYTHIA or ISAJET programs produce? I read in a CMS TDR (Compact Muon Solenoid Techincal Design Report) that "PYTHIA or ISAJET programs were run to produce minimum bias, QCD jet, top, Standard Model higgs, MSSM higgs or SUSY sparticle event $n$-tuples." Can somebody explain what these event $n$-tuples contain? Also, what does minumum bias mean in the above statement.
 A: I am going to shamelessly simplify here. Each event generated by PYTHIA or ISAJET consist of $n$ particles. For each particle, the information consists, initially, of the type of particle and its four-momentum. Then these programs can also cluster the produced particles in jets, applying the exact same algorithms that will be used for the analysis of measured data. They are used to produce a large number of such events, with a probability for each event matching what the theory says it should be, with further tweaking from previous measurements. 
Why tweaking? Theoretical computations predict the production of quark, gluons, leptons, etc. But then the quarks and gluons will form hadrons, in processes that the theory cannot fully rigorously compute. So PYTHIA and ISAJET use semi-empirical models, which contains adjustable parameters that can only be determined from measurements. To do that, experimentalists choose some very well understood Standard Model channel, and tweak their parameters to fit the data. Then they reuse the same parameters for channels where they expect to see new physics (supersymmetry, etc). 
As for minimum bias, I will give you the gist of it (for the benefit of other users of the site too) but I don't know what to recommend you as a technical reference. I am just reminiscing discussions with particle physicists here but I am not in the business anymore! 
So, first, minimum bias, is a rather generic term which can apply to a lot of techniques, but in the context of your question, it is safe to assume it refers to one particular issue. The total cross-section can be broken in the following terms:
$$\sigma_{total} = \sigma_{elastic} + \sigma_{sd} + \sigma_{dd} + \sigma_{nd} + \sigma_{cd}$$
The first term is the elastic collision case $pp\to pp$ where each proton is unscathed. The second term, Single Diffraction, is the case where one of the proton is unscathed but the other one fragments. The third case, Double Diffraction, is the case where both proton fragments. In all the cases so far, the final particle momenta will be very close to the beam line. And in the latter case, there will therefore be a huge rapidity gap between the jets produced by each proton, which helps to eliminate them. The next-to-last term, Non Diffractive, is really what LHC wants to see. Those are all the collisions where some constituent of one proton collide with some constituent of the other proton to produce everything LHC experiments seek to discover. The last term, Central Diffractive Dissociation, is a nasty case where each proton radiate a Pomeron and the interaction of the two pomerons give rise to particle with high transverse momentum (hence Central for central region of the detector).
So the minimum bias cross-section is then
$$\sigma_{\text{MB}} = \sigma_{dd} + \sigma_{nd}$$
Why this combination? My understanding is that Minimum Bias event are selected by a trigger, that it to say in real time on the detectors. Thus the criteria to eliminate the other events should be really quick to compute. 


*

*For elastic or single diffraction: nothing but a single hit in one-half of the rapidity range (positive side or negative side, I mean): quick to filter out

*$\sigma_{cd}$: not completely sure here. For one thing, those are quite rarer actually iiuc. And perhaps with one hit at very negative rapidity, one hit at very positive rapidity, and a relatively narrow band of hits around a zero rapidity, it may be quick to filter out too.
On the contrary, the double diffractive events have lots of hits everywhere except in the central rapidity range. This can be used after collection but online there is no quick criteria that would not also reject some interesting events where jets happen to be out of the central region.
I know that this is a bit of hand waving but unless you get dirty with the details, as good as it gets! 
