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Everyone has its own method. Bugs come in various species. Be curious and ask yourself questions. Start with the "Five Ws" (https://en.wikipedia.org/wiki/Five_Ws) . Rinse and repeat and soon you will be able to recognize them then to classify them. Then you will be able to spot them. Then you will be able to see the trace they leave. Then, for example, ...
There was a presentation at BlackHat Europe 2015 about weaknesses in Lastpass.
It's not clear what your intent is or what kinds of attacks you want to carry out, but it sounds like you simply need programs running that are configured to listen to or poll a configurable Command server, which would be one of your VMs. The commands the bots receive then determine their actions towards the victim. If you are shopping for a source of ...
There's a network designed for this purpose called DETER, and they both publish a great deal of information and make their "range" available to other researchers. http://deter-project.org/about_deterlab
Botnets are a large and varied class of software, which do a variety of tasks, so it's not necessarily easy to provide exact examples. With that said, if you take a typical task of creating Denial of Service conditions in the target system, then it's relatively easy to replicate the actions of a botnet with standard software. For example say you want to ...
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