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Technological advances in cyberinfrastructure have paved the way for research grade computational simulation tools, such as those available on nanoHUB.org. Even though benefits have been acknowledged for incorporating these tools into teaching and learning environments, difficulties have also been identified. To address some of these difficulties researchers have emphasized that inquiry learning with simulations, in order to be successful, needs adequate but not intrusive scaffolding. As a response to this need, nanoHUB.org affiliated faculty have proposed tool-based curricula to be used for training 21st century engineers in the nanoelectronics field. Motivated and informed by our previous work and related literature on inquiry learning with simulation, a transparency and scaffolding framework is proposed to be integrated into existing nanoHUB tool-based curricula.