If You’re Not Modeling, You’re Just Programming: Modeling Throughout an Undergraduate Software Engineering Program

Modeling is a hallmark of the practice of engineering. Through centuries, engineers have used models ranging from informal “back of the envelope” scribbles to formal, verifiable mathematical models. Whether circuit models in electrical engineering, heat-transfer models in mechanical engineering, or queuing theory models in industrial engineering, modeling makes it possible to perform rigorous analysis that is the cornerstone of modern engineering. By considering software development as fundamentally an engineering endeavor, RIT’s software engineering program strives to instill a culture of engineering practice by exposing our students to both formal and informal modeling of software systems throughout the entire curriculum. This paper describes how we have placed modeling in most aspects of our curriculum. The paper also details the specific pedagogy that we use in several courses to teach our students how to create, analyze and implement models of software systems

Concurrent system design: Applied mathematics & modeling in software engineering education

A hallmark of engineering design is the use of models to explore the consequences of design decisions. Sometimes these models are physical prototypes or informal drawings, but the sine qua non of contemporary practice is the use of formal, mathematical models of system structure and behavior. Whether circuit models in electrical engineering, heat-transfer models in mechanical engineering, or queuing theory models in industrial engineering, mathematics makes it possible to perform rigorous analysis that is the cornerstone of modern engineering. Until recently, such modeling was impractical for software systems. Informal models abounded, such as those created in UML1, but rigorous models from which one could derive significant properties were either so rudimentary or so tedious to use that it was difficult to justify the incremental benefit in other than the most critical of systems. In part this is a reflection of the relative immaturity of software engineering, but it also reflects a key distinction between software and traditional engineering: whereas the latter builds on numerical computation and continuous functions, software is more appropriately modeled using logic, set theory, and other aspects of discrete mathematics. Most of the models stress relationships between software components, and numerical computation is the exception rather than the norm. Recent advances in both theory and application have made it possible to model significant aspects of software behavior precisely, and to use tools to help analyze the resulting properties2,3,4. In this paper, we focus on a course developed by James Vallino and since taught and modified by Michael Lutz, to present formal modeling to our software engineering students at RIT. Our overall goals were three-fold: To acquaint our students with modern modeling tools, to connect the courses they take in discrete mathematics to real applications, and to persuade them that mathematics has much to offer to the engineering of quality software

Control System Plant Simulator: A Framework For Hardware In The Loop Simulation

Control systems courses are common in undergraduate engineering programs. These courses focus on the design of the controller\u27s mathematical model but rarely have students explore the practical issues of implementing the controller. Real-time and embedded systems courses focus on these practical issues with students implementing controllers for simplified Hardware-in-the- Loop plants such as a digital servo motor. Designing controllers for complex physical plants is difficult due to prohibitive costs or the risk of accidents caused by faulty controllers. These difficulties can be overcome if a simulator replaces the hardware-in-the-loop physical plant. We designed and implemented the Control System Plant Simulator (CSPS) as a flexible framework for simulating plant models in control system implementation projects. The framework allows the user to model continuous and discrete plants defined as transfer functions or systems of state-space equations. This paper describes the design of the CSPS framework by highlighting the expansion and modification flexibility it provides with its operating system, non-real-time user interface, and physical device abstraction layers. The CSPS framework has advantages over commercial tools that can provide a hardware-in-the-loop plant simulation. The framework\u27s scope of usage is much narrower than the commercial tools making it easier to learn how to use and modify. Also, we distribute the framework as an open-source project making it readily available for use in any course without licensing, and ensuring that deeper and more complex customizations are possible. The paper concludes with a discussion of our successful experience using the framework in real-time systems course projects, and porting to two operating environments (standard Windows XP and Ardence RTX Real-Time Extensions for Windows), two user interfaces (C-based text, Visual Basic GUI), and two data acquisition devices (USB data acquisition, simulated multi-channel IO device)

Embedded Systems Courses at RIT

A three-course sequence of cross-disciplinary real-time and embedded systems courses has been introduced at RIT ¢. We are teaching these courses in a studio-lab environment teaming computer engineering and software engineering students. The courses introduce students to programming both microcontrollers and more sophisticated targets, use of a commercial real-time operating system and development environment, modeling and performance engineering of these systems, and their interactions with physical systems

The Road We’ve Traveled: 12 Years of Undergraduate Software Engineering at the Rochester Institute of Technology

In 1996, the Rochester Institute of Technology launched the first undergraduate software engineering program in North America. This paper briefly reviews the development of the program, and describes the program’s evolution up to the present. We illuminate both the constant aspects of the program – what we believe we got right – as well as the changes made in light of pedagogical, technological and disciplinary advances. We conclude by considering the current and future challenges for undergraduate software engineering education both at RIT and elsewhere

Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents

The size and biogeochemical impact of the subseafloor biosphere in oceanic crust remain largely unknown due to sampling limitations. We used reactive transport modeling to estimate the size of the subseafloor methanogen population, volume of crust occupied, fluid residence time, and nature of the subsurface mixing zone for two low-temperature hydrothermal vents at Axial Seamount. Monod CH4 production kinetics based on chemostat H2 availability and batch-culture Arrhenius growth kinetics for the hyperthermophile Methanocaldococcus jannaschii and thermophile Methanothermococcus thermolithotrophicus were used to develop and parameterize a reactive transport model, which was constrained by field measurements of H2, CH4, and metagenome methanogen concentration estimates in 20–40 °C hydrothermal fluids. Model results showed that hyperthermophilic methanogens dominate in systems where a narrow flow path geometry is maintained, while thermophilic methanogens dominate in systems where the flow geometry expands. At Axial Seamount, the residence time of fluid below the surface was 29–33 h. Only 1011 methanogenic cells occupying 1.8–18 m3 of ocean crust per m2 of vent seafloor area were needed to produce the observed CH4 anomalies. We show that variations in local geology at diffuse vents can create fluid flow paths that are stable over space and time, harboring persistent and distinct microbial communities

The temporal response of the length of a partially stratified estuary to changes in river flow and tidal amplitude

Author Posting. © American Meteorological Society, 2009. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 39 (2009): 915-933, doi:10.1175/2008JPO3933.1.The temporal response of the length of a partially mixed estuary to changes in freshwater discharge Qf and tidal amplitude UT is studied using a 108-day time series collected along the length of the Hudson River estuary in the spring and summer of 2004 and a long-term (13.4 yr) record of Qf, UT, and near-surface salinity. When Qf was moderately high, the tidally averaged length of the estuary L5, here defined as the distance from the mouth to the up-estuary location where the vertically averaged salinity is 5 psu, fluctuated by more than 47 km over the spring–neap cycle, ranging from 28 to >75 km. During low flow periods, L5 varied very little over the spring–neap cycle and approached a steady length. The response is quantified and compared to predictions of a linearized model derived from the global estuarine salt balance. The model is forced by fluctuations in Qf and UT relative to average discharge Qo and tidal amplitude UTo and predicts the linear response time scale τ and the steady-state length Lo for average forcing. Two vertical mixing schemes are considered, in which 1) mixing is proportional to UT and 2) dependence of mixing on stratification is also parameterized. Based on least squares fits between L5 and estuary length predicted by the model, estimated τ varied by an order of magnitude from a period of high average discharge (Qo = 750 m3 s−1, τ = 4.2 days) to a period of low discharge (Qo = 170 m3 s−1, τ = 40.4 days). Over the range of observed discharge, Lo Qo−0.30±0.03, consistent with the theoretical scaling for an estuary whose landward salt flux is driven by vertical estuarine exchange circulation. Estimated τ was proportional to the discharge advection time scale (LoA/Qo, where A is the cross-sectional area of the estuary). However, τ was 3–4 times larger than the theoretical prediction. The model with stratification-dependent mixing predicted variations in L5 with higher skill than the model with mixing proportional to UT. This model provides insight into the time-dependent response of a partially stratified estuary to changes in forcing and explains the strong dependence of the amplitude of the spring–neap response on freshwater discharge. However, the utility of the linear model is limited because it assumes a uniform channel, and because the underlying dynamics are nonlinear, and the forcing Qf and UT can undergo large amplitude variations. River discharge, in particular, can vary by over an order of magnitude over time scales comparable to or shorter than the response time scale of the estuary.This study was generously funded by Hudson River Foundation Grant 005/03A and NSF Grant OCE-0452054. Lerczak also received partial support from the Woods Hole Center for Oceans and Human Health, NSF Grant OCE-0430724 and NIEHS Grant 1-P50-ES012742-01

Seafloor incubation experiment with deep-sea hydrothermal vent fluid reveals effect of pressure and lag time on autotrophic microbial communities

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fortunato, C. S., Butterfield, D. A., Larson, B., Lawrence-Slavas, N., Algar, C. K., Zeigler Allen, L., Holden, J. F., Proskurowski, G., Reddington, E., Stewart, L. C., Topçuoğlu, B. D., Vallino, J. J., & Huber, J. A. Seafloor incubation experiment with deep-sea hydrothermal vent fluid reveals effect of pressure and lag time on autotrophic microbial communities. Applied and Environmental Microbiology, 87, (2021): e00078-21, https://doi.org/10.1128/AEM.00078-21Depressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this knowledge gap, we developed a remotely operated vehicle (ROV)-powered incubator instrument to carry out and compare results from in situ and shipboard RNA stable isotope probing (RNA-SIP) experiments to identify the key chemolithoautotrophic microbes and metabolisms in diffuse, low-temperature venting fluids from Axial Seamount. All the incubations showed microbial uptake of labeled bicarbonate primarily by thermophilic autotrophic Epsilonbacteraeota that oxidized hydrogen coupled with nitrate reduction. However, the in situ seafloor incubations showed higher abundances of transcripts annotated for aerobic processes, suggesting that oxygen was lost from the hydrothermal fluid samples prior to shipboard analysis. Furthermore, transcripts for thermal stress proteins such as heat shock chaperones and proteases were significantly more abundant in the shipboard incubations, suggesting that depressurization induced thermal stress in the metabolically active microbes in these incubations. Together, the results indicate that while the autotrophic microbial communities in the shipboard and seafloor experiments behaved similarly, there were distinct differences that provide new insight into the activities of natural microbial assemblages under nearly native conditions in the ocean.This work was funded by Gordon and Betty Moore Foundation grant GBMF3297; the NSF Center for Dark Energy Biosphere Investigations (C-DEBI) (OCE-0939564), contribution number 562; NOAA/PMEL, contribution number 5182; and the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) under NOAA cooperative agreement NA15OAR4320063, contribution number 2020-1113. The RNA-SIP methodology used in this work was developed during cruise FK010-2013 aboard the R/V Falkor supported by the Schmidt Ocean Institute. The NOAA/PMEL supported this work with ship time in 2014 and through funding to the Earth Ocean Interactions group. NSF provided ship time for the 2015 expedition through OCE-1546695 to D.A.B. and OCE-1547004 to J.F.H

Revisiting the Gaia Hypothesis: Maximum Entropy, Kauffman’s ‘Fourth Law’ and Physiosemeiosis

Recently, Kleidon suggested to analyze Gaia as a non-equilibrium thermodynamic system that continuously moves away from equilibrium, driven by maximum entropy production which materializes in hierarchically coupled mechanisms of energetic flows via dissipation and physical work. I relate this view with Kauffman's 'Fourth Law of Thermodynamics', which I interprete as a proposition about the accumulation of information in evolutionary processes. The concept of physical work is expanded to including work directed at the capacity to work: I offer a twofold specification of Kauffman's concept of an 'autonomous agent', one as a 'self-referential heat engine', and the other in terms of physiosemeiosis, which is a naturalized application of Peirce's theory of signs. The conjunction of these three theoretical sources, Maximum Entropy, Kauffman's Fourth Law, and physiosemeiosis, shows that the Kleidon restatement of the Gaia hypothesis is equivalent to the proposition that the biosphere is generating, processing and storing information, thus directly treating information as a physical phenomenon. There is a fundamental ontological continuity between the biological processes and the human economy, as both are seen as information processing and entropy producing systems. Knowledge and energy are not substitutes, with energy and information being two aspects of the same underlying physical process

Datacube MV200 and ImageFlow User's Guide

The Datacube MaxVideo 200 is a high-speed image processing system that can provide video rate processing of images. A user writes programs using the Datacube ImageFlow libraries to control the hardware. Learning the details of ImageFlow programming is a daunting task for the new user. This learning task is made more difficult because the manuals for the MaxVideo 200 hardware and ImageFlow software are rather obscure to the typical novice user. This user's guide describes several simple ImageFlow programs. Emphasis is placed on providing some of the folklore that is needed to get started in MV200/ImageFlow programming. Also, the organization of the information in the Datacube manuals is described so that the new user can continue exploring on their own system features that are not in the sample programs