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Computer-Aided System Engineering and Analysis (CASE/A) Programmer's Manual, Version 5.0

The Computer Aided System Engineering and Analysis (CASE/A) Version 5.0 Programmer's Manual provides the programmer and user with information regarding the internal structure of the CASE/A 5.0 software system. CASE/A 5.0 is a trade study tool that provides modeling/simulation capabilities for analyzing environmental control and life support systems and active thermal control systems. CASE/A has been successfully used in studies such as the evaluation of carbon dioxide removal in the space station. CASE/A modeling provides a graphical and command-driven interface for the user. This interface allows the user to construct a model by placing equipment components in a graphical layout of the system hardware, then connect the components via flow streams and define their operating parameters. Once the equipment is placed, the simulation time and other control parameters can be set to run the simulation based on the model constructed. After completion of the simulation, graphical plots or text files can be obtained for evaluation of the simulation results over time. Additionally, users have the capability to control the simulation and extract information at various times in the simulation (e.g., control equipment operating parameters over the simulation time or extract plot data) by using "User Operations (OPS) Code." This OPS code is written in FORTRAN with a canned set of utility subroutines for performing common tasks. CASE/A version 5.0 software runs under the VAX VMS(Trademark) environment. It utilizes the Tektronics 4014(Trademark) graphics display system and the VTIOO(Trademark) text manipulation/display system.

Knox, J. C.↗

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Version 1.5 and 1.x.

EDGE bioinformatics was developed to help biologists process Next Generation Sequencing data (in the form of raw FASTQ files), even if they have little to no bioinformatics expertise. EDGE is a highly integrated and interactive web-based platform that is capable of running many of the standard analyses that biologists require for viral, bacterial/archaeal, and metagenomic samples. EDGE provides the following analytical workflows: quality trimming and host removal, assembly and annotation, comparisons against known references, taxonomy classification of reads and contigs, whole genome SNP-based phylogenetic analysis, and PCR analysis. EDGE provides an intuitive web-based interface for user input, allows users to visualize and interact with selected results (e.g. JBrowse genome browser), and generates a final detailed PDF report. Results in the form of tables, text files, graphic files, and PDFs can be downloaded. A user management system allows tracking of an individual’s EDGE runs, along with the ability to share, post publicly, delete, or archive their results.

Chain, Patrick↗

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Version 1.5 and 1.x.

EDGE bioinformatics was developed to help biologists process Next Generation Sequencing data (in the form of raw FASTQ files), even if they have little to no bioinformatics expertise. EDGE is a highly integrated and interactive web-based platform that is capable of running many of the standard analyses that biologists require for viral, bacterial/archaeal, and metagenomic samples. EDGE provides the following analytical workflows: quality trimming and host removal, assembly and annotation, comparisons against known references, taxonomy classification of reads and contigs, whole genome SNP-based phylogenetic analysis, and PCR analysis. EDGE provides an intuitive web-based interface for user input, allows users to visualize and interact with selected results (e.g. JBrowse genome browser), and generates a final detailed PDF report. Results in the form of tables, text files, graphic files, and PDFs can be downloaded. A user management system allows tracking of an individual’s EDGE runs, along with the ability to share, post publicly, delete, or archive their results.

Chain, Patrick↗

The Acoustic Emission signal acquired by the microphones placed in the CABRI test device along the fourteen last R.I.A. experiments: an example of reproducible research in nuclear science

The CABRI facility is an experimental nuclear reactor of the French Atomic Energy Commission. It is located at the Cadarache Research Centre in southern France and it is designed to act as a support to the French nuclear infrastructure. The purpose of the new testing programme termed, 'CABRI International Programme' (CIP) is to study the behaviour of PWR-type fuel rods at high burnup, equipped with an 'advanced' cladding, under Reactivity Initiated Accident (RIA) conditions (such as the scenario of a control rod ejection). Within the framework of this programme, piloted and funded by the French Institute of Nuclear Radioprotection and Safety (IRSN), ten tests are to be conducted with a frequency of two tests per year. The LPRE laboratory of the CEA which is in charge of the Preparation, realisation and breakdown of the test results studies the possibility to set up a new test analysis based on the processing of signals coming from sensors placed within the test equipment. During the experimental phase, the behaviour of the fuel element generates acoustic waves which can be detected by two microphones placed upstream and downstream of the test device. Studies showed the interest to realize temporal and spectral analyses on these signals by showing the existence of signatures which can be correlated with physical phenomena as the rod failure or the test shutdown (i.e. scram). The work presented in this article results from the will to consolidate these studies. Since the main phenomenon to be tracked is the fuel rod failure, the aim would be to highlight specific events which would have been precursors of the rod failure in order to use in the future these signals for further interpretation. Such an antecedent works resumption leads to a better understanding of the experimental needs and constitutes a good initial state to prepare the new very fast digital data acquisition systems. Although all the raw data are accessible in the form of text files, analyses and graphics representations were not straightforward to reproduce from the ancient studies since that, on one hand, people who were in charge of the original work left the laboratory and on the other hand because it is not easy when the time passes, even with our own work, to be able to remember the steps of data manipulations and the exact setup: - During the ancient experiments the use of analog data acquisition systems required to digitize tapes to be able to realize computer treatments. That had had for consequence to lose the initial dating. This one must be correctly edited to do temporal comparisons. - Analyses require functions for calculations whose parameters has to be well-known to reach the same results. We thus wished to manage our workflow in the idea that it can be easily reproducible on all the experiments. The object of the work presented in this article was to put in practice this strong bind between the data, treatments and generation of the document in order not to hesitate to do the iteration principle in action. We do not have to be afraid by the data driven analyses. According to the philosophy of the literate programming, the text of the technical document is woven with the computer code that produces all the printed output as tables, graphs for the study eliminating hence the unrealistic cut and paste. This difficulty is not specific to the nuclear domain. For many years, researchers have been worked out solutions to this mundane issue. And, presently, new technologies and high-level programming languages offer us actual answers. We will firstly present the tools applied in our laboratory to implement this workflow, then we will describe the global perception carried out to continue the study of the Acoustic Emission signals recorded by the two microphones during the fourteen last CABRI R.I.A. test.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

A simple json format for storing and exchanging code calculation and experimental results

Calculation codes and code systems give their results in a plethora of different formats and/or files. For instance, MCNP gives a user the MCNP specific output file, the mctal file, the ptrac file, etc. while PARTISN has a PARTISN specific output file and a number of binary files with various kinds of information about the calculation. However, the results we are interested in are always the same. These can be single values such as the effective multiplication factor k eff or the effective delayed neutron fraction β eff . It can be histogram data (such as particle spectra, reaction rates, sensitivity profiles, etc.) or even pointwise data (for example the nuclide composition as a function of time, etc.). It is also worthwhile to note that this would also apply to experimental data that we may wish to compare with as well. Calculation and experimental results can basically be split into two components: attributes (or metadata) and the actual result itself. Attributes represent information about the result that are not necessarily required for its’ interpretation but that are still good to have. Often, these attributes are what we will want to filter results on. This means that these attributes are often the answer to specific questions we may have about the result. The following is a non exhaustive list of such basic questions: what type of result is it: e.g. the effective multiplication factor k eff , the effective delayed neutron fraction β eff , etc.; which case does it relate to: e.g. a specific ICSBEP case such as PU-MET-FAST-001-001; which code and version produced this result: e.g. MCNP 6.2, etc.; which nuclear data library was used to obtain the result: e.g. ENDF/B-VIII.0 or JEFF 3.3; which nuclide and reaction does it apply to (for reaction rates and sensitivity profiles); which volume in the geometry was it calculated in? The second component of the calculation or experimental result is the actual numerical data of the result. It is this data that we want to compare, exchange, plot, interpret, etc. It consists of values with optional uncertainties and units. It also includes the underlying structure (if any structure is required to interpret the result). Depending on the type of result, it may be a single value (e.g. the effective multiplication factor), an array of values (e.g. a reaction rate or particle spectrum) or even a multidimensional array. In order to exchange results between different organisations, for instance for benchmarking, people often resort to spreadsheets or custom text files that need to be filled out. While this approach works well if little information is to be exchanged, it can become cumbersome when dealing with large amounts of data (like for instance particle spectra for thousands of cases). In addition, such an approach does not always capture the metadata we may be interested in to allow for automated processing of these files. The purpose of this report is to propose a standardised json structure to store any type of result and present an associated python interface to interact with these results directly. For such a structure to be useful, it must fulfill a specific set of functional requirements that we try to meet with this proposal. The format must allow for the calculation result to stand by itself. This means that we should not have to look in multiple places to be able to understand it. For example, if the result relates to a particle spectrum, the group structure in which the result is given should be stored with it. The format should be code agnostic. This means that we do not need to know where it came from to understand it. The format should be result type agnostic. This means that the format must be generic enough so that we can even use it for results we have not thought of yet. The format should be relatively easy to interact with through different scripting or programming languages (i.e. the machine interface) while still providing a clean structure that can be used directly by any human.

97 MATHEMATICS AND COMPUTING↗

A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling

Mechanistic models of how single cells respond to different perturbations can help integrate disparate big data sets or predict response to varied drug combinations. However, the construction and simulation of such models have proved challenging. Here, we developed a python-based model creation and simulation pipeline that converts a few structured text files into an SBML standard and is high-performance- and cloud-computing ready. We applied this pipeline to our large-scale, mechanistic pan-cancer signaling model (named SPARCED) and demonstrate it by adding an IFNγ pathway submodel. We then investigated whether a putative crosstalk mechanism could be consistent with experimental observations from the LINCS MCF10A Data Cube that IFNγ acts as an anti-proliferative factor. The analyses suggested this observation can be explained by IFNγ-induced SOCS1 sequestering activated EGF receptors. This work forms a foundational recipe for increased mechanistic model-based data integration on a single-cell level, an important building block for clinically-predictive mechanistic models.

60 APPLIED LIFE SCIENCES↗

Development of output user interface software to support analysis

Data processing software packages such as VSOP and MCNPX are softwares that has been scientifically proven and complete. The result of VSOP and MCNPX are huge and complex text files. In the analyze process, user need additional processing like Microsoft Excel to show informative result. This research develop an user interface software for output of VSOP and MCNPX. VSOP program output is used to support neutronic analysis and MCNPX program output is used to support burn-up analysis. Software development using iterative development methods which allow for revision and addition of features according to user needs. Processing time with this software 500 times faster than with conventional methods using Microsoft Excel. PYTHON is used as a programming language, because Python is available for all major operating systems: Windows, Linux/Unix, OS/2, Mac, Amiga, among others. Values that support neutronic analysis are k-eff, burn-up and mass Pu{sup 239} and Pu{sup 241}. Burn-up analysis used the mass inventory values of actinide (Thorium, Plutonium, Neptunium and Uranium). Values are visualized in graphical shape to support analysis.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

P SI4 1.4: Open-source software for high-throughput quantum chemistry

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree–Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4 's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. We announce a rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Python Tool for Aqueous Plutonium Nitrate Density Law Input Preprocessing in MCNP6

Here, this work develops a predictive density tool in Python, named Plutonium Nitrate Solutions (PuNS), to reduce bias and uncertainty in nuclear criticality safety calculations for plutonium nitrate systems. The Pitzer method and an empirical method were implemented into the PuNS tool to generate atom densities for use in MCNP6 material cards. These material cards are directly prepared into an MCNP6 input text file and are calculated based on customizable user inputs of plutonium content, nitric acid content, temperature, and plutonium isotope weight percentages. The PuNS tool is validated and verified against the International Criticality Safety Benchmark Evaluation Project Handbook experiments and is observed to predict densities within a root mean square error of 0.89% for the Pitzer method and 1.82% for the empirical method. These errors in density lead to up to 1569 pcm difference in MCNP6 calculated k eff for the Pitzer method and up to a 1751 pcm difference for the empirical method when compared to experimental benchmarks. Simultaneous work is also being performed at Los Alamos National Laboratory and the University of New Mexico to create a similar tool for plutonium chloride solutions, named Plutonium Chloride Solution, which aims to provide the accreditation of the chlorine absorption. These capabilities will not only provide more accurate models but also facilitate an improved understanding of solution systems and a potential relaxation in the conservatism of current aqueous plutonium processing criticality safety limits.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Erratum: Polarization transfer observables in elastic electron-proton scattering at Q 2 =2.5 , 5.2, 6.8, and 8.5GeV 2 [Phys. Rev. C 96 , 055203 (2017)]

Subsequent to the release of our original paper, we discovered in the context of preparing our technical supplement [1] for journal publication that a typographical error had existed in the text file that the analysis program used to construct the beam polarization "database" for both the original analysis, published in Ref. [2], and our final analysis. The electron-beam polarization P e and the analyzing power A y cancel exactly in the ratio R, which is proportional to the ratio P t / P l of the transferred polarization components. On the other hand, the extraction of the relative e dependence of P l / P Born l relies on knowledge of the beam polarization. As such, data taking was interrupted roughly every two days during the GEp - 2γ experiment to perform invasive measurements of the beam polarization using the Hall C Moller polarimeter [3].

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Reproducible Data Processing Research for the CABRI R.I.A. experiments Acoustic Emission signal analysis

The CABRI facility is an experimental nuclear reactor of the French Atomic Energy Commission (CEA) designed to study the behaviour of fuel rods at high burnup under Reactivity Initiated Accident (R.I.A.) conditions such as the scenario of a control rod ejection. During the experimental phase, the behaviour of the fuel element generates acoustic waves which can be detected by two microphones placed upstream and downstream from the test device. Studies carried out on the last fourteen tests showed the interest in carrying out temporal and spectral analyses on these signals by showing the existence of signatures which can be correlated with physical phenomena. We want presently to return to this rich data in order to have a new point of view by applying modern signal processing methods. Such an antecedent works resumption leads to some difficulties. Although all the raw data are accessible in the form of text files, analyses and graphics representations were not clear in reproducing from the former studies since the people who were in charge of the original work have left the laboratory and it is not easy when time passes, even with our own work, to be able to remember the steps of data manipulations and the exact setup. Thus we decided to consolidate the availability of the data and its manipulation in order to provide a robust data processing workflow to the experimentalists before doing any further investigations. To tackle this issue of strong links between data, treatments and the generation of documents, we adopted a Reproducible Research paradigm. We shall first present the tools chosen in our laboratory to implement this workflow and, then we shall describe the global perception carried out to continue the study of the Acoustic Emission signals recorded by the two microphones during the last fourteen CABRI R.I.A. tests. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Modeling and Analysis of Hybrid Pixel Detector Deficiencies for Scientific Applications

Semiconductor hybrid pixel detectors often consist of a pixellated sensor layer bump bonded to a matching pixelated readout integrated circuit (ROIC). The sensor can range from high resistivity Si to III-V materials, whereas a Si CMOS process is typically used to manufacture the ROIC. Independent, device physics and electronic design automation (EDA) tools are used to determine sensor characteristics and verify functional performance of ROICs respectively with significantly different solvers. Some physics solvers provide the capability of transferring data to the EDA tool. However, single pixel transient simulations are either not feasible due to convergence difficulties or are prohibitively long. A simplified sensor model, which includes a current pulse in parallel with detector equivalent capacitor, is often used; even then, spice type top-level (entire array) simulations range from days to weeks. In order to analyze detector deficiencies for a particular scientific application, accurately defined transient behavioral models of all the functional blocks are required. Furthermore, various simulations, such as transient, noise, Monte Carlo, inter-pixel effects, etc. of the entire array need to be performed within a reasonable time frame without trading off accuracy. The sensor and the analog front-end can be modeling using a real number modeling language, as complex mathematical functions or detailed data can be saved to text files, for further top-level digital simulations. Parasitically aware digital timing is extracted in a standard delay format (sdf) from the pixel digital back-end layout as well as the periphery of the ROIC. For any given input, detector level worst-case and best-case simulations are performed using a Verilog simulation environment to determine the output. Each top-level transient simulation takes no more than 10-15 minutes. The impact of changing key parameters such as sensor Poissonian shot noise, analog front-end bandwidth, jitter due to clock distribution etc. can be accurately analyzed to determine ROIC architectural viability and bottlenecks. Hence the impact of the detector parameters on the scientific application can be studied.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

SU-E-T-141: Automated Dose Point Placement for Cervical Cancer Brachytherapy Using Tandem and Ovoid Applicators

Purpose: To develop a standalone application, which automatically and consistently calculates the coordinates of points A and H based solely on the implanted applicator geometry for cervical cancer HDR brachytherapy. Methods: Manchester point A and ABS point H are both located 2cm lateral from the central tandem plane. While both points are located 2cm above the cervical os, surrogates for the os differ. Point A is defined relative to the anatomical cervical os. Point H is defined relative to the intersection of the tandem with the superior aspects of the ovoids. The application takes an input text file generated by the treatment planning system (TPS, BrachyVision, Varian) that specifies the source geometries. It then outputs the 3D coordinates of points A and H in both the left and right directions. The algorithm was implemented and tested on 34 CT scans of 7 patients treated with HDR brachytherapy delivered using tandem and ovoids. A single experienced user retrospectively and manually placed points A and H on the CT scans, whose coordinates were used as the gold standard for the comparison to the automatically calculated points. Results: The automatically calculated coordinates of points A and H agree within 0.7mm with the gold standard. The averages and standard deviations of the 3D coordinate difference between points placed by the two methods are 0.3±0.1 and 0.4±0.1mm for points A and H, respectively. The maximum difference in 3D magnitude is 0.7mm. Conclusion: The algorithm consistently calculates dose point coordinates independently of the planner for cervical cancer brachytherapy treated with tandem and ovoids. Automated point placement based on the geometry of the implanted applicators agrees in sub-millimeter with careful manual placements by an experienced user. This algorithm expedites the planning process and eliminates dependencies on either user input or TPS visualization tools.

60 APPLIED LIFE SCIENCES↗

SU-E-T-778: Use of the 2D MatriXX Detector for Measuring Scanned Ion Beam Parameters

Purpose: The quality assurance (QA) procedure has to check the most relevant beam parameters to ensure the delivery of the correct dose to patients. Film dosimetry, which is commonly used for scanned ion beam QA, does not provide immediate results. The purpose of this work is to answer whether, for scanned ion beam therapy, film dosimetry can be replaced with the 2D MatriXX detector as a real-time tool. Methods: MatriXX, equipped with 32×32 parallel plate ion-chambers, is a commercial device intended for pre-treatment verification of conventional radiation therapy.The MatriXX, placed at the isocenter, and GAFCHROMIC films, positioned on the MatriXX entrance, were exposed to 131.44 MeV proton and 221.45 MeV/u Carbon-ion beams.The OmniPro-I’mRT software, applied for the data taking of MatriXX, gives the possibility of acquiring consecutive snapshots. Using the NI LabVIEW, the data from snapshots were logged as text files for further analysis. Radiochromic films were scanned with EPSON scanner and analyzed using software programs developed in-house for comparative purposes. Results: The field dose uniformity, flatness, beam position and beam width were investigated. The field flatness for the region covering 6×6 cm{sup 2} square field was found to be better than 2%. The relative standard deviations, expected to be constant over 2×2, 4×4 and 6×6 pixels from MatriXX measurement gives a uniformity of 1.5% in good agreement with the film results.The beam center position is determined with a resolution better than 200 µm for Carbon and less than 100 µm for proton beam.The FWHM determination for a beam wider than 10 mm is satisfactory, whilst for smaller beams the determination is uncertain. Conclusion: Precise beam position and fast 2D dose distribution can be determined in real-time using MatriXX detector. The results show that MatriXX is quick and accurate enough to be used in charged-particle therapy QA.

60 APPLIED LIFE SCIENCES↗

COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database

We introduce COnTORT ( CO mprehensive T ranscriptomic OR ganizational T ool), a publicly available program that retrieves all available gene expression data and associated metadata for an organism from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. The data are compiled into text files that can be used for downstream bioinformatic applications.

Myers, Kevin S.↗

brulilo, Version 0.x

brulilo is a Python package for building and evolving thermonuclear reaction networks, such as those used in astrophysical explosion calculations. It is very much a current work in progress, and much of the intended functionality is still under development. The main goal of brulilo is an easy-to-use code for quick calculations or post-processing, as well as a learning tool to test various implementations of solvers on both CPUs and GPUs. Currently, brulilo parses an input text file that specifies the reactions to be included in the network. The notation of the inputs are in the typical astrophysical notation; i.e. hydrogen burning to deuterium in the sun, "p + p + e --> d + neutrino", is given as "p(p,)d." Each reaction is added to a list comprising the reaction network, and once completed, the network contains a list of all isotopes and reactions involved. brulilo then parses publicly available nuclear data (binding energy, spin, partition function data, etc.) for each isotope from the WebNucleo group's data at nucleo.ces.clemson.edu. Fits to reaction rate data for each reaction are obtained from the publicly available data provided by the Joint Institute for Nuclear Astrophysics' Reaclib database. Reverse reactions are calculated from detailed balance. The reaction network then consists of a sparse system of mathematically stiff ordinary differential equations (ODEs). Physically, "stiffness" here means that there are some reaction rates that are occurring much faster than others; the ratio of the fast to slow often being greater than 10^15 in astrophysics. Numerical integration of such systems typically involves implicit integration schemes, which brulilo will leverage from the scientific computing Python package, Numpy, as well as implement its own. There has recently been work from researchers at Oak Ridge National Lab who have found good results from applying quasi-equilibrium and quasi-asymptotic conditions to the stiff system of ODEs, which effectively remove some of the stiffness and allow for efficient explicit integration techniques to be used. The original intent of brulilo was to implement these stiffness-alleviating techniques with explicit integrators and compare the performance to traditional implicit integrations of the full stiff system. This is still underway, as the code is very much in an alpha-release state. Furthermore, explicit integrators are often much easier to parallelize than their implicit counterparts. brulilo will implement parallelization of these techniques, leveraging both the Python implementation of MPI, mpi4py, as well as highly parallelized versions targeted at GPUs with PyOpenCL and/or PyCUDA.

Malone, Chris↗

SNL-SWAN

Sandia National Laboratories has modified Simulating WAves Nearshore (SWAN), the Delft University of Technology code,, to include functionality to better model wave energy converters (WECs). The code modified by SNL has been named SNL-SWAN. SNL-SWAN includes a frequency dependent WEC Module that builds upon the traditional obstacle module in SWAN. In SNL-SWAN, a frequency dependent transmission coefficient is calculated to model power absorbed by WEC devices. The power transmission coefficients are calculated based on the WEC's power performance, which is defined by the user in the input text files. Two methods of defining WEC power performance have been implemented: a user-specified power matrix, and a user-specified relative capture width. These methods allow the user to define the WEC's frequency dependent energy absorption as a function of period and/or wave height. SWAN test cases were run to verify the compiled code's functionality, and verification of the frequency dependent WEC Module in SNL-SWAN has also been performed. SNL-SWAN code is will be released as open source code and will be made publicly available.

Chartrand, Chris↗