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- Creator:
- Polly, P. David
- Description:
- n/a
- Keyword:
- Phylogenetics, Ancestral Node Reconstruction, and Newick Trees
- Citation to related publication:
- Polly, P. D. 2012. Phylogenetics for Mathematica. Version 2.1. Department of Geological Sciences, Indiana University: Bloomington, Indiana. http://mypage.iu.edu/~pdpolly/Software.html
- Title:
- Phylogenetics for Mathematica (Ver. 2.1)
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- Creator:
- Zhu, Chen, Zhang, Yilun, Hu, Bin, and Teng, Yanguo
- Description:
- n/a
- Citation to related publication:
- Zhang YL, Hu B, Teng Y, Tu K, Zhu C (2019) A library of BASIC scripts of reaction rates for geochemical modeling using PHREEQC. Computers & Geosciences
- Title:
- A library of BASIC scripts of rate equations for geochemical modeling using PHREEQC
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- Creator:
- Polly, P. David and Goswami, Anjali
- Description:
- n/a
- Keyword:
- Cranial Integration, Statistical Analysis, Phenotypic Analysis, Geometric Morphometrics, Modularity, and Evolution
- Citation to related publication:
- Polly, P.D. and A. Goswami. 2010. Modularity for Mathematica, Version 1.0. Goswami, A. & Polly, P. D. 2010 Methods for studying morphological integration, modularity and covariance evolution. In Quantitative Methods in Paleobiology. Paleontological Society Short Course, October 30th, 2010, vol. The Paleontological Society Papers (ed. J. Alroy & G. Hunt), pp. 213-243. Chicago: The Paleontological Society.
- Title:
- Modularity for Mathematica
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- Creator:
- Polly, P. David
- Description:
- n/a
- Keyword:
- Geometric Morphometrics, Thin-plate splines, Mathematica, Procrustes, and Principal Components of shape
- Citation to related publication:
- Polly, P. D. 2012. Geometric morphometrics for Mathematica. Version 9.0. Department of Geological Sciences, Indiana University: Bloomington, Indiana. http://mypage.iu.edu/~pdpolly/Software.html
- Title:
- Geometric Morphometrics for Mathematica (Ver. 9.0)
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- Description:
- Data variables can be found in Yanites, 2018 Journal of Geophysical Research: Earth Surface as well as in the model code uploaded to the Community Surface Dynamic Modeling System infrastructure.
- Title:
- Data scripts for modeling dynamic width and slope evolution of actively eroding rivers
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- Creator:
- Porter, Jack, Kumar, Prashant, and Pohl, Nicola L. B.
- Description:
- Jupyter Notebook pages that include automation protocols were created for each step in the the multistep continuous-flow synthesis of a D-glucuronic acid building block through a series of optimised and modular transformations, including O-p-methoxyphenyl (PMP) glycosylation, Zemplén deacylation, 4,6-O-benzylidene protection/deprotection, 2-O-benzoylation, and C6 oxidation/methylation. The Jupyter Notebooks serve as a versatile platform for both writing Python code and comprehensively documenting automated chemical procedures, including reaction setups, protocols, and execution logs. To ensure experimental reproducibility, the necessary chemical information is stored externally in JSON files. The Notebooks process this data to dynamically generate stoichiometry tables and apparatus descriptions, while simultaneously controlling the laboratory’s liquid handling systems.
- Keyword:
- automated continuous flow synthesis, carbohydrates, glucuronic acid, organic synthesis, lab automation, MechWolf, Methyl (p-methoxyphenyl 2-O-benzoyl-3-O-benzyl-β-D-glucopyranosyluronate), ), p-Methoxyphenyl 2,3,4,6-tetra-O-acetyl-β-D-glucopyranoside, p-Methoxyphenyl β-D-glucopyranoside, p-Methoxyphenyl 4,6-O-benzylidene-β-D-glucopyranoside, p-Methoxyphenyl 2-O-benzoyl-3-O-benzyl-4,6-O-benzylidene-β-D-glucopyranoside, p-Methoxyphenyl 2-O-benzoyl-3-O-benzyl-β-D-glucopyranoside, , p-Methoxyphenyl 2-O-benzoyl-3-O-benzyl-β-D-glucopyranosyluronate, FAIR, and reproducible
- Title:
- Continuous-Flow Synthesis of Carbohydrate Building Blocks: D-Glucuronate Monosaccharide
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- Creator:
- Rutkowski, Leslie, Svetina, Dubravka, and Liaw, Yuan-Ling
- Description:
- This is supplementary material, including appendices, data, and syntax to reproduce all empirical and simulation results.
- Keyword:
- multiple-groups models, ordinal variables, collapsing categories, and model fit
- Title:
- The Effects of Collapsing Ordered Categorical Variables on Tests of Measurement Invariance
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- Description:
- Download the software applications used for the 2016 Student Cluster Competition by clicking the URLs below: Gromacs (6 MB); Paraview (6 GB); ParConnect (800 MB); Distributed Password Auditing/Recovery (125 MB). ParConnect sequence data were produced by the US Department of Energy Joint Genome Institute http://www.jgi.doe.gov/ in collaboration with the user community. Note that download times may vary.
- Title:
- 2016 Student Cluster Competition
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- Description:
- Kindly report errors to Professor Chen Zhu ( supcrt@indiana.edu). Tutorials, corrections, and updates may be found at Professor Zhu’s research web site https://hydrogeochem.earth.indiana.edu. Users of this program should also acknowledge and cite these articles: Parkhurst, D.L., Appelo, C., 2013. Description of input and examples for PHREEQC version 3--A computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations. Techniques and Methods 6-A43, U.S. Geological Survey, Reston, VA., 497. Johnson, J.W., Oelkers, E.H. and Helgeson, H.C. (1992) SUPCRT92 - A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1-bar to 5000-bar and 0°C to 1000°C. Computer & Geosciences 18:899-947. Zimmer, K., Zhang, Y., Lu, P., Chen, Y., Zhang, G., Dalkilic, M., Zhu, C., 2016. SUPCRTBL: A revised and extended thermodynamic dataset and software package of SUPCRT92. Computer & Geosciences 90, 97-111. This work was partly supported by NSF grant EAR-19267343 and the Office of the Vice Provost for Research of Indiana University.
- Title:
- SupPHREEQC
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- Description:
- Download the software applications used for the 2015 Student Cluster Competition by clicking the URLs below: HPC Repast (4 MB); MILC (2 GB); Trinity (64 GB); WRF (5 GB). Note that download times may vary and that due to its size the Trinity file could take several hours.
- Title:
- 2015 Student Cluster Competition
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- Description:
- A single ".ova" file encompassing an Ubuntu-based (v. 16.04) virtual machine (VM). This VM is the "artifact" used in the artifact evaluation of the corresponding PPoPP17 paper. It contains the complete software, such as example programs and benchmark programs, necessary to reproduce the results of the paper. Scripts are included in the virtual machine to automatically run benchmarks and compare their results. Download the VM by clicking the link below under "Link(s) to data and video for this item."
- Title:
- Bundled VM artifact to accompany paper entitled SC-Haskell: Sequential Consistency in Languages That Minimize Mutable Shared Heap
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- Description:
- This is a sample Ubuntu image for use with Openstack. This is an example of an image to be saved from Jetstream.
- Title:
- Ubuntu 14.04 Trusty Tahr TLS Sample Image
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- Creator:
- Lewis, Jared C., Roux, Benoît, Li, Ying, and Upp, David
- Description:
- To gain insight into how the POP scaffold might give rise to the observed ArM selectivity, molecular dynamics simulations were conducted on models of 5-G that involved different starting coordination states of dirhodium cofactor 1. Three starting coordination states (5-G apo, 5-G with parameterized Rh-His bond, 5-G without Rh-His bond) were studied. The initial structure of 5-G apo was constructed from the crystal structure of POP, with the following amino acids mutations made using VMD17: S477F/E104A/F146A/K199A/D202A/S301G/G99S/Y326H/Q98P/S99H/V71G/E283G. The 5-G with Rh-His and 5-G without Rh-His bond models were constructed by mutating S477Z (Z is azidophenylalanine, where dirhodium cofactor 1 covalently links to the protein), which is the only other mutation from 5-G apo. No other changes where made to the model without a Rh-His bond. The Rh-His model contains a parameterized H326 bond to one of the dirhodium atoms, as shown in Figure 2D. MD simulations were performed for the 5-G apo, with Rh-His and no Rh-His POP enzymes. All three structures were bathed in a 0.15M KCl solution using the Solution Builder Module in CHARMM-GUI.18 These systems were roughly 100 100 100 Å3 in dimension and contained ~ 110,000 atoms. The periodic boundary conditions were counted using the particle-mesh Ewald method with an automatic generated grid size. Once the simulation systems were generated, they were subjected to equilibration at 358.15 K. The system was first equilibrated in an NVT ensemble for 10 ns. The equilibration simulations were performed using NAMD2.14 GPU acceleration version package19 on Nvidia’s P100 GPUs. After equilibration, the systems were simulated for 1000 ns each in an NPT ensemble with temperature set to 358.15 K and the isotropic pressure set to 1 atm. Langevin thermostats with a damping coefficient of 1 ps-1 were used to keep the temperature constant. The cutoff of the van der Waals interactions and short-range electrostatic interactions were set to ~25 Å as suggested by the guesser script. The additive C36 force field was used in all the simulations performed here.20,21,22,23 The force field parameters for the covalently linked dirhodium cofactor 1 were generated using the GAAMP server.24
- Title:
- 5-G MD Simulations