Download the software applications and data used for the 2017 Student Cluster Competition by clicking the URLs below: Model for Prediction Across Scales (MPAS); Born seismic imaging tool; MrBayes program for Bayesian inference and model choice; LAMMPS molecular dynamics (MD) code. Note that download times may vary.
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 3/2 100 3/2 100 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
Supporting datasets for drill-down topic modeling workflow described in "Multi-level computational methods for interdisciplinary research in the HathiTrust Digital Library." PLOS ONE. https://doi.org/10.1371/journal.pone.0184188
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Supporting Data for "Multi-level computational methods for interdisciplinary research in the HathiTrust Digital Library"
The evigene_corn2016 archive package contains a complete, reconstructed gene set of Zea mays, corn plant, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Zea mays, corn plant reconstructed with EvidentialGene
The evigene_wasp_nasvit2012 archive package contains a complete, reconstructed gene set of Nasonia vitripennis, jewel wasp, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Nasonia vitripennis, jewel wasp reconstructed with EvidentialGene
The two major components of this supplement are packaged as two separate UNIX tar files available through links below. The two tar file names are:
(1) ModelConstructionDetails.tar - this contains the pdf file with the text (file name SupplementText.pdf) describing the technical details of how the 3D model was constructed. The package also contains a directory called Figures that contain five interactive figures. The SupplementText.pdf file contains links to these files that will resolve only if the files are left in that directory. There is also a small README text file to make the set of files more self contained.
(2) DataSupplement.tar - this is the package of data files that form the data supplement. The organization of the files in the package and file descriptions are described in the pdf file with the name DataSupplementDescription.pdf. That file can also be accessed directly from the link below.
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Electronic Supplement to “A Unified Three-dimensional Model of the Lithospheric Structure at the Subduction Corner in Southeast Alaska: Summary Results from STEEP”
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.
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Data scripts for modeling dynamic width and slope evoluton of actively eroding rivers
The evigene_catfish2013 archive package contains a complete, reconstructed gene set of Ictalurus punctatus, catfish, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Ictalurus punctatus, catfish reconstructed with EvidentialGene
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."
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Bundled VM artifact to accompany paper entitled SC-Haskell: Sequential Consistency in Languages That Minimize Mutable Shared Heap
The evigene_locust_locumig2013 archive package contains a complete, reconstructed gene set of Locusta migratoria migratoria, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Locusta migratoria migratoria reconstructed with EvidentialGene
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.
The evigene_honeybee_apismel2014 archive package contains a complete, reconstructed gene set of Apis mellifera, honey bee, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Apis mellifera, honey bee reconstructed with EvidentialGene
The evigene_shrimp_litova2013 archive package contains a complete, reconstructed gene set of Litopenaeus vannamei, white shrimp, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Litopenaeus vannamei, white shrimp reconstructed with EvidentialGene
Thesis (D.M.) - Indiana University, Jacobs School of Music, 2020. The EPUB for this item is available for download under "Link(s) to data and video for this item."
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Teaching Pre-College Organ Students: Methods of the Twenty-First Century
The evigene_aphid_acypi2011 archive package contains a complete, reconstructed gene set of Acyrthosiphon pisum, pea aphid, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Acyrthosiphon pisum, pea aphid reconstructed with EvidentialGene
The evigene_daphnia_similoides2017 archive package contains a complete, reconstructed gene set of Daphnia similoides, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Daphnia similoides reconstructed with EvidentialGene
There are two components to this project: a video documentary and a paper. The documentary, entitled "Silver Angel and Apollo X: A Glimpse into Nadina Mackie Jackson’s Canadian Bassoon Concerto Project," introduces Nadina Mackie Jackson’s career as a solo bassoonist and follows preparations for the premieres of Silver Angel and Apollo X. The paper focuses on Nadina Mackie Jackson’s career as a solo bassoonist and Paul Frehner’s Apollo X. Video Documentary Parts: 1 Introducing Nadina Mackie Jackson; 2) Meet Paul Frehner and Constantine Caravassilis; 3) Preparing to Write for the Bassoon; 4) Writing the Concertos: 5) The Nitty Gritty of the Concertos; 6) The Premieres; 7) On Being a Solo Bassoonist; 8) Final Thoughts. All eight parts are available as one zip file by clicking on the link under "Link(s) to data and video."
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Silver Angel and Apollo X: A Glimpse into Nadina Mackie Jackson's Canadian Bassoon Concerto Project
The evigene_arabidopsis2017 archive package contains a complete, reconstructed gene set of Arabidopsis thaliana, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Arabidopsis thaliana reconstructed with EvidentialGene
The evigene_beetle_pogocha2013 archive package contains a complete, reconstructed gene set of Pogonus chalceus, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Pogonus chalceus reconstructed with EvidentialGene
The evigene_pinetree2013 archive package contains a complete, reconstructed gene set of Pinus taeda, loblolly pine tree, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents. Click on the PURL link below in the "External Files" section to download the dataset.
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Genes of Pinus taeda, loblolly pine tree reconstructed with EvidentialGene
The evigene_zebrafish2017 archive package contains a complete, reconstructed gene set of Danio rerio, zebrafish, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Danio rerio, zebrafish reconstructed with EvidentialGene
The evigene_beetle_tribolium2014 archive package contains a complete, reconstructed gene set of Tribolium castaneum, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Tribolium castaneum reconstructed with EvidentialGene
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.
Click on the PURL link below in the "Link(s) to data and video for this item" section to download the dataset.
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Data for "Spatially variable increase in rock uplift in the northern U.S. Cordillera recorded in the distribution of river knickpoints and incision depths"
The evigene_tick_ixoscap2014 archive package contains a complete, reconstructed gene set of Ixodes scapularis, deer tick, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Ixodes scapularis, deer tick reconstructed with EvidentialGene
The evigene_cacao2013 archive package contains a complete, reconstructed gene set of Theobroma cacao, chocolate tree, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Theobroma cacao, chocolate tree reconstructed with EvidentialGene
The evigene_seaurchin_lytvar2017 archive package contains a complete, reconstructed gene set of Lytechinus variegatus, green sea urchin, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Lytechinus variegatus, green sea urchin reconstructed with EvidentialGene
The evigene_daphnia_pulex2010 archive package contains a complete, reconstructed gene set of Daphnia pulex, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Daphnia pulex reconstructed with EvidentialGene
The evigene_mosquito_aedes2016 archive package contains a complete, reconstructed gene set of Aedes aegypti, mosquito, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Aedes aegypti, mosquito reconstructed with EvidentialGene
The evigene_whitefly_bemitab2017 archive package contains a complete, reconstructed gene set of Bemisia tabaci, whitefly, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Bemisia tabaci, whitefly reconstructed with EvidentialGene
The evigene_tick_rhipic2014 archive package contains a complete, reconstructed gene set of Rhipicephalus pulchellus, zebra tick, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Rhipicephalus pulchellus, zebra tick reconstructed with EvidentialGene
The evigene_daphnia_galeata2016 archive package contains a complete, reconstructed gene set of Daphnia galeata, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Daphnia galeata reconstructed with EvidentialGene
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.
The evigene_killifish2014 archive package contains a complete, reconstructed gene set of Fundulus heteroclitus, atlantic killifish, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Fundulus heteroclitus, atlantic killifish reconstructed with EvidentialGene
The evigene_pig2018 download contains a complete, reconstructed gene set of model animal Pig, Sus scrofa, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of the Pig, Sus scrofa, reconstructed with EvidentialGene
The evigene_mosquito_anoalb2016 archive package contains a complete, reconstructed gene set of Anopheles albimanus, mosquito, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Anopheles albimanus, mosquito reconstructed with EvidentialGene
The evigene_shrimp_penamon2013 archive package contains a complete, reconstructed gene set of Penaeus monodon, tiger shrimp, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Penaeus monodon, tiger shrimp reconstructed with EvidentialGene
The evigene_daphnia_magna2014 archive package contains a complete, reconstructed gene set of Daphnia magna, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Daphnia magna reconstructed with EvidentialGene
The evigene_daphnia_pulex2017 archive package contains a complete, reconstructed gene set of Daphnia pulex, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Daphnia pulex reconstructed with EvidentialGene
The evigene_mosquito_anofun2016 archive package contains a complete, reconstructed gene set of Anopheles funestus, mosquito, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Anopheles funestus, mosquito reconstructed with EvidentialGene
