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.
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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Title:
Genes of Tribolium castaneum 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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Title:
Genes of Danio rerio, zebrafish 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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Title:
Genes of Pinus taeda, loblolly pine tree 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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Title:
Genes of Pogonus chalceus reconstructed with EvidentialGene
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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Title:
Genes of Arabidopsis thaliana 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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Title:
Silver Angel and Apollo X: A Glimpse into Nadina Mackie Jackson's Canadian Bassoon Concerto Project
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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Title:
Genes of Daphnia similoides reconstructed with EvidentialGene
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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Title:
Genes of Acyrthosiphon pisum, pea aphid 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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Title:
Teaching Pre-College Organ Students: Methods of the Twenty-First Century
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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Title:
Genes of Litopenaeus vannamei, white shrimp reconstructed with EvidentialGene
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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Title:
Genes of Apis mellifera, honey bee 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_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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Title:
Genes of Locusta migratoria migratoria 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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Title:
Bundled VM artifact to accompany paper entitled SC-Haskell: Sequential Consistency in Languages That Minimize Mutable Shared Heap
Quantitative measurement of intact alpha-synuclein proteoforms from post-mortem control and Parkinson's disease brain tissue by intact protein mass spectrometry
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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Title:
Genes of Ictalurus punctatus, catfish reconstructed with EvidentialGene
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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Title:
Data scripts for modeling dynamic width and slope evoluton of actively eroding rivers
