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Process and extract clinical information from Electronic Medical Records.

Two-community model fitting and pre-processing code along with modelled chlorophyll and phytoplankton carbon vertical profiles for 33 years of in-situ data from the Bermuda Atlantic Time-series Study (BATS) site in the Sargasso Sea. This model code and data output is related to the paper "Climate variability shifts the vertical structure of phytoplankton in the Sargasso Sea" by Johan Viljoen, Xuerong Sun and Bob Brewin. Paper available here: https://www.nature.com/articles/s41558-024-02136-6. Downloaded original BATS data was converted to CSV format before used in this code (see paper Data Availability). We acknowledge all researchers, technicians and data managers who contributed to the BATS site for the profound wealth of data produced since sampling started in the late 1980's. See paper and associated supplemental information for model output visualisation and an example model fit to a single profile of HPLC Chla and POC at BATS.

This is the release of a new version (v2.0.0) of TREvoSim. The first release and the underlying model was described in detail in the following paper: Keating, J.N., Sansom, R.S., Sutton, M.D., Knight, C.G. & Garwood, R.J. 2020. Morphological phylogenetics evaluated using novel evolutionary simulations. Systematic Biology 69(5): 897-912. doi:10.1093/sysbio/syaa012 Version 2.0.0 accompanies the preprint and paper below: Mongiardino Koch, N., Garwood, R.J. & Parry, L.A. Preprint. Fossils improve phylogenetic analyses of morphological characters. bioRxiv. doi: 10.1101/2020.12.03.410068v1 Mongiardino Koch, N., Garwood, R.J. & Parry, L.A. 2021. Fossils improve phylogenetic analyses of morphological characters. Proceedings of the Royal Society B: Biological Sciences The code is archived on zenodo.org: Documentation: TREvoSim Online Documentation Change log: The changes in v2.0.0 are described and discussed fully in the associated paper. In brief, these allow TREvoSim v2.0.0 trees and data to achieve benchmarks calculated from twelve total evidence analyses, as well as respresenting ongoing development of the package. Changes are: Addition of multiple playing fields option. Playing fields can have independent or identical environments. The option to overwrite a random individual when a juveniles is returned to the playing field (instead of the least fit one). User control of the fitness target in the fitness algorithm (see Keating et al. 2020). A fitness histogram functionality to assess the fitness landscape in the simulation. User control of the strength of selection (see Mongiardino Koch et al. 2021 for discussion). Multiple environments per playing field. Organism fitness is assessed against each environment, and the fitness of an organism is defined by the environment they are best suited to. The code has been refactored (the biggest change being to the underlying data structures/classes), and the simulation now uses Qt QRandomGenerator tools rather than incorporating random data. A user-accessible test suite has been added. Release information: Windows A zip containing all required binaries can be downloaded from the assets below. Alternatively an installer is provided. See notes below: Note 1: The .zip archive contains an executable TREvoSim_2.0.0.exe. The .zip can be extracted and the program run by double clicking this.exe file in the ./bin folder. All the required libraries have been included and are found in the ./bin folder. Mac A zip containing TREovSim can be downloaded from the assets below. To install the software, drag and drop the required .app folder(s) into the Applications folder. You may be required to the approve the software in security and privacy settings before it will launch. Linux Any Linux users willing to test a Linux build should contact palaeoware@gmail.com.

mmCSM-PPI is a tool for predicting the effects of multiple point mutations on protein-protein interactions.

Draft version for submission of fireMIP benchmark paper

CamoGAN uses Generative Adversarial Networks to simulate an evolutionary arms race between camouflage of a synthetic prey and its predator. CamoGAN can be used to evolve progressively more effective concealment against an artificial predator.

This version is used for producing all the publicly released fits for NNPDF4.0.

This work has been sponsored by the European Union's Horizon 2020 Research and Innovation Action under grant agreement No. 862644 (FET-OPEN project: Quantum readout techniques and technologies, QUARTET) and by the EPSRC via the Quantum Communications Hub (Grant No. EP/M013472/1 and EP/T001011/1). This zip file contains the code used to generate the figures in the paper: "Bounds on amplitude damping channel discrimination". See the README for more details on the files.

R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling or enzymatic genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.

Version 6.0.1 of the UniDec software source code. UniDec is a Bayesian deconvolution program for deconvolution of mass spectra and ion mobility-mass spectra. It was originally published in: M. T. Marty, A. J. Baldwin, E. G. Marklund, G. K. A. Hochberg, J. L. P. Benesch, C. V. Robinson, Anal. Chem. 2015, 87, 4370-4376. Detailed descriptions of the algorithm are provided in the paper and subsequent papers. Please cite us if you use UniDec in your research. This software is made freely available under a modified BSD license. Please refer to the LICENSE and readme.md files within any of the Zip files for details. For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu