Legacy - Performance 3.5 Software


Scope

This document details the changes and updates made in the latest version release of the Metworx Image (v3.1.0).

Release Notes

Software Installation Updates

R update: (v3.5.1)
R version (v3.5.1) (http://www.r-project.org/) is the current release of the open source statistical and graphics software on CRAN. Validation of the R installation and supporting packages will be mediated via the Chef recipe mrgQual::R (v0.3.0), which was developed to validate the core R installation through completion of example execution for the required and suggested base packages using the R function metrumrg::accept().

Rstudio-server update: (v1.1.463)
The latest version of Rstudio-server will be installed. Rstudio-server is an interactive development environment (IDE) for code development, and acts as the primary interface to workflows. Additionally, Rstudio-server acts as a possible mechanism for data transfer to METWORX workflows.

Pirana desktop update: (v2.9.9)
Pirana is an IDE for NONMEM development, allowing for tracking of model development, interfacing with PsN for NONMEM job submission and R for model diagnostics. This tool provides an alternative interface to NONMEM for users who prefer using a desktop GUI and has a longer history of support and acceptance in the Pharmacometrics community, as compared to PiranaJS. Pirana is a desktop application and will be accessed via Guacamole.

MATLAB update: (v9.5.0.9444444)
MathWorks MATLAB is a matrix-based language for solving computational mathematics. MATLAB traction lies mostly in the realm of engineering, but it is also preferred by many systems biology groups for being a high-level language with high capabilities for systems of differential equations and graphics. MATLAB will be installed as a desktop application, to be accessed via Guacamole.

Monolix Suite update: (v2018R2)
Monolix is software for non-linear mixed effects modeling (NLME) in pharmacometrics. Monoolix provides an alternative to NONMEM using the SAEM algorithm, and can be used for preclinical and clinical population PK/PD modeling and for systems pharmacology. Monolix utilizes a desktop installation and will be accessed via Guacamole.

Rstudio desktop update (v1.1.463)
The desktop version of Pirana has functionality to interface with Rstudio, but does not work with Rstudio-server. To allow this functionality to be utilized by METWORX users, the desktop version of Rstudio is additionally installed.

Shiny-server update (v1.5.10.990)
Shiny-serve (pro) will be installed to enable the ENVISION platform on METWORX. Shiny-server is the server version of the engine developed by Rstudio for hosting R code as interactive web interfaces via javascript and HTML. The METWORX ENVISION platform surfaces shiny functionality to METWORX users, and provides a tool within the METWORX app for user management and publishing of METWORX user developed shiny applications.

NGINX update: (v1.14.2)
Linux Web Server providing reverse proxy in front of web based tools used for the ability to access Guacamole and RStudio via HTTPS.

Guacamole update: (v0.9.14)
Apache Guacamole is a clientless remote desktop gateway, requiring no client side applications other than a browser. Users will access an xfce desktop on running METWORX workflows.