20.06 Software

Scope

This document summarizes the software available on the Metworx 20.06 Blueprint release.

Metworx 20.06 Software

Docker: (v19.03.11)

Docker is a tool which is used to automate the deployment of applications in lightweight containers so that applications can work efficiently in different environments (note: a container is a software package that consists of all dependencies required to run an application). This is the tool used by MRG to manage and update Metworx.

Git: (v2.17.1)

Git is a distributed version-control system for tracking changes in source code during software development. It is designed for coordinating work among programmers, but it can be used to track changes in any set of files. Its goals include speed, data integrity, and support for distributed, non-linear workflows.

GNU Fortran: (v7.5.0)

The GNU Fortran compiler fully supports the Fortran 77, 90, and 95 standards, parts of the Fortran 2003 and 2008 standards, as well as several vendor extensions.

Guacamole: (v1.1.0)

Apache Guacamole is a clientless remote desktop gateway, requiring no client side applications other than a browser. Users will access a kde desktop on running Metworx workflows.

LaTeX: (v2020)

LaTeX is a document preparation system for high-quality typesetting. Users write in plain text, then use markup tagging conventions to define the general structure of a document, to stylise text throughout a document, and add citations and cross references. It then uses the TeX typesetting program for formatting the associated output. It allows users to create professional, accurate scientific documents that accurately reflect precise equations and other graphics needed to express the user’s work.

MATLAB: (2019b)

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: (v2019R2 & v2018R2)

Monolix is software for non-linear mixed effects modeling (NLME) in pharmacometrics. Monolix 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.

MPN: (2020-06-25)

MPN (Metrum Package Network) is a tool developed and maintained by MetrumRG to ensure a reproducible analysis environment for R users. MPN provides a repository of stable, curated snapshots of R packages (from CRAN and other repositories). By installing packages from a specific MPN snapshot, rather than directly from CRAN, you can ensure it is always the same version of a given package.

NONMEM: (v7.3.3 & v7.4.4)

NONMEM is a software package for population pharmacokinetic modeling, allowing users to do NON-linear Mixed Effects Modeling.

pkgr: (v1.2.1)

pkgr is a rethinking of the way packages are managed in R. Namely, it embraces the declarative philosophy of defining the ideal state of the entire system, and working towards achieving that objective. Furthermore, pkgr is built with a focus on reproducibility and auditability of what is going on, a vital component for the pharmaceutical sciences + enterprises.

With pkgr, you can, in a parallel-processed manner, do things like:

  • Install a number of packages from various repositories, when specific packages must be pulled from specific repositories
  • Install Suggested packages only for a subset of all packages you'd like to install

  • Customize the installation behavior of a single package in a documentable and reproducible way

    • Set custom Makevars for a package that persist across system installations
    • Install source versions of some packages but binaries for others
  • Understand how your R environment will be changed before performing an installation or action.

PsN (Perl speaks NONMEM): (v4.9.0)

Perl-speaks-NONMEM (PsN) is a collection of Perl modules and programs aiding in the development of non-linear mixed effect models using NONMEM. The functionality ranges from solutions to simpler tasks such as parameter estimate extraction from output files, data file sub setting and resampling, to advanced computer-intensive statistical methods. PsN includes stand-alone tools for the end-user as well as development libraries for method developers.

Pirana desktop: (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. Pirana is a desktop application and will be accessed via Guacamole.

Python: (v3.6.9 & v2.7.17)

Users are able to use either Python3 or Python2 on their workflows. Python2 is officially end-of-lifed, however a large ecosystem of tooling still requires it, so we will continue to provide it. Conda-4.0 is installed at the latest patch version available upon release of Metworx 20.06.

R: (v4.0.2(default), v3.6.3, v3.5.3)

R version (v4.0.2) (http://www.r-project.org/) is the current release of the open source statistical and graphics software on CRAN.

The executables are available at the paths:

/opt/R/4.0.2/bin/R --> also symlinked to usr/bin/R

/opt/R/3.6.3/bin/R

/opt/R/3.5.3/bin/R

RStudio Connect: (v1.8)

RStudio Connect is developed by Rstudio for hosting R code as interactive web interfaces via javascript and HTML.

RStudio Desktop: (v1.2.5)

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.

RStudio Server Pro: (v1.3.9)

The latest version of RStudio-Server Pro is installed with this version of Metworx. RStudio-Server is an interactive development environment (IDE) for code development, and acts as the primary interface to workflows.

SGE: (v8.1.9)

SGE (Sun Grid Engine) is a grid computing computer cluster software system that allows users to perform parallel computing, improving efficiency and turnaround times for researchers.

Stan: (v2.21.0 & v2.19.1)

Stan is a probabilistic programming language for statistical inference written in C++. The Stan language is used to specify a Bayesian statistical model with an imperative program calculating the log density function. Users specify log density functions in Stan’s probabilistic programming language and get:

  • Full Bayesian statistical inference with MCMC sampling.
  • Approximate Bayesian inference with variational inference.
  • Penalized maximum likelihood estimation with optimization.

Stan can be called from a variety of areas, including the command line, R, Python, Matlab, and others. METWORX allows users to use their preferred Stan interface using the remote desktop/UI.

Subversion: (v1.9.7)

Subversion (SVN) is a software versioning and revision control system distributed as open source under the Apache License. It can be used to maintain current and historical versions of files such as source code, web pages, and documentation.

Torsten: (v0.87.2)

Torsten is a collection of stan functions to facilitate analysis of pharmacometric data using Stan. The current version includes:

  • Specific linear compartment models:

    • One compartment model with first order absorption.
    • Two compartment model with elimination from and first order absorption into central compartment
  • General linear compartment model described by a system of first-order \underline{linear} Ordinary Differential Equations (ODEs).
  • General compartment model described by a system of first order ODEs.
  • Mix compartment model with PK forcing function described by a linear one or two compartment model.

Ubuntu (OS): (v18.04.4)

Ubuntu is a complete Linux operating system, freely available with both community and professional support.