Scope

This document summarizes the software available on the Metworx 22-04.00.00 Blueprint release, including any details on changes from previous Metworx Blueprint versions.

Metworx 24-04 Software

bbi: (v3.3.0)

bbi is a tool for managing projects involving modeling and simulation with a number of software solutions used in pharmaceutical sciences including NONMEM. Most components are written in Go.

Change Summary:

Latest version upgraded from v3.2.3.

DCV Remote Desktop: (v2023.1)

DCV 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.

Change Summary:

DCV has been implemented in Metworx 24-04 as a replacement for Guacamole remote desktop (v1.4.0).

Docker: (v24.0.7)

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).

Change Summary:

Upgraded from Docker v.20.10.17. Release notes for Docker version 20.10.18 can be found here: https://docs.docker.com/engine/release-notes/24.0/#2407

Git: (v2.25.1)

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.

Change Summary:

Upgraded from Git v.2.17.1. Release notes can be found at https://github.com/git/git/blob/master/Documentation/RelNotes/2.25.1.txt.

Git-Annex: (v2.17.1)

Git Annex is an extension to Git, designed to manage large files efficiently within a Git repository. It allows you to track changes to these files without storing their actual content directly within the repository. This helps keep repository size manageable and prevents performance issues that can arise when dealing with large files in Git alone. Git Annex is particularly useful for handling binary files, media files, and datasets that are impractical to manage with Git alone.

Change Summary:

Newly added to Metworx 24-04

GNU Fortran: (v9.4.0)

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.

Change Summary:

Updated from v7.5.0

Go: (v1.21.4)

Go is an open-source programming language developed by Google. It's concurrency mechanisms make it easy to write programs that get the most out of multicore and networked machines, while its novel type system enables flexible and modular program construction. Go compiles quickly to machine code yet has the convenience of garbage collection and the power of run-time reflection. It's a fast, statically typed, compiled language that feels like a dynamically typed, interpreted language.

Change Summary:

Upgraded from Go v.1.18.2. Release notes can be found at https://tip.golang.org/doc/go1.21.

Julia: (v1.10.2.)

Julia is a flexible, high-level, high-performance dynamic language, appropriate for scientific and numerical computing, with performance comparable to traditional statically-typed languages. Julia features optional typing, multiple dispatch, and good performance, achieved using type inference and just-in-time (JIT) compilation, implemented using LLVM. It is multi-paradigm, combining features of imperative, functional, and object-oriented programming. Julia provides ease and expressiveness for high-level numerical computing, in the same way as languages such as R, MATLAB, and Python, but also supports general programming. To achieve this, Julia builds upon the lineage of mathematical programming languages, but also borrows much from popular dynamic languages, including Lisp, Perl, Python, Lua, and Ruby.

Change Summary:

Upgraded from the Julia 1.7 series to the Julia 1.10 series. The detailed release notes for the Julia 1.10 series can be found here https://docs.julialang.org/en/v1.10/.

JupyterLab: (v4.0.9)

JupyterLab is a next-generation web-based user interface for Project Jupyter that enables users to work with documents and activities such as Jupyter notebooks, text editors, terminals, and custom components in a flexible, integrated, and extensible manner. You can arrange multiple documents and activities side by side in the work area using tabs and splitters. Documents and activities integrate with each other, enabling new workflows for interactive computing, for example:

• Code Consoles provide transient scratchpads for running code interactively, with full support for rich output. A code console can be linked to a notebook kernel as a computation log from the notebook, for example.
• Kernel-backed documents enable code in any text file (Markdown, Python, R, LaTeX, etc.) to be run interactively in any Jupyter kernel.
• Notebook cell outputs can be mirrored into their own tab, side by side with the notebook, enabling simple dashboards with interactive controls backed by a kernel.
• Multiple views of documents with different editors or viewers enable live editing of documents reflected in other viewers. For example, it is easy to have live preview of Markdown, Delimiter-separated Values, or Vega/Vega-Lite documents.

JupyterLab is accessible via Posit Workbench on Metworx.

Change Summary:

Upgraded from JupyterLab v3.1.6. Change log information can be found at https://jupyterlab.readthedocs.io/en/4.0.x/getting_started/changelog.html#id16.

Jupyter Notebook: (v6.5.6)

Jupyter Notebook extends the console-based approach to interactive computing in a qualitatively new direction, providing a web-based application suitable for capturing the whole computation process: developing, documenting, and executing code, as well as communicating the results. It combines two components:

• A web application: a browser-based tool for interactive authoring of documents which combine explanatory text, mathematics, computations, and their rich media output.
• Notebook documents: a representation of all content visible in the web application, including inputs and outputs of the computations, explanatory text, mathematics, images, and rich media representations of objects.

Jupyter Notebook is accessible via Posit Workbench on Metworx.

Change Summary:

Upgraded from Jupyter Notebook v6.4.3. Change log information can be found at

MATLAB: (v2023a)

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 DCV remote desktop.

Change Summary:

MATLAB was updated from version 2022a. Release highlights associated with MATLAB 2022a can be found at https://www.mathworks.com/products/matlab/whatsnew.html.

MonolixSuite: (v2024R1)

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 population PK/PD modeling and systems pharmacology.

Change Summary:

Replaced MonolixSuite versions 2020R1 and 2021R1. Release highlights can be found at https://monolixsuite.slp-software.com/getting-started/2024R1/release-notes-monolixsuite-2024r1.

MPN Snapshot: (v2024-03-01)

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.

Change Summary:

Upgraded from MPN 2022-08-3. Release highlights can be found at https://mpn.metworx.com/docs/snapshots/2024-03-01.

NGINX: (v1.18.0)

NGINX is a high-performance web server known for its efficiency in handling heavy traffic loads. Its asynchronous, event-driven architecture makes it ideal for serving static content, reverse proxying, and load balancing across multiple servers. NGINX is favored by many developers and sysadmins for its speed, reliability, and robust feature set in managing web applications.

Change Summary:

Upgraded from v 1.14.0

NONMEM: (v7.5.1, v7.4.4, v7.3.0)

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

Change Summary:

Upgraded from v7.5.0 to 7.5.1. More information can be found at https://www.iconplc.com/solutions/technologies/nonmem

Open MPI: (v3.3.2)

Open MPI is an open-source project focused on providing a Message Passing Interface. Maintained by research academics and industry partners, it provides resources specifically geared for the HPC community.

Change Summary:

Newly added to Metworx 24-04

Perl: (v5.3.1)

Perl-speaks-NONMEM: (v5.3.1)

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.

Change Summary:

Pearl updated from version 5.3.0

Pirana: (v23.20.1)

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.

Change Summary:

Upgraded from version 2.9.9

pkgr: (v3.1.1)

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.

Change Summary:

Updated from version 3.1.0 to 3.1.1

Posit Connect: (v2023.12.1)

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

Change Summary:

Updated from RStudio Connect v2022.3.0

Posit Workbench: (v2023.12.1)

Posit Workbench is an interactive development environment (IDE) for code development, and acts as the primary interface to Metworx workflows, providing users with the ability to use their preferred IDE, whether that is RStudio, JupyterLab, Jupyter Notebook, or VS Code.

Change Summary:

Updated from RStudio Workbench v2022.02.1

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.

Change Summary:

No changes made from 22.09 blueprint

SLURM: (v20.11.8)

SLURM, short for Simple Linux Utility for Resource Management, is a highly efficient workload manager and job scheduler designed for large-scale computing clusters. It enables organizations to effectively allocate and manage computing resources, scheduling tasks across nodes based on predefined policies to optimize performance and resource utilization.

Change Summary:

New feature: more information can be found at https://www.schedmd.com/slurm-version-23-11-8-is-now-available/.

TexLive: (v2023)

TexLive 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 stylize 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.

Change Summary:

Upgraded from LaTex v2021. Additional documentation can be found at https://tug.org/texlive/doc.html.

Visual Studio Code (VS Code): (v1.87.0)

Visual Studio Code is a powerful lightweight source code editor which runs on desktop, available for Windows, macOS, and Linux. It comes with built-in support for JavaScript, TypeScript, and Node.js with a variety of extensions for other languages.

Change Summary:

Upgraded from VS Code v1.59.0. Additional documentation can be found at https://code.visualstudio.com/updates/v1_87.