[Paper Review] A Unified, Cross-Platform Framework for Automatic GUI and Plugin Generation in Structural Bioinformatics and Beyond

Sikao Guo, Edoardo Sarti+1 more|arXiv (Cornell University)|Feb 17, 2026

Genomics and Phylogenetic Studies0 citations

TL;DR

The paper presents a three-phase workflow and toolkit that automatically generates cross-platform GUI plugins for CLI tools, using an MVP architecture and a single formal specification to target VMD, PyMol, and web platforms.

ABSTRACT

We present a workflow and associated toolkit to automate the creation of graphical user interfaces (GUI) for executables run from command line interfaces (CLI). The workflow consists of three phases, namely (Step 1) the plugin design, (Step 2) the formal (platform independent) specification of the GUI, and (Step 3) the plugin code generation for the targeted platforms. Our architecture is aligned with the Model--View--Presenter (MVP) pattern: steps one and two build the Model and View descriptions, while step three implements the Presenter layer that binds inputs, invokes the CLI, and updates outputs. Once Step one has been (manually) completed, steps two and three are fully automated. The decoupled MVP design and platform-specific generator modules enable reuse of logic, portability across ecosystems, and significant reductions in engineering effort for complex interactive applications. We primarily use our workflow to generate GUI in structural bioinformatics for CLI executables from the Structural Bioinformatics Library (SBL), targeting three platforms, namely VMD, Pymol and Web servers. The workflow can be used as a guideline, while its implementation available in the package Plugin_manager from the SBL, see https://sbl.inria.fr/doc/Plugin_manager-user-manual.html.

Motivation & Objective

• Provide a workflow to automate GUI plugin creation for CLI tools in structural bioinformatics and beyond.
• Ensure consistency, maintainability, and portability across multiple host platforms.
• Leverage a single formal specification to propagate changes across all targets.
• Demonstrate cross-platform plugin generation for VMD, PyMol, and web environments.
• Centralize project structure to aid collaboration and onboarding.

Proposed method

• Define a plugin design phase that selects CLI options and determines GUI layout.
• Automatically generate a formal JSON specification from the GUI design and CLI flags.
• Automatically generate platform-specific code from the JSON specification using dedicated generators.
• Organize code according to the Model–View–Presenter (MVP) pattern to separate concerns.
• Enable cross-platform integration with VMD, PyMol, and Panel web environments via tailored backends.
• Provide a post-analysis script to translate CLI outputs into GUI outputs and visualizations.

Experimental results

Research questions

• RQ1 How can a single formal specification enable consistent GUI generation across multiple platforms for CLI tools?
• RQ2 Can MVP-based generated code maintain separation of concerns across VMD, PyMol, and web targets?
• RQ3 What is the workflow to move from design to fully functional cross-platform GUI plugins?
• RQ4 How effectively can the framework adapt to new platforms or visualization engines with minimal manual effort?

Key findings

• A three-phase workflow (design, formal specification, code generation) enables automatic cross-platform GUI plugin creation.
• A single specification plus platform-specific code generators reduce development effort from n×m to n+m for n applications and m targets.
• The MVP architecture maintains separation of concerns, facilitating maintainability and portability across Tkinter/VMD, Qt/PyMol, and Panel/Web backends.
• Plugins are generated for multiple environments from the same design artifacts, reusing layout and flags across targets.
• The framework supports direct integration with VMD, PyMol, and web viewers (NGL/Three.js) through tailored communication mechanisms.
• A post-analysis script standardizes outputs for GUI, 3D viewers, and downstream visualizations across platforms.