Please redesign the Software page of my AcademicPages/Jekyll website to focus almost exclusively on my main bioinformatics software project: SCALPEL.

Repository: https://github.com/franzake/franzake.github.io

SCALPEL repository: https://github.com/plasslab/SCALPEL

Goals:

• Modern academic software showcase
• Clean Stanford/OpenAI-style aesthetic
• Compact and elegant
• Research/software engineering oriented
• Strong visual presentation
• GitHub Pages compatible

Requirements:

1. Remove the current bulky text-heavy “Major Projects” layout.
2. The main and primary software showcased should be: SCALPEL (Single-Cell Alternative Polyadenylation and Isoform Exploration)
3. Use the SCALPEL GitHub repository to gather:

• project description
• workflow overview
• key functionalities
• technologies
• relevant figures/images
• README assets

1. Include a preview image from the SCALPEL GitHub repository directly on the page. this image show the SCALPEL pipeline
2. Create a modern compact project card layout similar to a startup/software showcase.

Desired structure:

⸻

SCALPEL

Short scientific/software summary.

[ Preview image on the right or top ]

Key Features:

• Isoform quantification at single-cell resolution
• Alternative polyadenylation analysis
• Differential isoform usage analysis
• Reproducible Nextflow workflows
• Scalable HPC/cloud execution
• nf-core-oriented design principles

Technologies: Nextflow · Python · R · Docker · Singularity · scRNA-seq

Links: [GitHub] [Documentation] [Paper if available]

⸻

1. Keep the page visually light and readable.
2. Avoid giant blocks of text.
3. Add subtle separators/cards.
4. Responsive design for mobile.
5. Remove the old “RNA-seq Fusion Detection Workflows” section entirely.
6. Add GitHub badges if visually clean:

• stars
• license
• workflow status
• last commit

1. Add a concise scientific/software engineering summary: “SCALPEL is a scalable computational framework for transcript isoform quantification and alternative polyadenylation analysis at single-cell resolution.”
2. Styling goals:

• compact cards
• subtle borders
• modern typography
• image rounded corners
• no oversized sections
• elegant spacing

1. Keep all modifications compatible with: bundle exec jekyll serve
2. Generate all required HTML/CSS/Markdown edits directly.
3. If possible, add:

• hover effect on the project card
• clickable GitHub repository button
• compact feature badges
• small technology pills

1. The final result should resemble:

• a modern computational biology software portfolio
• an academic software showcase
• a polished research engineering page suitable for Stanford and industry AI/bioinformatics visibility.