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Update Research page, add Join us section
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‎.github/copilot-instructions.md‎

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# Copilot Instructions for mathis-group.github.io
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## Project Overview
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This is a static website for the Mathis Group at ASU, built using Jekyll and the [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs). The site is primarily managed with Markdown, YAML, HTML (Liquid), and SCSS files.
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## Key Structure
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- **Content:**
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- `index.md`, `_members/`, `_posts/`, `blog/`, `projects/`, `research/`, `team/` — Main site content in Markdown.
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- `_data/` — YAML files for structured data (citations, members, projects, etc.).
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- `_includes/`, `_layouts/` — HTML/Liquid templates for site rendering.
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- `_styles/` — SCSS for custom site styling.
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- **Custom Code:**
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- `_plugins/` — Custom Ruby plugins for Jekyll (e.g., `array.rb`, `file.rb`).
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- `_cite/` — Python scripts for citation management (`cite.py`, `util.py`).
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## Developer Workflows
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- **Local Build:**
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- Use `./.docker/run.sh` to build locally (requires Docker). Adjust line endings if you encounter issues.
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- **Content Editing:**
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- Add or update Markdown files in `_members/`, `_posts/`, etc. for new content.
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- Update YAML files in `_data/` for structured data changes.
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- **Custom Plugins:**
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- Ruby plugins in `_plugins/` extend Jekyll functionality. Review these for custom site logic.
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- **Citation Management:**
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- Python scripts in `_cite/` manage citations. Dependencies are listed in `_cite/requirements.txt`.
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## Conventions & Patterns
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- **YAML Front Matter:** All content Markdown files use YAML front matter for metadata.
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- **Data-Driven Content:** Many site sections (members, projects, citations) are generated from YAML in `_data/`.
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- **SCSS Organization:** Custom styles are modularized in `_styles/` and imported via `all.scss`.
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- **No JavaScript Build Step:** JS in `_scripts/` is used as-is; there is no bundler or transpiler.
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## Integration Points
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- **Jekyll:** Site is built and served by Jekyll (via Docker for local dev).
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- **Lab Website Template:** Provides base layouts and structure; customizations are layered on top.
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- **Python Citation Tools:** Used for managing and updating citation data.
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## Examples
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- To add a new member: create a Markdown file in `_members/` with appropriate front matter.
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- To update citations: edit `_data/citations.yaml` and/or use `_cite/cite.py`.
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- To add a new custom layout: create an HTML file in `_layouts/` and reference it in content front matter.
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## References
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- See `README.md` for build instructions.
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- Review `_plugins/` and `_cite/` for custom logic.
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- Consult the [Lab Website Template docs](https://greene-lab.gitbook.io/lab-website-template-docs) for base system details.

‎_data/projects.yaml‎

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- title: Modelling the Origin(s) of Life.
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- title: Modeling the Origin(s) of Life.
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group: featured
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image: images/modeling-acs.jpg
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description: We use numerical simulation, and statistical modelling to explore properties of living systems and understand how they can emerge from simpler, non-living components.
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description: We use numerical simulation, and statistical modeling to explore properties of living systems and understand how they can emerge from simpler, non-living components.
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- title: Life Detection from First Principles.
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group: featured

‎_includes/project-focus.html‎

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<section class="project-focus" style="margin-bottom:2em;">
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<div style="display:flex;align-items:flex-start;gap:1.5em;flex-wrap:wrap;">
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{% if include.project.image %}
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<img src="/{{ include.project.image }}" alt="{{ include.project.title }}" style="max-width:220px;min-width:120px;border-radius:8px;box-shadow:0 2px 8px rgba(0,0,0,0.08);margin-bottom:0;">
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{% endif %}
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<div style="flex:1;min-width:220px;">
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<h2 style="margin-top:0;">{{ include.project.title }}</h2>
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<p>{{ include.project.description }}</p>
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</div>
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</div>
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</section>

‎index.md‎

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{% capture text %}
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The Mathis Group is broadly interested in the origin and detection of life. Our goal is to understand the emergence of life, develop tools to facilitate life detection in the solar system, and help make life in the lab. We conduct interdisciplinary research focuses on the intersection of physics, chemistry, computer science and biology.
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The Mathis Group is broadly interested in the origin and detection of life. Our goal is to understand the emergence of life, develop tools to facilitate life detection in the solar system, and help make life in the lab. We conduct interdisciplinary research focuses on the intersection of physics, chemistry, computer science and biology.
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{%
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include button.html

‎research/index.md‎

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# {% include icon.html icon="fa-solid fa-microscope" %}Research
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The Mathis Group studies the origin of living systems, and life detection. We also hope to use the insights and tools we develop to better understand the future of our planet and ourselves. We're just getting started. Check back soon to keep up!
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{% include section.html %}
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# Research Focus
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{% include list.html component="card" data="projects" filters="group: featured" %}
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{% assign featured_projects = site.data.projects | where: "group", "featured" %}
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{% for project in featured_projects %}
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{% include project-focus.html project=project %}
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{% endfor %}
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{% include section.html %}
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‎team/index.md‎

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{% include section.html dark=true %}
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# Interested in Joining?
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### Postdoctoral Scholars:
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We're hiring! Details and application portal are available here: [apply.interfolio.com](https://apply.interfolio.com/175255)
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### Graduate Students:
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We do not currently have funding lines to support new graduate students. Students interested in joining us are encouraged to apply to the PhD program in the School of Complex Adaptive Systems, and contact Prof. Cole Mathis about applying for independent funding through the [NSF's Graduate Research Fellowship Program](https://www.nsf.gov/funding/opportunities/grfp-nsf-graduate-research-fellowship-program) or [NASA Future Investigators in NASA Earth and Space Science Technology](https://science.nasa.gov/earth-science/early-career-opportunities/) programs.
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*SESE Graduate Students:* If you are a newly admitted SESE PhD student, and are interested in a research project with us please email Prof. Cole Mathis.
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### Undergraduate Students:
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We support undergraduate students interested in research through the [_Biocomputing Scholars_ program](https://asu-bd-bss.github.io). Barret Honors students interested in thesis projects should email Prof. Cole Mathis directly and/or contact [Prof. Kelle Dhein](https://www.kelledhein.com) for more information about thesis projects in the School of Complex Adaptive Systems.
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{% include section.html %}
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# About the name
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The Mathis Group aims to conduct high quality, reproducible, interdisciplinary research. Research of this nature requires a team with a diverse skillset, and with diverse backgrounds — the most interesting questions cannot be answered by a single mind. The name 'Mathis-Group' does not imply the PI is the only intellectual contributor to the team's success. The name was chosen because it is simple, and unambiguously locates the entire team with the most persistent individual in the group. This is important considering the ever-shifting Arizona State University ecosystem, including the Biodesign Institute, and the School of Complex Adaptive Systems, which have their own idiosyncratic naming conventions.
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The Mathis Group aims to conduct high quality, reproducible, interdisciplinary research. Research of this nature requires a team with a diverse skill set, and with diverse backgrounds — the most interesting questions cannot be answered by a single mind. The name 'Mathis-Group' does not imply the PI is the only intellectual contributor to the team's success. The name was chosen because it is simple, and unambiguously locates the entire team with the most persistent individual in the group. This is important considering the ever-shifting Arizona State University ecosystem, including the Biodesign Institute, and the School of Complex Adaptive Systems, which have their own idiosyncratic naming conventions.

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