BioCompLabSynthetic Biological Hardware and Biological Computer Organization Research Laboratory
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Projects

Concrete programs, not abstract claims.

These are the laboratory initiatives that are now visible on the website, organized by maturity and tied back to the new reference files.

Program count

6

Visible laboratory programs and cataloged support artifacts.

Active work

3

Programs currently presented as active initiatives.

Supporting items

3

Documentation, education, archival, and provenance work.

active

Biological Systems Simulation Models for the Physical Synthesis of Digital Circuits in Bacteria

A research program on simulation models that connect biological system dynamics with the physical synthesis of digital circuits in bacterial hosts.

Model assembly, hybrid biological simulation, bacterial implementation constraints, and the translation between computational circuit behavior and living-cell execution.

Open project
active

GenESyS Whole-Cell Modeling

Hybrid biochemical, metabolic, stochastic, and compartment-aware whole-cell modeling for prokaryotic and eukaryotic scenarios.

Deterministic biochemical networks, flux balance models, stochastic transcription/translation, growth, checkpoints, and division logic.

Open project
active

BioCompLab Web Portal

The public and member-facing portal that organizes research, tools, courses, news, account access, and publication records.

Evidence-first information architecture, provenance-aware cataloging, and a clean separation between public and member-only workflows.

Open project
education

Biological Computing Foundations Course

A structured learning path that connects molecular biology, bioinformatics, systems biology, modeling, and synthetic biology.

A long-form course with modules, linked tools, guided activities, and a scientific study track for members.

Open project
documentation

Publications and Provenance Catalog

A catalog that distinguishes papers, technical reports, datasets, software artifacts, and reproducibility packages.

Traceability, metadata quality, publication status, and conservative handling of what is ready for public display.

Open project
archival

Reference Library

A curated archive of documents, papers, manuals, and research references used to improve the portal and project pages.

Whole-cell modeling references, synthetic biology references, systems biology textbooks, and project source material.

Open project

Active initiatives

Biological Systems Simulation Models for the Physical Synthesis of Digital Circuits in Bacteria

A research program on simulation models that connect biological system dynamics with the physical synthesis of digital circuits in bacterial hosts.

GenESyS Whole-Cell Modeling

Hybrid biochemical, metabolic, stochastic, and compartment-aware whole-cell modeling for prokaryotic and eukaryotic scenarios.

BioCompLab Web Portal

The public and member-facing portal that organizes research, tools, courses, news, account access, and publication records.

Supporting projects and artifacts

Biological Computing Foundations Course

education

A long-form course with modules, linked tools, guided activities, and a scientific study track for members.

Evidence: Course configuration in the portal · Locally archived teaching and modeling material

Publications and Provenance Catalog

documentation

Traceability, metadata quality, publication status, and conservative handling of what is ready for public display.

Evidence: Lab papers folder · Research project report · Proposal and technical documents

Reference Library

archival

Whole-cell modeling references, synthetic biology references, systems biology textbooks, and project source material.

Evidence: nonGit_AIassistant_referenceFiles directory

Editorial rule

Project pages should remain evidence-first: if a project is exploratory, it must be marked as documentation, education, planned work, or archival context rather than as a scientific result.

Review publication catalog

Protected PDF shelf

Project PDFs will use the protected reader stack.

This page is now wired to the same hidden PDF catalog model as courses. Project PDFs will live in hiddenPDF/projects and can later be opened with the same authenticated page-image reader.

Courses

Protected course PDFs and teaching materials.

5 PDFs
Folder: coursesMetadata: courses-metadata.json

Projects

Protected project PDFs and supporting artifacts.

0 PDFs
Folder: projectsMetadata: projects-metadata.json

Publications

Protected publication PDFs and editorial records.

2 PDFs
Folder: publicationsMetadata: publications-metadata.json
Open course PDF catalog

The same protected PDF pipeline used for courses will serve project and publication PDFs once they are added.