Skip to content

README.md

Latest commit

 

History

History
225 lines (164 loc) · 10.2 KB

README.md

File metadata and controls

225 lines (164 loc) · 10.2 KB

🔬 K R&D Lab — SPHERE I / SCIENCE

Science sphere entry point for K-RnD Lab

GitHub HF Learning Playground HF Cancer Research Suite License

Computational approaches to biology, medicine, plant science, ecology, chemistry, cognition, and longitudinal life-pattern research

⚠️ Research use only. All models are experimental and hypothesis-generating.

Scope

This repository maps SPHERE I — SCIENCE inside K R&D Lab. Scientific questions stay here; reusable tooling, scoring systems, and dashboards belong in SPHERE-III-TECHNOLOGY.

Documentation Workflow

  • docs/ = active research staging and execution materials
  • archived_docs/ = superseded planning, older operating notes, and historical strategy layers

If a file is still needed to scope, execute, or stage an active study, it stays in docs/. If it has already been superseded by lane maps, execution status files, or actual research starter packs, it moves to archived_docs/.

Current Science Directions

SPHERE I — SCIENCE
│
├── 🩺 S1 — Biomedical & Oncology
├── 🌿 S2 — Plant Science & Phytochemistry
├── 🌾 S3 — Agricultural Biology & Biofertilizers
├── ⚗️ S4 — Biochemistry & Metabolomics
├── 🧠 S5 — Neuroscience & Aging
├── 🌍 S6 — Ecology & Environmental Science
└── 📚 S7 — K Life OS

Science Boundaries

  • S1 Biomedical & Oncology
    Computational oncology, RNA therapeutics, delivery systems, biomarkers, and rare-cancer hypotheses.
  • S2 Plant Science & Phytochemistry
    Plant-intrinsic biology: phytochemicals, plant metabolites, bioactive compounds, and plant molecular traits.
  • S3 Agricultural Biology & Biofertilizers
    Applied agro-biology: soil, rhizosphere, biofertilizers, crop-growth systems, and intervention logic.
  • S4 Biochemistry & Metabolomics
    Cross-organism biochemical mechanisms, pathway logic, and metabolomic signatures.
  • S5 Neuroscience & Aging
    Neurobiology, cognition, neuroinflammation, aging, and computational vulnerability patterns.
  • S6 Ecology & Environmental Science
    Ecosystems, biodiversity, environmental communities, and climate/pollution-linked system effects.
  • S7 K Life OS
    Science-facing work on measurable life systems, cognition, adaptive training, self-tracking, and longitudinal human-pattern research.

Conference-Aligned Expertise

The current conference-style expertise map is best treated as an overlay on top of the existing S1 structure rather than a replacement for it.

Conference area Current home in the lab
Nucleic-acid therapeutics: technologies and applications S1-B PHYLO-RNA and S1-D PHYLO-LNP
Recombinant proteins and mAb development technologies Future S1-G if it becomes a repeated line of work
Gene editing technologies and applications in medicine Future S1-H if it becomes a repeated line of work
Advanced cell therapies Future S1-I if it becomes a repeated line of work
Bioinformatics and AI in biomedical research Cross-cutting method layer across S1 and SPHERE-III
Biomarkers and molecular diagnostics S1-E PHYLO-BIOMARKERS
Other translational research Cross-cutting umbrella across S1, E, and T
Structural biology Future S1-J, or part of S1-C when tied to molecular design

Potential future S1 expansion tracks, only if they grow into repeated study series:

  • S1-G Biologics & Antibody Engineering
  • S1-H Gene Editing & Functional Therapeutics
  • S1-I Cell Therapies & Translational Platforms
  • S1-J Structural Biology & Molecular Design

Active Concentration Today

🩺 S1 — Biomedical & Oncology

Current active concentration includes:

  • genomics and variant interpretation
  • RNA therapeutics
  • RNA-directed drug discovery
  • nanoparticle delivery
  • biomarkers and liquid-biopsy logic
  • rare cancer frontier studies

📚 S7 — K Life OS

Current active lane:

Current project:

Example Directions Outside S1

  • S2: phytochemical atlas, compound-target prioritization, plant stress-response signatures
  • S3: rhizosphere microbiome scoring, biofertilizer efficacy modeling, soil-health predictors
  • S4: metabolite signature classifier, pathway perturbation maps, enzyme/substrate inference
  • S5: neuroinflammation biomarker panels, cognitive aging predictors, vulnerability scoring
  • S6: environmental microbiome sentinels, biodiversity stress markers, pollutant-response networks

Primary Sphere And Hybrid Combos

SPHERE-I remains the home sphere for scientific questions, hypotheses, and validation logic. Hybrid combo labels are added only when a study clearly crosses into reusable tooling or translational decision-making:

  • S for pure scientific questions and hypothesis work
  • S+T for science-facing methods, scoring systems, or reusable analytical tooling
  • S+E for translational opportunity framing grounded in a science problem
  • S+E+T for work that simultaneously connects domain research, implementation, and venture logic

Hugging Face is treated as an interactive delivery layer for demos and interfaces, not as a separate sphere.

Cross-Sphere Registry

The first shared registry scaffold across SCIENCE, ENTREPRENEURSHIP, and TECHNOLOGY lives in SPHERE-III:

Source Of Truth

  • GitHub repo: research structure, manuscripts, notebooks, data snapshots
  • Hugging Face Spaces: interactive demos and app wrappers
  • Local spaces/ directory: mirrored copies of the current HF app layer for audit and sync

Deploy Entrypoints

Public app launchers that need ASCII-safe hosted paths live in deploy/.

Current example:

  • deploy/k_ecologic_lab.py
    • public wrapper for the K-EcoLOGIC Lab environmental platform
  • live app
    • https://k-ecologic-lab.streamlit.app/
    • module pages:
      • Home
      • SortSmart Ukraine
      • Packaging & Sorting Guide
      • Environmental Briefs
      • Sorting Assistant
      • Activist Requests
      • Air & Exposure
      • Water Watch
      • Polluters & Permits
      • Radiation & Risk

Interactive Spaces

The current live app environment is split across these Spaces:

Space Purpose Local mirror
Learning Playground Interactive sandbox for miRNA, siRNA, LNP, flow-corona, and variant-learning tabs spaces/learning-playground
Cancer Research Suite Live research-gap exploration, real-data lookups, and research assistant workflows spaces/cancer-research-suite
PHYLO BRCA2 miRNA Demo Dedicated BRCA2 miRNA study demo spaces/phylo-brca2-mirna

More detail is documented in spaces/README.md and docs/hf-space-sync.md.

Repository Layout

SPHERE-I-SCIENCE/
|-- S1 — Biomedical & Oncology/
|-- S2 — Plant Science & Phytochemistry/
|-- S3 — Agricultural Biology & Biofertilizers/
|-- S4 — Biochemistry & Metabolomics/
|-- S5 — Neuroscience & Aging/
|-- S6 — Ecology & Environmental Science/
|-- S7 — K Life OS/
|-- spaces/
|   |-- learning-playground/
|   |-- cancer-research-suite/
|   `-- phylo-brca2-mirna/
|-- docs/
|   `-- hf-space-sync.md
`-- tools/
    `-- sync_hf_spaces.ps1

Sync Workflow

When the app layer changes in Hugging Face, refresh the local mirrors with:

powershell -ExecutionPolicy Bypass -File .\tools\sync_hf_spaces.ps1

Recommended workflow:

  1. Update research assets in GitHub.
  2. Update app/runtime wrappers in the relevant Hugging Face Space.
  3. Run the sync script to mirror the current Space state into spaces/.
  4. Commit both the research edits and the refreshed mirrors when they should move together.

Citation

If you cite the repository, use the project-level metadata in CITATION.cff.

Disclaimer

All computational models are research-grade and experimental. Results labeled simulated require validation before clinical, pharmaceutical, agricultural, educational, or commercial application.

Built with Python · Gradio · scikit-learn · pandas · matplotlib
© 2026 Oksana Kolisnyk · KOSATIKS GROUP · MIT License