MorphoLang is an open source toolkit that operationalizes the "Bioelectric Code." It treats biological pattern formation as a computational process, allowing researchers to compile high level anatomical goals (e.g., "Build an Eye") into low level molecular interventions.
"If bioelectric dynamics... can be treated as a kind of software, the next revolution in biology could be... driven by the realization that we do not have to manipulate living systems at the level of their 'machine code' (affecting specific molecules), but at the level of information.". Levin & Martyniuk, 2017
Status: 🧬 BETA v0.4 - Genetic Interface (Research Use Only)
Bioelectricity is the trigger; genetics is the machinery. v0.4 connects them:
- 🧬 Downstream Biomarkers: Protocols now verify that voltage changes successfully trigger specific genes (e.g., Rx1, Msx1, Notch).
- ⏱️ Temporal Profiles: Models oscillating vs. constant signals ("pulsatile" vs "steady-state").
New tool to read voltage patterns and predict morphology:
- 🔮
predict_morphology.py: Input a voltage map, output a predicted organ.- Example: "Warning: -40mV pattern in ventral ectoderm matches Ectopic Eye."
Traditional regenerative medicine attempts to micromanage individual cell fates. MorphoLang takes a top down pattern homeostasis approach:
- Hardware: Ion channels and gap junctions
- Software: Spatio-temporal Vmem patterns
- Control Loop: Closed loop feedback to maintain target states
- Interface: Coupling bioelectric triggers to transcriptional networks
git clone https://github.com/tlcdv/MorphoLang.git
cd MorphoLang
pip install -r requirements.txtfrom compiler.experiment_gen import BioCompiler
compiler = BioCompiler()
protocol = compiler.find_subroutine(organ="eye", species="Xenopus laevis")
print(compiler.generate_protocol(protocol))Output includes:
[PHASE 4: HOMEOSTATIC MAINTENANCE]
Monitoring Schedule: Every 6 hours
Feedback Decision Tree: IF Vmem > -25mV → Apply booster
[PHASE 5: SAFETY & VERIFICATION]
(!) VERIFICATION METHOD: Ratiometric Voltage Imaging
SECONDARY VERIFICATION (Genetic Markers):
> Gene: Rx1 (Retinal Homeobox)
Expected: UPREGULATED
Timing: Stage 12.5
You observe a hyperpolarized patch (-40mV) in the ventral ectoderm. What is the tissue building?
from compiler.predict_morphology import BioDecoder
decoder = BioDecoder()
prediction = decoder.predict(vmem=-40.0, spatial_domain="ventral_ectoderm")
print(decoder.generate_report(prediction))Output:
PREDICTION #1: INDUCE EYE
Mechanism: Hyperpolarized domain mimicking Anterior Neural Field
Confidence: High
Verifiers: Check for expression of Rx1, Pax6
| Subroutine | Target | Mechanism | Biomarkers |
|---|---|---|---|
xenopus_eye_v1 |
Induce Eye | Kv1.5 (1-2 ng) | Rx1, Pax6 |
xenopus_tail_v1 |
Regenerate Tail | H+ Pump (500 pg) | Notch, Msx1 |
planaria_head_v1 |
Remodel Head | Octanol (127 μM) | ndk, smed-prep |
xenopus_limb_v1 |
Regenerate Limb | Monensin (10 mM) | Msx1 |
We welcome bioelectric subroutines! To contribute:
- Fork the repo
- Create a JSON file in
/subroutinesfollowingsubroutine_schema.json - Include:
downstream_biomarkers(gene targets)control_loopparameterstemporal_profile(constant/oscillating)
- Submit a Pull Request.
- Research Use Only: Protocols are for controlled laboratory environments.
- Animal Ethics: IACUC approval required for all animal work.
- Tumor Risk: Stop conditions prevent indefinite interventions.
MIT License - See LICENSE for details
Based on the research of Dr. Michael Levin (Tufts University) and the principles of bioelectric pattern homeostasis.