Use Cases

bsim serves diverse needs across research, education, and industry.

Academic Research

Systems Biology Research

Problem: Researchers need to test hypotheses about biological systems but setting up simulation environments is time-consuming.

Solution: bsim provides instant access to curated models and simulation infrastructure.

Example Workflow:

Search for existing models of your pathway of interest
Run baseline simulations to understand normal behavior
Modify parameters to test your hypothesis
Compare results to experimental data
Export figures for publication

Benefits:

Weeks of setup reduced to minutes
Reproducible simulation configurations
Easy collaboration with co-authors

Pharmacology & Drug Discovery

Problem: Predicting drug effects requires understanding complex pharmacokinetic and pharmacodynamic relationships.

Solution: bsim enables PKPD modeling and parameter exploration.

Example Workflow:

Find or upload a PKPD model for your drug class
Set physiological parameters for target population
Run dose-response simulations
Identify optimal dosing regimens
Share results with regulatory teams

Benefits:

Rapid screening of dosing scenarios
Multi-compartment model support
Integration with clinical trial design

Computational Neuroscience

Problem: Neural models are computationally intensive and require specialized software.

Solution: bsim runs neural simulations in the cloud with interactive visualization.

Example Workflow:

Browse Hodgkin-Huxley and similar neural models
Configure membrane potentials and ion channel parameters
Run action potential simulations
Analyze spike timing and frequency
Compare wild-type vs mutant channel behavior

Benefits:

No NEURON/GENESIS installation needed
Instant visualization of membrane dynamics
Easy parameter sensitivity analysis

Education

University Courses

Problem: Students need hands-on experience with biological modeling but software setup creates barriers.

Solution: bsim provides zero-setup access to classic models with interactive exploration.

Course Integration:

Systems Biology 101: Explore Michaelis-Menten kinetics, gene regulatory networks
Computational Neuroscience: Hodgkin-Huxley, integrate-and-fire neurons
Pharmacology: PKPD modeling, drug-drug interactions
Ecology: Predator-prey dynamics, population modeling

Benefits for Instructors:

Assign simulations as homework
Create guided tutorials
Track student progress
Share model collections

Benefits for Students:

Learn by doing, not installing
Immediate visual feedback
Experiment without breaking things
Access from any device

MOOCs and Online Learning

Problem: Online courses can’t assume students have specific software installed.

Solution: bsim runs entirely in the browser with no prerequisites.

Integration Options:

Embed interactive simulations in course materials
Link to pre-configured model runs
Use API for automated grading
Provide course-specific model collections

Industry Applications

Pharmaceutical R&D

Problem: Drug development requires extensive modeling to predict efficacy and safety.

Solution: bsim accelerates early-stage modeling and hypothesis testing.

Applications:

Target validation through pathway modeling
PKPD parameter estimation
Virtual patient population simulations
Drug combination modeling

Benefits:

Faster time-to-insight
Reduced reliance on specialized consultants
Standardized modeling workflows
Audit trails for regulatory compliance

Biotechnology

Problem: Bioprocess optimization requires understanding cellular metabolism under different conditions.

Solution: bsim enables metabolic modeling and flux analysis.

Applications:

Metabolic pathway optimization
Strain engineering predictions
Bioreactor condition screening
Media optimization

Benefits:

Reduce wet lab experiments
Explore parameter space systematically
Document optimization rationale
Collaborate with CRO partners

Healthcare & Diagnostics

Problem: Precision medicine requires patient-specific model predictions.

Solution: bsim can run personalized simulations based on individual parameters.

Applications:

Drug dosing personalization
Disease progression modeling
Treatment response prediction
Biomarker discovery

Benefits:

Rapid model customization
HIPAA-compliant deployment options
Integration with clinical systems
Scalable to patient populations

Research Collaborations

Multi-Site Projects

Problem: Collaborators at different institutions need to share models and results.

Solution: bsim provides centralized project spaces with fine-grained access control.

Features:

Shared project workspaces
Role-based permissions (viewer, editor, admin)
Version-controlled model updates
Comment and discussion threads

Open Science

Problem: Publishing a paper doesn’t guarantee reproducibility of computational results.

Solution: bsim enables public sharing of complete simulation environments.

Features:

Public project URLs
DOI assignment for cited simulations
Embeddable results widgets
Complete parameter logging

Integration Scenarios

Workflow Automation

# Example: Automated parameter sweep
import bsim
 
client = bsim.Client(api_key="...")
 
# Run parameter sweep
results = []
for k1 in [0.1, 0.2, 0.5, 1.0]:
    run = client.create_run(
        model_id="BIOMD0000000012",
        duration=100,
        parameters={"k1": k1}
    )
    results.append(run.wait())
 
# Analyze results
sensitivities = analyze_sensitivity(results)

Data Pipeline Integration

# Example: Airflow DAG
tasks:
  - name: run_simulation
    operator: BSimOperator
    model_id: "BIOMD0000000012"
    parameters:
      k1: "{{ params.k1 }}"
 
  - name: process_results
    operator: PythonOperator
    python_callable: analyze_results
    depends_on: run_simulation

Lab Information Systems

REST API integration for automated workflows
Webhook notifications for completed runs
Batch job submission and monitoring
Results export in standard formats

Success Stories

Academic Lab Case Study

“bsim reduced our model setup time from weeks to hours. We can now test hypotheses the same day we conceive them.” — Dr. Jane Smith, University of Example

Biotech Startup Case Study

“We used bsim to screen 10,000 parameter combinations overnight, identifying optimal fermentation conditions that increased yield by 40%.” — CTO, BioStartup Inc.

Educational Case Study

“My students can focus on understanding the biology rather than debugging software installations. Engagement has increased dramatically.” — Prof. John Doe, Example State University

Overview Pricing