Biotech Cell Simulations

Articles

• Biodynamics
  • R.Pearlstein et al: Improving the preclinical and clinical success rates of LMW drugs depends on radical revisions to the status quo scientific foundations of medicinal chemistry: a case study on COVID Mpro inhibition (2023)
  • H. Wan, R. Pearlstein: Toward a first principles understanding of the activation and deactivation mechanisms of class A G-protein coupled receptors and voltage-gated cation channels (2022)

Tools

• Cell-OS
  • CTag announcement
• NVidia WaterWorks, WaveWorks
  • Used in videogaming
• Novartis/watMD
• CompuCell3D - open-source, allows researchers to create detailed models of cells and tissues and simulate their behaviors in 2D or 3D environments.
• BioNetGen - modeling and simulation of biochemical reaction networks
• Virtual Cell - modeling and simulating biological systems at the cellular level. Visual interface for constructing and simulating computational models of cellular processes, such as signal transduction, gene regulation, and cell signaling
• COPASI (Complex Pathway Simulator) - simulation and analysis of biochemical networks. GUI for building and simulating models of cellular processes and offers various analysis features, including parameter estimation, sensitivity analysis, and optimization.
• NetLogo - agent-based modeling platform that allows for simulating and studying complex systems, including cellular processes. Simple programming language and a user-friendly interface
• Amber, free to academis. Charges $25,000 for pharma companies.
• Alphafold - can predict structure of protein from sequence from aminoacic sequence. There are 20 aminoacids. Determines shape of molecule. But, can be amended for
• CellOS in matlab
• Symbiology is add on to Matlab.
• CellML (like XML) and SBML (Systems Biology Markup Language)

Other

• Artificial Intelligence
• Biotech
• Biotech Cell Simulations
• Biotech Software Stacks
• Cloud Data Platform
• Cognitive Science
• Computation Theory
• GPUs
• Language Models
• Meta Learning
• MLOps
• Probabilities and Statistics
• Robotics
• Self Driving Cars
• Computational Topology