Posts tagged systems biology
The limitations of deterministic modeling in biology
The limitations of deterministic modeling in biology

There are excellent reasons for biologists to consider looking beyond differential equations as their tool of choice for modeling and simulating biological systems.

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Modeling & Simulation, Computational Biology, Systems Biology, Mathematical BiologyGordon Webstermodeling, simulation, calculus, differential equations, dynamic modeling, deterministic modeling, stochastic modeling, agent-based modeling, computational biology, systems biology, cell signaling pathways, cell biology, cell signaling
If you really want to understand how a biological pathway works, build one
If you really want to understand how a biological pathway works, build one

Amber Biology was recently commissioned by a biotechnology company, to build a dynamic, agent-based model of a biological pathway.

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Bioinformatics, Biomarkers, Computational Biology, Modeling & Simulation, Systems Biology, Cell SignalingAlex Lancastercomputational biology, systems biology, bioinformatics, modeling, simulation, stochastic modeling, dynamic modeling, deterministic modeling, calculus, differential equations, cell signaling, cell signaling pathway, cell signaling network, cell biology, molecular biology
A Collaborative Cloud-Based Biological Modeling Platform
A Collaborative Cloud-Based Biological Modeling Platform

A brief video demo of a collaborative, cloud-based biological modeling platform running in a web browser.

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Computational Biology, Mathematical Biology, Modeling & Simulation, Systems BiologyGordon Webstercomputational biology, systems biology, bioinformatics, modeling, simulation, stochastic modeling, dynamic modeling, deterministic modeling, calculus, differential equations, cell signaling, cell signaling pathway, cell signaling network, cell biology, molecular biology
Amber Biology presenting on biological pattern formation at Jan 23 Boston Python Meetup
Amber Biology presenting on biological pattern formation at Jan 23 Boston Python Meetup

Amber Biology is presenting at the Boston Python Meetup, on the modeling of biological pattern formation ...  

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Amber Biology, Bioinformatics, Mathematical Biology, Modeling & Simulation, Python, Software Development, Systems Biology, TrainingAlex Lancastercomputational biology, systems biology, bioinformatics, modeling, simulation, stochastic modeling, dynamic modeling, deterministic modeling, calculus, differential equations
A spring surprise: computational analysis unearths potential prions in plants
A spring surprise: computational analysis unearths potential prions in plants

A new paper involving Amber Biology consultants, illustrates the power of bioinformatics to find intriguing features in proteomes …

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Computational Biology, Mathematical Biology, Modeling & Simulation, Systems BiologyAlex Lancastercomputational biology, systems biology, bioinformatics, modeling, simulation, stochastic modeling, dynamic modeling, deterministic modeling, calculus, differential equations, prions
The Central Role Of User Experience Design In Scientific Modeling
The Central Role Of User Experience Design In Scientific Modeling

Data is not knowledge. Data can reveal relationships between events –

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Computational Biology, Mathematical Biology, Modeling & Simulation, Software Development, Systems Biology, BioinformaticsGordon Webstercomputational biology, systems biology, bioinformatics, modeling, simulation, stochastic modeling, dynamic modeling, deterministic modeling, calculus, differential equations, software, software development, programming, coding, python, computation, computer science, programming language, ux, user experience, user experience design, ux design
All Big Data is equal, but some Big Data may be more equal than others
All Big Data is equal, but some Big Data may be more equal than others

It’s often widely assumed that decisions made by algorithms are more “neutral” and “fair” than those made by people.  

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Bioinformatics, Computational Biology, Mathematical Biology, Statistical AnalysisAlex Lancastercomputational biology, systems biology, bioinformatics, modeling, simulation, stochastic modeling, dynamic modeling, deterministic modeling, calculus, differential equations, big data, data science, data analysis
Biological models: Much more than just a weather forecast
Biological models: Much more than just a weather forecast

Biological modeling is not yet in the mainstream of biological research in the way that it is in other scientific and technical areas like physics and engineering ...

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Biomarkers, Cell Signaling, Computational Biology, Mathematical Biology, Modeling & Simulation, Systems Biology, AlgorithmsGordon Webstercomputational biology, systems biology, bioinformatics, modeling, simulation, stochastic modeling, dynamic modeling, deterministic modeling, calculus, differential equations
Biologists Flirt With Models
Biologists Flirt With Models

Early developments in biological modeling hold the potential to forge a knowledge revolution in biology  and to bring modeling into the mainstream of biological research … 

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Algorithms, Biomarkers, Cell Signaling, Computational Biology, Mathematical Biology, Modeling & Simulation, Systems BiologyGordon Webstercomputational biology, systems biology, bioinformatics, modeling, simulation, stochastic modeling, dynamic modeling, deterministic modeling, calculus, differential equations, complex adaptive systems
An "Uncertainty Principle" for mathematical approaches to biological modeling
An "Uncertainty Principle" for mathematical approaches to biological modeling

If you’re a biological modeler, chances are there are two words that keep you up at night. Those two words are combinatorial complexity … 

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Algorithms, Computational Biology, Cell Signaling, Mathematical Biology, Modeling & Simulation, Systems BiologyGordon Webstercomputational biology, systems biology, bioinformatics, modeling, simulation, stochastic modeling, dynamic modeling, deterministic modeling, calculus, differential equations, complex adaptive systems