Posts in Modeling & Simulation
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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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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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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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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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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The Central Role Of User Experience Design In Scientific Modeling

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

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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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Python for next-generation sequencing

A story about how a challenging genome sequencing project demonstrated once again, what an awesome tool Python can be ...

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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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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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