Difference between revisions of "Team:Brasil-USP/Modeling/Optimizations"
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| + | <h1>Crash-course on Python</h1> | ||
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| + | <p>The first thing we did was to level-up everyone interested with modeling, and created a small material that can be used to quickly understand how to use python and get ready for real-world problems as soon as possible. For instance, <a href="https://github.com/thmosqueiro/modeligem/wiki/Installing-Python-with-Anaconda-%28Windows%29" target="_blank">here</a> we have a step-by-step tutorial on how to install Python with Anaconda, and <a href="http://nbviewer.ipython.org/github/thmosqueiro/modeligem/blob/master/notebooks/Python_Intro.ipynb" target="_blank">here</a> the course itself.</p> | ||
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| + | <p>This material was used with <a href="https://2015.igem.org/Team:UFSCar-Brasil" target="_blank">UFSCar-Brasil</a> team during our collaboration day of modeling (described <a href="https://2015.igem.org/Team:Brasil-USP/Collaborations">here</a>).</p> | ||
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<h1>Numerical techniques</h1> | <h1>Numerical techniques</h1> | ||
| + | <p>Numerical methods are always a problems when someone from a biological area wants to simulate something. For several applications, there are 3rd party software that can very well simulate your system. But sometimes you may want to do it yourself. For this reason, we created another complementary material (available <a href="http://nbviewer.ipython.org/github/thmosqueiro/modeligem/blob/master/notebooks/Deterministic_Modeling_Repressilator.ipynb" target="_blank">here</a>) that demonstrates how to use state-of-art numerical methods to simulate differential equations and plot them. These techniques cover most of the simulation issues people have during their first trials.</p> | ||
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Revision as of 02:17, 19 September 2015
BioInformatics
Modeling
Table of contents
We have developed several libraries in Python and a comprehensive guide through our material and code. Our main idea is to spread further several techniques on modeling and simulations for synthetic biology. Everything is hosted on GitHub and publicly available for anyone in the world. We really tried to close the gap between modeling and experimentation as much as possible. For instance, the software we developed was used to analyze our Interlab Study and all results from the wet lab.
This material will be continuously be available and in the following we will go through some of what we have developed.
Crash-course on Python
The first thing we did was to level-up everyone interested with modeling, and created a small material that can be used to quickly understand how to use python and get ready for real-world problems as soon as possible. For instance, here we have a step-by-step tutorial on how to install Python with Anaconda, and here the course itself.
This material was used with UFSCar-Brasil team during our collaboration day of modeling (described here).
Numerical techniques
Numerical methods are always a problems when someone from a biological area wants to simulate something. For several applications, there are 3rd party software that can very well simulate your system. But sometimes you may want to do it yourself. For this reason, we created another complementary material (available here) that demonstrates how to use state-of-art numerical methods to simulate differential equations and plot them. These techniques cover most of the simulation issues people have during their first trials.