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Robert's Notebook

Computational Chemistry, Python, Politics, Policy. Next Steps With Swift. Jun 04, 2013. Let's try doing something a little more complicated with swift. Here's my new swift script. Basically, it's going to run a python script on each of a set of input files. Pythonscript; app (. Pythonscript script, File input ). Read On ↵. Jun 03, 2013. Is a parallel scripting language developed at the U. Chicago Computation Institute. It provides a way to manage heterogeneous clusters. I have. Read On ↵. May 26, 2013.

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Robert's Notebook | rmcgibbo.github.io Reviews

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Computational Chemistry, Python, Politics, Policy. Next Steps With Swift. Jun 04, 2013. Let's try doing something a little more complicated with swift. Here's my new swift script. Basically, it's going to run a python script on each of a set of input files. Pythonscript; app (. Pythonscript script, File input ). Read On ↵. Jun 03, 2013. Is a parallel scripting language developed at the U. Chicago Computation Institute. It provides a way to manage heterogeneous clusters. I have. Read On ↵. May 26, 2013.

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Robert's Notebook | rmcgibbo.github.io Reviews

https://rmcgibbo.github.io

Computational Chemistry, Python, Politics, Policy. Next Steps With Swift. Jun 04, 2013. Let's try doing something a little more complicated with swift. Here's my new swift script. Basically, it's going to run a python script on each of a set of input files. Pythonscript; app (. Pythonscript script, File input ). Read On ↵. Jun 03, 2013. Is a parallel scripting language developed at the U. Chicago Computation Institute. It provides a way to manage heterogeneous clusters. I have. Read On ↵. May 26, 2013.

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rmcgibbo.github.io

1

What is the uncertainty in an MSM?

http://rmcgibbo.github.io/blog/2013/05/26/what-is-the-uncertainty-in-an-msm

Computational Chemistry, Python, Politics, Policy. What is the uncertainty in an MSM? May 26, 2013. Two major sources of error characterize a Markov state model. The first is the convergence of the dataset - we can only model the processes that we've simulated, in some form or another. When the sampling is insufficient, its not like the MSM can make something out of nothing. This sampling error is hard to model, because we. If we split the dataset in half, are the halves look consistent with one another?

2

Robert's Notebook Archive

http://rmcgibbo.github.io/archives.html

Computational Chemistry, Python, Politics, Policy. Projects in the Pipeline. Faster PyYAML Parsing with LibYAML. What is the uncertainty in an MSM? Next Steps With Swift. Next Steps With Swift. What is the uncertainty in an MSM? Faster PyYAML Parsing with LibYAML. Projects in the Pipeline.

3

Robert's Notebook

http://rmcgibbo.github.io/category/misc.html

Computational Chemistry, Python, Politics, Policy. Next Steps With Swift. Jun 04, 2013. Let's try doing something a little more complicated with swift. Here's my new swift script. Basically, it's going to run a python script on each of a set of input files. Pythonscript; app (. Pythonscript script, File input ). Read On ↵. Jun 03, 2013. Is a parallel scripting language developed at the U. Chicago Computation Institute. It provides a way to manage heterogeneous clusters. I have. Read On ↵. May 26, 2013.

4

Projects in the Pipeline

http://rmcgibbo.github.io/blog/2013/05/23/projects-in-the-pipeline

Computational Chemistry, Python, Politics, Policy. Projects in the Pipeline. May 23, 2013. A few of the projects on my mind right now. Some are father along than others. GBVI: We need to push on this. Currently, not a lot has been done. Optimal-K: At this point, the framework for choosing the optimal number of states, at least under euclidean metrics, is low hanging fruit. Getting this finished and out the door is academic priority number 1. Posted by Robert McGibbon. May 23, 2013. Next Steps With Swift.

5

Faster PyYAML Parsing with LibYAML

http://rmcgibbo.github.io/blog/2013/05/23/faster-yaml-parsing-with-libyaml

Computational Chemistry, Python, Politics, Policy. Faster PyYAML Parsing with LibYAML. May 23, 2013. This morning, Christian. Submitted a great pull request. To speed up YAML parsing in MSMBuilder using LibYAML. In MSMBuilder, we use a YAML file to save the "project", which is keeps the path to all of the files associated with an MSMBuilder project, such as the different trajectories, and a PDB for the protein's topology. Python -c from yaml import CLoader. Wget http:/ pyyaml.org/download/libyaml/yam...

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Robert's Notebook

Computational Chemistry, Python, Politics, Policy. Next Steps With Swift. Jun 04, 2013. Let's try doing something a little more complicated with swift. Here's my new swift script. Basically, it's going to run a python script on each of a set of input files. Pythonscript; app (. Pythonscript script, File input ). Read On ↵. Jun 03, 2013. Is a parallel scripting language developed at the U. Chicago Computation Institute. It provides a way to manage heterogeneous clusters. I have. Read On ↵. May 26, 2013.

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rmcgibbo

Robert T. McGibbon. Robert T. McGibbon. I'm currently a fourth year PhD student in the Department of Chemistry at Stanford University. I work with Vijay Pande. At the intersection of biophysics. On quantitative statistical analysis of protein dynamics via long-timescale physics-based simulation and Markov models. I graduated from Princeton University, where I studied Chemistry and Computer Science. While there, I worked with Andrew Bocarsly. My research at Stanford with Vijay Pande.

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