Blog Archives

A few thoughts on the existing code parallelization

September 17, 2016
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A few weeks ago I worked on some old code parallelization. The whole process made me think about how efficient parallelization of the existing code in R can really be and what should be considered efficient. There is a lot … Continue reading →

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Network visualization – part 5: Cytoscape (an update) – RCy3

August 7, 2016
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Network visualization – part 5: Cytoscape (an update) – RCy3

A few years ago I wrote a series of blogs about network visualization in R (1, 2, 3, and 4), as a mean of keeping organized notes on how to do it for myself but also for (hopefully) helping others … Continue reading →

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Networks, mazes, and R (Rmaze)

July 20, 2016
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Networks, mazes, and R (Rmaze)

Like many people who work with networks (aka graphs), I like to emphasize their usability and applicability to different problems. If some phenomena can be described by its objects and relationships among those objects – well, hello networks. One of … Continue reading →

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One function to run them all… Or just eval

May 15, 2016
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When I was writing a sysBio package, I needed a function that can be customized based on the user specified model. Such function would include user specified variables (parameters, rates, etc.) with assigned values, functions/expression that use those variables, and … Continue reading →

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Modeling in systems biology with R

May 4, 2016
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Modeling in systems biology with R

A couple of years ago, I was interested in a pharmacokinetic/pharmacodynamics (PK/PD) modeling and simulation project developed at the institute where I worked. It seemed that Matlab and its SimBiology toolbox was the tool everybody around me went with. While … Continue reading →

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Network visualization – part 4: 3D networks

September 20, 2013
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Network visualization – part 4: 3D networks

In the fourth and final part of my graph visualization series, I’ll show how to create 3D network plots. 3D plots are more than just pretty plots – they allow you to rotate, scale, and zoom in and out of … Continue reading →

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Network visualization – part 3: Hive plots

September 15, 2013
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Network visualization – part 3: Hive plots

In the third part of “how to quickly visualize networks directly from R” series, I’ll write about the hive plots and “HiveR” package. The concept of hive plots is fundamentally different from the Cytoscape and Gephi plots. Cytoscape and Gephi … Continue reading →

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Network visualization – part 2: Gephi

July 26, 2013
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Network visualization – part 2: Gephi

In the second part of my “how to quickly visualize networks directly from R” series, I’ll discuss how to use R and the “rgexf” package to create network plots in Gephi. Gephi is a great network visualization tool that allows … Continue reading →

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