Wednesday, February 20, 2013

NetGestalt for Data Visualization in the Context of Pathways

Many of you may be familiar with WebGestalt, a wonderful web utility developed by Bing Zhang at Vanderbilt for doing basic gene-set enrichment analyses. Last year, we invited Bing to speak at our annual retreat for the Vanderbilt Graduate Program in Human Genetics, and he did not disappoint! Bing walked us through his new tool called NetGestalt.

NetGestalt provides users with the ability to overlay large-scale experimental data onto biological networks. Data are loaded using continuous and binary tracks that can contain either single or multiple lines of data (called composite tracks). Continuous tracks could be gene expression intensities from microarray data or any other quantitative measure that can be mapped to the genome.  Binary tracks are usually insertion/deletion regions, or called regions like ChIP peaks.  NetGestalt extends many of the features of WebGestalt, including enrichment analysis for modules within a biological network, and provides easy ways to visualize the overlay of multiple tracks with Venn diagrams.

Netgestalt provides a very nice interface for interacting with data. Extensive documentation on how to use it can be found here.  Bing and his colleagues also went the extra mile to create video tutorials on how to use their web tool, and walk you through an analysis of some tumor data.

Tuesday, February 12, 2013

"Document Design and Purpose, Not Mechanics"

If you ever write code for scientific computing (chances are you do if you're here), stop what you're doing and spend 8 minutes reading this open-access paper:

Wilson et al. Best Practices for Scientific Computing. arXiv:1210.0530 (2012). (Direct link to PDF).

The paper makes a number of good points regarding software as a tool just like any other lab equipment: it should be built, validated, and used as carefully as any other physical instrumentation. Yet most scientists who write software are self-taught, and haven't been properly trained in fundamental software development skills. 

The paper outlines ten practices every computational biologist should adopt when writing code for research computing. Most of these are the usual suspects that you'd probably guess - using version control, workflow management, writing good documentation, modularizing code into functions, unit testing, agile development, etc. One that particularly jumped out at me was the recommendation to document design and purpose, not mechanics. 

We all know that good comments and documentation is critical for code reproducibility and maintenance, but inline documentation that recapitulates the code is hardly useful. Instead, we should aim to document the underlying ideas, interface, and reasons, not the implementation.

For example, the following commentary is hardly useful:

# Increment the variable "i" by one.
i = i+1

The real recommendation here is that if your code requires such substantial documentation of the actual implementation to be understandable, it's better to spend the time rewriting the code rather than writing a lengthy description of what it does. I'm very guilty of doing this with R code, nesting multiple levels of functions and vector operations:

# It would take a paragraph to explain what this is doing.
# Better to break up into multiple lines of code.
sapply(data.frame(n=sapply(x, function(d) sum(, function(dd) mean(dd))

It would take much more time to properly document what this is doing than it would take to split the operation into manageable chunks over multiple lines such that the code no longer needs an explanation. We're not playing code golf here - using fewer lines doesn't make you a better programmer.

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Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.