Comparing data structure enumeration speeds in C#
Determining which data structure to use for storing data involves trade-offs between how much memory they require and how long different operations, such as insertions, deletions, or searches take. In...
View ArticleHow to remove the “Trial Edition” banner from the VisiFire open source chart kit
Visifire is a very good graphing component for making silverlight or WPF applications. The component was first released as an open source library on GoogleCode, but since then has been made a closed...
View ArticleSoftware Patents
In the dark moments when one wonders if their research is doing enough to better the world, it’s always nice to remember you’re not a patent lawyer. The radio program This American Life did a...
View ArticleJava vs. C# Performance Comparison for Parsing VCF Files
Making a comparison with a reasonably complex program ported between the two languages. Update 3/10/2014: After writing this post I changed the C# parser to remove an extra List<> allocation in...
View ArticleAccessing dbSNP with C# and the .NET Platform
NCBI Entrez can be accessed with many different platforms (python, R, etc.) , but I find .NET one of the best because the static typing makes it easy to infer what all the datafields mean, and navigate...
View ArticleMono.Simd and the Mandlebrot Set.
C# and .NET are some of the fastest high level languages, but still cannot truly compete with C/C++ for low level speed, and C# code can be anywhere from 20%-300% slower. This is despite the fact that...
View ArticleUsing Selectome with .NET Bio, F# and R
The Bio.Selectome namespace has features to query Selectome.Selectome is a database that merges data from Ensembl and the programs in PAML used to compute the ratio of non-synonymous to synonymous...
View ArticleThe .NET Bio BAM Parser is Smoking Fast
The .NET Bio library has an improved version of it’s BAM file parser, which makes it significantly faster and easily competitive with the current standard C coded SAMTools for obtaining sequencing data...
View ArticleNuMTs, mtDNA sequencing and Aligners
There are a lot of NuMTs (nuclear encoded mitochondrial sequences) in the genome, and when the mtDNA is sequenced, so reads may align to the nuclear genome instead of the mtDNA because of this. But...
View ArticleC# vs. Java, Xamarin vs. Oracle, Performance Comparison version 2.0
Today I noticed the SIMD implementation of the Mandelbrot set algorithm I blogged about last year was successfully submitted to the language shootout webpage. However, I was a bit disappointed to see...
View ArticleProfiling Rcpp package code on Windows
Profiling Rcpp code on Unix/Mac is easy, but is difficult on Windows because R uses a compilation toolchain (MinGW) that produces files that are not understood by common Windows profiling programs....
View ArticleWhy R Math Functions on Windows are Slow, and How to Fix It
R on windows has much slower versions of the log, sine and cosine functions than are available on other platforms, and this can be a serious performance bottleneck for programs which frequently call...
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.NET Bio is Significantly Faster on .Net Core 2.0
Summary: With the release of .NET Core 2.0, .NET Bio is able to run significantly faster (~2X) on Mac OSX due to better compilation and memory mangement. The .NET Bio library contains libraries for...
View ArticleHow to Decompile / Reverse Engineer PyInstaller Binaries
Sharing Python programs is a pain, and one solution to this problem is to package up all of the python code, the interpreter and the dependencies into an executable for distribution. PyInstaller is a...
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