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The interface for creating such an intermediate result file is implemented into WPS [4] and described in a separate manuscript (Yi and Stephens unpublished work).
The data file is implemented very simply using the sparse file feature of Linux and most other UNIX-like operating systems.
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Subsequently, first-pass quality control and genotype calling from the raw data in the form of CEL files were implemented with Affymetrix Power Tools v1.16.0 (APT) software using the Axiom GT1 algorithm.
A file system called Hybrid Memory File System (HMFS) is implemented based on this framework.
When using USB or Bluetooth link, a file transfer protocol is implemented which sends at first the filename, then the file size, and then its data bytes.
Although computing capabilities of nodes are a significant performance factor, each node also needs the capability to read and write large amounts of data to and from the distributed file system that is implemented on remote nodes.
The command lines used to run these tools are listed at the end of the Additional file 1. MOST+ is implemented in C++.
Functional classification of the Clusters of Orthologous Groups (COGs) (Additional file 1: Figure S3, Additional file 3: File S5) was implemented to identify orthologous protein sets [ 49].
The cache is implemented using two files for each file that is cached: a bitmap file that has a bit set for each file block in cache and a data file that contains the actual blocks of data.
R libraries of the probe and CDF packages, and annotation of the remapped probe sets are provided in Additional File 3. The probe remapping protocol is implemented in a Perl script, and provided in Additional File 4. Exlink, the gene definition proposed by Ensembl was used in the study in order to organize transcripts from multiple databases [ 6].
While the parsing of the KGML pathway files to produce adjacency matrices is implemented in R, the integral linear program (LP) that optimizes grid arrangements is written in C++, using CPLEX (ILOG, Gentilly, France) as an LP solver.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com