New Statistical Algorithms for the Analysis of Mass - FU Berlin, FB MI ...

162CHAPTER 6. PROTEOMICS.NET - PRODUCT-ORIENTED CASE STUDIES
29
30 // open t a s k found
31 c h a n g e s t a t e ( ” P r o c e s s i n g Task ID : ” + c u r t a s k I D ) ;
32
33 // p r o c e s s t a s k
34
35 S t r i n g s o u r c e f i l e = params [ 1 ] ;
36 S t r i n g t a r g e t f i l e = s o u r c e f i l e + ” . f i l t e r e d ” ;
37 S t r i n g tophat param = params [ 2 ] ;
38 S t r i n g t a r g e t d i r = params [ 4 ] ;
39
40 S t r i n g cmd = ”/home/ c o c k t a i l / conrad /work/phd/PROTEOMICS WORKER/
41 PROTEOMICSWORKER apply tophat/ UseTopHat ” +
42 s o u r c e f i l e + ” ” + tophat param ;
43
44 exec cmd (cmd ) ;
45
46 . . .
47
48
49 // Move f i l e to new d i r e c t o r y
50 r e s = f s o u r c e . renameTo (new F i l e ( t a r g e t d i r h a n d l e ,
51
52 . . .
6.2.6 Allowing for Easy Creation and Integration of Grid Applications
on the Example of Analyzing Molecular Dynamics
Simulations
Background
The goal of this project was to build a pipeline for dimensionality reduction
and analysis of molecular dynamics simulation data. This is a three step
process:
Import data into the system: To enable access to the data it must be
copied to a temporary directory of this project accessible by the server.
Subsequently, the datasets can be selected for import. This includes extraction
of meta-data (such as structure of the simulated molecule) and
conversion into the “trr” (Gromacs trajectory format) format, which
is used internally. After successful conversion the transformed data is
moved to the project directory and a description, metadata and an ID
is inserted into the database. The ID is necessary to access the data in
further analyses.
Transform data: To prepare the data for analysis it must be converted to
an internal binary format that can be read by the analysis algorithms.
Because an analysis only needs parts of the full dataset this step is not
included in the import process.
Analyze data: The analysis of the transformed data is performed and the
results written to the database.
Since the data is usually quite large (several Gigabytes) it makes perfectly
sense to process many datasets in parallel.