A highly optimized grid deployment: the metagenomic analysis example.
Computational resources and computationally expensive processes are two topics that are not growing at the same ratio. The availability of large amounts of computing resources in Grid infrastructures does not mean that efficiency is not an important issue. It is necessary to analyze the whole process to improve partitioning and submission schemas, especially in the most critical experiments. This is the case of metagenomic analysis, and this text shows the work done in order to optimize a Grid deployment, which has led to a reduction of the response time and the failure rates. Metagenomic studies aim at processing samples of multiple specimens to extract the genes and proteins that belong to the different species. In many cases, the sequencing of the DNA of many microorganisms is hindered by the impossibility of growing significant samples of isolated specimens. Many bacteria cannot survive alone, and require the interaction with other organisms. In such cases, the information of the DNA available belongs to different kinds of organisms. One important stage in Metagenomic analysis consists on the extraction of fragments followed by the comparison and analysis of their function stage. By the comparison to existing chains, whose function is well known, fragments can be classified. This process is computationally intensive and requires of several iterations of alignment and phylogeny classification steps. Source samples reach several millions of sequences, which could reach up to thousands of nucleotides each. These sequences are compared to a selected part of the "Non-redundant" database which only implies the information from eukaryotic species. From this first analysis, a refining process is performed and alignment analysis is restarted from the results. This process implies several CPU years. The article describes and analyzes the difficulties to fragment, automate and check the above operations in current Grid production environments. This environment has been tuned-up from an experimental study which has tested the most efficient and reliable resources, the optimal job size, and the data transference and database reindexation overhead. The environment should re-submit faulty jobs, detect endless tasks and ensure that the results are correctly retrieved and workflow synchronised. The paper will give an outline on the structure of the system, and the preparation steps performed to deal with this experiment.
Aparicio
Gabriel
G
Universidad Politécnica de Valencia - ITACA. gaparicio@itaca.upv.es
Blanquer
Ignacio
I
Hernández
Vicente
V
D019295:Computational Biology; D003201:Computers; D003205:Computing Methodologies; D003628:Database Management Systems / Q000458:organization & administration*; D030541:Databases, Genetic; D023281:Genomics / Q000458:organization & administration*; D014943:Global Health; D006801:Humans; D016347:Medical Records Systems, Computerized / Q000458:organization & administration*; D017422:Sequence Analysis, DNA; D012984:Software; D013030:Spain; D014584:User-Computer Interface