Speaker
Describe the added value of the Grid for the scientific/technical activity you (plan to) do on the Grid. This should include the scale of the activity and of the potential user community and the relevance for other scientific or business applications
The availability of a collection of evolutionary conserved sequences among different
organisms could be of great importance for scientific community for the functional
annotation of genomes and for the identification of regulatory elements.
Given the reliability and sensitivity of CSTminer software it would be very useful to
perform genome wide comparisons of several genomes. Unfortunately given the
complexity of CSTminer alignment step and the size of the genomes (3 and 2.6 Gbp for
Human and Mouse genomes respectively) it would be impossible to carry out such
analysis even on very powerful servers.
This is the reason why we exploited the possibility to use the EGEE infrastructure
and the power of a Grid approach.
Report on the experience (or the proposed activity). It would be very important to mention key services which are essential for the success of your activity on the EGEE infrastructure.
In order to have a more efficient jobs we grouped together a lot of comparison (about
1000), in this way we can reduce the overhead do to files transfer and environment
setting-up.
We have developed a job submission tool (JST) that allows the submission of large
number of jobs in an almost unattended way. It is based on the concept of “task” to
be executed. Only if all steps are correctly executed, the status of that particular
task on the central DB is updated to “Done”. In this way the central DB provides a
monitoring of the task execution and no manual intervention is required to manage the
resubmission of the failed tasks.
The most important services needed in order to run this application is WMS in order
to submit jobs optimizing the utilization of each resource available.
We also exploit successfully the data transport services using gsiftp in order to
copy files both for input and output.
With a forward look to future evolution, discuss the issues you have encountered (or that you expect) in using the EGEE infrastructure. Wherever possible, point out the experience limitations (both in terms of existing services or missing functionality)
We can foresee to build a web interface in which the user can easily submit its own
comparison with between a given genome and a new one (provided by the user itself).
In this way this application can be established as a service for the user even if not
expert of the EGEE infrastructure.
Describe the scientific/technical community and the scientific/technical activity using (planning to use) the EGEE infrastructure. A high-level description is needed (neither a detailed specialist report nor a list of references).
One of the major task of genomic analysis is the identification of genes and
regulatory elements of gene expression. Among the different methods used to solve
this task, comparative analysis have shown their strength and reliability.
CSTminer is a comparative analysis tool developed to compare two or more sequences to
identify conserved sequences and to classify them as coding (likely genes) or
non-coding (potential regulatory regions) upon the computation of a coding potential
score (CPS).
