The workflows that were designed for this purpose have been submitted to a workflow repository at http://www.myexperiment.org/packs/319.html[ 15].
The proteins were submitted to an annotation workflow that included HMM-based annotations from InterPro, SMART, PRINT, Prosite and Pfam.
These were submitted to the MHOLline workflow http://www.mholline.lncc.br to construct 3D protein structure models by comparative modelling.
This non redundant dataset of T. cruzi was submitted to the MHOLline workflow to construct the 3D protein models.
Afterwards, these sequences were submitted to the MHOLline workflow and we were able to construct models for 3,286 sequences (26.6% of the total).
Assembled reads with homology to viral hits in the taxonomic analyses were submitted to the RAMMCAP workflow against the PFAM, TIGRFAM, and COGs databases, which is implemented in CAMERA, with an expected E value of <10−3 to assign a functional annotation to the reads.
In several cases, the workflow submitted to Track II described only a specific slice of a larger curation process, so that the full curation process for some of these databases (MGI, in particular) may be considerably broader than what is captured in Table 4. Generally speaking, MODs report that most papers contain all the information needed for making annotations.
Workflow-as-a-service: Multiple workflow instances submitted to the resource manager.
For analysis with MetaCore, the gene list of proteins found to be up-regulated in the mouse plasma and secreted/shed in mouse and human cancer cell lines (total of 58 genes) was submitted to an enrichment and network workflow.
After the analysis customization, the workflow can be submitted to the queue system.
Alternatively, WINGS can generate execution-ready workflows that can be submitted to either Apache OODT [ 39] or the Pegasus/Condor execution engine [ 40], which are designed for large-scale distributed data processing in a variety of environments, such as local clusters, shared infrastructure, or cloud resources.
