transPLANT Cloud Infrastructure

trnsPLANT Cloud

The cloud infrastructure is a virtualization platform, that provides access to specific genomic applications and workflows. It is based on OpenNebula to control the underlying hardware infrastructure. Applications are run in virtual machines that are instantiated dynamically following the requirements of the analysis workflow.

Workflows are defined by the use of COMPSs programming model. COMPSs is able to discover implicit parallelism in the pipelines, and hence, execute otherwise serial operations with an optimal use of a parallel environment. COMPSs workflows can be defined using Java, C++, or Python. COMPSs has been adapted to control the virtualization layer, making it transparent to the user, and also allowing to execute the same workflow in a series of environment, from single workstations, to HPC or grid/cloud facilities. Applications where the use of COMPSs would not be desirable can be also executed in their native environment, exploiting already existing parallelism if any.

Cloud applications

Complex applications are stored in the system as a collection of pre-packed virtual machines that include the application itself and the necessary software environment. Virtual machines developed here are fully compatible with most common cloud infrastructures.
>> Offer of applications

Not only dynamic virtual machines are supported, but also static web based applications, which can take profit of the HPC facilites if they need to perform heavy back-end calculations.

vcf-viewer

Visualizer for variant call format files

URL: 

http://transplantdb.bsc.es/vcf-viewer

lailaps

Integrative search engine for plant genomics data

URL: 

http://transplantdb.bsc.es/lailaps

GWAPP worker

Computational back-end worker for GWAPP,
a GWAS web application

URL: 

http://gwapp.gmi.oeaw.ac.at/


Cloud access

Access to TransPLANT local infrastructures is made accessible through the Programing Model Enacting Service (PMES). The user can interact with the service programmatically, and also via specifically designed web-based tools.

Web based access

DASHBOARD: 

The web based tool offers a user-friendly interface that allows a full control of the infrastructure, and it is useful for managing small analysis and workflows. To obtain an account for the dashboard, please contact us.

URL: 

https://transplantdb.bsc.es/pmes

Guest user: 

guest : gu3st2014

DATA MANAGER: 

The web utility allows to transfer I/O data to the transPLANT cloud via HTTPS. If large transferences are required, accession through alternative vias are available. To consult them, or gain access to the application, please, contact us.

GALAXY: 

The widly used galaxy interface can also query the PMES service though a collection of galaxy tools. The cloud shed installed into our Galaxy server include utilities to transfer user data to the cloud, as well as other PMES applications.

URL: 

http://inb.bsc.es/galaxy/

Guest user: 

inb@bsc.es : gu3st2014

EGI: 

A replica of a the TransPlant Cloud infrastructure is supported by the federated EGI cloud, a public research e-infrastructure composed by a grid of academic private clouds and virtualised resources.

URL:

https://147.228.242.36:8443/pmes/
Replica of TransPlant cloud endorsed by fedcloud.egi.eu

RESOURCE:

https://appdb.egi.eu/store/vappliance/transplant.base
Base image for the TransPlant cloud at EGI marketplace

DOCUMENTATION: 
 

Programmatic Access

PMES offers access to the infrastructure through the Basic Execution Service (BES) web service. To help web services clients to define and submit jobs, a java-based client API is also provided. Here are listed the collection of PMES web-services developed.

>> Web-services

WEB SERVICES REGISTRY: 

The complete list of transplant web services can be found in the registry, which is powered by BioSWR (Bio Semantic Web Registry), a web-based tool that allows users to navigate and search them. Additionally, web services providers can register and annotate their own services, by login into the application. Contact us to gain an access.

URL: 

http://transplantdb.bsc.es/registry

Guest user: 

guest : gu3st2014

DOCUMENTATION: