Compute platform

MuGVRE Compute Platform is a virtualization platform (adapted from TransPLANT European project), 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.

transPlantCloudschema

 

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.


 
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.

 

BigNASim
Database structure and analysis portal for nucleic acids simulation data.
Nucleosome Dynamics
Perform and visualize nucleosome-related analysis based on MNase-seq experimental data.
TADbit
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data.
TADkit 3D
3D representations of chromatin conformations modeled from 3C-based interaction matrices.
Flexibility Browser
Description of the structure and flexibility of DNA, as a function of its local tetranucleotide sequence.
Genome Browser

Select reference genome:

 
 

Cloud access

 

Access to MuGVRE 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.
 

LINK:
Click here to access the Dashboard
Guest user:
guest : gu3st2014

 

DATA MANAGER:

The web utility allows to transfer I/O data to the MuGVRE 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.
 

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