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MDWeb and MDMoby:
MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs).
The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb).
Adam Hospital, Pau Andrio, Carles Fenollosa, Damjan Cicin-Sain, Modesto Orozco, Josep Lluís Gelpí MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics, 2012, 28(9):1278-1279.
Availability: http://mmb.irbbarcelona.org/MDWeb/
MDWeb Setup tutorial:
A complete setup tutorial using MDWeb can be found here:
http://mmb.irbbarcelona.org/MDWeb/help.php?id=tutorial
or here in pdf format :
http://mmb.irbbarcelona.org/MDWeb//htmlib/help/MDWeb_Tutorial.pdf
A complete manual of MDWeb can be found here in pdf format
http://mmb.irbbarcelona.org/MDWeb//htmlib/help/MDWeb_Manual.pdf
All the Web Services and Workflows offered by MDWeb server are also accessible programmatically (see reference paper for more details). In order to ease the installation of the needed libraries (specially BioMoby libraries), we have built a docker container.
MDMoby Docker Container:
We have prepared a docker container to easily install the required libraries and play with MDMoby Workflows. To install a docker engine (if you don’t have it already installed), please go to the docker home page and follow the easy steps explained in Get Started with Docker to install the required software for your specific OS (Mac, Windows or Linux):
https://www.docker.com/
After that, pull the prepared MDMoby docker container:
#!docker docker pull adamhospital/mdmobydocker
To run the docker container, type:
#!docker docker run -it adamhospital/mdmobydocker /bin/bash
Availability: https://hub.docker.com/r/adamhospital/mdmobydocker/
MDMoby Web Services, Workflows and Ontology:
Information about all the WS implemented in MDMoby can be found here:
http://mmb.irbbarcelona.org/MDWeb/help.php?id=ops
Information about all the Workflows implemented in MDMoby can be found here:
http://mmb.irbbarcelona.org/MDWeb/help.php?id=workflows
Information about the MD ontology created to use with MDMoby WSs and Workflows can be found here:
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