Information

Install BioSimSpace

Currently there are two options for installing BioSimSpace: 1) Download and run a docker container docker run chryswoods/biosimspace 2) Automatic installer For Linux and macOS there is an automatic installer script available here. This will download, install, and configure a clean BioSimSpace application. With a decent network connection, the full installation process should take around...

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Getting Started

This page describes how to get started with BioSimSpace after it has been installed. It will walk you through a simple "Hello World" style example, showing how to use a BioSimSpace workflow component from both the command line and from within the Knime workflow engine.

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Citing BioSimSpace

This page suggest how you should cite your use of BioSimSpace. I am very keen that we generate the citation information automatically from the workflow component, e.g. "component --get-citation" should return the full citation list of the BioSimSpace together with all of the software used by that component. I am a strong supporter of correct...

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Software and Dependencies

This page will list and link to all of the software dependencies of BioSimSpace, including linking to their licenses and places where their source can be downloaded. This is both necessary to comply with license terms, and also good community practice to ensure that we can advertise all of the other projects on which we...

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Interoperable

BioSimSpace is designed to make it easy to interoperate between different molecular simulation packages. Indeed, interoperability is BioSimSpace's reason to exist. To achieve this, BioSimSpace has an advanced internal representation of molecular information, together with a wide support for a range of molecular file formats. This enables BioSimSpace to automatically translate a file from one...

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Interactive

BioSimSpace can be used in many different environments, e.g. from the command line, within a workflow engine such as Knime, and also interactively in a online Jupyter notebook. Information about the Jupyter notebooks.

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Open Source

BioSimSpace is Open Source, with most components released under the GPL license. Something more about the licensing... BioSimSpace relies on lots of different pieces of software to work. More information about these, and their licenses is available here.

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About this website

This website is hosted on the Microsoft Azure Cloud in the Azure Kubernetes Service. The website uses Kubernetes to autoscale a Wordpress / Bitnami MariaDB installation that was installed from the Kubeapps Helm Chart. The free Allegiant theme from CPO Themes provides the base styling. All graphics were produced via either molecule renders produced using VMD,...

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