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[bioontology-support] NCBO Virtual Appliance download. Future: Vagrant? Docker?

John Graybeal jgraybeal at stanford.edu
Mon Mar 6 14:00:40 PST 2017


Hi Rafael,

Re (1), I'm corresponding separately to get the information we need.

Re (2), I want to make sure we start from the same understanding. I reference Paul Alexander's helpful input yesterday, which I think addresses the *mechanical* aspect of your request:

I think the description on the wiki is a little misleading. The actual VM distribution is done using OVF, which allows the VM to be used in VirtualBox, VMWare, Xen, KVM, etc. There are instructions for each of these here:
https://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_use_the_OVF_image_with_my_virtualization_software.3F_.28VMware.2C_VirtualBox.2C_KVM.2C_Xen.2C_etc.29

VirtualBox is a direct import without any modifications needed. Other platforms need to convert the file and set configuration as appropriate.

Your question here also emphasizes the currency of the system—"an automated  (i.e. always-up-to-date) VM creation mechanism". I'll discuss this with the team of course, as it is definitely a desirable target. I know there are likely to be a lot of technical challenges (perhaps Vagrant will be a helpful technology to help us solve them).

One example is that our internal deployment processes evolve over time to make best use of our 20-odd machine instances that support the many facets of BioPortal, with its latest re-factorings and optimizations. A second issue is that must support an extensive collection of plug-in libraries and software languages, which often add a special challenge to the deployment scenario.

That said, we'll have a look at the options going forward. Can you help make the case for your favored approach(es), say Vagrant vs Docker vs OVF?

John



On Mar 4, 2017, at 11:40 AM, Rafael Richards <rmrich5 at gmail.com<mailto:rmrich5 at gmail.com>> wrote:

Re:  https://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance


Dear Bioportal team,


1. Could you send the link to download and run the VCBO  VM?

2. Are you planning to migrate to an automated  (i.e. always-up-to-date) VM creation mechanism such as Vagrant?


Thank you.


Rafael Richards MD MS
202-469-1527

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research



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