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[bioontology-support] Bioportal installation

Paul R Alexander palexander at stanford.edu
Tue Aug 21 10:53:01 PDT 2012


Konstantinos,

The instructions you refer to are over two years old from before we had 
the Appliance available and should be mainly replicated in the docs that 
are included in the respective codebases.

Because of the diverse infrastructure requirements and various 
codebases, we've found that using the Appliance is simpler that 
installing the code in every case. So long as your CPU supports 64bit 
instructions, running the Appliance from virtualization software like 
VirtualBox or VMWare should work.

If you cannot find a machine to run the Appliance on, we also have a 
version that runs on Amazon's EC2.

Paul


On 8/21/12 2:11 AM, Konstantinos Giannoutakis wrote:
> Hi,
>
> I was thinking of installing the software without the use of the 
> Appliance, since I encounter problems as described in my previous 
> email. I will try installing the Appliance on another PC...
>
> By the way, I saw in this thread
>
> https://mailman.stanford.edu/pipermail/bioontology-support/2010-June/002010.html
>
> some wiki pages with installation details (like 
> http://www.bioontology.org/wiki-internal/index.php/How_to_install_Bioportal#Install_the_bioportal_admin_application_.28optional.29), 
> how can I gain access to this internal wiki?
>
> Thank you very much for your support so far!!!
>
>
> On 21/8/2012 3:51 ??, Paul R Alexander wrote:
>> Konstantinos,
>>
>> We don't support installing the software without the use of our 
>> Appliance. However, the all of NCBO's software is open source so you 
>> can definitely give it a shot. Here's information on the main pieces 
>> of software that we write. You'll also need Tomcat, Ruby, Rails, 
>> MySQL, and 4store.
>>
>> https://bmir-gforge.stanford.edu/gf/project/bioportal_core/scmsvn/?action=AccessInfo
>> https://bmir-gforge.stanford.edu/gf/project/bioportalui/scmsvn/?action=AccessInfo
>> https://bmir-gforge.stanford.edu/gf/project/obs/scmsvn/?action=AccessInfo
>>
>> There should be some documentation in the /docs/ folder of each 
>> repository.
>>
>> Paul R Alexander
>> Senior Software Engineer
>> NCBO BioPortal
>> Stanford Center for Biomedical Informatics Research
>>
>>
>> On 8/20/12 5:56 AM, Konstantinos Giannoutakis wrote:
>>> Hi again,
>>>
>>> I downloaded the file from the page you mentioned, and tried to open 
>>> the .ovf file with VirtualBox manager, but when it starts the 
>>> following error appears:
>>>
>>> This kernel requires an x86-64 CPU, but only detected an i686 CPU.
>>> Unable to boot - please use a kernel appropriate for your CPU.
>>>
>>>
>>> My CPU is an Intel i5.
>>>
>>> Is there any way to install manually the bioportal framework on a PC 
>>> without using ready images?
>>>
>>> Thank you
>>>
>>>
>>> On 17/8/2012 6:52 ??, Trish Whetzel wrote:
>>>> Certainly! The page at: 
>>>> http://bioportal.bioontology.org/virtual_appliance has links for 
>>>> the download as well as links for documentation on installing and 
>>>> working with the Appliance. If you have any questions about the 
>>>> install, please either review the support archives or email 
>>>> support at bioontology.org <mailto:support at bioontology.org>.
>>>>
>>>> For our record keeping, can you tell us a bit about the reason for 
>>>> requesting the Virtual Appliance? For example, do you plan to use 
>>>> the Appliance for ontologies outside of the biomedical domain or do 
>>>> you plan to use the Annotator for private/proprietary data?
>>>>
>>>> Thanks!
>>>> Trish
>>>>
>>>>
>>>> On Aug 17, 2012, at 12:18 AM, Konstantinos Giannoutakis wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> My username in BioPortal is "kgiannou". Thank you very much!!!
>>>>>
>>>>> Best regards
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 16/8/2012 8:01 ??, Trish Whetzel wrote:
>>>>>> Please send me your BioPortal username. We can then provide this 
>>>>>> account access the download page.
>>>>>>
>>>>>> Trish
>>>>>>
>>>>>>
>>>>>> Trish Whetzel, PhD
>>>>>> Outreach Coordinator
>>>>>> The National Center for Biomedical Ontology
>>>>>> Ph: 650-721-2378
>>>>>> http://www.bioontology.org <http://www.bioontology.org/>
>>>>>>
>>>>>> "Like" NCBO on Facebook: http://on.fb.me/bioontology
>>>>>>
>>>>>> Follow NCBO on Twitter: http://twitter.com/#!/bioontology 
>>>>>> <http://twitter.com/#%21/bioontology>
>>>>>>
>>>>>> Join in Discussions on LinkedIn: http://linkd.in/ncbo-group
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Aug 16, 2012, at 7:23 AM, Konstantinos Giannoutakis wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I am willing to install Bioportal in my local machine, thus I 
>>>>>>> would like to ask you for a "Virtual Appliance" as stated in the 
>>>>>>> page:
>>>>>>> http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance
>>>>>>>
>>>>>>> Thank you very much!
>>>>>>>
>>>>>>> -- 
>>>>>>> Konstantinos Giannoutakis, PhD
>>>>>>> Research Associate
>>>>>>> Informatics and Telematics Institute
>>>>>>> Centre for Research and Technology Hellas
>>>>>>> 6th Km Charilaou-Thermi Road
>>>>>>> GR 57001
>>>>>>> Thermi, Thessaloniki, Greece
>>>>>>> www.iti.gr/~kgiannou
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> bioontology-support mailing list
>>>>>>> bioontology-support at lists.stanford.edu
>>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>
>

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