[Proteopedia] Website back online!

Thu Apr 2 19:20:55 EDT 2009

2009/4/2 Eran Hodis <eran.hodis at weizmann.ac.il>:
> Dear Dan,
>
> You wrote:
> "Great news that the site is back up. w.r.t the above, how do you
> intend to fix the problems? Will you manually update each script, or
> has the PDB provided a computer readable list of changes? I'm curious
> to know because this update is affecting 1000's of PDB users."
>
> Eric helpfully suggested several solutions to the problem. Jaim and I met today to discuss the issue and decided the best way to fix the problem of the old scripts not working will be to download any un-remediated files (from the PDB snapshot) that those scripts use, and store them locally, and have the old scripts refer to them. In the case of new scripts, to avoid problems with future PDB updates, Proteopedia will begin to locally save the PDB files that our (your) scripts use.
>
> No need to update the scripts manually, we can do this automatically.

Right, sounds like an ideal solution given the circumstances. I'm
baffled as to why the PDB apparently can't even produce a list of
which files have changed, never mind specifically how they may have
changed.

All the best,
Dan.

> Eran
>
> -----Original Message-----
> From Dan Bolser <dan.bolser at gmail.com>
> Sent Thu 4/2/2009 6:50 PM
> To Forum for the Proteopedia User Community <proteopedialist-for-users at bioinformatics.org>
> Cc eran.hodis at weizmann.ac.il
> Subject Re: [Proteopedia] Website back online!
>
> 2009/4/2 Eran Hodis <eran.hodis at weizmann.ac.il>:
>> Update (April 2 2009)
>>
>> The Proteopedia website is now back up and fully functional! Thank you again
>> for your patience.
>>
>> Our sincere apologies for any inconvenience the delays in the upgrade
>> process may have caused. It is very important to us that such a period of
>> protracted downtime never occurs again.
>>
>> You'll find a yellow notice at the top of each page in Proteopedia
>> indicating that the website is back up and functional -- this is to alert
>> users that may not be on the mailing list that the website is back to a
>> functional state. We'll remove the banner in a day or so.
>>
>> You'll also notice, when logged in, a grey banner indicating that some
>> scenes, in particular those with DNA, are not displaying correctly.  This is
>> due to the recent remediation of the PDB database, and will be fixed soon
>> (hopefully within one week).
>
> Great news that the site is back up. w.r.t the above, how do you
> intend to fix the problems? Will you manually update each script, or
> has the PDB provided a computer readable list of changes? I'm curious
> to know because this update is affecting 1000's of PDB users.
>
>
>>
>> Best regards,
>>
>> Eran
>>
>> On Apr 2, 2009, at 1:18 AM, Eran Hodis wrote:
>>
>>> Update (April 1 2009):
>>>
>>> The upgrade process is not going smoothly, as I'm sure you've noticed by
>>> now. We really apologize for these delays, and are doing our best to
>>> finish the upgrade.
>>>
>>> We know that the website is running very slowly at the moment -- please
>>> bear with us.
>>>
>>> Eran
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>> Update (March 31 2009):
>>>>
>>>> Thank you again for your patience. The upgrade is progressing but is
>>>> taking longer than expected due to a small mix-up in the upgrade process.
>>>>
>>>> Again, the Proteopedia website is accessible for viewing, but not editing
>>>> -- however due to the upgrade process it may load a bit slowly.
>>>>
>>>> We hope to have the upgraded website up and running by tomorrow morning
>>>> (Israel time). Should we encounter more difficulties, (let's hope not!)
>>>> we
>>>> will let you know here.
>>>>
>>>> Eran
>>>>
>>>>
>>>> -----Original Message-----
>>>>>
>>>>> From Eran Hodis <eran.hodis at weizmann.ac.il>
>>>>
>>>> Sent Mon 3/30/2009 4:05 PM
>>>> To Forum for the Proteopedia User Community
>>>> <proteopedialist-for-users at bioinformatics.org>
>>>> Subject [Proteopedia] UPDATE : Re:  Temporary Read-only Database
>>>>
>>>> Update:
>>>>
>>>> The Proteopedia website is now accessible, with the ability to edit
>>>> pages temporarily disabled.  (Previously the website was completely
>>>> down.)
>>>>
>>>> The upgrade of Proteopedia's storage capacities is proceeding as
>>>> planned, and we expect to allow editing on the website either by later
>>>> tonight (Israel time) or early tomorrow morning (also Israel time).
>>>>
>>>> We will update you with an email to this mailing list. Thanks again
>>>> for your patience!
>>>>
>>>> Eran
>>>>
>>>>
>>>> On Mar 30, 2009, at 12:47 PM, Eran Hodis wrote:
>>>>
>>>>> Hi Everyone,
>>>>>
>>>>> As Jaim mentioned in the previous email, below, today we are
>>>>> upgrading Proteopedia's storage capacities.
>>>>>
>>>>> We had expected access to Proteopedia to continue unaffected, with
>>>>> the ability to edit pages temporarily disabled.
>>>>>
>>>>> However, due to some unforeseen issues, the Proteopedia website is
>>>>> currently not accessible. This should be fixed shortly as the
>>>>> upgrade process is completed. We will update you with an email to
>>>>> this mailing list.  Thanks for your patience!
>>>>>
>>>>> Best,
>>>>> Eran
>>>>>
>>>>> On Mar 29, 2009, at 7:50 AM, Jaime.Prilusky at weizmann.ac.il wrote:
>>>>>
>>>>>> Dear All,
>>>>>>
>>>>>> This Monday March 30th, we'll upgrade Proteopedia's storage.
>>>>>>
>>>>>> During the process, access to Proteopedia will be read-only, it will
>>>>>> not be possible to create or edit pages, but searching and displaying
>>>>>> pages will remain unaffected.
>>>>>>
>>>>>> Jaim
>>>>>> --
>>>>>> Dr Jaime Prilusky                      |
>>>>>> Jaime.Prilusky at weizmann.ac.il
>>>>>> Head Bioinformatics                    |
>>>>>> R&D Bioinformatics and Data Management |
>>>>>> Department of Biological Services      |
>>>>>> Weizmann Institute of Science          | fax: 972-8-9344113
>>>>>> 76100 Rehovot - Israel                 | tel: 972-8-9344959
>>>>>>
>>>>>> OCA, http://oca.weizmann.ac.il (the protein structure/function
>>>>>> database)
>>>>>> Proteopedia, http://proteopedia.org (because life has more than 2D)
>>>>>>
>>>>>> ------------------------------------------------------------------------
>>>>>>
>>>>>> _______________________________________________
>>>>>> Proteopedialist-for-users mailing list
>>>>>> Proteopedialist-for-users at bioinformatics.org
>>>>>>
>>>>>> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users
>>>>>
>>>>> Eran Hodis
>>>>> eran.hodis at weizmann.ac.il
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Proteopedialist-for-users mailing list
>>>>> Proteopedialist-for-users at bioinformatics.org
>>>>> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users
>>>>
>>>> Eran Hodis
>>>> eran.hodis at weizmann.ac.il
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Proteopedialist-for-users mailing list
>>>> Proteopedialist-for-users at bioinformatics.org
>>>> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users
>>>>
>>>>
>>>> _______________________________________________
>>>> Proteopedialist-for-users mailing list
>>>> Proteopedialist-for-users at bioinformatics.org
>>>> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users
>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Proteopedialist-for-users mailing list
>>> Proteopedialist-for-users at bioinformatics.org
>>> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users
>>
>> Eran Hodis
>> eran.hodis at weizmann.ac.il
>>
>>
>>
>>
>> _______________________________________________
>> Proteopedialist-for-users mailing list
>> Proteopedialist-for-users at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users
>>
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