Welcome to Panorama support 

Welcome to the Panorama support forum. If you have a question about using Panorama, or if you encounter a problem, you can post your questions here.

Support is provided by the creators of the software, as time allows, though we hope others will share their experience as the user community grows.

In order to post to the forum, you'll need to sign up for an account. If you already have an account but have forgotten your password, you can reset your password using the "Forgot your password?" link on the Sign-in page.

When you post a question, please include the following information:

  • A detailed description of your problem or question, including instructions for re-creating any problem that you are encountering
  • The web-browser you were using when you encountered the problem
  • If the problem occurred while publishing a document through Skyline please include the version of the Skyline software you were using, your operating system, and any other information that may help us to answer the question

If you are including text output from a tool, please attach files to your message, rather than pasting in long text.

 

You can also sign up to request a project on PanoramaWeb.


Messages 
Showing: all messages
set password does nothing
Tobias Kockmann 2017-07-20
Hi there,

I am trying to set a pw for a new user, but nothing happens after hitting the return key. Who should I contact?

A more general question: We are using autoQC and during the test phase all uploading of data was done using my personal account. Now, I would like to release the system to the whole group. Which user status is required for

- uploading data to autoQC folders?
- adding annotations/guide sets?
- viewing the data

Greetings,
Tobi
view message
Upload error
(3 responses) phains 2017-07-18
Hi,

I am having similar issues to those already described. First off, I'm using LabKey 17.2 (just upgraded, but the issues were occurring with the prior version), AutoQC is V 1.1.0.10626 and Skyline is V3.7.0.10940, all 64-bit, Win 10 for AutoQC and Skyline or Win server 2012 for LabKey.

All my current AutoQC methods are working fine. These were made sometime ago with an earlier version of Skyline. The problem occurs when I try to make a NEW AutoQC config. I opened up one of my working methods, saved the Skyline file using the latest version of Skyline and now it does not work.

The symptoms: When I start the config in AutoQC it does not make an AutoQC.log file. If I make one manually this part then works fine. The file are imported in to Skyline but the Panorama upload fails.

The AutoQC log and Panorama log are attached.

By the way, we still have the issue with AutoQC giving up the ghost every few days when monitoring network drives. It’s annoying, but we just stop the config and start it again...

Thanks,

Peter
 AutoQC.log  Panorama.log 
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Skyline 3.7 Support
(3 responses) mdowns2 2017-06-14
Hi Panorama Team,

I've just recently updated to Skyline 3.7, and I'm unable to import data to a QC folder on Panorama. (See error messages below.)

Do you know when Skyline 3.7 files will be supported in the QC folders? Or is there some other issue going on?


Thanks,
Melanie Downs



14 Jun 2017 15:17:10,169 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
14 Jun 2017 15:17:10,172 INFO : Starting to import Skyline document from 2017-05-05_P6P_PRM-3_2017-06-14_17-14-51.sky.zip
14 Jun 2017 15:17:10,172 INFO : Expanding 2016_09_07_6ProteinDigest.blib
14 Jun 2017 15:17:10,174 INFO : Expanding 2016_09_07_6ProteinDigest.redundant.blib
14 Jun 2017 15:17:10,186 INFO : Expanding 2017-05-05_P6P_PRM-3.skyd
14 Jun 2017 15:17:10,953 INFO : Expanding 2017-05-05_P6P_PRM-3.sky.view
14 Jun 2017 15:17:10,953 INFO : Expanding 2017-05-05_P6P_PRM-3.sky
14 Jun 2017 15:17:10,973 WARN : The version of this Skyline document is 3.7. This is newer than the highest supported version 3.6
14 Jun 2017 15:17:11,033 INFO : Updating previously imported data for sample file F:\RawDataQE\20161215_P6P.raw in QC folder.
14 Jun 2017 15:17:11,157 INFO : Inserting sp|P02769|ALBU_BOVIN
14 Jun 2017 15:17:12,951 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
14 Jun 2017 15:17:12,952 ERROR: Uncaught exception in PipelineJob: (DONE) Skyline document import - 2017-05-05_P6P_PRM-3_2017-06-14_17-14-51.sky.zip
org.postgresql.util.PSQLException: ERROR: insert or update on table "generalmoleculechrominfo" violates foreign key constraint "fk_gmchrominfo_samplefile"
  Detail: Key (samplefileid)=(375166) is not present in table "samplefile".
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Signal Data Module on PanaramaWeb
(1 response) Jim Collett 2017-05-08
Would it be possible for the PanoramaWeb admin team to install to the LabKey Signal Data Module on PanoramaWeb?

https://labkey.org/Documentation/wiki-page.view?name=signalData
https://github.com/LabKey/signalData

Thanks,

Jim
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Feature Request - Manual Reference Ranges
(1 response) Will Thompson 2017-04-18
Hi Skyline Panorama Team,

We have been using AutoQC for a few years now (wow time flies!) and we have noticed that the most difficult portion of using the tool in practical 'go/no go' decisions is defining the "guide set" of runs. This is because it is very difficult to find a set of runs which have enough variation for all the metrics, without having too much variation for any of them, to properly capture the reference range. A good example would be retention time; If you perform 5 injections on 5 separate days, while running samples, you might get a good handle on most of the metrics for AutoQC. However if you are using commercial columns the retention time may be extremely tight within that window (say <15-30 seconds variability) which is too narrow to accommodate a column change or larger drifts over time, which may be somewhere in the neighborhood of +/- 1 minute. If we then start using larger sets of runs for guide sets, it is very difficult to find a set of runs over weeks or maybe even a month, which do not contain a single outlier for any of the metrics (and we in theory would not want to have outliers in the 'guide set'). Additionally, some metrics (such as mass accuracy) would make sense to have an 'absolute' cutoff window as opposed to a guide set in any case; for instance, we want all ions to have standard deviation of +/- 1.5 ppm. Allowing the user to utilize historical data to manually set a range for each metric may be more time-consuming for the user to set up, but it would perhaps lead to more accurate go/no go decisions. Another (slightly less appealing) option might be to still use the software to establish a 'guide set', but allow the user to exclude specific runs from specific individual metrics.

Thanks

Will
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No upload to Panorama from AutoQC
(6 responses) michael plank 2017-04-12
Hi all,
I`m trying to use AutoQC, but the data do not end up on Panorama. I`m wondering if you might have a look at my settings if I`m getting anything wrong: Screenshots attached.
I set the 'Expected acquisition duration' short, as the files are not written to the folder by the instrument, but I copy-paste them there.

AutoQC says "running", already for several hours on this configuration.
Panorama says "
20170410_RapMock2nd_1
No sample files imported"

I`m also attaching a copy of today`s log entries.


Thanks a lot for your help.
Michael
 sc1.png  sc2.png  20170411_todaysLog.txt 
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log file does not exist
(5 responses) n wildburger 2017-04-09
Hi

I keep getting an error message "log file does not exist" when ever I try to start AutoQC after building a configuration.

I have never seen this error before, and the is not the first time I have installed AutoQC on a system before granted this is an older computer.

Thanks,

Norelle
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Panorama AutoQC not updating since 3/1
(2 responses) Will Thompson 2017-03-24
Hi Vagisha and team,

We have an issue with the most recent results not showing up in Panorama folder /Duke Proteomics Core/QC. Since 3/1, the AutoQC Loader on the PC loads the data into Skyline and then the log shows that it is pushed to Panorama, but the data never shows up in the Levy-Jennings or other plots. The data HAS been loaded to panorama because I can see them listed in the "RUNS" tab. Please take a look and let me know what you find. I have given admin access to that folder to vsharma@uw.edu.

Cheers

Will
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Error in Panorama Upload
(5 responses) Todd 2017-03-20
Hi,

We have been uploading DDA runs to Panorama (through AutoQC) for several months now without any major issues. We have used the latest Skyline-daily builds (currently 3.6.1.10556). Since about 3/9/2017, we have been getting errors at the end of the skyline file upload both when using AutoQC, or when trying to manually upload the files from within the Skyline application. I have attached the logs for the AutoQC (v1.1.0.10005) and the Skyline applications, and an example sky.zip file. We can't remember exactly whether this error coincided with our latest upgrade of Skyline-daily to the most recent build, but it might be related.

Thanks,
Todd
 293_PRTC_std_2017-03-20_15-05-10.sky.log  AutoQC.log 
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AutoQC "stalling"
(12 responses) phains 2017-03-15
Hi,

we have AutoQC setup to monitor several MS with a number of different configuration files. All of them work *most* of the time. We have noticed that after a few days (we are still working out how long), AutoQC stops working for some of the configurations. If you stop the individual configuration (as opposed to the AutoQC application) and restart it, the files are successfully processed. It is possible ALL the configurations are doing this, it’s just that we haven’t noticed as those particular configurations aren’t supposed to be processing any files at this point in time. As such, it may be a global issue, or a local issue, we aren't 100% sure as yet.

We have other software running on the same PC doing a very similar thing (syncing files) and it is not experiencing any issues, so we don’t think it’s related to computer sleep issues (the PC is set to stay wake all the time, ditto the HDD).

Any ideas?

Thanks,

Peter
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AutoQC not sending files to Panorama
(11 responses) n wildburger 2017-02-09
Currently, I am using AutoQC on our Fusion so we can monitor instrument performance with the PRTC mix from Thermo.
Auto QC runs fine, but no files or results are on our folder on Panorama.


Attached is the Skyline template for of PRTC peptides we monitor, which to me looks fine. However, the instrument method used for the PRTC standard is a targeted MS2, meaning there is no MS1. I think this is why the AutoQC fails since a lot of the metrics are from the MS1 (correct me if I'm wrong). And since there is no MS1 my database search with PEAKS fails so I cannot create a spectral library.

Any input would be appreciated.
 SkylineTemplate_Fusion_QA-QC_5Feb2017.sky.view 
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"unknown error connecting to the server panoramaweb.org"
(4 responses) nod2007 2016-11-15
I started getting the message:

"unknown error connecting to the server panoramaweb.org"

about a week ago and have been unable to upload any results since. I haven't made any changes to the AUTOQC settings.
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Publish to Panorama Error
(4 responses) mdowns2 2016-11-01
I am having an issue with using the Publish to Panorama option in Skyline to publish to our PanoramaWeb project. When I attempt the upload I can see the appropriate project and subfolders, but I receive the following 404 error message:"The remote server returned an error: (404) Not Found." I have attached a screen grab with details.

Any advice you can give would be appreciated.

-Melanie
 PubToPanoramaError.JPG 
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AutoQC Loader stuck - error message
(4 responses) allikrest 2016-10-05
I keep getting the error message below. Sometimes it appears as below but I have also had a pop-up error that causes the AutoQC Loader app to quit altogether, which is problematic since I have other configurations actively importing files when the Loader quits. I am trying to import a .raw file. I have made sure that it is newly added to the "watch" folder, that it is not in the skyline document, and that it is not already uploaded as a "sample file" on Panorama. Now, AutoQC Loader just seems to be stuck. It won't recognize any new raw files that I drop into the "watch" folder for this particular configuration. I have attached the log file showing the errors.

An exception occurred while importing the file.
   at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
   at System.IO.FileStream.Init(String path, FileMode mode, FileAccess access, Int32 rights, Boolean useRights, FileShare share, Int32 bufferSize, FileOptions options, SECURITY_ATTRIBUTES secAttrs, String msgPath, Boolean bFromProxy, Boolean useLongPath, Boolean checkHost)
   at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess access, FileShare share)
   at AutoQC.AutoQcLogger.WriteToFile(String message)
   at AutoQC.AutoQcLogger.LogError(String message)
   at AutoQC.AutoQcLogger.LogException(Exception ex)
   at AutoQC.ConfigRunner.RunConfiguration(Object sender, DoWorkEventArgs e)
   at System.ComponentModel.BackgroundWorker.OnDoWork(DoWorkEventArgs e)
   at System.ComponentModel.BackgroundWorker.WorkerThreadStart(Object argument)
 AutoQC.log 
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no mass accuracy data
(1 response) allikrest 2016-10-04
Is mass accuracy data stored in skyline or controlled by a setting in the skyline document? I have 4 AutoQC folders and can see mass accuracy data for the runs in all of them except for one ("AutoQC_BSA_Fus") (see attached screen shot). I have compared the settings in all four skyline documents and cannot seem to find anything that is different in the file associated with the folder in which runs have no mass accuracy data.

Thanks,
Allison
 Weekly BSA_Fus.sky  no mass accuracy.jpg 
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Error: test library not found in settings
(7 responses) allikrest 2016-09-30
Hello,

I am getting this error whenever AutoQC Loader tries to import my skyline document to Panorama. I am using Skyline version 3.5.0.9319, 64-bit. Any idea what is going on?

Thanks,
Allison

30 Sep 2016 07:14:18,818 INFO : Starting to import Skyline document from Weekly_Yeast_QEx_2016-09-30_10-13-58.sky.zip
30 Sep 2016 07:14:18,818 INFO : Expanding Weekly_Yeast_QEx.skyd
30 Sep 2016 07:14:18,859 INFO : Expanding Weekly_Yeast_QEx.sky.view
30 Sep 2016 07:14:18,860 INFO : Expanding Weekly_Yeast_QEx.sky
30 Sep 2016 07:14:18,861 WARN : The version of this Skyline document is 3.5. This is newer than the highest supported version 2.62
30 Sep 2016 07:14:19,525 INFO : Inserting peptides1
30 Sep 2016 07:14:19,570 ERROR: Skyline document import failed
java.lang.IllegalStateException: 'test' library not found in settings.
    at org.labkey.targetedms.SkylineDocImporter.insertPrecursor(SkylineDocImporter.java:1244)
    at org.labkey.targetedms.SkylineDocImporter.insertPeptideOrSmallMolecule(SkylineDocImporter.java:1040)
    at org.labkey.targetedms.SkylineDocImporter.insertPeptideGroup(SkylineDocImporter.java:923)
    at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:533)
    at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:149)
    at org.labkey.targetedms.pipeline.TargetedMSImportPipelineJob.run(TargetedMSImportPipelineJob.java:85)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
 Weekly_Yeast_QEx2.sky 
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Programmatic access to data in Panorama
(4 responses) gabe 2016-09-09
Hi, I'm wondering where I can find descriptions or documentation on APIs or programmatic access to Skyline data in Panorama. This PDF suggests that APIs exist (page 23) but I can't find any more info anywhere. Thanks Gabe
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AutoQC: Error getting status of file
(2 responses) Christian.Frese 2016-08-02
Hi,

I get the following error message when I start runnign AutoQC:

ERROR: Error getting status of file D:\Data\BSA\20160726_UC_ColID_163_CKF_BSA_50fmol_test2.raw
ERROR: Exception details can be found in the AutoQC log in C:\Users\Q1\Documents\PRM
Adding D:\Data\BSA\20160726_UC_ColID_163_CKF_BSA_50fmol_test2.raw to re-import queue.

I atached the logfile. Any idea what's going on?

best,
Christian
 AutoQC_2016_08.txt 
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Problems with Autoqc
(1 response) mhardt 2016-04-28
Hi there,

ive set up a skyline file with MRM transitions for 8 small molecules and the data is successfully imported by the autoqc daemon and uploaded to the panorama server. Unfortunaterly, panorama doesnt display the data and gives an error message...

There were no records found. The date filter applied may be too restrictive.

But there is no filter set up. Can anybody help?

Thanks,

Fabian.
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*_annotated_minimized_* vs *_minimized_annotated_*
(1 response) c.chung 2016-04-15
On Apr 14, 2016 8:27 AM, c.chung wrote:

In the Panorama pagehttps://panoramaweb.org/labkey/project/LINCS/GCP/begin.view?TargetedMSRuns.sort=Created the GCP files can be:
*_annotated_minimized_*
or
*_minimized_annotated_*
I sorted by date, three out of the 15 files the naming is swapped.
Is there a difference in the protocol for naming them slightly different?


On Apr 14, 2016 2:20 PM, PCCSE support wrote:

Thank you for your question, there are no protocol differences between these two naming conventions, just user error in naming them in the wrong order.

I will shortly be reuploading these files in the correct order (annotated_minimized)
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Skyline with discovery content (DDA)
(1 response) An Staes 2016-01-19
Hi,

We have a skyline file containing discovery data (DDA runs of which we build a spectral lib with the dat files from mascot) and no target data. When importing into panorama, it puts this skyline file in the "targeted MS runs" section. Is there a way to annotate that this is a discovery experiment, present in skyline?

Thanks!

Kind regards,
An
view message
error on import
(1 response) Giel Vandemoortele 2016-01-18
Hi,

We wanted to import our skyline files on our subfolder on Panorama, but we managed to import only 2 out of 10.
All the rest of the files throw the same error (see screenshot): java.lang.IllegalArgumentException: No enum constant org.labkey.targetedms.parser.DataSettings.AnnotationType.-1

Can you help us on this?

Thank you!

Kind regards,
Giel
 skyline_panorama_import_error.PNG 
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Display of ms/ms in Panorama
(1 response) Ida Suppanz 2015-10-30
Hello,
I imported a skyline document to Panorama that I zipped via the "share"-> "minimal" option. In my skyline document I have several replicates with ms/ms information. In the Panorama view only one ms/ms is displayed for a given peptide. How can I see which replicate (and wich r.t. if there are several ms/ms for one replicate) it belongs to?
Is it possile to choose which ms/ms will be displayed in Panorama before zipping the file? Or can I display the ms/ms information for all replicates?
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Error Same Key
(6 responses) bphinney 2015-10-22
So I duplicated my skyline file and removed the results and re saved it. I wanted to add a few more peptides to my QC. When I run autoQC again (pointing to the new skyline file and uploading to a new sub directory on Panorama) I get "An Item with the same key has already been added" and then an Error failed importing. Any ideas on how to fix this?

thanks!

Brett
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Auto QC Project
(4 responses) bphinney 2015-10-22
Hi, i'm trying to set up autoqc and publish to panaroma, but I can't figure out my project name to put in the "Folder on Panorama" box. I think my project has spaces in it which may be causing the problem

Thanks!

Brett
view message
autoQC client software
(1 response) Tobias kockmann 2015-10-21
Dear panorama support,

where can I find the panorama autoQC client software that needs to be installed on the instrument PC?

Greetings,
Tobi
view message
Empty Group Name??
zaulim3 2015-08-02
One year ago, I registered the panoramaWeb at Jul 18, 2014.
At that time, I didn't make the group name in spite of your recommendation.

I want to make a group in panoramaWeb to publish my MRM data.
Could you make a new group, LMP_KIST, in my account??

Thank you.

Heesung
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Error 412 Precondition failed
(4 responses) ykim 2015-07-27
Hi, I've been uploading files into Panorama without any issues, except that there are two files that give me this error: Error renaming temporary zip file: A remote server returned an error: (412) Precondition Failed. Any idea of how to fix this would be great! Thanks.
view message
Trouble uploading files
(1 response) brian flatley 2014-12-30
Hi Guys,

I am just getting some errors while trying to upload a file to Panorama from Skyline. I have tried to import the file using both manual upload of a zipped Skyline file and also uploading from Skyline directly to Panorama.

I have attached a screen shot of the error log.

"value too long for type character varying"

Thanks,

Brian
 Pamorama_Error_Dec_2014.png 
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The message to view email to fake email does not appear
(3 responses) yngvild bjorlykke 2014-10-02
I am following the tutorial for publishing data in Panorama. When doing: "If you use a fake email
address you can set the password for the account by clicking on a link to the email message that gets
generated for the new user.", the link to the message does not appear, instead I have:
"System membership status for new group members:
test@test.ts added as a new user to the system and emailed successfully."

Any idea on how to get unstuck?

Thank you!
view message
Error retrieving server folders
(1 response) brian flatley 2014-07-29
Hi,

When I try and publish files from Skyline to Panorama, I get the following error message

Error retrieving server folders:
Value cannot be null.
Parameter name:value

If I select "ok" to this error message the folder structure for panorama appears but is absent of any of our folders
e.g. UCD Pennington Lab or any of the subfolders.

I have attached a screenshot of both the error message and the file structure of Panorama.

Any help would be great,

Brian
 Screenshot_Panorama.jpg 
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RE: Panorama URL
(2 responses) tsbatth 2014-01-23
Hey Panorama team,

Thanks for good work. We're getting ready to upload a data set with a submition of apublication soon and we were wondering if it's possible to trim our current URL from

"https://panoramaweb.org/labkey/project/Joint%20BioEnergy%20Institute/begin.view?"

to something like


"https://panoramaweb.org/labkey/project/JBEI/begin.view?"

If it isn't too much trouble. Originally when I applied for panorama project I gave full name of the institution, but I think an abbreviation would be nicer. Thanks for your time.

Cheers,

Tanveer
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Cannot view or download the result (zip file)
(2 responses) mh167 2014-01-13
Hi there,

My collaborator just upload our MRM data to Panorama and I was able to view the result in the morning. After tried to download the Zip file and failed many times, I cannot see my result anymore ( I can still see the folder and the file but cannot see the chromatogram or other parts). Once I click the peptide, the panoroma stop working. I tried to download the zip file but always stopped after very long waiting. The web browser indicated some server error. Could you please give me some suggestions? Very appreciate.

MF
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Duplicate webparts
(1 response) tsbatth 2013-05-22
Hey,

I have a question regarding the Targeted MS Runs webpart in my project. I seem to be unable to remove webparts in a 'Targeted MS' folder. I have duplicate parts but seem to be unable to remove them (I'm admin for the project currently), I don't see the 'x' at top right of part title.

Regards,

T
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Changing filenames
(2 responses) tsbatth 2013-05-20
Hey,

Is it possible to rename files once they've been uploaded to Panorama via Skyline?

Thanks,

T
view message
How to add a new user account to an existing project
(4 responses) Tobias kockmann 2013-04-09
Hello Panorama support,

how to add a new user to an existing project? In the Admin tool one can only add pre-defined/default users. There is no function like create/invite user.

Greetings,
Tobi
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