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    0 0

    If you have command line access to the Linux back-end then the token authentication can quickly be tested for any Columbus user account using the curl tool.

    [columbus@columbus]$ curl -i -X POST -H 'Content-Type: application/json' -d '{"userName": "INSERT", "password": "INSERT", "urls": ["/api/1.1/images/*"]}' http://columbus/api/1.1/authentication/token

    Which should yield an output like this:

    HTTP/1.1 201 CREATED
    Server: nginx/1.0.8
    Date: Tue, 02 Aug 2016 13:36:32 GMT
    Content-Type: application/json
    Transfer-Encoding: chunked
    Connection: keep-alive
    Vary: Accept-Language
    Content-Language: en-us

    {"token": "a436ac1b-5965-4ad9-abf9-487f1b6031e0", "urls": ["/api/1.1/images/*"]}

    The authentication token can be used to test image retrieval. The example below requests image with ID 2801 and saves it to the local /tmp directory on the Columbus server.

    Note: The measurement containing image with ID 2801 must first be published via the Columbus web interface in order for the images to be accessible to the API.

    [columbus@columbus]$ curl -H 'PKI-Columbus-Authentication: a436ac1b-5965-4ad9-abf9-487f1b6031e0' http://columbus/api/1.1/images/2801.tiff -o /tmp/2801.tiff

    If the authentication fails, check the /var/log/columbus/web/columbus.log for details. Please contact the Informatics Support team if further assistance is required.


    0 0

    The changes suggested below will only become active once the Columbus service is restarted.

    [columbus@columbus]$ sudo /etc/init.d/columbus restart



    =========================================
    acapella user
    =========================================

    Acapella uses the value of environment variable TMP. Only if this does not exist, the /tmp directory is used. You can specify the TMP environment variable in the shell script which starts Acapella. For example, modify...

    /usr/local/PerkinElmerCTG/Acapella*/bin/acapella.sh

    ...and add the TMP setting near the end of the file, before the "exec $BINDIR/acapella "$@"" line:

    ...
    export TMP=/path/to/new/tmp/folder
    exec $BINDIR/acapella "$@"
    ...

    Please make sure the specified path exists and is writable for the user "acapella".


    =========================================
    columbus user
    =========================================

    Data bound for /tmp can be redirected by placing the following lines at the top of the /etc/init.d/columbus script...

    # redirect tmp data
    TMPDIR=/path/to/new/tmp/folder
    TMP=$TMPDIR
    TEMP=$TMPDIR
    export TMPDIR TMP TEMP


    Please make sure the specified path exists and is writable for the user "columbus".


    0 0

    Since recently the conformation of the drawn structures in ChemBioDrawUltra 14.0 changes when I press 'Apply Documents Setting from'. This didn't happen before or with older versions of ChemDraw where only graphical settings were changed but the geometry of the drawn structure remained like entered. In some cases the change of the conformation of the structure occurs only after pressing 'Apply Documents Setting from' for a second time.

    There is often a good reason to draw a structure in a certain conformation and I would really like that the structure remains as drawn but only fonts and bond length etc.. are adjusted to the values defined in the document settings. If I would like to change also the conformation of the structure I still can do that with the 'Clean Up Structure' function.

    Thanks for help and suggestions.


    0 0

    I have installed Chemdraw 16.0 (on a windows 10 platform) and the toolbars are way too small. How can I resize them?


    0 0

    Hey everyone,

    after latest windows 10 updates (which are impossible to avoid) Chemdraw 15.1 and 16.0 are incapable to simulate 1H and 13C NMR spectra anymore. The simulation windows remains blank (or rather grey) and no spectrum is visible (me and all other colleagues in lab with 10 are affected by this issue).

    Is this issue already reported and is there a workaround for this ?

    Thank you

    Cheers, Volker


    0 0
  • 12/23/16--20:13: Disappearing toolbars
  • I've had a problem with this for a while on multiple computers. Often when I open ChemDraw, the toolbars that I had customized for my use have either disappeared or moved around.

    How can I tell the program to keep them as they are?

    I have ChemDraw Professional (Chem Office 2015) and am running it in Windows 7. I'm using multiple screens, but mainly have ChemDraw open on my main screen.


    0 0

    We are have been having issues with a function of Volocity for a few years and I would like to see if we could find a solution to the problem. The issue pertains to the exposure times while using the acquisition setup.

    Our acquisition is only capturing a single frame with multiple channels. The exposure times for the channels are set prior to the acquisition and are saved. The issue occurs when running the acquisition, some exposure settings saved in the channels are not respected during the acquisition setup. For example in a blue fluorescent channel, the exposure time is set to 1s but when acquiring the shutter is only open for 0.001 seconds and does not capture the specific channel. This issue is usually only seen when running 3 channels but decreases in probability of occurring when dropping to less channels. In an attempt to solve this issue I have attempted to measure device latencies but I get an error when trying to do this.

    In the ideal situation, I would like to set the exposure times and get the acquisition running smoothly without having to cancel it because the shutters are closing too quickly. When I notice that the acquisition is not good, I usually stop it. I do notice that the channel's disk icon appears unsaved which means I need to go back into the channel and set the correct exposure amount. Some times to take one multichannel picture I need to take at least 5 acquisition before all channels respect their appropriate exposure times. As you might suspect this gets quite annoying.

    We have a Mac 5000 controller that controls the shutter speeds and a manual filters cube that is change through manual intervention pop up window that I have set to work.

    Any advice on what is wrong with the device latency measurement or else this sporadic exposure time issue. Let me know if you need any additional information.


    0 0

    A small, but I think useful new feature to the Background Job Status page would be to add a filter button for the Status column. The use case is wanting to know (only!) which jobs are currently running, or still Scheduled, etc. I often just do a browser Find > "Running" to see which jobs are not done yet. Especially in a multiple user environment, there can be many jobs Completed or in various stages of completion.

    An additional useful filter would be by User Name.

    Perhaps even better, a repoting mechanism, even simply email, that would send upon a whole Session ID being complete.

    Thanks,
    David


    0 0

    The command to use for this purpose would be as follows:

    $ ps -fU columbus

    This will list all processes associated with Columbus along with the relevant PID's.


    0 0

    In the below example we can see a number of active processes associated with the columbus user.

    If I wanted to target the 'python manage.py' processes and filter using the start time column one can use kstart_time as an argument to ps to sort by start time, then grep for python manage.py processes and output everything in the 5th row and after.

    e.g.

    $ ps kstart_time -fU columbus | grep 'python manage' | tail -n +5

    You might then wish to consider killing any of the old processes.

    e.g.

    $ sudo kill -9 15169

    -------------------------------

    RAH


    0 0

    The 502 bad gateway error tends to mean that there has been or is currently a communication issue between the client web interface and an up stream server, in this case it would indicate an issue communicating with the Columbus server.

    The last time I encountered the issue we were able to attribute it to too many python processes running which was effectively blocking communication between the clients and the Columbus server.

    Typically you might only expect to see 4 or 5 python manage.py processes running at any one time, and you should certainly not have any more than 10. If this is the case then it's likely there are some 'stale' or stalled processes that need killing - as was the case for me.

    A simple workaround for this is to just restart the Columbus web component:

    $ sudo /etc/init.d/columbus restart web

    This would bring the server back up but it didn't help with root cause analysis. You might wish to try the following workflow to verify that it's the same issue:

    $ sudo /etc/init.d/columbus stop web


    # now check if there are any "python manage.py..." processes still alive


    $ ps -fU columbus


    # if in this output list there are "python manage.py..." processes still listed, kill

    them manually:


    $ sudo kill manage.py command>



    # start columbus web again


    $ sudo /etc/init.d/columbus start web

    If the error goes away then this suggests that it's the number of python manage.py processes that is causing the issue.

    The problem with this approach is that it mean that any users currently logged in would potentially lose their work e.g. if building an analysis BB routine.

    Alternatively it might be sufficient for you to kill the stale "python manage.py...." processes from time to time. You can identify these stale processes by looking at the output of:


    $ ps -fU columbus

    As described here:

    http://forums.cambridgesoft.com/messageview.aspx?catid=55&threadid=3485&enterthread=y

    Following on from that you might then just need to filter out those older processes using a similar workflow as described here:

    http://forums.cambridgesoft.com/messageview.aspx?catid=55&threadid=3486&enterthread=y

    ------------------------------

    RAH


    0 0

    I've seen the following error crop up a couple of times when loading a specific data set in the Image Analysis view. Please note, the same data set will load without issue in the 'Browse' mode:

    The data set in question is a large single well multi field data set (~ 1500 fields in this example).

    The image analysis view loads information for all fields in a well which can take significant time for a dataset such as this. The fact that it isn't always reproducible is likely down to general server usage/load at the time the request is made.

    I believe the timeout in question and how Columbus deals with this type of large single well data set has been improved in recent releases and is set to continue in that vein but if you do see this error as a temporary workaround you could try increasing the timeout as follows.

    Locate the server.proc file in the following path:

    usr/local/PerkinElmerCTG/Acapella_version/AcapellaResources/AcapellaCore/StdLib/Databundle/server.proc

    (it's the same file mentioned in the on screen error)



    The pertinent line which we can edit is at the top of that file and reads:

    proc ServerInit(polytype xml in "Either xml structure or filename", int timeout@s=120 explicit in)

    You'd just need to change the 'int timeout@s=120 explicit in' to something like 'int timeout@s=240 explicit in' i.e. 4 minutes instead of 2...

    After making the change it is necessary to restart the Columbus services:

    $ sudo /etc/init.d/columbus restart



    check to make sure all processes are 'OK':



    $ sudo /etc/init.d/columbus status



    and then re-test to see if waiting that bit longer allows the data set to load.

    --------------------------------

    RAH


    0 0

    Yes, this is possible but be very careful - querying the db isn't necessarily recommended because if changes are inadvertently made to the db it may cause corruption. Always check to make sure you have a recent db backup:

    $ cd /OMERO/OMERO4_4/db_backup/

    Look for a recent .pg_dbdump file.

    For example if I wanted to run an sql query to list all of the active users and the screen, plate and group (owner) association I'd use the following steps :

    Connect to the omero database (columbus user):

    $ sudo su columbus

    $ psql omero4_4

    > select e.omename as user, s.name as screen, p.name as plate, eg.name as group from screen s join screenplatelink spl on spl.parent=s.id join plate p on spl.child=p.id join experimentergroup eg on eg.id=p.group_id join experimenter e on e.id=p.owner_id order by e.omename, s.name;

    The output would look something like this:

    ------------------------------

    RAH


    0 0

    Usually this is defined by cell compactness given as circumference normalized to area but this isn't readily available as a morphology readout in Columbus.

    Compactness is available as one of the STAR features, but that only allows you to use thresholds between 30 – 60% and not 0 or 100% (whatever would be equivalent to not applying a threshold at all).

    A method to dervive compactness is shown below.

    1) Find Nuclei

    2) Find Cytoplasm

    3) Select Population

    a. Common filters

    b. Remove Border Objects (to get rid of any incomplete cells/cells on edges so that the measurement is more accurate

    4) Calculate Morphology

    a. Membrane

    b. Standard

    i. Area

    ** because the membrane is 1px wide, calculating the area is essentially calculating the circumference

    5) Calculate Morphology Properties

    a. Cell

    b. Standard

    i. Area

    6) Calculate Properties

    a. By Formula

    b. A/B

    c. Variable A = Membrane Area

    d. Variable B = Cell Area

    e. Output property = compactness

    ---------------

    RAH


    0 0

    Hi there,

    I found out that chemdraw for excel does not work at all.

    Here is my work enviornment:

    1. Windows 10 version 1607 (OS build: 14393.576)

    2. MS Office 2013 32 bits

    3. ChemDraw Pro 16.0.0.82

    BTW, The chemdraw pro 16 excel add-in works on my windows 7 x64. Unfortunately out IT push all clients PC to windows 10 version 1607 (The Windows 10 Anniversary Update)

    Is any new chemdraw pro 16 patch to address this issue? Thanks lot.

    Regard,

    Peter


    0 0

    Here is a typical filesystem setup on a Columbus Conductor server:

    a. / 100GB
    b. /tmp 50GB
    c. /opt 8GB
    d. /srv 8GB
    e. /usr 100GB
    f. /var 100GB

    The important filesystems here are /var (where the database tables live) and /tmp (which is used to cache import data for certain import methods). If either of these locations become saturated then the Columbus database will encounter problems.

    The system must also have at least 64GB of swap space.


    0 0

    Yes, the information from the Job Status page is backed up in the following location...

    Columbus 2.5 and below:
    ~acapella/.imacro/jobstatus.PORT.log

    Columbus 2.6 and above:
    ~acapella/.Acapella/4.*/jobstatus.PORT.log

    (where PORT is the TCP port of the Acapella master server)

    Entries over 31 days old are removed from the disk file.


    0 0

    Yes, the 'Transfer to Columbus' Export method can be used to copy data from one user account to another. The data is duplicated during the process, so that the data appears in both source and destination user accounts.


    0 0

    Users can be members of many groups at a time, however, a user can only be active in one group at a time - this is their 'Default Group'. User can specify this group using the Default group control under the My Account page, any data imported by the user will be imported into this specified default group.

    For non-admin users the 'Default Group' is set via the 'Administration' link ...'My account'. For admin users it would be 'Administration' link ...'Users & Groups' ...'My Account'.


    0 0

    Batch Analysis is only possible using data stored in the Screen tree. Project data must be converted into Screen data before Batch Analysis can be performed.

    The URL below links to a zip file download containing a custom Image Analysis script which can be used to convert the Project data, as well as a PowerPoint file detailing the workflow to follow to perform the conversion.

    https://perkinelmer.box.com/v/ProjectDataConversion

    Note, the conversion script contained in the zip archive is valid for use with Columbus version 2.6 and above. Please contact the support team at informatics.support@perkinelmer.com to request conversion scripts compatible with legacy versions of Columbus.


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