Torrent Suite SoftwareAdministration Guide

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Torrent Suite Software space on Ion Community

Administration Guide TOC

Manage Sequencer Instrument Settings from the Torrent Browser

From your Torrent Browser, you can do the following remotely:

• Set FTP information
• Set Update server address
• Monitor the state of the Ion S5, Ion PGM or Ion Proton sequencing instrument,such as Idle or In experiment
• View the most recent alarms
• Get the software versions

Connect the sequencer instrument to the Torrent Server

This section uses the Ion PGM Sequencer as an example of how to connect an Ion sequencer to the Torrent Server.

On the Ion PGM Sequencer Advanced screen, you can set Torrent Server login information, e.g. server address ( Torrent Server ), username ( TS UserName ), and password ( TS Passwd ), to connect to the Torrent Server. The Torrent Server field turns green to indicate thatthe login information is correct.

Connect for the first time

If this is first time that this Ion S5, Ion PGM, or Ion Proton Sequencer is connected to the Torrent Server, the sequencer instrument pulls the FTP information and update server information from server. Any subsequent update to these fields, such as FTP server, is sent back to the Torrent Browser.

If the Torrent Suite Software has never seen this Ion S5, Ion PGM , or Ion Proton instrument before,then the instrument name is not listed under Rigs , and the Torrent Browser copies the settings from a template orthe model sequencer name default . You can modify the model default to suite your site deployment, but you should not delete the model instrument named default .

Once the Ion S5, Ion PGM or Ion Proton instrument is connected

As mentioned before, any subsequent updates to the fields will also be updated in Torrent Browser by the Ion S5, Ion PGM or Ion Proton instrument . Changing the name of the Ion PGM ( PGM Name ) has a different implication. It creates a new rig with the information for the new Ion S5, Ion PGM or Ion Proton instrument , rather than for the model Ion PGM.

Update information on an Ion S5, Ion PGM or Ion Proton instrument via the Torrent Browser

Ion S5, Ion PGM , and Ion Proton instrument information is stored inside Rigs under Site administration. First click on the Config tab; under Database Administration section, click on Admin Interface . It prompts for user name and password. The user needs to have staff status and the permission to update Rigs ( rundb | rigs ). By default, ionadmin has this permission.

FTP Information

The FTP information on Torrent Browser can be updated anytime whether or not there is the experiment going on the Ion PGM instrument . The FTP information is sent to the Ion PGM instrument and is effective immediately.

To change the FTP information, go to Rigs under Site administration and click on the name of the Ion PGM instrument .

Update home

Update home is the URL to the Ion S5, Ion PGM , or Ion Proton instrument update server. By default it is set to the Torrent Server, which acts as the sequencing instrument update server. To change the update home URL, go to Rigs under Site administration and click on the name of the sequencing instrument .

Reference library and barcode

On the Ion S5, Ion PGM , or Ion Proton instrument, during a run, you can enter information about the experiment,or run, on Run Info screen. The Ion S5, Ion PGM, or Ion Proton instrument gets the lists of reference library and barcode set from the Torrent Browser. The information is queried in real time.

For example, while at this Run Info screen on the Ion S5, Ion PGM , or Ion Proton instrument , you realize the reference library has not been added on Torrent Browser. You can go to Reference tab (with the Admin gear menu References option) on Torrent Browser and add a new reference library. Back at the sequencing instrument , you see the new reference library when pressing the drop-down menu (in red below, shown on an Ion PGM instrument):

View Ion S5, Ion PGM , or Ion Proton instrument s tatus and information

You can view the status of Ion S5, Ion PGM or Ion Proton instrument in the State field. It can be Idle , Initing , or In Experiment . You also can view the recent alarm such "No connectivity to ftp server". You can find out the software versions in the Version field.

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