Thermo Fisher Scientific Ion Chef User guide

Type
User guide
For Research Use Only. Not for use in diagnostic procedures.
Ion Chef Instrument Network Connection
USER GUIDE
Publication Number MAN0013444
Revision C.0
Manufacturer: Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256
The information in this guide is subject to change without notice.
DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL,
INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT,
INCLUDING YOUR USE OF IT.
Revision history: Pub. No. MAN0013444
Revision Date Description
C.0 October 2, 2018 This revision includes information to:
Connect an Ion Chef Instrument to an Ion GeneStudio S5
Sequencer
Share Planned Runs using Ion Mesh
Monitor consumables using Ion Mesh
B.0 December 18, 2015 Various revisions.
A.0 January 27, 2015 New document.
Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you accept
the terms and conditions of all applicable Limited Use Label Licenses.
TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.
©2018 Thermo Fisher Scientific Inc. All rights reserved.
Contents
CHAPTER 1 Introduction ................................................ 5
Overview ....................................................................... 5
About the Torrent Server .................................................... 5
Networking guidelines and best practices ...................................... 6
Network setup workflow ..................................................... 6
Collect the required network information ...................................... 6
CHAPTER 2 Connections between Torrent Server and the
Ion Chef Instrument ..................................................... 7
General requirements ........................................................... 7
Direct connection ........................................................... 7
DHCP IP ................................................................... 8
Static IP ................................................................... 8
Add the Torrent Server IP address ................................................. 9
Edit the Torrent Server firewall tables to allow the LAN port IP ...................... 10
Create a firewall exception for the Torrent Server .............................. 10
Connect directly to the Torrent Server ............................................ 11
Connect by network to the Torrent Server ......................................... 13
CHAPTER 3 Connections between the Ion S5 or Ion
GeneStudio S5 Systems and the Ion Chef Instrument ............. 15
General requirements .......................................................... 15
Direct connection .......................................................... 15
DHCP IP .................................................................. 16
Static IP .................................................................. 16
Add the sequencer IP address ................................................... 17
Edit the Torrent Server firewall tables to allow the LAN port IP ...................... 18
Create a firewall exception for the Torrent Server .............................. 18
Connect directly to the Ion S5, Ion GeneStudio S5, or Ion GeneStudio S5
Plus Sequencer ................................................................ 19
Connect by network to the Ion S5 or Ion GeneStudio S5 Sequencer ................. 20
Ion Chef
Instrument Network Connection User Guide
3
CHAPTER 4 Monitor runs, share Planned Runs, and manage
consumables with Ion Mesh ............................................. 21
Set up Ion Mesh ................................................................ 21
View sequencing runs on multiple sequencers with Ion Mesh ........................ 22
Transfer a Planned Run to a Torrent Server with Ion Mesh .......................... 23
Remove a server from an Ion Mesh configuration .................................. 24
Change server nickname in an Ion Mesh configuration .............................. 24
Enable or disable an Ion Mesh connection ......................................... 24
Track Ion Chef flexible workflows for Ion 550 chips with Ion Mesh .................. 25
Related documentation .................................................. 26
Customer and technical support ................................................. 26
Limited product warranty ....................................................... 27
Contents
4
Ion Chef
Instrument Network Connection User Guide
Introduction
If your Torrent Server, Ion S5, Ion GeneStudio S5, or Ion GeneStudio S5 Plus
sequencer was not connected to the Ion Chef Instrument during installation, or if
you move the equipment in your laboratory, the procedures in this guide might apply
to you.
Overview
This document describes how to congure the Ion Chef Instrument to connect with a
Torrent Server. The guide also explains how to connect an Ion Chef Instrument to
the internal Torrent Server in Ion S5, Ion GeneStudio S5, and Ion GeneStudio S5
Plus sequencers. When you connect to a Torrent Server, you can use Torrent Suite
Software to plan and monitor instrument runs, review run reports, and download run
results from the connected instruments.
You can use the following types of network connections to connect a Ion Chef
Instrument to a Torrent Server or a Torrent Server that is embedded in an Ion
GeneStudio S5 Sequencer:
A local area network (LAN) by DHCP IP connection
A direct connection
A local area network (LAN) by Static IP connection
If you add multiple Torrent Servers to a network, you can congure connections
between servers, if you use Torrent Suite Software 5.6 and later. Connections that use
an Ion Mesh conguration, enable you to do the following:
Share Planned Runs with Torrent Servers that are included in the Ion Mesh
conguration.
Track reagent and cartridge usage across Ion Chef Instrument exible
workows from dierent Ion Chef Instruments connected to dierent Torrent
Servers.
View and monitor all runs of interest across multiple Torrent Servers on the
screen in Torrent Suite Software.
Torrent Server in this guide refers to the server component of the PGM, Ion Proton,
Ion S5 XL, or Ion GeneStudio S5 Prime System. Torrent Suite Software is the
software that resides on the Torrent Server. You can transfer Planned Runs between
servers that use the same versions of Torrent Suite Software and are connected to the
same subnet.
The Ion S5, Ion GeneStudio S5, and Ion GeneStudio S5 Plus sequencers have
embedded Torrent Servers and this guide describes how to target the sequencer IP
addresses to form network connections.
1
About the Torrent
Server
Ion Chef
Instrument Network Connection User Guide
5
We recommend that you consult a network administrator before connecting the
Ion Chef Instrument to your laboratory network. See the Ion Chef System Site
Preparation Guide (Pub. No. MAN0007956) for more information about the Ion Chef
Instrument networking requirements.
Collect the required network information.
q
Connect the Ion Chef Instrument to the configured LAN port.
q
Configure the Ion Chef Instrument with the required information.
q
Monitor the Ion Chef Instrument to test the network connection.
q
Share Planned Runs and monitor consumables with Ion Mesh.
Before you begin the procedures in this guide, obtain the following information from
your network administrator:
Network policy for obtaining IP addresses (DHCP IP or static IP).
If the network requires static IP addresses, obtain the static IP address, subnet
mask, gateway address, and DNS server name for the LAN port.
Note: For the Planned Run sharing and le transfer protocol (FTP) functionality to be
successful, the subnet must be the same on all Torrent Servers and Ion Chef
Instruments on the LAN.
Networking
guidelines and
best practices
Network setup
workflow
Collect the
required network
information
Chapter 1 Introduction
Overview
1
6
Ion Chef
Instrument Network Connection User Guide
Connections between Torrent Server
and the Ion Chef Instrument
This chapter describes how to connect the standalone Torrent Server component of the
PGM, Ion Proton, Ion S5 XL, or Ion GeneStudio S5 Prime System to an Ion Chef
Instrument.
General requirements
The following diagrams illustrate common network congurations to which an
Ion Chef Instrument and Torrent Server might be added. See the Ion Chef System
Site Preparation Guide (Pub. No. MAN0007956) for more information.
For a direct connection, the Ion Chef Instrument is connected directly to the Torrent
Server.
1
23
1Network
2Ion Chef Instrument
3Torrent Server
2
Direct connection
Ion Chef
Instrument Network Connection User Guide
7
In a DHCP IP network, the Ion Chef Instrument and the Torrent Server connect to
the network.
1
34
2
1DHCP Server
2Network
3Ion Chef Instrument
4Torrent Server
In a static IP network, the Ion Chef Instrument and the Torrent Server are connected
to the network.
1
23
1Network
2Ion Chef Instrument
3Torrent Server
To share Planned Runs and successful FTP functionality, the subnet must be the same
for all Torrent Servers and Ion Chef Instruments on the LAN.
DHCP IP
Static IP
Chapter 2 Connections between Torrent Server and the Ion Chef Instrument
General requirements
2
8
Ion Chef
Instrument Network Connection User Guide
Add the Torrent Server IP address
The rst time that an instrument is connected to a Torrent Server, or any time the
connection conguration is changed, for example from a direct connection to a
connection over a network, you must add the IP address of the server to the
instrument. To add the Torrent Server IP address from the Ion Chef Instrument.
After you complete this procedure the IP address is available to select on the
Ion Chef Instrument.
1. Sign in to Torrent Suite Software.
2. Click (Seings)4Services.
3. Record the server IP address that is displayed on the System Services screen.
Later you will enter the IP address on the instrument screen.
4. Return to the Ion Chef Instrument user interface, then tap Manage. The
Manage Connections dialog opens.
Chapter 2 Connections between Torrent Server and the Ion Chef Instrument
Add the Torrent Server IP address
2
Ion Chef
Instrument Network Connection User Guide
9
5. Enter the server IP address or Torrent Server host name in the Server eld and
repeat for Update site. Click Save.
The Torrent Server host name or IP address is linked to the Ion Chef Instrument.
Edit the Torrent Server firewall tables to allow the LAN port IP
When connecting through a LAN, the Torrent Server rewall seings need to be
modied for both DHCP and Static LAN connections.
Note: When directly connected, instruments are on the 192.168.20x.x subnet from
which all trac is enabled, so modication of rewall seings is not required.
Any exception would mean that editing the local rewall tables to include the LAN IP
is required. Also, if the Ion Chef Instrument is geing a DHCP address from your
network, you need to create an exception for the entire DHCP subnet.
Consult your system administrator or Thermo Fisher Field Service Engineer (FSE) or
Field Application Specialist (FAS) for this procedure. On the Torrent Server, edit
the /etc/iptables.custom le and add a rewall rule to allow all trac from the IP
address of the Ion Chef Instrument. (This is a blank le initially and is intended for
custom rewall conguration.)
IMPORTANT! Only edit the /etc/iptables.custom le and not /etc/iptables.rules,
because /etc/iptables.rules is overwrien when software is updated.
1. Enter sudo^nano^/etc/iptables.custom, then add the three lines below:
*filter
-A INPUT -s xxx.xxx.xxx.xxx -j ACCEPT
COMMIT
Note: -A INPUT -s xxx.xxx.xxx.xxx -j ACCEPT adds the rule to the
format. Enter the IP address of the Ion Chef instrument in place of
"xxx.xxx.xxx.xxx". When nished editing, save changes by pressing CTRL +
O and CTRL + X.
Create a firewall
exception for the
Torrent Server
Chapter 2 Connections between Torrent Server and the Ion Chef Instrument
Edit the Torrent Server firewall tables to allow the LAN port IP
2
10
Ion Chef
Instrument Network Connection User Guide
2. After this command, manually apply the change:
sudo^iptables-restore^--noflush^<^/etc/iptables.custom
Note: You can also list the rewall rules with: sudo^iptables-L.
If this command returns with no output, it means it succeeded.
3. If the Ion Chef Instrument is geing a DHCP address from your network, create
the exception for the entire DHCP subnet.
The example below assumes that the DHCP address for the Ion Chef
Instrument is 172.16.48.0 and the DHCP subnet range is 172.16.48.1 to
172.16.48.254. Add these three lines:
*filter
-A INPUT -s 172.16.48.0/24 -j ACCEPT
COMMIT
4. Restart the server.
5. (Optional) If you need to make corrections, repeat this process and completely
drop all rules and start fresh. Enter the following:
sudo^iptables-F
sudo^iptables-restore^<^/etc/iptables.rules
sudo^iptables-restore--noflush^</^etc/iptables.custom
Removing a rule from either of these les would remove it from the active
rewall rules, because the iptables-restore command does not overwrite
rules, it adds them to all active rules.
Connect directly to the Torrent Server
You can directly connect the Torrent Server to the Ion Chef Instrument.
1. Verify Torrent Server connection to Ion Chef Instrument.
a. Plug the connector from the Ion Chef Instrument directly into one of the
available ports on the back of the server.
The Ion Chef Instrument is assigned a default IP address, for example
192.168.201.1, based on the Torrent Server port you connect to.
Chapter 2 Connections between Torrent Server and the Ion Chef Instrument
Connect directly to the Torrent Server
2
Ion Chef
Instrument Network Connection User Guide
11
b. On the Home screen, tap Seings4Instrument Seings4About4About
Instrument, then verify the IP address for the server connection on the Ion
Chef Instrument.
2. Connect the Ion Chef Instrument.
a. On the Home screen, tap Seings4 Torrent Server.
b. Verify that the server seings are correct. Ensure that the Torrent Suite
Software password is correct.
The Torrent Suite Software URL is the IP address of the port you connected
to on the back of the server (192.168.20x.1).
The server and instrument are now connected.
Chapter 2 Connections between Torrent Server and the Ion Chef Instrument
Connect directly to the Torrent Server
2
12
Ion Chef
Instrument Network Connection User Guide
3. To set the password, tap Manage, then enter the password to the ionadmin
account password on the selected Torrent Server.
4. Tap Save.
The Torrent Server is directly connected to the Ion Chef Instrument, an icon ( ) on
the lower left side of the home screen appears. You can now use Ion Mesh to share
Planned Runs and monitor consumables.
Connect by network to the Torrent Server
To connect to the Torrent Server through the company LAN, you need to target
ServerPortIP (Eth1), see “Add the Torrent Server IP address“ on page 9 for more
information. When the LAN is set to DHCP, the IP, Gateway, Netmask, and DNS
Name Servers populate automatically. You will also need to modify the Torrent Server
rewall seings. See “Edit the Torrent Server rewall tables to allow the LAN port
IP“ on page 10 for more information.
1. On the Home screen, tap Seings4Instrument Seings4Network
Conguration.
2. Select the appropriate IP conguration:
Option Description
DHCP Dynamic Host Configuration Protocol is a client/server protocol that
automatically provides an Internet Protocol (IP) host with its IP address
and other related configuration information such as the subnet mask and
the gateway.
Static IP Static Internet Protocol (IP) address is a permanent number assigned to a
computer by an Internet Service Provider (ISP).
Chapter 2 Connections between Torrent Server and the Ion Chef Instrument
Connect by network to the Torrent Server
2
Ion Chef
Instrument Network Connection User Guide
13
3. Ensure that the information is correct, then tap Done.
The Torrent Server is connected to the company LAN, an icon ( ) on the lower left
side of the home screen appears. You can now use Ion Mesh to share Planned Runs
and monitor consumables.
Chapter 2 Connections between Torrent Server and the Ion Chef Instrument
Connect by network to the Torrent Server
2
14
Ion Chef
Instrument Network Connection User Guide
Connections between the Ion S5 or
Ion GeneStudio S5 Systems and the
Ion Chef Instrument
This chapter describes how to connect an Ion Chef Instrument to the internal Torrent
Server component in an Ion S5, Ion GeneStudio S5, or Ion GeneStudio S5 Plus
Sequencer.
General requirements
The following diagrams illustrate common network congurations to which an
Ion Chef Instrument and a Ion S5, Ion GeneStudio S5, or Ion GeneStudio S5 Plus
Sequencer with an internal Torrent Server might be added. See the Ion Chef System
Site Preparation Guide (Pub. No. MAN0007956) for more information.
For a direct connection, the Ion Chef Instrument is connected directly to an Ion S5,
Ion GeneStudio S5, or Ion GeneStudio S5 Plus Sequencer with an embedded server.
1
23
1Network
2Ion Chef Instrument
3Ion S5, Ion GeneStudio S5, or Ion GeneStudio S5 Plus Sequencer with an embedded
server
3
Direct connection
Ion Chef
Instrument Network Connection User Guide
15
In a DHCP IP network, the Ion Chef Instrument and the Ion S5, Ion GeneStudio
S5, or Ion GeneStudio S5 Plus Sequencer with an embedded server connect to the
DHCP IP network.
1
34
2
1DHCP Server
2Network
3Ion Chef Instrument
4Ion S5, Ion GeneStudio S5, or Ion GeneStudio S5 Plus Sequencer with an embedded
server
In a static IP network, the Ion Chef Instrument and the Ion S5, Ion GeneStudio S5,
or Ion GeneStudio S5 Plus Sequencer with embedded server are connected to the
network.
1
23
1Network
2Ion Chef Instrument
3Ion S5, Ion GeneStudio S5, or Ion GeneStudio S5 Plus Sequencer with an embedded
server
To share Planned Runs and successful FTP functionality, the subnet must be the same
for all sequencers and Ion Chef Instruments on the LAN.
DHCP IP
Static IP
Chapter 3 Connections between the Ion S5 or Ion GeneStudio S5 Systems and the Ion Chef Instrument
General requirements
3
16
Ion Chef
Instrument Network Connection User Guide
Add the sequencer IP address
The rst time that an instrument is connected to an Ion S5, Ion GeneStudio S5, or
Ion GeneStudio S5 Plus Sequencer with an embedded Torrent Server or any time the
connection conguration is changed, for example from a direct connection to a
connection over a network, you must add the IP address of the sequencer to the
instrument. After you complete this procedure the IP address is available to select on
the Ion Chef Instrument.
1. If you are connecting the Ion Chef Instrument to a Ion S5, Ion GeneStudio S5,
or Ion GeneStudio S5 Plus Sequencer with an embedded Torrent Server over a
network, click Seings4Instrument Seings4About on the sequencer and
locate the target IP address displayed on the sequencer user interface screen.
2. Return to the Ion Chef Instrument user interface, then tap Manage. The
Manage Connections dialog opens.
3. Enter the sequencer IP address or host name in the Server eld and repeat for
Update site. Click Save.
The sequencer IP address is linked to the Ion Chef Instrument.
Chapter 3 Connections between the Ion S5 or Ion GeneStudio S5 Systems and the Ion Chef Instrument
Add the sequencer IP address
3
Ion Chef
Instrument Network Connection User Guide
17
Edit the Torrent Server firewall tables to allow the LAN port IP
When connecting through a LAN, the rewall seings of an Ion S5, Ion GeneStudio
S5, or Ion GeneStudio S5 Plus Sequencer with an embedded Torrent Server need to
be modied for both DHCP and Static LAN connections.
Note: When directly connected, instruments are on the 192.168.20x.x subnet from
which all trac is enabled, so modication of rewall seings is not required.
Any exception would mean that editing the local rewall tables to include the LAN IP
is required. Also, if the Ion Chef Instrument is geing a DHCP address from your
network, you need to create an exception for the entire DHCP subnet.
Consult your system administrator or Thermo Fisher Field Service Engineer (FSE) or
Field Application Specialist (FAS) for this procedure. On the Ion S5, Ion
GeneStudio S5, or Ion GeneStudio S5 Plus Sequencer with an embedded Torrent
Server, edit the /etc/iptables.custom le and add a rewall rule to allow all trac from
the IP address of the Ion Chef Instrument. (This is a blank le initially and is
intended for custom rewall conguration.)
IMPORTANT! Only edit the /etc/iptables.custom le and not /etc/iptables.rules,
because /etc/iptables.rules is overwrien when software is updated.
1. Enter sudo^nano^/etc/iptables.custom, then add the three lines below:
*filter
-A INPUT -s xxx.xxx.xxx.xxx -j ACCEPT
COMMIT
Note: -A INPUT -s xxx.xxx.xxx.xxx -j ACCEPT adds the rule to the
format. Enter the IP address of the Ion Chef instrument in place of
"xxx.xxx.xxx.xxx". When nished editing, save changes by pressing CTRL +
O and CTRL + X.
2. After this command, manually apply the change:
sudo^iptables-restore^--noflush^<^/etc/iptables.custom
Note: You can also list the rewall rules with: sudo^iptables-L.
If this command returns with no output, it means it succeeded.
3. If the Ion Chef Instrument is geing a DHCP address from your network, create
the exception for the entire DHCP subnet.
The example below assumes that the DHCP address for the Ion Chef
Instrument is 172.16.48.0 and the DHCP subnet range is 172.16.48.1 to
172.16.48.254. Add these three lines:
*filter
-A INPUT -s 172.16.48.0/24 -j ACCEPT
COMMIT
Create a firewall
exception for the
Torrent Server
Chapter 3 Connections between the Ion S5 or Ion GeneStudio S5 Systems and the Ion Chef Instrument
Edit the Torrent Server firewall tables to allow the LAN port IP
3
18
Ion Chef
Instrument Network Connection User Guide
4. Restart the server.
5. (Optional) If you need to make corrections, repeat this process and completely
drop all rules and start fresh. Enter the following:
sudo^iptables-F
sudo^iptables-restore^<^/etc/iptables.rules
sudo^iptables-restore--noflush^</^etc/iptables.custom
Removing a rule from either of these les would remove it from the active
rewall rules, because the iptables-restore command does not overwrite
rules, it adds them to all active rules.
Connect directly to the Ion S5, Ion GeneStudio S5, or Ion
GeneStudio S5 Plus Sequencer
The Ion S5, Ion GeneStudio S5, and Ion GeneStudio S5 Plus sequencers include a
built-in server. You can connect an Ion Chef Instrument and the sequencer directly
and plan runs for both instruments through the Torrent Suite Software.
Before you can complete this procedure the Ion Chef Instrument and the Ion S5,
Ion GeneStudio S5, or Ion GeneStudio S5 Plus Sequencer must be connected
directly through a cable connection. See the your site administrator or the Ion Chef
System Site Preparation Guide (Pub. No. MAN0007956) for more information about this
connection and Ion Chef Instrument networking requirements.
1. Connect the Ion Chef Instrument directly to the Ion S5, Ion GeneStudio S5, or
Ion GeneStudio S5 Plus Sequencer, then click Seings4Instrument
seings4Torrent Server.
2. Record the following information from the screen:
Setting Example Value
Update site 192.168.201.1
Server 192.168.201.1
Username (browser) ionadmin
Password (browser) ionadmin
Username (ftp) ionguest
Password (ftp) ionguest
3. To connect the instruments for the rst time, tap Manage on the Ion Chef
Instrument, then enter the recorded information in the Manage Connections
dialog, and click Save.
The Ion Chef Instrument is now connected to the Ion S5, Ion GeneStudio S5, or
Ion GeneStudio S5 Plus Sequencer, an icon ( ) on the lower left side of the home
screen appears. You can now use Ion Mesh to share Planned Runs and monitor
consumables.
Chapter 3 Connections between the Ion S5 or Ion GeneStudio S5 Systems and the Ion Chef Instrument
Connect directly to the Ion S5
, Ion GeneStudio
S5, or Ion GeneStudio
S5 Plus Sequencer
3
Ion Chef
Instrument Network Connection User Guide
19
Connect by network to the Ion S5 or Ion GeneStudio S5 Sequencer
To connect to an Ion Chef Instrument to an Ion S5, Ion GeneStudio S5, or Ion
GeneStudio S5 Plus Sequencer with an embedded Torrent Server through the
company LAN, you need to target ServerPortIP (Eth1), see “Add the sequencer IP
address“ on page 17 for more information. When the LAN is set to DHCP, the IP,
Gateway, Netmask, and DNS Name Servers populate automatically. You will also
need to modify the Ion S5 or Ion S5, Ion GeneStudio S5, or Ion GeneStudio S5
Plus Sequencer rewall seings. See “Edit the Torrent Server rewall tables to allow
the LAN port IP“ on page 18 for more information.
1. On the Home screen, tap Seings4Instrument Seings4Network
Conguration.
2. Select the appropriate IP conguration:
Option Description
DHCP Dynamic Host Configuration Protocol is a client/server protocol that
automatically provides an Internet Protocol (IP) host with its IP address
and other related configuration information such as the subnet mask and
the gateway.
Static IP Static Internet Protocol (IP) address is a permanent number assigned to a
computer by an Internet Service Provider (ISP).
3. Ensure that the information is correct, then tap Done.
The Ion S5, Ion GeneStudio S5, or Ion GeneStudio S5 Plus Sequencer is connected
to the company LAN, an icon ( ) on the lower left side of the home screen appears.
You can now use Ion Mesh to share Planned Runs and monitor consumables.
Chapter 3 Connections between the Ion S5 or Ion GeneStudio S5 Systems and the Ion Chef Instrument
Connect by network to the Ion S5
or Ion GeneStudio
S5 Sequencer
3
20
Ion Chef
Instrument Network Connection User Guide
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Thermo Fisher Scientific Ion Chef User guide

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