BioNano Genomics 90023 Setup Manual Download Page 1

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For Research Use Only. Not for use in diagnostic procedures.
Copyright © 2022 Bionano Genomics Inc. All Rights Reserved

Saphyr Networking and Setup Guide

Document Number: 30251
Document Revision: F

Summary of Contents for 90023

Page 1: ...For Research Use Only Not for use in diagnostic procedures Copyright 2022 Bionano Genomics Inc All Rights Reserved Saphyr Networking and Setup Guide Document Number 30251 Document Revision F...

Page 2: ...rument Controller Bionano Access Server Cabling 11 Connect Bionano Access Server to Compute on Demand COD 19 Saphyr Bionano Compute Server s Cabling and Operation 21 Introduction of Saphyr and Bionano...

Page 3: ...TO THIS DOCUMENT EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE TO THE FULLEST EXTENT ALLOWED BY LAW IN NO EVENT SHALL BIONANO GENOMICS...

Page 4: ...ute Option B Steps Access txt and Legacy image D Added port 3002 for Compute On Demand connectivity Added firewall configuration for ICS v5 2 E Clarified that the Instrument controller can t be connec...

Page 5: ...chitecture of the Saphyr system and its requirements for integration within their organization Please contact Support bionanogenomics com prior to implementing steps within Figure 1 Saphyr System Refe...

Page 6: ...grades o Bionano Access Server 1 Static IP assigned Compute on Demand if applicable Software Upgrades Data Center for Compute Server Solution Available rack space for 2U Server s o Saphyr Compute o Bi...

Page 7: ...com http wustat windows com http ntservicepack microsoft com http go microsoft com http dl delivery mp microsoft com https dl delivery mp microsoft com ICS Controller Bionano Access Server TeamViewer...

Page 8: ...in RAID 1 256 GB C drive Space Height 46 cm 18 in Width 18 cm 7 in Depth 47 cm 18 5 in Power 100 240 VAC at 50 60 Hertz Power Consumption 300 Watts 2m long IEC 60320 C13 power cord Network 2 1 gigabit...

Page 9: ...For Research Use Only Not for use in diagnostic procedures 30251 Rev F Saphyr Networking and Setup Guide Page 9 of 36 Customer Network...

Page 10: ...ifications Provided By Bionano Software CentOS 7 x Bionano Access Bionano Tools PostgresSQL Nodejs Perl Python R Docker Memory 128 GB RAM Data Storage 40 TB with RAID Controller Space Height 46 cm 18...

Page 11: ...System Configuration is comprised of one Saphyr instrument left Saphyr Instrument Controller middle and a Bionano Access Server right Actual physical placement may be modified to meet site specific ne...

Page 12: ...Controllers 60368 and one Bionano Access Server middle Bionano Access Server NIC Card Four ports p5p4 to p5p1 descending order left to right P5p4 To Saphyr Instrument Controller 2 60368 NIC Card Adapt...

Page 13: ...no Access Tethering 2 1 Configure ICS Controller to Bionano Access Server network 2 1 1 On ICS PC desktop navigate to Control Panel Network Internet and click View network status and tasks 2 1 2 Selec...

Page 14: ...n diagnostic procedures 30251 Rev F Saphyr Networking and Setup Guide Page 14 of 36 2 1 3 Select Internet Protocol Version 4 Ipv4 and click Properties 2 1 4 Input ICS PC IP address 111 111 111 111 and...

Page 15: ...ivity 2 2 1 Open a web browser and input https 111 111 111 1 3005 to confirm Bionano Access page loads 2 2 2 If not successful open Putty and connect to confirm Access connection Note Contact BNG Supp...

Page 16: ...Configuration Connection to BAS 2 3 1 In Saphyr ICS select the Bionano Access icon and input the Bionano Access configuration Server Name 111 111 111 1 Port 3005 Important If Bionano Access has been c...

Page 17: ...Standalone mode no downstream analysis 3 BAS Server Static IP Configuration Below are steps to obtain the Bionano Access Server p5p1 MAC address for static IP assignment 3 1 Connect to the BAS termin...

Page 18: ...TPROTO to static and input the customer provided Access static IP Netmask Gateway DNS addresses The file should look similar to this Generated by dracut initrd NAME p5p1 DEVICE p5p1 ONBOOT yes NETBOOT...

Page 19: ...ng Enter the following command systemctl status access Note If Access is not Running enter the following command to start Access systemctl start access 4 Connect Bionano Access Server to Compute on De...

Page 20: ...phyr Networking and Setup Guide Page 20 of 36 Note Newly registered systems will require the appropriate Region inputted 4 5 Confirm connection status Note If COD is unable to connect contact customer...

Page 21: ...ion requires one static IP address for the Saphyr1a Compute Node in the data center The remaining compute nodes will be on a separate custom subnet The Saphyr1a node will be dual homed It will have on...

Page 22: ...itional Bionano Computes are added to scale the cluster to fit your specific demands A single Bionano Access Server can be configured to interact with multiple compute clusters if required Each Comput...

Page 23: ...United States are required to supply two 2m long country specific IEC 60320 C13 power cord in some cases the FSE may be able to provide the suitable power cord Network Minimum 1 1 GB Ethernet connect...

Page 24: ...etc hosts 1 1 3 Edit to include Saphyr1A static IP Enter xxx xxx xxx xxx saphyr1a 1 1 4 Ctrl x to save Y for yes and Enter 2 Saphyr Compute Server Configuration Steps 2 1 Option A Configuration 2 1 1...

Page 25: ...r 2 1 1 8 Restart network with the following command sudo systemctl restart network 2 1 2 Edit Saphyr1a Host File 2 1 2 1 Edit the Saphyr1A hosts file with the following command sudo nano etc hosts 2...

Page 26: ...2 6 Proceed to Section 3 Verify SGE 2 2 Option B Configuration 2 2 1 Perform all steps within Section 2 1 Option A Configuration Note Once Option A steps Section 2 1 are completed the FSE can access t...

Page 27: ...Enter the command sudo nano etc hosts 2 2 7 Input all Nodes and BAS Static IPs provided by customer IT Dept 2 2 8 Exit and save with the following command Enter Y ctrl x 2 2 9 Enter the following comm...

Page 28: ...h bionano1b etc 2 3 Edit saphyr1a Hosts file 2 3 1 From saphyr1a edit saphyr1a Host file Enter the following command and input all the Node Static IPs provided by customer IT Dept sudo nano etc hosts...

Page 29: ...Saphyr1a node IP address Enter command ssh saphyr1a Note If a password prompt displays please contact Bionano Technical Support 3 2 4 Enter exit to return to Access 4 Configure Bionano Access Server a...

Page 30: ...are home bionano access share irysSolveShare home bionano access share irysSolveListenIP xxx xxx xx xx Add Access Static IP icsShareRelPath chips webServerShareJobs jobs webServerRelLocalFiles webServ...

Page 31: ...customer Never share bionano credentials with customers 5 1 Putty into the BAS with BNG login credentials 5 2 Create a username login Input line command Note The username should be unique to the Insti...

Page 32: ...tic procedures 30251 Rev F Saphyr Networking and Setup Guide Page 32 of 36 Appendix A Legacy Saphyr Compute Options Below is the configuration for Dell with two port network cards Below are the config...

Page 33: ...full proxy URL and optionally the proxy credentials and click Apply Proxy Settings HTTPS proxy URLs are not supported Note There must be a tethered connection between the Instrument Controller and the...

Page 34: ...ation Appendix C Verifying Firewall Configuration for Saphyr ICS 1 Log in to Saphyr ICS using the SysAdmin credentials 2 Select the lock icon in the top toolbar to display the Saphyr Assure dropdown a...

Page 35: ...and higher If the network test was successful but Saphyr ICS connections still aren t functional an internal DNS server may be interfering To test this in Saphyr ICS Main Menu select System Settings...

Page 36: ...tation on Bionano products SDS s certificates of analysis frequently asked questions and other related documents from the Support website or by request through e mail and telephone Type Contact Email...

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