Bionumerics Databases

A core component of PulseNet International is the ability to compare genotyping results produced in different laboratories. This is facilitated by using normalising electrophoresis gels against a common standard, and the use of the same names for database fields. PulseNet certified laboratories should contact their regional coordinator for PulseNet standardised databases including script customisations.

 

Bionumerics Usage Guidelines (2011 Training Sessions)

The following PDFs are from presentations at the 2011 PulseNet Training sessions, and describe the use of BioNumerics. The PDFs can be viewed by clicking on the image or the link in the text.

PulseNet MasterScripts and Database Management Tools - PDF 1457KB pdf icon  1. PulseNet MasterScripts and Database Management Tools
Presented by Lisa Theobald, April 2011
PDF 1457 KB, 22 pages
Creating Databases and Installing MasterScripts - PDF 946KB pdf icon  2. Creating Databases and Installing MasterScripts 
Presented by Lisa Theobald, April 2011
PDF 946 KB, 21 pages
Analyzing a TIFF - PDF 5331KB pdf icon  3. Analyzing a TIFF, Linking Lanes, and Entering Data
Presented by Beth McGlinchey, April 2011
PDF 5331 KB, 66 pages
Creation and File Location of PulseNet Bundle Files - PDF 1876KB pdf icon  4.Creation and File Location of PulseNet Bundle Files
Presented by Chris Bailey, April 2011
PDF 1876 KB, 16 pages
Querying and Performing Comparisons- PDF 4027KB pdf icon  5. Querying and Performing Comparisons
Presented by Shannon Dalton, April 2011
PDF 4027 KB, 39 pages
Using Chart & Statistics Tool and Groups - PDF 2066KB pdf icon  6. Using the Chart & Statistics Tool and Groups
Presented by Steven Stroika, April 2011
PDF 2066 KB, 34 pages
Importing Data in BioNumerics - PDF 1484KB pdf icon  7. Importing Data In BioNumerics
Presented by Jen Castleman, April 2011
PDF 1484 KB, 18 pages
PFGE: Tips and Tricks - PDF 3249KB pdf icon   8. PFGE: Tips and Tricks to Success and Interpretation of Results for Foodborne Outbreak Investigations
Presented by Molly Freeman, April 2011
PDF 3249 KB, 29 pages
Advanced Tools - PDF 2708KB pdf icon  9. Advanced Tools
Presented by Kelley B. Hise, April 2011
PDF 2708 KB, 37 pages

 

Bionumerics Usage Guidelines (2009 Training Sessions)

The following PDFs are from presentations at the 2009 PulseNet Training sessions, and describe the use of BioNumerics. The PDFs can be viewed by clicking on the image or the link in the text.

Introduction to BioNumeric 5.0 and PulseNet scripts - PDF 1640KB pdf icon  1. Introduction to BioNumeric 5.0 and PulseNet scripts
Presented by Molly Leeper, May 2009
PDF 1640 KB, 29 pages
How to create a new database and install pulsenet scripts - PDF 915KB pdf icon  2. How to create a new database and install PulseNet scripts
Presented by Molly Leeper, May 2009
PDF 915 KB, 23 pages
Gel anlaysis presentation - PDF 2228KB pdf icon  3. Analysis of tiff images in BioNumerics, linking of lanes to isolates and adding text data
Presented by Angie Dixon and Jen Castleman, May 2009
PDF 2228 KB, 68 pages
Import data using OBCD and export data to excel - PDF 1000KB pdf icon  4. How to import data using OBCD and export data to Excel
Presented by Beth McGlinchey, May 2009
PDF 1000 KB, 26 pages
Query local and national databases and making composite data sets - PDF 1780KB pdf icon  5. How to query local and national databases and making and using composite data sets
Presented by Erik Coleman, May 2009
PDF 1780 KB, 33 pages
Performing comparisons in BioNumerics - PDF 1887KB pdf icon  6. How to perform comparisons in BioNumerics
Presented by Erik Coleman, May 2009
PDF 1887 KB, 30 pages
Performing comparisons in BioNumerics - PDF 1887KB pdf icon  8. How to perform advanced queries in BioNumerics
Presented by Shannon Brown, May 2009
PDF 767 KB, 23 pages
How to change setting and layouts in BioNumerics including adding fields, changing order of fields, directory location, picklists, deleting databases - PDF 1151KB pdf icon  8. How to change setting and layouts in BioNumerics including adding fields, changing order of fields, directory location, picklists, deleting databases
Presented by Molly Leeper, May 2009
PDF 1151 KB, 26 pages
How to use the groups, charts and statistics tools in BioNumerics - PDF 1484KB pdf icon  9. How to use the groups, charts and statistics tools in BioNumerics
Presented by Shannon Brown, May 2009
PDF 1484 KB, 39 pages
Creation and File Location of PulseNet Bundle Files - PDF 432KB pdf icon  10. How to create bundle files, file location of the bundle file, and how to open bundle files
Presented by Angie Dixon, May 2009
PDF 432 KB, 17 pages
How to remove the navigator window, alter preferences, add database fields and freeze panes - PDF 326KB pdf icon  11. How to remove the navigator window, alter preferences, add database fields and freeze panes.
Presented by Lisa Theobald, May 2009
PDF 326 KB, 8 pages

PulseNet Regional Database & Server Requirements

Hardware and Software Requirements

Hardware:

  • Application Server
  • Database Server
  • Admin Workstation
  • Client Workstation

 Software:

  • BioNumerics Server Software (one for each server)
  • BioNumerics Client Software (one for each server and one for each client)
  • SQL or Oracle Software (one for the database server only)

Hardware and Software Configuration

Application Server:

  • Windows Server Operating System
  • BioNumerics Server Software
  • BioNumerics Client Software

 Database Server:

  • Windows Server Operating System
  • BioNumerics Server Software
  • BioNumerics Client Software
  • SQL or Oracle

Admin:

  • Windows Professional Operating System
  • BioNumerics Client Software
  • PulseNet Admin Scripts

Client:

  • Windows Professional Operating System
  • BioNumerics Client Software
  • PulseNet Client Scripts

*Note: Gel Compar (Applied Maths) Client Software can be substituted for BioNumerics Client Software

The costs for setting up a BioNumerics Online Server and Regional/National Database includes, but are not limited to, the servers and workstations, as well as the operating systems and the BioNumerics server and client software. The hardware costs will depend on current market prices, specifications and the manufacturer of the hardware. The software costs will depend on the BioNumerics version and the number of licenses needed.

The BioNumerics Online Server will need to be accessible to the BioNumerics clients via the Internet. Therefore, internet connectivity costs should be taken into consideration when planning costs.

The PulseNet standard configuration of BioNumerics includes the following modules:

  • Fingerprint Types
  • Character Types
  • Sequence Types
  • Comparison & Cluster Analysis
  • Identification and Libraries
  • Database Sharing Tools

The Sequence Types module is not required for analysis of PFGE data, and all basic PulseNet functions can be performed without the Identification and Libraries module, however, for some functions only slowly and manually.

Regional Database Personnel Requirements

Please note that one person may be able to perform more than one of the tasks mentioned below.

  • Database managers (for each organism)
  • Supervisor/coordinator of database managers
  • QA/QC manager responsible for the certification and proficiency program
  • Network administrator/engineer support, responsible for the installation, operation and maintenance of the BioNumerics applications on the servers and workstations

The costs are associated with compensation for database managers, supervisors, QA/QC manager and network administration/engineer support.

Regional Database Activity
  1. Regional reference laboratories (PulseNet participating laboratory): analyze and upload isolates from local client databases; and download, query and compare isolates submitted to the regional database using BioNumerics or Gel Compar software.
  2. Database manager: analyzes and uploads isolates for participants who are not analysis certified or who do not have the required resources; verify the accuracy of the bandmarkings of the uploaded isolates; assigns pattern names to isolates; maintains the integrity of the databases; identifies clusters and potential outbreaks; assists epidemiologists in outbreak investigations; provides classroom and on-site instructions and training for BioNumerics training; and attends Update Meetings.
  3. Supervisor/coordinator of database managers: supervises database managers in their daily work, as well as prepares and presents database team-related information and documentation, as requested.
  4. QA/QC manager: works with regional/national laboratories to prepare and distribute certification sets; evaluates gel and analysis certification submitted by laboratorians; works with regional/national laboratories to prepare and distribute proficiency sets; evaluates proficiency of gel and analysis; prepares updates and distributes quality control documentation.
  5. Network administrator/engineer support: responsible for the installation, operation and maintenance of the BioNumerics applications on the servers and workstations; provides access to the regional database; provides access to a discussion forum which is accessible by all regional PulseNet participants (including epidemiologists) through the Internet, and that would serve as the central communication tool for distributing information relevant to current clusters and outbreaks; as well as provides daily troubleshooting support for PulseNet participants.
Regional Data Management Flowchart - example from PulseNet Latin America

Data management flowchart

 

For further information please contact: The PulseNet International coordinator

Useful download: word iconPulseNet regional database/server requirements info sheet.
(Word doc. 254 KB)

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