Useful Tools in BioNumerics
Existing Applications and New Features of BioNumerics v4.5 and MasterScripts v3.0
Molly Joyner, CDCApril 5th, 2006
Existing Applications: Changing your settings
Can change settings of database
Can change order of information fields for comparisons
Can change directory
Highlights: BioNumerics v4.5: Start-Up Menu
Wider database list field
v4.0 v4.5
Highlights: BioNumerics v4.5: Start-up menu
Double-click on database name to open database
Highlights: BioNumerics v4.5: DatabasesShortcut: CTRL-A to select all entries in database
- A
- A
Use CTRL-A to select all entries in a comparisonAnd
Highlights: BioNumerics v4.5: Fingerprint TypesPop-up gelstrips in database can be lined up or
closed all at once
Right-click on a gel strip and select “line-up”or “close all”
Highlights: BioNumerics v4.5: ComparisonsEntries in a comparison can be converted to a subset
Highlights: BioNumerics v4.5: Comparisons
Comparison information can be shown when comparison is printed (title of comparison and field names)
Select Layout, “show comparison information”and/or “show field names
I’ve Uploaded my Patterns – Now What?•Detecting Local Clusters
•Bundle Files
•Working with Online Databases
•New Features
Detecting Local Clusters: Hot-List Search in Client
The “Hot-List” is a new addition to the PulseNet client scripts
Enter the number of days to search back
Isolates found within search
Detecting Local Clusters: 60-120 day searchTo detect a local cluster, start by searching for the past 60-120 days
Query by isolate & choose upload date range
Create a comparison with selected isolates
Pull up images and look for clusters
Creating Bundle Files
Choose a name for the bundle
Select entries to be saved in bundle:
-Ctrl + left-click
OR
-Shift + left-click
OR
-Left click + space bar
Next click “create PulseNet bundle”icon
Default setting selects every field but you can deselect a field by clicking on it
Opening Bundle Files
Bundle Location
“File/Open Bundle”
“Open/Close Existing Bundles” tool at top of toolbar
Two ways to open bundles in your database
OR
Reminder: PulseNet bundles only!Always check a bundle file’s information before opening it!
If it has extraneous fields, request a PulseNet bundle from the person from which you received the bundle file.
NON-PULSENET BUNDLES WILL BE DELETED FROM THE WEBBOARD.
A PulseNet bundle is denoted by a “PN” after the file name
Green dots = PulseNet fields
Red dots = non-PulseNet fields
Making a bundle permanent1. Save a bundle file from the WebBoard
to proper location
2. Rename bundle file with “@_” in front of name
3. Isolates in bundle file will appear in your database next time you open it
Making a bundle permanentAn example of when you would make a bundle permanent:
Annual & Quarterly reports are located on the WebBoard under “Important PulseNet Documents” / “2005 Reports”
Right click to extract bundle to where your bundles are saved
Rename with @_file-name
•Outbreak patterns are included in Annual/Quarterly Reports for that year/quarter
•Save bundle permanently to use for future reference
Online Databases: New Way to Connect (Using BN v4.0 or higher)
New tool for connecting to online server
Enter login & password
Enter the # of days for which you would like to search for data (10 is default)
Connecting this way can
•Reduce connection time
•Allow searches of a subset of the database
•Allow you to connect at “0” days and still upload
Online Databases: Change to Default Hot-List Search
When connected to the online database(s), the default days for the Hot List search has been changed from 60 to 30 days.
Keep number low to narrow your search
Online Databases: Searching the National Database
To decrease the number, search using more specific criteria (ex: serotype) in the hotlist that was just selected [notice use of wildcards (*)]
Much better!
Download these to your local database
Online Databases: Searching the National Database
Select local isolates that you would like to compare to those in the national database and choose “Copy selection”
Paste local selection into comparison with national database selection
Calculate cluster analysis
Online Databases: Searching the National Database
Now you can see that some of your local patterns cluster with patterns in the national database
Online Databases: Match Against Server (Using BN v4.0 or higher)
Open Entry Edit screen for an isolate for which you would like to find matches in the online database
Match Against Server Tool: Use to identify patterns from online server that are within a certain number of bands different from patterns in your local database
Using this tool, you can compare an isolate to anything in the database
Online Databases: Match Against Server
Select:
1) Enzyme
2) % Tolerance
3) Maximum number of bands different
4) Maximum number of entries to be selected
Note: Even if you are only connected for the past 10 days, you will be able to compare your local patterns to online patterns that were submitted prior to 10 days with “Match Against Server”
Online Databases: Match Against Server
Match results come up in a new window. To select each isolate, either hold down CTRL and click on each one or hold down SHIFT and select a range
Online Databases: Match Against Server
The isolates have been selected on the online server
To download these isolates for comparison, click on “download the selected entries from server”
Online Databases: Match Against Server
Copy local pattern into comparison to see if it matches any from online server
New Features: New Databases: Vibrio cholerae
Vibrio cholera
The V. choleraedatabase includes new fields, including:
•Serogroup
•O1 serotype
•BioType
•Onset Date
•Toxin
Note: There is no “Serotype” field in the V. choleraedatabase
New Features: New Databases: Yersinia Pestis
Yersinia pestis
There are 7 new fields that are used in the Y. pestis database:
•Species
•Agency ID (for cross-reference)
•BioType
•Diagnostic (for LRN testing). This takes the place of the Biochemical button.
Note: there is no “Serotype” field in the Y. pestis database
New Features: Fill Gel Information Field ScriptNew script under “PulseNet” menu: “Fill Gel-Information Field”
Select isolate(s) for which you want this information added and then run the script
The gel and lane information is added in the appropriate field “PFGE-enzyme-file”
Note: This field is now automatically filled when you upload patterns to the online database
New Features: New Fields: “Traveled to” & “Exposure”
New Fields: “Exposure” & “Traveled To” have been added to PulseNet databases
The pull-down menus have been populated; however these are just suggestions –other items can be added to your list
Note: Please do not put sensitive information in these fields such as company names, brands, etc.
New Features: New Fields: “Patient Age” in Days
New field: Patient age in number of days can now be added in the“patient age” field
Note: this field is for numbers only. Please do not enter “< or >” or other symbols into these fields. Also, the days field does not need to be filled if the person > / = 1 year old
New Features: Updates to Pull Down Menus•Always use the pull down menus in the Entry Properties window
Several serotypes have been added to the Salmonella & E. coli databases
Click on green “i” to open Entry Properties window
Salmonella serotype I 4, [5],12: i-has been moved from the top of the serotype pick-list. It is now grouped with the “I’s”.
New Features: Updates to Pull Down Menus
There have been items added to the “Type Details” field. This is not a required field; it is a place to add additional information about an isolate.
These are suggested items; you can add to your list
Use the Charts & Statistics tool to visually show database information
Ex: to see trends in a certain pattern, select isolates with that pattern
Then click on charts & statistics tool
Select field (component) that you want to graph and click on “Add”
Presenting Data: Charts & Statistics Tool
Click on “Date Variable” and select “Convert to interval data” to graph trends by day, month, or year
Click on “OK”to create graph
Presenting Data: Charts & Statistics Tool
Presenting Data: Charts & Statistics Tool
Use tools to change type of chart
Can select two components (such as age and city) and graph in a contingency table or 3D bar graph
Presenting Data: Collapse/Expand Branches
Use “Collapse Branch” tool to simplify large/complex dendrograms
•Select a group of closely related isolates
•Create dendrogram
•Choose “collapse/expand branch” under Clustering menu
Presenting Data: Swapping BranchesLet’s say you want to place 2 clusters next to each other, but do not want your dendrogram to go away…
Right-click to select branch, and choose “Swap branches”
Repeat as many times as needed
Now the clusters are next to each other for further inspection
Presenting Data: Using Groups in Posters/PublicationsGroups can be shown as colors for posters/presentations (default)
Groups can be shown as shapes for publications (or papers that will be in black & white)
OR
Conclusions
Utilize existing tools to:
• Maintain local database
• Search National Database
• Manage clusters/outbreaks
Features of Masterscripts v3.0 include:
• New databases: V. cholerae & Y. pestis
• Additions & changes to local databases
• Additions & changes to online databases
ConclusionsSome highlights of BioNumerics 4.5 include:
• Changes to start-up menu
• Changes to databases
• Changes to fingerprint types
• Changes to comparisons
Present data in various ways using tools such as:
• Charts & statistics
• Swapping/Expanding & Collapsing Branches
• Groups
AcknowledgementsThank you to the following laboratories / individuals for participating in testing of MasterScripts v3.0:
Alabama - Sherricka Simington
Los Angeles County - Eleanor Lehnkering
Hawaii - Precy Calimlim
New York - Dianna Schoonmaker-Bopp
Wyoming - Wanda Manley
Questions?