Useful Tools in BioNumerics - aphl.org...Useful Tools in BioNumerics Existing Applications and New Features of BioNumerics v4.5 and MasterScripts v3.0 Molly Joyner, CDC April 5th,

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


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


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”


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


The isolates have been selected on the online server

To download these isolates for comparison, click on “download the selected entries from 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



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?