next generation 2100 software - a wealth of new features

Next Generation 2100 Software - A Wealth of New Features

Chairperson: Ingrid Ginnutt

Content of the E-seminar

• 2100 expert software concept

• New features

• How to use new features?

• New product structure

• Your upgrade to new 2100 expert SW

• Summary


The Agilent 2100 Bioanalyzer

DNA 7500 LabChip kitSizing and Quantitation (100-7500bp) Restriction digests, PCR products

DNA 12000 LabChip kitSizing and Quantitation (100-12000bp) Restriction digests, larger DNA fragments

RNA 6000 Nano LabChip kitQC & Quantitation (up to 6000 bases)Total RNA, mRNA, microarray samples

DNA 1000 LabChip kitSizing and Quantitation (25-1000bp) Small PCR products, small restriction digests

Protein 200 Plus LabChip kitSizing and Analysis (14-200 kDa) Proteins

DNA 500 LabChip kitSizing and Quantitation (25-500bp)PCR products, restriction digests

Cell Fluorescence LabChip kitAnalysis of cell fluorescence parameters Cells

RNA 6000 Pico LabChip kitHigh Sensitivity QC (up to 6000 bases)Total RNA, mRNA

Protein 50 LabChip kitSizing and Analysis (5-50 kDa) Proteins


Winter 2004Dec 2003

2100 expert software- one version for all assays- Decl. of system validation

2100 expert security pack- 21 CFR part 11compliance- electronic records- electronic signatures- audit trails

2100 bioanalyzer - IQ and OQ/PV services- Declaration of conformity

Chips and reagents- Declaration of conformity

SW for Molecular Assays: “Bio sizing”

SW for Cell Assays: “Cell fluorescence”

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2100 Software Roadmap

* Biosizing and Cell fluorescence will be made obsolete

*

*

Past


2100 Expert Software – In Brief

• Replaces Biosizing and Cell fluorescence software

• One SW for electrophoresis and flow cytometry assays supporting the platform idea: “one platform – endless possibilities”

• Incl. all capabilities of the current “Biosizing” and “Cell fluorescence” SW

• One look and feel for the analysis of RNA, DNA, proteins and cells

• Support all existing and future LabChip kits and assays

• Import of old data files from Biosizing and Cell Fluorescence possible


2100 Expert Software – In Brief (cont.)

• Control of all bioanalyzers (old A- & B- and current C-versions)

• Data Organizer not compatible with 2100 expert

• License keys for software modules (electrophoresis, flow cytometry, security pack), no license for data review

• Runs on Windows 2000 and Windows XP

• Many new SW features


2100 Expert Requirements

• PC hardware (minimum requirements):• CPU: Pentium III with 800 MHz• RAM: 128 Mbyte• Ports: 1-2 serial ports• VGA: Resolution of 1024 x 768• HDD: 10 GB

• Operating system:• Windows 2000 Service Pack 4 (or higher)• Windows XP Service Pack 1 (or higher)• Not compatible with Windows NT

• 2100 bioanalyzer:

• A and B/C version, compliance services for B/C version only (serial number DE13701001 or higher)


2100 Expert New Features - Based on User Requirements• Improved integrator with manual integration

(change start/end point and baseline)

• Color coded result flagging (e.g. “mark all samples in green that contain a 38 kDa protein in a concentration above 75 ng/ul”)

• Compare results from different chips within the improved and integrated data comparison context (previously Data Evaluation Tool)

• Pattern recognition and smear analysis applicable to RNA, DNA and protein assays

• Normal and advanced user mode

• Improved reporting and printing functions

• Preview in file open window (e.g. gel-like image, sample names)


2100 Expert New Features - Based on User Requirements (cont.)

• Customizable result tables and gel like-image

• More export formats (txt, pdf, wmf, jpg, tif, bmp, ...)

• New context structure for easy access of software functionalities

• Extended diagnosis functionality

• Support of IQ & OQ/PV

• Prerequisite for 21 CFR part 11 compliance, prepared for security pack (with user authentication/user roles, archiving/revision control, audit trails, …..)

• And many more ……


2100 Expert Contexts

Instrument context

• Connect to up to 2 instruments

• Run a demo assay

• Run an assay

Data and Assay context

• Enter sample info

• Review results (gel-like image, E-gram, dot plot, histogram, result table)

• Change assay set points on sample or chip level (e.g. Min. Peak Height)

• Result flagging

• Create/modify new assays

Validation context

• Run IQ and OQ for hardware and software

Comparison context

• Compare results from different chips (gel-like image, E-gram, result table)


Tree view for navigation between samples and files

Contextmenu bar

Customizable gel-like image(change order)

Customizable result table (change order and add additional columns)

Single gel lane for selected E-gram

Task bar with context sensitive icons for different actions

Tabs for different data analysis functions


How to use old data files from Biosizing or Cell Fluorescence? • Go to File/Import

• Select old bioanalyzer files that

you would like to import

Note:

2100 expert files can not be imported in

Biosizing or Cell Fluorescence


Convenient switching between flow cytometric and electrophoretic assays

• Flow cytometric and

electrophoretic assays are

available in the Assay menu

• depending on the inserted

cartridge

• and the entered license key(s)


• Click on Electropherogram tab

• Switch to Manual Integration

mode

• select Menu/Manual

integration• or clicking on the “manual”

icon in the task bar

Easy access to manual integration in electropherogram tab


Integration of Soy Bean Protein- Get better quantitation precision with manual integration

Biosizing

10 11 12 13

Fluorescenc

e

Time (seconds)

77.5

80.0

82.5

85.0

87.5

90.0

92.5

95.0

97.5

28.5 29 29.5 30 30.5 31 31.5 32 32.5 33 33.5

123

4

Conc. [ug/ml]

Peak

24.834.738.029.7

4321

2100 expert - automatic integration

123

4

Conc. [ug/ml]

Peak

24.834.637.929.7

4321

123

4

Conc. [ug/ml]

Peak

28.638.044.433.6

4321

2100 expert - manual integration

1

Conc. [ug/ml]

Peak

144.6

1


How to move peak start/end point in manual integration mode?

• Peak start and end time are shown as blue dots

• (A) blue dot is on signal :• Click on blue dot• Dot turns green• Hold left mouse button and move

dot along signal

• (B) blue dot is on drop line (dotted line)• Click on blue dot• Dot turns green• Press Ctrl and hold left mouse

button to move dot along drop line

• Create a new drop line• Press Ctrl and hold left mouse

button to move dot along new drop line

(A)

(B)


How to modify columns displayed in result table?

• Right mouse click on table

headers• Select Configure columns• Select to be displayed column

headers


How to change the column order in the result table?

• Click on column header and move

it to desired place

• New location is indicated by green

arrow


How to apply set points from one data file to another?

• Go to Assay Properties tab in the

data context• Click on Import set points• Select the file from which you

want to apply the set points from


How to get a quick result overview using color-coded result flagging?

• Set up rules in Result flagging

(data and assay context)

• Apply rules

DNA fragment with 25, 70, 93 bp found

DNA fragment with 160, 206, 308 bp found

DNA fragment with 500, 610, 1000 bp found and total conc. > 50 ng/ul


How to re-arrange the gel-like image lanes for better comparison?

• Select the lane that you would like

to move• Hold left mouse click on lane• Move lane to new location

Initial gel-like image

Rearranged gel-like image


How to zoom in the gel-like image?

• Hold left mouse click on gel-like image

• Two horizontal lines appear (one line is

fixed)

• Move mouse while holding left button

• Release left button (second line is

fixed

• Both line define the zooming window

• Double-click to undo the zoom


How to do smear analysis for RNA, DNA or protein assays?

• Go to Assay properties

• Select Smear analysis in the

advanced sample set points

• Define size regions

• Results are displayed in new

Region table

• Regions are indicated by dotted

lines in the electropherogram


Compare chips in comparison context

Select sample from different chips

Electropherogram overlay

Legend for electropherogram overlay

Single gel lane for selected E-gram

Save selected samples in a comparison file

Switch between comparison summary, gel and electropherogram view


New Product Structure - Start with flow cytometry or electrophoresis functionality or both !

2100, Accs.

2100G2938C2100, PC, Accs., VM

SW on CD

Start-up service

2100 Desktop SystemG2940CA

2100, PC, Accs., VM

SW on CD

Start-up service

2100 Laptop SystemG2943CA

Electrophoresis SetG2947CA

Electrode Cartridge

Electroph. License

Flow Cytometry SetG2948CA

Pressure Cartridge

Check.&Test chip kit

Flow Cyt. License

System IQ and OQ/PV Services:Per incident:IQ (R1015A)OQ/PV (R1016A)


Your upgrade to 2100 expert software

• Free upgrade of current 2100 users, if registered

• after 2100 installation

• with LabChip kit fax back form

• Software and electrophoresis licenses are in the post or have been shipped already

• if you have not receive your copy by March 2004, please contact your local sales representative

• current cell fluorescence users please contact your local sales representativeto acquire a flow cytometry license

• 2100 expert software can be run in parallel to Biosizing or Cell fluorescence software


Compliance for the Agilent 2100 bioanalyzer systems - A 2-phased approach

• Phase I – GMP/GLP compliance:

• 2100 expert software

• IQ & OQ/PV services

• "Declarations of Conformity" for all LabChip kits

• Phase II – full compliance:

• Security Pack for full 21 CFR Part 11 compliance


Reasons to switch to 2100 expert software

• Nothing to loose – all features from Biosizing and Cell fluoresence included

• Benefit from many new software features

• Take first step towards full 21 CFR part 11 compliance

• New assays and LabChip kits will only be developed for 2100 expert

“One software, one platform

for analysis of cells, proteins, RNA and DNA”

next generation 2100 software - a wealth of new features

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