Using IVART online

Preparation of data

Correct data management and preparation is crucial for successful use of IVART Online. Data for IVART online processing must:

• be organised in a 96-well plate format with 8 horizontal rows and 12 vertical columns.
• be annotated by a system of “Tags” to identify results plates and drug layouts
• include at least two drug-free controls on each plate
• be saved in Microsoft Excel 2007 format (.xlsx)

 

“Tags” are strings of text placed in the cell immediately below and to the right of the cells corresponding to a 96-well plate of results or drug concentration data. Tags are critical to defining the location of a plate and ensure that results are matched correctly with drugs and concentrations. Result tags contain information about samples and the study (Table 1).

 

table4IVART

Variable in the result tag	Description	Value
ID1	Sample ID1	Required
ID2	Sample ID2	Optional
Date	Date of sampling from patient (dd/mm/yyyy)	Optional
DrugLayout	Name of Drug concentration layout	Required
Country	Country patient infected	Optional
StudySiteName	Location of study	Optional
Method	Readout method + duration of test	Optional
Lat	Latitude	Optional
Lon	Longitude	Optional
SampleType	Reference clone	Required only for references; leave blank for field isolates
Batch	Date of preparation of drug plate batch (dd/mm/yyyy)	Optional

 

There are two options to prepare data files for IVART analysis:

1. Copy & Paste data into the IVART Data Template – an easy solution in order to immediately begin your analysis and a helpful step that allows for data organisation in prospective studies.
2. Add tags to identify drug concentration layouts and result plates in your own data files according to the Example Tagging file. Users who become familiar with this more complex approach can process large datasets more quickly.

 

IVART Data Template

In the sheet Drug concentration Layouts of the IVART data template, the drug and its concentration (nM) in each well of the 96-well plate is specified. The layout can be adapted to your specific data set, organised by column or row, with increasing or decreasing concentrations. More than one drug concentration layout with its own unique name may be added. The template automatically generates a drug layout tag seen in the dark blue cell used by IVART to extract data (Fig. 1). The layout only has to be created once.

 

Figure 1: Defining your drug concentrations in the IVART data template

 

In the sheets Results Isolates and Results References the test results (i.e. counts per minute, absorbance, microscope count etc.) are pasted in the 96-well format for each drug and concentration. Information relevant for each plate, sample, and study can be entered in the white cells to the left of the plate. The template will automatically generate the plate tag (dark blue, lower right) when the variables Sample ID1 and DrugLayout, required for IVART analyses, are filled in (Fig. 2).

Figure 2: Copy and paste test results and enter plate information in the IVART data template

 

Tagging data in an existing file

To specify the drug concentration used in each 96-plate well, a drug concentration layout worksheet is created following the Example Tagging file. The tag “DRUG-LAYOUT:NAME” is placed in the cell immediately below and to the right of the drug concentration layout. The Drug-Layout tag defines an area of 12 columns x 8 rows from which IVART extracts drug concentration values (in nM).

Figure 3: Creating a drug concentration layout when tagging your data

 

Result plates are annotated by adding a tag in the lower right corner of the each plate - N12 in Figure 4. The tag can be copied from the Example Tagging file and it contains references to cells where information about the sample and study is located or can be filled in. The function of the tag can be changed to retrieve values from different cells and to have default values.

Figure 4: Tagging the result plates in your data file by using the tag in the Example file

Data Upload and Analysis

Tagged data files can be uploaded to IVART and will be securely stored on WWARN’s servers where the access is limited to the user. The Plate Assistant provides feedback on any tagging errors, helping IVART to extract data correctly. It highlights problems with the file organisation that should be resolved before the file can be analysed and it issues warnings of inconsistencies in the data file. Once the data is ready, it can be analysed. A data set with a thousand assays can be processed within five minutes; the results are available for immediate download.

Selected data sets can be shared with WWARN through the IVART online system. It is not a requirement to share data with WWARN to use IVART Online. Details regarding the use of IVART Online are specified in the Terms of Use and in the Step-by-step User Guide available to download.