Running AntigenMap jobs involves four screens (steps) - input, review, color, and result. At each screen you are provided with help messages as popup buttons for major input parameters.

The input screen provides form fields required to run AntigenMap. It starts with a choice to choose Map Display Option. The main data is your HI Table (either by file upload or direct input). Other parameters include: Low Reactor Threshold, Normalization Method, Rank, Number of Iterations, and an option to run AntigenMap using temporal model.

Map Display Option

We provide 2D and 3D map types for antigenic cartography visualization. This is the first choice to be determined.

HI Data

There are three types of data points presented in the HI matrix: observed/regular values, unobserved/missing values, and low reactors

  • Regular Entries: Regular data entries should be of Integer type.
  • Missing Values: If the testing antigen and antiserum did not react or you simply did no perform such pair of reaction in your experiment, please put 0 at this entry.
  • Low Reactors: If the reaction values are smaller than a certain confidence threshold, please indicate such an entry by prefixing it with <. For example, <20 means this entry has a value that is less than 20 but user does not know the exact and reliable value.

For detailed HI table format, please click on input screen, next to the section title "Data: HI Table"

Click to automatically paste our example HI table input text field.


Low Reactor Threshold: Choose an appropriate threshold value such that any entry with a value smaller than this threshold would be treated as low reactors. Setting different threshold will influence the final result.

Normalization Method: We provide five methods to normalize HI table. N4 and N5 require that you provide reference values in your HI input header line.

Temporal Model: Choose whether to treat your HI input as temporal data and use our temporal model to determine antigenic distances between testing antigens.

Rank: Provide an appropriate rank value of your input data matrix. The default rank is 2. Choose a higher value if your data set is larger.

Number of Iteration: Choose the maximum iteration number during low rank matrix completion step in AntigenMap program.

Submit Input Form

Once you are ready, click to submit input form. Your input will be automatically checked. You will be prompted with a warning window if any of your input does not pass validation.

Once your input data have passed the initial validation, all parameters and HI table will be presented on the second screen for review purpose.

The entries in HI table are highlighted with different background colors.
  • Antigen names are on green background.
  • Group ID's are on blue background.
  • Observed/regular HI entries are on white background.
  • Unobserved/missing HI entries are on grey background.
  • Low reactors are on yellow background.
  • Invalid fields are on red background.
If you do not think the input data are correct, you can click to go back to the first screen.
Otherwise, click to initiate AntigenMap computation job.
Modify On-the-Fly
You are also presented with the opportunity on review screen to modify any entry in HI table on-the-fly. Just click an data entry cell, you will be prompt with a editable field. Once you are done, click anywhere outside the field will make the update. Any update will be validated immediately. An invalid entry will be highlighted on red background.
If you want to display antigen names as data point labels on antigenic cartography map, please check corresponding checkboxes in front of these antigen names.
If there is any invalid entry, you will not be able to proceed to the final screen, but appears instead.

While the computation job is running, you are then prompted to choose the color scheme of each data group. Click each color palette to choose from predefined color options. Once you are ready, click .

Once you have chosen color scheme AND the computation job is completed, you will be presented with the final antigenic cartography map, either 2D or 3D depending on your initial choice on input screen.

Map Manipulation

If there is more than one group of data entries, a legend box will appear inside map area. This box is draggable for your convenience.

Click on group label inside the legend box will toggle all data points belonging to selected group.

Click and drag a rectangle selection will zoom in for viewing local details. This is especially useful if multiple data points are heavily clustered together. Click button "Reset Zoom" will bring the view back to the original scale.

Map Export

Click the top-right button inside the map will prompt you a few exporting options to save constructed map AS-IS.


Public users will see a watermark embedded in constructed map. In order to remove this watermark, you are encouraged to register with us.

Job Tracking

You are also provided with a direct URL to current job. This is especially useful if your job runs longer than usual. Keep this URL for your future reference. Periodically check at this URL to see if your job has completed. Email notification is coming soon for AntigenMap and other web application services on our website.

There is another advantage with a registered account - you are able to keep track of ALL jobs (completed and/or running) once you are logged in.