How to submit a Challenge 2013 entry

This page contains important information for participants in the PhysioNet/CinC Challenge 2013. Please read it carefully before submitting Phase 2 or 3 entries!

Entries must be submitted as tarballs or zip files

To simplify uploading of challenge entries, and to permit automated scoring for events 4 and 5, all of the files associated with an entry must be included in a single zip file or tarball, either of which can be made using many widely available file archivers.

Sample entry

A sample entry is available as a tarball or as a zip archive. If you download and unpack either version of the sample entry, you will have a complete set of required files, arranged as required in two directories. The tarball or zip archive that you create from your own files should have the same structure as the sample entry.

Important note about file names

Files stored on PhysioNetWorks may have names that contain any of these 66 printing characters:

ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789.+_-
Any other character in the name of a file in your entry will be replaced by an underscore (_). Do not include files with names that contain spaces or other disallowed characters in your entry, especially in names of source files, because they may make it difficult or impossible for us to score your entry properly.

Required contents

Directories: Create a directory (folder) named annotations, and a second folder named sources.

Set B annotations: All entries must include an annotation file for each of the 100 records in test set B (b00, b01, b02, ..., b99). These files may be in either of the formats used for the reference annotation files provided for set A: either text format, or PhysioBank-compatible binary format.

If PhysioBank-compatible binary format is used, the names of the files must be b00.ann, b01.ann, b02.ann, ... b99.ann.

If text format is used, the names of the files must be b00.txt, b01.txt, b02.txt, ..., b99.txt. In this format, each line contains an integer that specifies the time of occurrence of a fetal QRS complex, in units of milliseconds elapsed since the beginning of the record. The times must appear in chronological order. Compare your files with the .fqrs.txt files provided for set A. It is important to use the correct format so that the autoscorer can calculate your scores correctly.

These files are the basis for calculating the scores for events 4 and 5. All of them must be collected in the annotations directory.

README.txt: Include a short text file with the names of your team members, their affiliations, and contact information (postal and email addresses). Put it in your sources directory.

Optional contents

QT measurements:

Event 3 (QT measurements of set C) is open to participants who submit sources for their software. If you wish to participate in event 3, your software should produce for each record a one-line text file named "qt.txt", containing its estimate of the QT interval in milliseconds.

Although event 6 (QT measurements of set B) has been cancelled, you may include QT measurements for set B records in your submission if you wish. Please submit them in the same format as for event 3, but the individual files should be named b00.qt, b01.qt, b02.qt, ..., b99.qt, so that we can associate them with the correct records. Include them within the annotations directory. If we obtain a sufficient number of such measurements, we will attempt to derive a crowd-sourced set of QT measurements from them for further study.

Source files: If you wish to enter events 1, 2, and (optionally) 3, include a set of source files for your software in the sources directory. Sources in C, C++, Java, MATLAB m-code, Perl, Python, or R are acceptable.

Submitting an entry

Use the zip- or tar-compatible file archiver of your choice to create a zip file or tarball containing the annotations and sources directories. (It should not include any higher-level directories, or any other extraneous files. Archives in .zip, .tar, .tar.gz, and .tar.bz2 formats are acceptable.)

If you unpack the files in your zip file or tarball, they should be arranged like this:

   annotations/
     b00.ann       <-- or b00.txt, etc.
     b01.ann
      ...
   sources/
     README.txt
and not like this:
   entry/     <-- incorrect:  do not include any directories above annotations
     annotations/
        b00.ann
        b01.ann
          ...
     sources/
        README.txt

Go to your Challenge 2013 Participant Page, click on or (which of these you see depends on your browser), select the zip file or tarball containing your entry, then click on . Be patient and do not interrupt the upload while it is in progress (note that your browser may not indicate that anything is happening). When the upload is complete, the autoscorer will calculate your event 4 and 5 scores, which may require another minute or so. They will be added to your participant page once they have been calculated.