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Competitions for the 2012 SBML Hackathon


In time for the 2012 SBML Hackathon (an integral part of HARMONY 2012), the SBML Team is running three new competitions. The details of the are described on this page.

We are serious about these competitions, and so to encourage participation, the winners will receive significant travel support to attend HARMONY 2012 in Maastricht. Each competition is independent, and offers separate prizes; except as indicated, there are no restrictions on the number of competitions the same person may win (i.e., you can win more than one competition if you enter more than one).

Competition #1: A new SBML t-shirt design

SBML logo shirts have proved popular in the past. We are going to hold a competition for a new shirt design. One design will be chosen, and the creator of the winning design will receive US$ 200 of travel support to attend HARMONY 2012 as well as two t-shirts with the logo printed on it. The winning design will be chosen by a popular vote to be held during March, 2012, and announced on the sbml-discuss mailing list.

Image:Done.gif The design submission phase of the contest has closed. The deadline for submitting shirt designs was March 9, 2012. The guidelines we used for design submissions are still available on a separate page.

Image:Done.gif The voting phase has ended. Six designs were put up for a vote. The deadline for submitting votes was midnight (EST) on March 29.

And the award goes to...
See Mort Yao's winning design in our SBML t-shirt design contest and place your order for the latest in haute tech couture. The deadline for ordering t-shirts is April 20.

Competition #2: SBML Test Suite test cases

Image:Done.gif The competition is now closed.

In an effort to gather more test cases and make simulator support for all of SBML more robust, we are soliciting new test cases for the SBML Test Suite. Submissions must be received by May 12. The rest of this section details the rules.

Points for each unique (as defined below), original test will be awarded as follows:

  • 1 point: The test case consists of the absolute minimum: a test model in SBML format, a results file in .csv format, and a settings file in the format used by current SBML Test Suite test cases.
  • 3 points: There is a properly-formatted test directory, with valid SBML file(s) and properly-formatted model (.m), settings, and results files, including a cogent summary of what your test is supposed to be testing.
  • 3 points: Getting all the Test Suite tags for your test correct.
  • 3 points: Getting the results for your test correct. If there is controversy over the proper interpretation of your test, the correct results will be determined either by consensus among the simulator writers, or by the SBML editors.

Unique test in this context means uniqueness in conceptual design, not numerical precision. Multiple submitted models where nothing changes but the numbers count as a single entry. Entries that match the conceptual design of an existing test suite test too exactly may likewise be discarded. (To compare, find the models in the test suite with exactly the same set of test tags as yours.)

In addition, your tests taken as a whole will gain points for the following:

  • 20 points: Providing one or more tests with a unique set of tags whose combination is covered by fewer than 3 tests in the test suite. The libSBML team must agree the tag combination is well-integrated, meaning that each component influences the other components. (20 points per combination.)

    Note that it will be most helpful to simulator writers if you provide a test that contains the least number of tags that nevertheless reveals the problem in the simulator. We already have a 'kitchen sink' model in the test suite (model 1000) so we don't need more tests of that type. What we do need is focused tests that pinpoint specific issues with particular combinations of tags, and tests that use existing tags in new ways.
  • 50 points: Revealing inconsistent interpretations of SBML: If two or more simulators from our test bed get different results from your test, but both groups (not including your own) claim that their interpretation is correct, we'll resolve the dispute among the editors and/or the community, and award you 50 points/controversy.
  • 50 points: Per simulator in our test bed that generally handles models with the same tags correctly, produces no warnings or error messages, but fails to produce the expected results. 50 points per issue, max 1/test. No points given for integration errors; the test suite expressly does not try to test integration, but SBML concepts.

As many of these items are somewhat subjective, we will strive to evaluate them as anonymously as possible. Entries are to be submitted to Linda Taddeo (, who will remove identifying information from the submissions and then pass them on to the libSBML Team for assessment.

The following prizes are available for different point levels:

  • 50 points or more: An SBML T-shirt in the size of your choice.
  • 250 points or more: An SBML T-shirt plus US$ 200 of travel support to attend HARMONY 2012.
  • Highest number of points across all submissions: An SBML T-shirt, travel support to HARMONY 2012, plus a gift certificate for $100 at

A maximum of three (3) awards of travel support will be made. If more than three individuals or group garner 250 points or more, we will select the three awardees based on precedence: those submitted chronologically earliest will win.

All decisions of the team will be final.

Competition #3: SBML tutorials

Image:Done.gif The competition is now closed.

Help us build up a collection of developer-oriented tutorials about SBML to be made available on Currently, there are no such tutorials available, yet there is a clear need for explanations of SBML details in a form more accessible than the SBML specification documents. The purpose of this competition is to jump-start the creation of this tutorial collection.

All submissions will be considered for inclusion on, with credit given to the author(s). In addition, the winners of this competition will also receive prizes. Submissions must be received by May 12.

Here are the specifics about what to submit:

  • Keep in mind that the eventual collection of tutorials will be a web page with various topic headings on it, and then for each heading, a list of subtopics, each with links to tutorials. Therefore, tutorials should be modular and focused on technical aspects of SBML, rather than general "what is SBML" type tutorials.
  • A given tutorial should focus on a single aspect of SBML. It can get right to the point; it does not have to begin with an introduction about what SBML is.
  • The most basic tutorial would be a collection of presentation slides with onscreen notes. Optionally, for extra points, we welcome screencasts (if appropriate in the context) and audio commentary (in English, with good audio quality).
  • Do not bother styling your slides beyond basic text formatting (bold, typewriter font, etc.) and level/sublevel organization, because we will import the slides into a common set of slide format templates. Note, however, that we will not have time to do wholesale slide editing, so do be careful about the quality of your writing (and your spoken commentary, if there is one) – your tutorial will very likely be made public on, so keep that in mind.
  • Please use one of the following formats: Microsoft PowerPoint, Apple Keynote, Google Docs Presentation, or OpenOffice/NeoOffice/LibreOffice Impress.

Submit your tutorial(s) via email to (To prevent mail server errors, do not include more than 10 MB of attachments in any given email message; instead, use an online facility to store your files, then email a link.)

Scoring will be performed as follows. Each tutorial will be scored on the following characteristics and given the points indicated. The points will be added for each tutorial to produce an overall total score for the tutorial:

  • Content
    • 2 points: the presentation clearly explains an element of SBML or a substantive aspect of using SBML
    • 3 points: there is a mathematical explanation of the use of the element (where appropriate)
    • 3 points: there is pseudocode that illustrates the use of the element (where appropriate)
  • Presentation
    • 10 points: a screencast is included
    • 20 points: audio commentary is included
  • Bonus
    • 30 points: clearest of all tutorials submitted to the competition
    • 50 points: a tutorial that explains how to handle one of the following:
      • multiple compartments, with compartment sizes ≠ 1
      • the hasOnlySubstanceUnits attribute on species objects
      • fast reactions
      • priorities on events (in SBML Level 3)
      • algebraic rules
      • delay differential equations
      • variable stoichiometries

It is possible for a submission to get 0 points if it is judged to be of low quality, irrelevant, wrong, or otherwise unsuitable. (Hopefully, that won't happen, but we still need to say it.)

The tutorials will be judged anonymously (so do not put your name on the actual slides!). The judging will be performed by the SBML Team and the SBML Editors. The tutorials will be anonymized before they are passed to the judges.

The following prizes are available for different point levels:

  • 50 points or more: An SBML T-shirt in the size of your choice.
  • 125 points or more: The T-shirt plus US$ 200 of travel support to HARMONY 2012.
  • Highest number of points: The T-shirt and travel support, plus a gift certificate for US$ 100 at

A maximum of three (3) awards of travel support will be made. If more than three individuals or group garner 125 points or more, we will select the three awardees based on precedence: those submitted chronologically earliest will win.

All decisions will be final.

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