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Supplementary documents for the 2009 SBML Hackathon

(Best Poster Competition)
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New this year, we are introduce small competitions with '''prizes''' for the winners. The prizes are [http://www.sandisk.com/Products/Item(2729)-SDCZ7-016G-A11-Cruzer_Titanium_USB_Drive_16GB.aspx 16 GB SanDisk Cruzer Titanium Ultra] USB drives. There are three competitions (and three prizes). The competitions are scored independently; individuals may participate in more than one, but their scores in each competition are kept separate and are not added up.
New this year, we are introduce small competitions with '''prizes''' for the winners. The prizes are [http://www.sandisk.com/Products/Item(2729)-SDCZ7-016G-A11-Cruzer_Titanium_USB_Drive_16GB.aspx 16 GB SanDisk Cruzer Titanium Ultra] USB drives. There are three competitions (and three prizes). The competitions are scored independently; individuals may participate in more than one, but their scores in each competition are kept separate and are not added up.
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The competition will close at 16:00 (4 PM) on Friday, so that we can announce winners at the dinner on Friday night.
=== Matrix Competition ===
=== Matrix Competition ===

Revision as of 12:59, 26 March 2009

Contents

Here you will find additional materials for the 2009 SBML Hackathon.

Suggested activities for the SBML Hackathon

Whether you are coming to the hackathon with goals in mind already, or whether you are exploring SBML, the following list of possible activities may be helpful to keep you productive (and in some cases, to help SBML and the SBML community at the same time!). These are only suggested activities, meant to serve as starting points if you are unsure where to start; you are of course free to do other things!

The "competitions" mentioned in this table are described in a separate section below.

Category Activity alternatives
1 Testing existing SBML support • Use the online validator to test & debug your SBML output
• Attend SBML Test Suite tutorial
2 Upgrading existing SBML support • Attend libSBML 4.x-beta tutorial, then install libSBML 4 and start hacking!
3 Implementing new SBML support • If libSBML is the answer, download libSBML & start hacking!
• If SBMLToolbox is the answer, download SBMLToolbox & start hacking!
• Else, let's talk about alternatives
4 Enhancing SBML interoperability • Get together with someone else and exchange models between your software
• Work on the Matrix Competition (see below)
• Work on the LibSBML Documentation Competition (see below)
5 Learning more about SBML • Read the SBML intro, then the SBML Level 2 Version 4 specification
• Find attendees with interesting software & talk to them about SBML
6 Helping the SBML community • Work on the Best Practices Competition (see below)
• Work on the Matrix Competition (see below)
• Work on the LibSBML Documentation Competition (see below)

Competition rules

www.sandisk.com/Products/Item(2729)-SDCZ7-016G-A11-Cruzer_Titanium_USB_Drive_16GB.aspx 16 GB SanDisk Cruzer Titanium Ultra] USB drives. There are three competitions (and three prizes). The competitions are scored independently; individuals may participate in more than one, but their scores in each competition are kept separate and are not added up.//www.sandisk.com/Products/Item(2729)-SDCZ7-016G-A11-Cruzer_Titanium_USB_Drive_16GB.aspx 16 GB SanDisk Cruzer Titanium Ultra] USB drives. There are three competitions (and three prizes). The competitions are scored independently; individuals may participate in more than one, but their scores in each competition are kept separate and are not added up.

The competition will close at 16:00 (4 PM) on Friday, so that we can announce winners at the dinner on Friday night.

Matrix Competition

The SBML Software Guide includes descriptions of known SBML-compatible software packages as well as a matrix of those packages' features. Although the SBML Team requests that software authors send updates about their software, few do. It is likely that there are many out-of-date entries in the matrix, but the SBML Team simply doesn't have the staff to check every single entry. This is a situation where a bit of distributed parallel processing could be put to great effect.

The goal of this competition is to validate entries in the Matrix (and optionally in the accompanying longer descriptions of the entries). Scoring is simply based on finding and correcting errors. The scoring rules are as follows:

  1. Every square in the matrix is worth 2 points.
    • Example: you find that the matrix claims software package "BIGSBML" supports DAEs, but you investigated it and found that in fact it does not. This is a correction to one square in the matrix, and is worth 2 points.
    • Example: you find that the matrix claims software package "GREATSBML" has no dependencies, but you check, and discover that it actually needs MATLAB. This is a correction to one square in the matrix, and is worth 2 points.
  2. Finding a no-longer-existent package entry is worth 5 points.
    • Explanation: there are 20 columns in the matrix. Without a special case, removing a whole row would constitute changing 20 squares (= 40 points), yet it would not reflect the same amount of work as checking the 20 individual features of an existing package.
  3. Adding a missing package and filling out its features is worth 30 points.
    • Explanation: adding a whole new entry is generally less time consuming than checking 20 columns of an existing entry (which would otherwise constitute 40 points total).
  4. Bonus points:
    1. +5 points for providing a new or updated paragraph for use in the software summary page.

To participate, each individual should compose a single document listing every change they propose in the matrix. The format of this document can be anything (e.g., plain text) and should describe each change in a way that makes it possible for a judge to easily understand what is meant. It can be simple and uncomplicated, but it has to be unambiguous enough so that judges can evaluate the results without having to consult the author.

Each individual's score will be tallied separately from every other person's. It does not matter if more than one person reports the same specific correction; all persons reporting the correction are attributed the same number of points.

In cases of conflicting reports between multiple people for the same matrix correction, a knowledgeable person will seek to determine which report is correct. The person(s) who made the correct report get(s) the points.

LibSBML Documentation Competition

Due to its size and continuously-changing nature, the libSBML API documentation by now probably contains errors. Simple lack of time and staff prevent the libSBML Team from being able chase down errors in a timely fashion, yet correcting the documentation is obviously an important thing to do. This is another situation where engaging multiple people (especially libSBML users) is likely to yield good results.

The activity in this competition concerns finding and reporting errors of content in the libSBML API documentation. Here are the scoring rules:

  1. Each correction to a specific matter is worth 3 points.
    • Explanation: the focus here is on claims about a feature or behavior that are contrary to the actual features or behaviors exhibited by a method, class or other API element. Due to the nature of documentation, the explanation of a feature or behavior may take several sentences, which makes finding an appropriate scoring metric difficult. The most sensible approach seems to be to focus on topics and not (for example) single words, sentences or paragraphs.
  2. Missing argument or return type descriptions are worth 2 points per instance.
  3. Wholly missing documentation for a method or class is worth 1 point.
    • Explanation: spotting completely missing documentation is much easier than finding errors in the content.
  4. Corrections are counted separately for each method or class where it applies
    • A correction that affects multiple methods (e.g., a missing parameter description) is counted multiple times, once for each method where the correction is repeated.
  5. Things that do not count as corrections:
    • Formatting bugs (but we appreciate reports of them nonetheless).
    • Reports of the same matter in the documentation for different programming languages
      • Explanation: the libSBML documentation is generated from a single common source, so a bug in one language almost certainly exists in the others as well. Counting them separately would be unfair.
    • Documentation bugs that arise from the documentation generation system, and not from author errors

You may report the errors for whichever language API you prefer to use.

sourceforge.net/tracker/?func=add&group_id=71971&atid=942737 issue tracker on SourceForce]. Please make sure to log in so that your identity is tracked and we know to whom the report should be attributed. Report one issue/matter/bug/etc. per submission, otherwise it will be difficult for us to tally the results.//sourceforge.net/tracker/?func=add&group_id=71971&atid=942737 issue tracker on SourceForce]. Please make sure to log in so that your identity is tracked and we know to whom the report should be attributed. Report one issue/matter/bug/etc. per submission, otherwise it will be difficult for us to tally the results.

Each individual's score will be tallied separately from every other person's. It does not matter if more than one person reports the same specific correction; all persons reporting the correction are attributed the same number of points.

In cases of conflicting reports between multiple people for the same matrix correction, a knowledgeable person will seek to determine which report is correct. The person(s) who made the correct report get(s) the points.

Best Poster Competition

To recognize the effort put into preparing and presenting posters, we will have a competition for the best poster at the Hackathon. The posters will be ranked by everyone via electronic voting. The voting page allows you to vote on 3 posters, so please pick the 3 most notable posters you want to vote on out of the many that you saw. www.surveymonkey.com/s.aspx?sm=R5eEcT58lG8sVQ23zkZeuQ_3d_3d Go to the voting page]//www.surveymonkey.com/s.aspx?sm=R5eEcT58lG8sVQ23zkZeuQ_3d_3d Go to the voting page]

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