Supplementary materials for the 2010 SBML-BioModels.net Hackathon
Here you will find additional materials for the 2010 SBML-BioModels.net Hackathon.
Contents |
Suggested activities for the Hackathon
Whether you are coming to the SBML-BioModels.net hackathon with goals in mind already, or whether you are exploring SBML and/or the many BioModels.net initiatives, the following list of possible activities may be helpful to keep you productive (and in some cases, to help the SBML and BioModels.net communities 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 | Learning more about SBML Level 3 | • Read the SBML intro, then the SBML Level 3 Version 1 specification • Find attendees with interesting software & talk to them about SBML |
| 2 | Testing existing SBML support | • Use the online validator to test & debug your SBML output • Develop additional test cases for the SBML Test Suite. |
| 3 | Upgrading existing SBML support | • Attend libSBML 5 introduction, then install libSBML and start hacking! • Attend the jSBML introduction, then get involved in hacking on jSBML |
| 4 | 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 |
| 5 | Enhancing SBML interoperability | • Get together with someone and exchange models between your software • Work on one of the competition topics (see below) |
| 6 | Learning about BioModels.net services | • Attend the BioModels.net Services training session • Attend the BioModels.net community development session • Work on one of the competitions tasks (see below) |
| 7 | Learning about SED-ML | • Attend the SED-ML update talk • Implement SED-ML support in your software |
| 8 | Gaining experience in model annotation | • Attend the BioModels.net Services training session • Annotate models using, e.g., semanticSBML or SAINT • Help Ron and Dagmar in tagging models in BioModels Database |
Competition rules
Following the success of this idea at last year's hackathon, this year we are once again going to hold small competitions with prizes for the winners. The prizes will be a Canary Wireless Hotspotter and $25 gift certificates to Amazon. 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. Also, there must be more than one contestant in a given competition for that competition to be considered valid. (In other words, there won't be winners by default.)
The competition will close at 8PM on Monday, in order that we can have enough time to tally the results and announce winners in the morning on Tuesday.
The following are preliminary descriptions of the activities; detailed rules will be provided in time for the hackathon.
BioModels.net facilities bashing
The objective of this competition is to look for and report problems in the various BioModels.net facilities (both BioModels Database and the other BioModels.net services). Scoring is based on the number and type of suggestions, bug reports, and other useful comments provided by people. Here are the detailed rules:
- BioModels Database model errors:
- Downloading a model and finding an error in the model is worth 3 points per error. An error in this case can be an incorrect simulation result, an error in a parameter value compared to the published model, an incorrect annotation, or similar significant problem.
- BioModels.net services behavior errors:
- A report of an error or clearly unexpected behavior in any of the web services or web pages for the BioModels.net efforts (i.e., BioModels Database, SBO, MIRIAM Resources, etc.) is worth 2 points.
- Documentation errors:
- Finding and reporting an error in the documentation for the BioModels.net efforts is worth 1 point.
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 issue; all persons reporting the issue are attributed the same number of points.
In cases of conflicting reports between multiple people for the same problem, a knowledgeable person will seek to determine which report is correct. The person(s) who made the correct report will get the point(s).
Improving jSBML
The jSBML library is currently in development. This competition will focus on developing new features for jSBML. You can check out the latest source code from the jSBML project on SourceForge. Scoring is based simply on the following rules:
- Implementation of new functionality (e.g., implementation of new methods, enhancement of existing methods): 2 points per line of source code.
- Writing documentation:
- 2 points per sentence of user documentation (not code documentation, but separate documentation explaining how to use jSBML).
- 1 point per line of documentation in the code. This can be comments explaining certain lines of code are doing, or explaining the purpose of a class, or the purpose of a variable.
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.
The voting page is closed.
Competition winners!
We announced the winners of the competition on the last day of the hackathon. The winners were:
- BioModels.net hacking: Michael Hoehl
- Best poster: Deepak Chandran, for his poster on TinkerCell
We had unfortunately no winners in the jSBML competition, because there was only 1 contestant and the rules require at least two participants in a contest for that that contest to be valid.