{"action":"created","issue":{"url":"https://api.github.com/repos/nrnb/GoogleSummerOfCode/issues/33","repository_url":"https://api.github.com/repos/nrnb/GoogleSummerOfCode","labels_url":"https://api.github.com/repos/nrnb/GoogleSummerOfCode/issues/33/labels{/name}","comments_url":"https://api.github.com/repos/nrnb/GoogleSummerOfCode/issues/33/comments","events_url":"https://api.github.com/repos/nrnb/GoogleSummerOfCode/issues/33/events","html_url":"https://github.com/nrnb/GoogleSummerOfCode/issues/33","id":129404322,"number":33,"title":"Interconversion between the systems biology modeling formats SBML and BioPAX","user":{"login":"draeger","id":1740827,"avatar_url":"https://avatars.githubusercontent.com/u/1740827?v=3","gravatar_id":"","url":"https://api.github.com/users/draeger","html_url":"https://github.com/draeger","followers_url":"https://api.github.com/users/draeger/followers","following_url":"https://api.github.com/users/draeger/following{/other_user}","gists_url":"https://api.github.com/users/draeger/gists{/gist_id}","starred_url":"https://api.github.com/users/draeger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/draeger/subscriptions","organizations_url":"https://api.github.com/users/draeger/orgs","repos_url":"https://api.github.com/users/draeger/repos","events_url":"https://api.github.com/users/draeger/events{/privacy}","received_events_url":"https://api.github.com/users/draeger/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/nrnb/GoogleSummerOfCode/labels/BioPAX","name":"BioPAX","color":"d4c5f9"},{"url":"https://api.github.com/repos/nrnb/GoogleSummerOfCode/labels/Difficulty:%202","name":"Difficulty: 2","color":"000000"},{"url":"https://api.github.com/repos/nrnb/GoogleSummerOfCode/labels/Java","name":"Java","color":"d4c5f9"},{"url":"https://api.github.com/repos/nrnb/GoogleSummerOfCode/labels/SBML","name":"SBML","color":"0052cc"},{"url":"https://api.github.com/repos/nrnb/GoogleSummerOfCode/labels/XML","name":"XML","color":"bfe5bf"}],"state":"open","locked":false,"assignee":{"login":"draeger","id":1740827,"avatar_url":"https://avatars.githubusercontent.com/u/1740827?v=3","gravatar_id":"","url":"https://api.github.com/users/draeger","html_url":"https://github.com/draeger","followers_url":"https://api.github.com/users/draeger/followers","following_url":"https://api.github.com/users/draeger/following{/other_user}","gists_url":"https://api.github.com/users/draeger/gists{/gist_id}","starred_url":"https://api.github.com/users/draeger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/draeger/subscriptions","organizations_url":"https://api.github.com/users/draeger/orgs","repos_url":"https://api.github.com/users/draeger/repos","events_url":"https://api.github.com/users/draeger/events{/privacy}","received_events_url":"https://api.github.com/users/draeger/received_events","type":"User","site_admin":false},"milestone":null,"comments":0,"created_at":"2016-01-28T10:05:27Z","updated_at":"2016-03-15T20:40:09Z","closed_at":null,"body":"### Background\r\n\r\n[BioPAX](http://biopax.org) and [SBML](http://sbml.org) belong to the most popular modeling and data exchange languages in systems biology. While SBML focusses on quantitative modeling and dynamic simulation of models, BioPAX concentrates mainly on visualization and qualitative analysis of pathway maps. BioPAX describes reactions and relations. In contrast, SBML core exclusively describes quantitative processes such as reactions. The SBML extension for [Qualitative Models (qual)](http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-7-135), makes interconversion between both formats possible. The tools BioPAX2SBML and SBML2BioPAX have been developed for interconversion. Since then, both SBML and BioPAX have further developed and come now with enhanced model components that are not yet covered by neither converter.\r\n\r\n### Goal\r\n\r\nIn this project, we will enhance [BioPAX2SBML](http://bioinformatics.oxfordjournals.org/content/28/20/2648) in response to experiences with its use and specific feedback from the BioPAX community. We will also enhance [SBML2BioPAX](http://sbfc.sourceforge.net/mediawiki/index.php/SBML2BioPAX) to translate more SBML constructs, handle SBML Level 3 packages to the extent possible, and add features requested by the BioPAX community. Both programs should be incorporated into one common framework.\r\n\r\n### Technologies\r\n\r\n * [BioPAX2SBML](http://www.cogsys.cs.uni-tuebingen.de/software/BioPAX2SBML/)\r\n * [SBML2BioPAX](http://sbfc.sourceforge.net/mediawiki/index.php/SBML2BioPAX)\r\n * [SBML qual](http://co.mbine.org/specifications/sbml.level-3.version-1.qual.version-1.release-1.pdf)\r\n\r\n### Potential mentors\r\n\r\nAndreas Dräger, Michael Hucka, Nicolas Rodriguez, Akira Funahashi\r\n\r\n### Contact\r\n\r\n[SBML Team](mailto:sbml-team@caltech.edu)"},"comment":{"url":"https://api.github.com/repos/nrnb/GoogleSummerOfCode/issues/comments/197011079","html_url":"https://github.com/nrnb/GoogleSummerOfCode/issues/33#issuecomment-197011079","issue_url":"https://api.github.com/repos/nrnb/GoogleSummerOfCode/issues/33","id":197011079,"user":{"login":"abhishek0198","id":17585135,"avatar_url":"https://avatars.githubusercontent.com/u/17585135?v=3","gravatar_id":"","url":"https://api.github.com/users/abhishek0198","html_url":"https://github.com/abhishek0198","followers_url":"https://api.github.com/users/abhishek0198/followers","following_url":"https://api.github.com/users/abhishek0198/following{/other_user}","gists_url":"https://api.github.com/users/abhishek0198/gists{/gist_id}","starred_url":"https://api.github.com/users/abhishek0198/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/abhishek0198/subscriptions","organizations_url":"https://api.github.com/users/abhishek0198/orgs","repos_url":"https://api.github.com/users/abhishek0198/repos","events_url":"https://api.github.com/users/abhishek0198/events{/privacy}","received_events_url":"https://api.github.com/users/abhishek0198/received_events","type":"User","site_admin":false},"created_at":"2016-03-15T20:40:09Z","updated_at":"2016-03-15T20:40:09Z","body":"@draeger @mhucka @niko-rodrigue @funasoul \r\nI am Abhishek, computer science undergraduate student from India. I am very interested in working on this project. I went through the documentation of SBML (http://sbml.org/Main_Page) and JSBML library (http://sbml.org/Software/JSBML) and understood the format and parsing mechanism. \r\n\r\nI would like to get started by setting up local dev to be more specific on my proposal for this project. I am assuming I need BioPAX2SBML and SBML2BioPAX in order to get started. Are there any dev docs avaialble to get started?\r\n\r\nAlso what is the best method to communicate regarding questions/issues? \r\n\r\nThanks"}}