{"action":"created","issue":{"url":"https://api.github.com/repos/kroneckerbio/kroneckerbio/issues/24","labels_url":"https://api.github.com/repos/kroneckerbio/kroneckerbio/issues/24/labels{/name}","comments_url":"https://api.github.com/repos/kroneckerbio/kroneckerbio/issues/24/comments","events_url":"https://api.github.com/repos/kroneckerbio/kroneckerbio/issues/24/events","html_url":"https://github.com/kroneckerbio/kroneckerbio/issues/24","id":68166076,"number":24,"title":"External dependency handling","user":{"login":"xpspectre","id":4530441,"avatar_url":"https://avatars.githubusercontent.com/u/4530441?v=3","gravatar_id":"","url":"https://api.github.com/users/xpspectre","html_url":"https://github.com/xpspectre","followers_url":"https://api.github.com/users/xpspectre/followers","following_url":"https://api.github.com/users/xpspectre/following{/other_user}","gists_url":"https://api.github.com/users/xpspectre/gists{/gist_id}","starred_url":"https://api.github.com/users/xpspectre/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/xpspectre/subscriptions","organizations_url":"https://api.github.com/users/xpspectre/orgs","repos_url":"https://api.github.com/users/xpspectre/repos","events_url":"https://api.github.com/users/xpspectre/events{/privacy}","received_events_url":"https://api.github.com/users/xpspectre/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/kroneckerbio/kroneckerbio/labels/question","name":"question","color":"cc317c"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2015-04-13T18:47:14Z","updated_at":"2015-04-18T23:41:20Z","closed_at":null,"body":"Until now, kroneckerbio has been fully contained within Matlab and its toolboxes. This makes deployment and use very easy (it's even advertised as such in the documentation). Having integrated integrators/optimizers is also one of Matlab's key strengths. However, with direct SBML conversion (issue #23) and potentially other forms of parsing/input/output (issue #6), external libraries become very attractive. Other types of analyses, like stochastic simulation, also require C/C++ code and MEX routines.\r\n\r\nlibSBML represents a general case where installing dependencies complicates installation, especially if you're not on Windows. In Windows, downloading the compiled binaries suffices. In Linux, as usual, you download the source, compile the shared libraries, and compile and setup the Matlab/MEX files. Haven't tested on Mac yet.\r\n\r\nIssues to consider:\r\n1. Do we want to include the binaries? Which ones? They add ~20 Mb.\r\n2. Do we include detailed installation instructions for specific platforms?\r\n\r\nAny other issues, thoughts?"},"comment":{"url":"https://api.github.com/repos/kroneckerbio/kroneckerbio/issues/comments/94213897","html_url":"https://github.com/kroneckerbio/kroneckerbio/issues/24#issuecomment-94213897","issue_url":"https://api.github.com/repos/kroneckerbio/kroneckerbio/issues/24","id":94213897,"user":{"login":"drhagen","id":2952478,"avatar_url":"https://avatars.githubusercontent.com/u/2952478?v=3","gravatar_id":"","url":"https://api.github.com/users/drhagen","html_url":"https://github.com/drhagen","followers_url":"https://api.github.com/users/drhagen/followers","following_url":"https://api.github.com/users/drhagen/following{/other_user}","gists_url":"https://api.github.com/users/drhagen/gists{/gist_id}","starred_url":"https://api.github.com/users/drhagen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drhagen/subscriptions","organizations_url":"https://api.github.com/users/drhagen/orgs","repos_url":"https://api.github.com/users/drhagen/repos","events_url":"https://api.github.com/users/drhagen/events{/privacy}","received_events_url":"https://api.github.com/users/drhagen/received_events","type":"User","site_admin":false},"created_at":"2015-04-18T23:41:20Z","updated_at":"2015-04-18T23:41:20Z","body":"After talking to the people at JSBML, someone from libSBML found my post and pointed me to a [portable Matlab version of libSBML](https://sourceforge.net/projects/sbml/files/libsbml/5.11.4/stable/MATLAB%20interface/ ), which looks like it only recently came out. I tried it and it worked perfectly for the one test case I tried. If you want to try parsing with a free library, I would recommend starting here."}}