{"push_id":1458132034,"size":65,"distinct_size":62,"ref":"refs/heads/model_checker","head":"75d833ab62fb8cf98cc5d6bf110eea2a1bb4253c","before":"686b929c6848075e95eafe9d9b534c0f7a7e431e","commits":[{"sha":"0088ad7949ffa531d2ebfcef0cbcb5fdbd9db081","author":{"name":"Ben Gyori","email":"2da2c81b23ded5af8dcb52b535e3929154f0ddfb@gmail.com"},"message":"Additional prioritizations for DRUM terms","distinct":false,"url":"https://api.github.com/repos/johnbachman/indra/commits/0088ad7949ffa531d2ebfcef0cbcb5fdbd9db081"},{"sha":"8d3d6e004c359a09494c623b43d4e1992a67164d","author":{"name":"Ben Gyori","email":"2da2c81b23ded5af8dcb52b535e3929154f0ddfb@gmail.com"},"message":"Deprioritize non-human proteins for DRUM matches","distinct":false,"url":"https://api.github.com/repos/johnbachman/indra/commits/8d3d6e004c359a09494c623b43d4e1992a67164d"},{"sha":"0d6878505ba2b1867eeeb067a58ab3e91495328e","author":{"name":"Ben Gyori","email":"2da2c81b23ded5af8dcb52b535e3929154f0ddfb@gmail.com"},"message":"Remove unnecessary print","distinct":false,"url":"https://api.github.com/repos/johnbachman/indra/commits/0d6878505ba2b1867eeeb067a58ab3e91495328e"},{"sha":"5bec95e735ffd6c084b5c4e42d77a6c38c6507d9","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Smoke test for a yet nonexistent ModelChecker","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/5bec95e735ffd6c084b5c4e42d77a6c38c6507d9"},{"sha":"0d3327db6b3d22b92affbb62aa97830b561921d1","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Test now trivially passes","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/0d3327db6b3d22b92affbb62aa97830b561921d1"},{"sha":"52644467a2caf955542b7ed58229d4d42e9735c4","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Elementary monomer_pattern embedding\n\nMight be better off in PySB, but it's OK here for now.","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/52644467a2caf955542b7ed58229d4d42e9735c4"},{"sha":"355b1d57a7a7a16d72e7c8d51c3042bcd55a13ec","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Tests of cp_embeds_into","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/355b1d57a7a7a16d72e7c8d51c3042bcd55a13ec"},{"sha":"dc5719d5fa4859530b4b40fb37cdaa79fb384d70","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Match CPs to either LH or RH side of rules\n\nIdea is to find rules that take a particular complex pattern as one\ntheir inputs, and take a different (target) pattern as one of their\noutputs.","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/dc5719d5fa4859530b4b40fb37cdaa79fb384d70"},{"sha":"66c9ea244d8306f2739b3bc2607055e3086481b5","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Proof-of-concept model checking using influence map\n\nIdentifies rules in the model that have the input node among the\nreactant patterns, and output rules that have the output nodes among the\nproduct patterns. Then checks the influence map to see if there is a\npath in the influence map between these rules.\n\nThis could also be done using the species_graph or reaction network, but\nthis would not be robust to combinatorially complex models.","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/66c9ea244d8306f2739b3bc2607055e3086481b5"},{"sha":"72a3b803dcfc8ad141681bbae34d5478192f9459","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Fix capitalization of kin act site name in PysbAssembler","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/72a3b803dcfc8ad141681bbae34d5478192f9459"},{"sha":"acc3a4799fed087cfbda49bb991f3378fbff9d9d","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Test PysbAssembler assembly policies\n\nOne step and two step both produce Pysb models that satisfy the\nphosphorylation constraint, whereas the interactions only policy does\nnot.","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/acc3a4799fed087cfbda49bb991f3378fbff9d9d"},{"sha":"624848bbd0e23f6f36dd55a4b9d4ad57cf5ff2ce","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Path polarity computation\n\nNeeded because even though the influence map has directional edges, many\nof these edges are actually inhibitory (i.e., the firing of one rule\nactually diminishes the activity of another rule). So it is necessary to\ncompute the polarity of the overall path and check if it matches the\nconstraint.","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/624848bbd0e23f6f36dd55a4b9d4ad57cf5ff2ce"},{"sha":"4b9aecfb5f76c508eaefb214662b727261fbed18","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Model checking with path polarity","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/4b9aecfb5f76c508eaefb214662b727261fbed18"},{"sha":"1e926bb01866fc0b2e4add7f0b73c5d44c780c76","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Target rules must be production rules\n\nThat is, the target pattern must not be present on the left hand side\nand be present on the right hand side.","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/1e926bb01866fc0b2e4add7f0b73c5d44c780c76"},{"sha":"be8181d441fca5815b7c5357db37c6525348b0ef","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Find paths to both prod and consumption rules","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/be8181d441fca5815b7c5357db37c6525348b0ef"},{"sha":"af82207fc72a5957a64471d9480506e2773c38b4","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Support dephosphorylation (exmple of demodify rule)","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/af82207fc72a5957a64471d9480506e2773c38b4"},{"sha":"69b55dbf53723bfabf49971cce3111342abcfff9","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Build more expansive Sif networks","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/69b55dbf53723bfabf49971cce3111342abcfff9"},{"sha":"25054586406024e082f9836884d5198ffa669f5b","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Save the results of ras network","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/25054586406024e082f9836884d5198ffa669f5b"},{"sha":"c5446f5dfccfaade48c3341183c6cbbd859fbfeb","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Make model_checker python 3 compatible","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/c5446f5dfccfaade48c3341183c6cbbd859fbfeb"},{"sha":"999661541010b14a62960783f3deff9be57daf70","author":{"name":"John Bachman","email":"42d6a13776d54e4d0631f6221d2e91b54716b2ee@gmail.com"},"message":"Handle case where a modification is not observed","distinct":true,"url":"https://api.github.com/repos/johnbachman/indra/commits/999661541010b14a62960783f3deff9be57daf70"}]}
{"actor":{"display_login":"johnbachman"}}