{"action":"created","comment":{"url":"https://api.github.com/repos/biopython/biopython/pulls/comments/65592544","id":65592544,"diff_hunk":"@@ -0,0 +1,271 @@\n+\\chapter{Bio.phenotype: analyse phenotypic data}\n+\\label{chapter:phenotype}\n+\n+This chapter gives an overwiev of the functionalities of the\n+\\verb|Bio.phenotype| package included in Biopython. The scope of this\n+package is the analysis of phenotypic data, which means parsing and\n+analysing growth measurements of cell cultures.\n+In its current state the package is focused on the analysis of\n+high-throughput phenotypic experiments produced by the\n+\\href{https://en.wikipedia.org/wiki/Phenotype_microarray}{Phenotype Microarray technology},\n+but future developments may include other platforms and formats.\n+\n+\\section{Phenotype Microarrays}\n+\\label{sec:phenotypemicroarrays}\n+\n+The \\href{https://en.wikipedia.org/wiki/Phenotype_microarray}{Phenotype Microarray}\n+is a technology that measures the metabolism of bacterial\n+and eukaryotic cells on rhoughly 2000 chemicals, divided in twenty 96-well","path":"Doc/Tutorial/chapter_phenotype.tex","position":18,"original_position":18,"commit_id":"cdcdf856517f6ecc4db3e41b5be5d9c5c4f04898","original_commit_id":"cdcdf856517f6ecc4db3e41b5be5d9c5c4f04898","user":{"login":"cbrueffer","id":2705287,"avatar_url":"https://avatars.githubusercontent.com/u/2705287?v=3","gravatar_id":"","url":"https://api.github.com/users/cbrueffer","html_url":"https://github.com/cbrueffer","followers_url":"https://api.github.com/users/cbrueffer/followers","following_url":"https://api.github.com/users/cbrueffer/following{/other_user}","gists_url":"https://api.github.com/users/cbrueffer/gists{/gist_id}","starred_url":"https://api.github.com/users/cbrueffer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cbrueffer/subscriptions","organizations_url":"https://api.github.com/users/cbrueffer/orgs","repos_url":"https://api.github.com/users/cbrueffer/repos","events_url":"https://api.github.com/users/cbrueffer/events{/privacy}","received_events_url":"https://api.github.com/users/cbrueffer/received_events","type":"User","site_admin":false},"body":"Typo, \"rhoughly\"","created_at":"2016-06-02T18:25:18Z","updated_at":"2016-06-02T18:25:18Z","html_url":"https://github.com/biopython/biopython/pull/836#discussion_r65592544","pull_request_url":"https://api.github.com/repos/biopython/biopython/pulls/836","_links":{"self":{"href":"https://api.github.com/repos/biopython/biopython/pulls/comments/65592544"},"html":{"href":"https://github.com/biopython/biopython/pull/836#discussion_r65592544"},"pull_request":{"href":"https://api.github.com/repos/biopython/biopython/pulls/836"}}},"pull_request":{"url":"https://api.github.com/repos/biopython/biopython/pulls/836","id":72358131,"html_url":"https://github.com/biopython/biopython/pull/836","diff_url":"https://github.com/biopython/biopython/pull/836.diff","patch_url":"https://github.com/biopython/biopython/pull/836.patch","issue_url":"https://api.github.com/repos/biopython/biopython/issues/836","number":836,"state":"closed","locked":false,"title":"Updated Bio.phenomics","user":{"login":"peterjc","id":63959,"avatar_url":"https://avatars.githubusercontent.com/u/63959?v=3","gravatar_id":"","url":"https://api.github.com/users/peterjc","html_url":"https://github.com/peterjc","followers_url":"https://api.github.com/users/peterjc/followers","following_url":"https://api.github.com/users/peterjc/following{/other_user}","gists_url":"https://api.github.com/users/peterjc/gists{/gist_id}","starred_url":"https://api.github.com/users/peterjc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/peterjc/subscriptions","organizations_url":"https://api.github.com/users/peterjc/orgs","repos_url":"https://api.github.com/users/peterjc/repos","events_url":"https://api.github.com/users/peterjc/events{/privacy}","received_events_url":"https://api.github.com/users/peterjc/received_events","type":"User","site_admin":false},"body":"How does this look @mgalardini to replace #830?\r\n\r\nI've created ``test_phenomics_scipy.py`` for the fitting test which needs SciPy, although there is a warning here you might be able to help with:\r\n\r\n```\r\n$ python2.7 test_phenotype_scipy.py\r\ntest_WellRecord (__main__.TestPhenoMicro)\r\nTest basic functionalities of WellRecord objects. ... /home/xxx/lib/python2.7/site-packages/scipy/optimize/minpack.py:690: OptimizeWarning: Covariance of the parameters could not be estimated\r\n  category=OptimizeWarning)\r\nok\r\n\r\n----------------------------------------------------------------------\r\nRan 1 test in 0.774s\r\n\r\nOK\r\n```\r\n\r\n```\r\n$ python3.5 test_phenotype_scipy.py\r\ntest_WellRecord (__main__.TestPhenoMicro)\r\nTest basic functionalities of WellRecord objects. ... /home/xxx/lib/python3.5/site-packages/scipy/optimize/minpack.py:690: OptimizeWarning: Covariance of the parameters could not be estimated\r\n  category=OptimizeWarning)\r\nok\r\n\r\n----------------------------------------------------------------------\r\nRan 1 test in 0.842s\r\n\r\nOK\r\n```\r\n\r\nThese are both using SciPy 0.17.1 in case that 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