{"id":24092,"date":"2024-01-10T17:20:26","date_gmt":"2024-01-10T09:20:26","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24092"},"modified":"2024-01-10T17:20:27","modified_gmt":"2024-01-10T09:20:27","slug":"%e5%bc%ba%e5%8a%9b%e6%8e%a8%e8%8d%90%ef%bc%81higlass%e5%8f%af%e8%a7%86%e5%8c%96contact%e7%9f%a9%e9%98%b5%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24092","title":{"rendered":"\u5f3a\u529b\u63a8\u8350\uff01Higlass\u53ef\u89c6\u5316contact\u77e9\u9635\uff01"},"content":{"rendered":"

\u5c0f\u679c\u6700\u8fd1\u7814\u7a76\u4e09\u7ef4\u57fa\u56e0\u7ec4\u5e76\u4e14\u5df2\u7ecf\u5f97\u5230\u4e86contact\u77e9\u9635\uff08cool\u6587\u4ef6\uff09\uff0c\u90a3\u4e48\u600e\u4e48\u505a\u51fa\u6765\u7f8e\u89c2\u7684\u53ef\u89c6\u5316\u56fe\u5462\uff0c\u50cf\u4e0b\u9762\u7684\u56fe\u4e00\u6837<\/p>\n

<\/p>\n

\u60f3\u5b66\u7684\u5c0f\u4f19\u4f34\u4eec\u5c31\u8ddf\u7740\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u5427~<\/p>\n

\u9996\u5148\u5411\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e0bjupyte notebook\uff1ajupyter\u662f\u4e00\u4e2a\u57fa\u4e8eweb\u7684\u4ea4\u4e92\u5f0f\u8ba1\u7b97\u5e73\u53f0\u3002jupyter notebook\u662f\u4e00\u4e2a\u539f\u59cb\u7684web\u5e94\u7528\uff0c\u7528\u4e8e\u521b\u5efa\u548c\u5206\u4eab\u5305\u542b\u4ee3\u7801\u3001\u65b9\u7a0b\u3001\u6587\u672c\u3001\u53ef\u89c6\u5316\u3001\u4ea4\u4e92\u5f0f\u4eea\u8868\u76d8\u548c\u5176\u4ed6\u5a92\u4f53\u7684\u8ba1\u7b97\u6587\u6863\u3002jupyter\u652f\u6301\u8d85\u8fc740\u79cd\u7f16\u7a0b\u8bed\u8a00\uff0c\u5305\u62ecPython, R, Julia\u548cScala\u3002\u4f60\u53ef\u4ee5\u4f7f\u7528pip\u6216conda\u7b49\u5de5\u5177\u5b89\u88c5jupyter\uff0c\u6216\u8005\u5728\u6d4f\u89c8\u5668\u4e2d\u5728\u7ebf\u5c1d\u8bd5jupyter\u3002<\/p>\n

\u56e0\u4e3a\u5c0f\u679c\u4f7f\u7528\u7684\u662f\u670d\u52a1\u5668\uff0c\u6240\u4ee5\u5c0f\u679c\u5148\u5728\u670d\u52a1\u5668\u4e0a\u5b89\u88c5\u4e86\u4e00\u4e2ajupyter notebook(\u5982\u679c\u5927\u5bb6\u662f\u5b89\u88c5\u7684anaconda\u7684\u8bdd\u5c31\u4e0d\u7528\u5b89\u88c5\u4e86\u54e6\uff0canaconda\u81ea\u5e26jupyter notebook)\uff0c\u5982\u679c\u662fminiconda\u7684\u8bdd\u5219\u9700\u5b89\u88c5\uff0canaconda\u548cminiconda\u7684\u533a\u522b\u5728\u4e0b\u9762\u54af<\/p>\n

anaconda\u548cminiconda\u7684\u533a\u522b\u4e3b\u8981\u6709\u4e24\u4e2a\u65b9\u9762\uff1a<\/p>\n

    \n
  1. \u5305\u7684\u6570\u91cf\uff1aanaconda\u662f\u4e00\u4e2a\u5305\u542b\u4e86\u8d85\u8fc7150\u4e2a\u6570\u636e\u79d1\u5b66\u548c\u673a\u5668\u5b66\u4e60\u5305\u7684\u5b8c\u6574\u7684Python\u53d1\u884c\u7248\uff0c\u800cminiconda\u53ea\u5305\u542b\u4e86conda\u3001Python\u548c\u4e00\u4e9b\u5176\u4ed6\u7684\u5305\u3002\u56e0\u6b64\uff0canaconda\u7684\u5b89\u88c5\u6587\u4ef6\u6bd4\u8f83\u5927\uff0c\u9700\u8981\u66f4\u591a\u7684\u78c1\u76d8\u7a7a\u95f4\uff0c\u800cminiconda\u7684\u5b89\u88c5\u6587\u4ef6\u6bd4\u8f83\u5c0f\uff0c\u66f4\u52a0\u7075\u6d3b\u3002<\/li>\n
  2. \u754c\u9762\u7684\u7c7b\u578b\uff1aanaconda\u63d0\u4f9b\u4e86\u4e00\u4e2a\u56fe\u5f62\u7528\u6237\u754c\u9762\uff08GUI\uff09\u53eb\u505aNavigator\uff0c\u53ef\u4ee5\u901a\u8fc7\u5b83\u6765\u521b\u5efa\u73af\u5883\u3001\u5b89\u88c5\u5305\u3001\u542f\u52a8\u5f00\u53d1\u5e94\u7528\u7b49\u3002\u800cminiconda\u53ea\u63d0\u4f9b\u4e86\u4e00\u4e2a\u547d\u4ee4\u884c\u754c\u9762\uff08CLI\uff09\uff0c\u9700\u8981\u901a\u8fc7\u8f93\u5165\u547d\u4ee4\u6765\u7ba1\u7406\u73af\u5883\u548c\u5305\u3002<\/li>\n<\/ol>\n

    \u4f7f\u7528conda\u5b89\u88c5jupyter\uff1a<\/p>\n

    conda install jupyter<\/p>\n

    \u4e0b\u9762\u9700\u8981\u751f\u6210\u914d\u7f6e\u6587\u4ef6\uff1a<\/p>\n

    jupyter notebook –generate-config<\/p>\n

    \u7136\u540e\u4f1a\u5f97\u5230\uff1a<\/p>\n

    Writing default config to: \/root\/.jupyter\/jupyter_notebook_config.py<\/p>\n

    \u8bf4\u660e\u4e86\u914d\u7f6e\u6587\u4ef6\u7684\u5730\u5740\uff0c\u7136\u540e\u4f7f\u7528vim\u6253\u5f00\u4fee\u6539\u914d\u7f6e\u6587\u4ef6\uff1a<\/p>\n

      \n
    1. c.NotebookApp.ip=’*’ #<\/li>\n
    2. c.NotebookApp.ip=’0.0.0.0′<\/li>\n
    3. c.NotebookApp.open_browser =False # \u8bbe\u7f6e\u662f\u5426\u81ea\u52a8\u6253\u5f00\u6d4f\u89c8\u5668<\/li>\n
    4. c.NotebookApp.port =8888 # \u8bbe\u7f6e\u7aef\u53e3\uff0c\u53ef\u4ee5\u81ea\u5df1\u66f4\u6539<\/li>\n
    5. c.NotebookApp.allow_remote_access = True<\/li>\n<\/ol>\n

      \u4e4b\u540e\u5728\u547d\u4ee4\u884c\u8f93\u5165jupyter notebook\u53ef\u4ee5\u542f\u52a8jupyter notebook \uff0c\u5982\u679c\u9700\u8981\u4fdd\u6301jupyter notebook\u6302\u8d77\u7684\u8bdd\u53ef\u4ee5\u4f7f\u7528nohup \uff1a nohup jupyter notebook > jupyter.log 2>&1 &<\/p>\n

      \u5982\u679c\u9700\u8981\u7ed3\u675fjupyter\u8fdb\u7a0b\u7684\u8bdd\u53ef\u4ee5\u4f7f\u7528\u4e00\u4e0b\u4ee3\u7801\uff1a<\/p>\n

      ps -aux | grep jupyter | awk \u2018{print $2}\u2019 | xargs kill -9 -s<\/p>\n

      \u542f\u52a8jupyter notebook\u4e4b\u540e\uff0c\u6d4f\u89c8\u5668\u8f93\u5165\u76f8\u5e94\u7684ip\u548c\u7aef\u53e3\u5373\u53ef\u8fdb\u5165\uff0c\u9996\u6b21\u8fdb\u5165\u9700\u8981\u8f93\u5165token\uff0ctoken\u4f1a\u5728\u547d\u4ee4\u884c\u4e2d\u51fa\u73b0\uff0c\u8f93\u5165\u5373\u53ef<\/p>\n

      <\/p>\n

      \u8fdb\u5165\u540e\u53d1\u73b0\u53ea\u6709python3\u4e00\u4e2akernel\uff0c\u5982\u679c\u60f3\u4f7f\u7528\u5176\u4ed6\u865a\u62df\u73af\u5883\u8be5\u600e\u4e48\u529e\u5462<\/p>\n

      \u53ef\u4ee5\u53c2\u8003\u4e00\u4e0b\u6d41\u7a0b\uff1a<\/p>\n

        \n
      1. \u9996\u5148\u5728\u4f60\u60f3\u8981\u4f7f\u7528\u7684\u865a\u62df\u73af\u5883\u4e2d\u5b89\u88c5ipykernel\u5305<\/li>\n<\/ol>\n

        conda activate YOUR_ENV_NAME<\/p>\n

        conda install ipykernel<\/p>\n

          \n
        1. \u5728\u4f60\u5b89\u88c5jupyter notebook\u7684\u73af\u5883\u91cc\u9762\u8fd0\u884c\u4ee5\u4e0b\u4ee3\u7801\uff1a<\/li>\n<\/ol>\n

          python -m ipykernel install –user –name YOUR_ENV_NAME –display-name YOUR_ENV_NAME<\/p>\n

          \u8fd9\u6837\u518d\u6b21\u6253\u5f00\u5c31\u4f1a\u51fa\u73b0\u4f60\u60f3\u4f7f\u7528\u7684\u865a\u62df\u73af\u5883\u5566<\/p>\n

          <\/p>\n

          \u4e0a\u9762\u662f\u73af\u5883\u7684\u914d\u7f6e\uff0c\u4e0b\u9762\u5f00\u59cb\u53ef\u89c6\u5316cool\u6587\u4ef6<\/p>\n

          \u9996\u5148\u6211\u4eec\u8981\u4f7f\u7528higlass-python\u8fd9\u4e2apython\u5305<\/p>\n

          \u4f7f\u7528pip\u5b89\u88c5\uff1a
          \npip install jupyter higlass-python<\/p>\n

          \u4e0b\u9762\u662f\u5173\u4e8ehiglass\u8f6f\u4ef6\u7684\u4e00\u4e9b\u4ecb\u7ecd\uff1ahiglass\u662f\u4e00\u4e2a\u7528\u4e8e\u53ef\u89c6\u5316\u5927\u89c4\u6a21\u6570\u636e\u7684\u7f51\u9875\u6d4f\u89c8\u5668\uff0c\u6700\u521d\u8bbe\u8ba1\u7528\u4e8e\u5904\u7406\u6d77\u91cf\u7684\u57fa\u56e0\u7ec4\u6570\u636e\u96c6\u3002higlass\u57fa\u4e8e\u7c7b\u4f3c\u4e8e\u57fa\u56e0\u7ec4\u6d4f\u89c8\u5668\u548c\u73b0\u4ee3\u5728\u7ebf\u5730\u56fe\uff08\u6240\u8c13\u7684\u6ed1\u52a8\u5730\u56fe\uff09\u7684\u6846\u67b6\uff0c\u5f62\u6210\u4e86\u4e00\u4e2a\u5feb\u901f\u3001\u7075\u6d3b\u548c\u53ef\u6269\u5c55\u7684\u591a\u5c3a\u5ea6\u6570\u636e\u6d4f\u89c8\u5668\u3002higlass\u652f\u6301\u591a\u79cd1D\u548c2D\u7684\u8f68\u8ff9\u7c7b\u578b\uff0c\u53ef\u4ee5\u663e\u793a\u4e0d\u540c\u6587\u4ef6\u683c\u5f0f\u7684\u6570\u636e\u3002higlass\u4f7f\u7528D3.js\u3001Pixi.js\u3001React\u7b49\u5f00\u6e90\u7ec4\u4ef6\u8fdb\u884c\u6570\u636e\u53ef\u89c6\u5316\u548c\u4ea4\u4e92\u3002<\/p>\n

          \u4e0b\u9762\u5c31\u662f\u53ef\u89c6\u5316\u5206\u6790\u7684\u4ee3\u7801\u5566<\/p>\n

          import higlass as hg<\/p>\n

          # \u52a0\u8f7d\u6587\u4ef6<\/p>\n

          tileset = hg.cooler(“software\/HiC-Pro\/Utils\/test\/.output.cool”)<\/p>\n

          track = tileset.track(“heatmap”)<\/p>\n

          view = hg.view(track, width=6)<\/p>\n

          # \u670d\u52a1\u5668\u8fd0\u884c\u9700\u8981\u52a0\uff0c\u4e0d\u7136\u8fd0\u884c\u4e0d\u51fa\u6765<\/p>\n

          tileset = hg.remote(<\/p>\n

          uid=”CQMd6V_cRw6iCI_-Unl3PQ”,<\/p>\n

          server=”http:\/\/higlass.io\/api\/v1\/”,<\/p>\n

          )<\/p>\n

          view = hg.view(<\/p>\n

          hg.track(“top-axis”),<\/p>\n

          tileset.track(“heatmap”, height=250).opts(<\/p>\n

          valueScaleMax=0.5,<\/p>\n

          ),<\/p>\n

          )<\/p>\n

          view<\/p>\n

          \u4e0b\u9762\u662f\u5c0f\u679c\u7684\u8fd0\u884c\u7ed3\u679c\uff0c\u5927\u5bb6\u4e00\u8d77\u8bd5\u4e00\u8bd5\u5427<\/p>\n

          <\/p>\n

          \u4eca\u5929\u7684\u5173\u4e8ehiglass\u53ef\u89c6\u5316\u7684\u5b66\u4e60\u5c31\u5230\u8fd9\u91cc\u5566\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u627e\u5c0f\u679c\u8ba8\u8bba\uff0c\u6709\u611f\u89c9\u751f\u4fe1\u5206\u6790\u590d\u6742\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528\u6211\u4eec\u7684\u751f\u4fe1\u5c0f\u5de5\u5177\u54e6\uff0c\u94fe\u63a5\u5728\u8fd9\uff1ahttp:\/\/www.biocloudservice.com\/home.html<\/a>\uff0c\u6211\u4eec\u660e\u5929\u89c1\u54af~<\/p>\n","protected":false},"excerpt":{"rendered":"

          \u5c0f\u679c\u6700\u8fd1\u7814\u7a76\u4e09\u7ef4\u57fa\u56e0\u7ec4\u5e76\u4e14\u5df2\u7ecf\u5f97\u5230\u4e86contact\u77e9\u9635\uff08cool\u6587\u4ef6\uff09\uff0c\u90a3\u4e48\u600e\u4e48\u505a\u51fa\u6765\u7f8e\u89c2\u7684\u53ef\u89c6\u5316\u56fe\u5462\uff0c\u50cf\u4e0b\u9762 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24092"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=24092"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24092\/revisions"}],"predecessor-version":[{"id":24100,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24092\/revisions\/24100"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=24092"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=24092"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=24092"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}