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            "Requirement already satisfied: terminado>=0.8.3 in /usr/local/lib/python3.10/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (0.18.1)\n",
            "Requirement already satisfied: prometheus-client in /usr/local/lib/python3.10/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (0.21.0)\n",
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            "Requirement already satisfied: ptyprocess>=0.5 in /usr/local/lib/python3.10/dist-packages (from pexpect>4.3->ipython>=4.0.0->ipywidgets>=7.6.0->ipycytoscape) (0.7.0)\n",
            "Requirement already satisfied: wcwidth in /usr/local/lib/python3.10/dist-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython>=4.0.0->ipywidgets>=7.6.0->ipycytoscape) (0.2.13)\n",
            "Requirement already satisfied: platformdirs>=2.5 in /usr/local/lib/python3.10/dist-packages (from jupyter-core>=4.6.1->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (4.3.6)\n",
            "Requirement already satisfied: notebook-shim>=0.2.3 in /usr/local/lib/python3.10/dist-packages (from nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (0.2.4)\n",
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            "Requirement already satisfied: jupyterlab-pygments in /usr/local/lib/python3.10/dist-packages (from nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (0.3.0)\n",
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            "Requirement already satisfied: mistune<4,>=2.0.3 in /usr/local/lib/python3.10/dist-packages (from nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (3.0.2)\n",
            "Requirement already satisfied: nbclient>=0.5.0 in /usr/local/lib/python3.10/dist-packages (from nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (0.10.0)\n",
            "Requirement already satisfied: packaging in /usr/local/lib/python3.10/dist-packages (from nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (24.1)\n",
            "Requirement already satisfied: pandocfilters>=1.4.1 in /usr/local/lib/python3.10/dist-packages (from nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (1.5.1)\n",
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            "Requirement already satisfied: fastjsonschema>=2.15 in /usr/local/lib/python3.10/dist-packages (from nbformat->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (2.20.0)\n",
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            "Requirement already satisfied: argon2-cffi-bindings in /usr/local/lib/python3.10/dist-packages (from argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (21.2.0)\n",
            "Requirement already satisfied: webencodings in /usr/local/lib/python3.10/dist-packages (from bleach!=5.0.0->nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (0.5.1)\n",
            "Requirement already satisfied: attrs>=22.2.0 in /usr/local/lib/python3.10/dist-packages (from jsonschema>=2.6->nbformat->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (24.2.0)\n",
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            "Requirement already satisfied: referencing>=0.28.4 in /usr/local/lib/python3.10/dist-packages (from jsonschema>=2.6->nbformat->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (0.35.1)\n",
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            "Requirement already satisfied: cffi>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from argon2-cffi-bindings->argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (1.17.1)\n",
            "Requirement already satisfied: soupsieve>1.2 in /usr/local/lib/python3.10/dist-packages (from beautifulsoup4->nbconvert>=5->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (2.6)\n",
            "Requirement already satisfied: pycparser in /usr/local/lib/python3.10/dist-packages (from cffi>=1.0.1->argon2-cffi-bindings->argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (2.22)\n",
            "Requirement already satisfied: anyio<4,>=3.1.0 in /usr/local/lib/python3.10/dist-packages (from jupyter-server<3,>=1.8->notebook-shim>=0.2.3->nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (3.7.1)\n",
            "Requirement already satisfied: websocket-client in /usr/local/lib/python3.10/dist-packages (from jupyter-server<3,>=1.8->notebook-shim>=0.2.3->nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (1.8.0)\n",
            "Requirement already satisfied: idna>=2.8 in /usr/local/lib/python3.10/dist-packages (from anyio<4,>=3.1.0->jupyter-server<3,>=1.8->notebook-shim>=0.2.3->nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (3.10)\n",
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            "Requirement already satisfied: exceptiongroup in /usr/local/lib/python3.10/dist-packages (from anyio<4,>=3.1.0->jupyter-server<3,>=1.8->notebook-shim>=0.2.3->nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets>=7.6.0->ipycytoscape) (1.2.2)\n",
            "Downloading ipycytoscape-1.3.3-py2.py3-none-any.whl (3.6 MB)\n",
            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m3.6/3.6 MB\u001b[0m \u001b[31m55.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hDownloading spectate-1.0.1-py2.py3-none-any.whl (11 kB)\n",
            "Downloading jedi-0.19.1-py2.py3-none-any.whl (1.6 MB)\n",
            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m1.6/1.6 MB\u001b[0m \u001b[31m55.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hInstalling collected packages: spectate, jedi, ipycytoscape\n",
            "Successfully installed ipycytoscape-1.3.3 jedi-0.19.1 spectate-1.0.1\n"
          ]
        }
      ],
      "source": [
        "#how to link python code to cytoscape\n",
        "\n",
        "!pip install networkx\n",
        "!pip install ipycytoscape"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "import networkx as nx\n",
        "import ipycytoscape\n",
        "from IPython.display import display\n",
        "from google.colab import output\n",
        "output.enable_custom_widget_manager()\n"
      ],
      "metadata": {
        "id": "o3qvE9jnZEnZ"
      },
      "execution_count": 3,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "G=nx.Graph()\n",
        "G.add_edges_from([(1,2),(2,3),(3,5),(3,4),(4,5),(1,3),(2,4),(4,1)])\n",
        "cyto=ipycytoscape.CytoscapeWidget()\n",
        "cyto.graph.add_graph_from_networkx(G)\n",
        "\n"
      ],
      "metadata": {
        "id": "cX-rGRLHZE3P"
      },
      "execution_count": 4,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "display(cyto)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 417,
          "referenced_widgets": [
            "304efd73356a4f22b004228771542713",
            "7870e243623a4d179d2168fdd04fd50a",
            "8f61fc5170e84015bb3cc4dcd72ac42b",
            "3c4f30265f4c4a4da7a86a44b7c01a05",
            "ba852b2a09ec4c09b419d9f47a889cf1",
            "4232c2060ea94dbf9626cd3b2f938aa3",
            "4d2af0c7e303449ea44b4eef14564685",
            "cb4eaed3758f4ce7ab7a1d51464d44ec",
            "2181c26a3f734e0c9ccff52f61542330",
            "ac36f3b81fa840b5816a9d2f14d6bdc9",
            "2f562bc3039c4510ab570b6b45e91c46",
            "a7e45817f45048fbaf59dc03199c6dfb",
            "58d3ffd0c5654c2786f9c27a1acbf85b",
            "2f0b800a53a14fdc82bb8355b51377dc",
            "e7cb2c1b1df64e4e94da2d1118120748",
            "ed7decda61684472b6e50114ec4d1657"
          ]
        },
        "id": "u-Xfq1TXZE7H",
        "outputId": "9de93e53-3ee8-4d95-858e-bdfba480ec96"
      },
      "execution_count": 5,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "CytoscapeWidget(cytoscape_layout={'name': 'cola'}, cytoscape_style=[{'selector': 'node', 'css': {'background-c…"
            ],
            "application/vnd.jupyter.widget-view+json": {
              "version_major": 2,
              "version_minor": 0,
              "model_id": "304efd73356a4f22b004228771542713"
            }
          },
          "metadata": {
            "application/vnd.jupyter.widget-view+json": {
              "colab": {
                "custom_widget_manager": {
                  "url": "https://ssl.gstatic.com/colaboratory-static/widgets/colab-cdn-widget-manager/2b70e893a8ba7c0f/manager.min.js"
                }
              }
            }
          }
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [],
      "metadata": {
        "id": "bhA2BFfGZE-M"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "Support for third party widgets will remain active for the duration of the session. To disable support:"
      ],
      "metadata": {
        "id": "0_GHk8IAapc8"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "Support for third party widgets will remain active for the duration of the session. To disable support:"
      ],
      "metadata": {
        "id": "mJmcGKu2avxZ"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "Support for third party widgets will remain active for the duration of the session. To disable support:"
      ],
      "metadata": {
        "id": "vc3MeXcmavip"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "Support for third party widgets will remain active for the duration of the session. To disable support:"
      ],
      "metadata": {
        "id": "7dfjxaFbavI4"
      }
    },
    {
      "cell_type": "code",
      "source": [],
      "metadata": {
        "id": "qXF1ZtxKZFBj"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [],
      "metadata": {
        "id": "kyexWiJJZFEw"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}