diff --git a/Makefile b/Makefile
index df95010..6a69aa6 100644
--- a/Makefile
+++ b/Makefile
@@ -2,7 +2,7 @@
 
 # Install development dependencies
 install:
-	uv sync --dev
+	uv sync --all-extras --dev
 
 # Run tests with coverage
 test:
diff --git a/pyproject.toml b/pyproject.toml
index 9365cd9..89f02d8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,14 +31,18 @@ dependencies = [
     "numpy",
     "openai",
     "ipykernel",
-    "fastmcp>=2.12.2",
-    "click>=8.2.1",
     'networkx',
     'igraph',
     'pyvis',
     'zstandard',
 ]
 
+[project.optional-dependencies]
+mcp = [
+    "fastmcp>=2.12.2",
+    "click>=8.2.1",
+]
+
 [project.scripts]
 tct-server = "main:main"
 
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index bab518f..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,13 +0,0 @@
-requests
-jsons
-pandas
-seaborn
-matplotlib
-ipycytoscape
-networkx
-openai
-ipykernel
-PyYAML
-ipywidgets
-zstandard
-igraph
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 3af9951..0000000
--- a/setup.py
+++ /dev/null
@@ -1,32 +0,0 @@
-from setuptools import setup, find_packages
-
-setup(
-    name='TCT',
-    version='0.1.6',
-    packages=find_packages(),
-    install_requires=[
-        # List your library's dependencies here
-        'requests',
-        'pandas',
-        'seaborn',
-        'matplotlib',
-        'ipycytoscape',
-        'networkx',
-        'numpy',
-        'openai',
-        'PyYAML',
-        'copy',
-    ],
-    entry_points={
-        'console_scripts': [
-            # Define any command-line scripts here
-        ],
-    },
-    url='https://github.com/NCATSTranslator/Translator_component_toolkit',
-    author='Guangrong Qin',
-    author_email='guangrong.qin@isbscience.org',
-    description='Translator Component Toolkit',
-    long_description=open('README.md').read(),
-    long_description_content_type='text/markdown',
-    license='MIT',
-)
diff --git a/tests/test_server.py b/tests/test_server.py
index 43b3863..fd1df2e 100644
--- a/tests/test_server.py
+++ b/tests/test_server.py
@@ -1,5 +1,10 @@
 """Simple tests for TCT MCP Server functionality."""
 
+import pytest
+
+# Skip this module entirely when the optional MCP extra (fastmcp) is not installed.
+pytest.importorskip("fastmcp")
+
 from TCT.server import mcp
 
 
diff --git a/uv.lock b/uv.lock
index 3f4c7e0..7eb6e9c 100644
--- a/uv.lock
+++ b/uv.lock
@@ -247,7 +247,7 @@ resolution-markers = [
     "python_full_version < '3.11'",
 ]
 dependencies = [
-    { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
+    { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" } },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/66/54/eb9bfc647b19f2009dd5c7f5ec51c4e6ca831725f1aea7a993034f483147/contourpy-1.3.2.tar.gz", hash = "sha256:b6945942715a034c671b7fc54f9588126b0b8bf23db2696e3ca8328f3ff0ab54", size = 13466130, upload-time = "2025-04-15T17:47:53.79Z" }
 wheels = [
@@ -318,7 +318,7 @@ resolution-markers = [
     "python_full_version == '3.11.*'",
 ]
 dependencies = [
-    { name = "numpy", version = "2.3.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+    { name = "numpy", version = "2.3.2", source = { registry = "https://pypi.org/simple" } },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/58/01/1253e6698a07380cd31a736d248a3f2a50a7c88779a1813da27503cadc2a/contourpy-1.3.3.tar.gz", hash = "sha256:083e12155b210502d0bca491432bb04d56dc3432f95a979b429f2848c3dbe880", size = 13466174, upload-time = "2025-07-26T12:03:12.549Z" }
 wheels = [
@@ -875,17 +875,17 @@ resolution-markers = [
     "python_full_version < '3.11'",
 ]
 dependencies = [
-    { name = "colorama", marker = "python_full_version < '3.11' and sys_platform == 'win32'" },
-    { name = "decorator", marker = "python_full_version < '3.11'" },
-    { name = "exceptiongroup", marker = "python_full_version < '3.11'" },
-    { name = "jedi", marker = "python_full_version < '3.11'" },
-    { name = "matplotlib-inline", marker = "python_full_version < '3.11'" },
-    { name = "pexpect", marker = "python_full_version < '3.11' and sys_platform != 'emscripten' and sys_platform != 'win32'" },
-    { name = "prompt-toolkit", marker = "python_full_version < '3.11'" },
-    { name = "pygments", marker = "python_full_version < '3.11'" },
-    { name = "stack-data", marker = "python_full_version < '3.11'" },
-    { name = "traitlets", marker = "python_full_version < '3.11'" },
-    { name = "typing-extensions", marker = "python_full_version < '3.11'" },
+    { name = "colorama", marker = "sys_platform == 'win32'" },
+    { name = "decorator" },
+    { name = "exceptiongroup" },
+    { name = "jedi" },
+    { name = "matplotlib-inline" },
+    { name = "pexpect", marker = "sys_platform != 'emscripten' and sys_platform != 'win32'" },
+    { name = "prompt-toolkit" },
+    { name = "pygments" },
+    { name = "stack-data" },
+    { name = "traitlets" },
+    { name = "typing-extensions" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/85/31/10ac88f3357fc276dc8a64e8880c82e80e7459326ae1d0a211b40abf6665/ipython-8.37.0.tar.gz", hash = "sha256:ca815841e1a41a1e6b73a0b08f3038af9b2252564d01fc405356d34033012216", size = 5606088, upload-time = "2025-05-31T16:39:09.613Z" }
 wheels = [
@@ -901,17 +901,17 @@ resolution-markers = [
     "python_full_version == '3.11.*'",
 ]
 dependencies = [
-    { name = "colorama", marker = "python_full_version >= '3.11' and sys_platform == 'win32'" },
-    { name = "decorator", marker = "python_full_version >= '3.11'" },
-    { name = "ipython-pygments-lexers", marker = "python_full_version >= '3.11'" },
-    { name = "jedi", marker = "python_full_version >= '3.11'" },
-    { name = "matplotlib-inline", marker = "python_full_version >= '3.11'" },
-    { name = "pexpect", marker = "python_full_version >= '3.11' and sys_platform != 'emscripten' and sys_platform != 'win32'" },
-    { name = "prompt-toolkit", marker = "python_full_version >= '3.11'" },
-    { name = "pygments", marker = "python_full_version >= '3.11'" },
-    { name = "stack-data", marker = "python_full_version >= '3.11'" },
-    { name = "traitlets", marker = "python_full_version >= '3.11'" },
-    { name = "typing-extensions", marker = "python_full_version == '3.11.*'" },
+    { name = "colorama", marker = "sys_platform == 'win32'" },
+    { name = "decorator" },
+    { name = "ipython-pygments-lexers" },
+    { name = "jedi" },
+    { name = "matplotlib-inline" },
+    { name = "pexpect", marker = "sys_platform != 'emscripten' and sys_platform != 'win32'" },
+    { name = "prompt-toolkit" },
+    { name = "pygments" },
+    { name = "stack-data" },
+    { name = "traitlets" },
+    { name = "typing-extensions", marker = "python_full_version < '3.12'" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/6e/71/a86262bf5a68bf211bcc71fe302af7e05f18a2852fdc610a854d20d085e6/ipython-9.5.0.tar.gz", hash = "sha256:129c44b941fe6d9b82d36fc7a7c18127ddb1d6f02f78f867f402e2e3adde3113", size = 4389137, upload-time = "2025-08-29T12:15:21.519Z" }
 wheels = [
@@ -923,7 +923,7 @@ name = "ipython-pygments-lexers"
 version = "1.1.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
-    { name = "pygments", marker = "python_full_version >= '3.11'" },
+    { name = "pygments" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/ef/4c/5dd1d8af08107f88c7f741ead7a40854b8ac24ddf9ae850afbcf698aa552/ipython_pygments_lexers-1.1.1.tar.gz", hash = "sha256:09c0138009e56b6854f9535736f4171d855c8c08a563a0dcd8022f78355c7e81", size = 8393, upload-time = "2025-01-17T11:24:34.505Z" }
 wheels = [
@@ -2784,11 +2784,9 @@ wheels = [
 
 [[package]]
 name = "tct"
-version = "0.1.6"
+version = "0.2.0"
 source = { editable = "." }
 dependencies = [
-    { name = "click" },
-    { name = "fastmcp" },
     { name = "igraph" },
     { name = "ipycytoscape" },
     { name = "ipykernel" },
@@ -2806,6 +2804,12 @@ dependencies = [
     { name = "zstandard" },
 ]
 
+[package.optional-dependencies]
+mcp = [
+    { name = "click" },
+    { name = "fastmcp" },
+]
+
 [package.dev-dependencies]
 dev = [
     { name = "codespell" },
@@ -2817,8 +2821,8 @@ dev = [
 
 [package.metadata]
 requires-dist = [
-    { name = "click", specifier = ">=8.2.1" },
-    { name = "fastmcp", specifier = ">=2.12.2" },
+    { name = "click", marker = "extra == 'mcp'", specifier = ">=8.2.1" },
+    { name = "fastmcp", marker = "extra == 'mcp'", specifier = ">=2.12.2" },
     { name = "igraph" },
     { name = "ipycytoscape" },
     { name = "ipykernel" },
@@ -2833,6 +2837,7 @@ requires-dist = [
     { name = "seaborn" },
     { name = "zstandard" },
 ]
+provides-extras = ["mcp"]
 
 [package.metadata.requires-dev]
 dev = [