diff --git a/CMakeLists.txt b/CMakeLists.txt
index 47a64c9..d2537af 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,74 +1,80 @@
 # Copyright 2018 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
 
 ################################################################################
 #    This file is part of NUISANCE.
 #
 #    NUISANCE is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
 #    the Free Software Foundation, either version 3 of the License, or
 #    (at your option) any later version.
 #
 #    NUISANCE is distributed in the hope that it will be useful,
 #    but WITHOUT ANY WARRANTY; without even the implied warranty of
 #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #    GNU General Public License for more details.
 #
 #    You should have received a copy of the GNU General Public License
 #    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
 ################################################################################
 cmake_minimum_required (VERSION 2.8 FATAL_ERROR)
 
 #Use the compilers found in the path
 find_program(CMAKE_C_COMPILER NAMES $ENV{CC} gcc PATHS ENV PATH NO_DEFAULT_PATH)
 find_program(CMAKE_CXX_COMPILER NAMES $ENV{CXX} g++ PATHS ENV PATH NO_DEFAULT_PATH)
 
 project(NUISANCE)
 
 include(ExternalProject)
 
 set (NUISANCE_VERSION_MAJOR 3)
 set (NUISANCE_VERSION_MINOR 0)
 set (NUISANCE_VERSION_REVISION 0)
 
 set (NUISANCE_VERSION_STRING "v${NUISANCE_VERSION_MAJOR}r${NUISANCE_VERSION_MINOR}")
 if(${NUISANCE_VERSION_REVISION} STRGREATER "0")
   set (NUISANCE_VERSION_STRING "${NUISANCE_VERSION_STRING}p${NUISANCE_VERSION_REVISION}")
 endif()
 
 #Set this to TRUE to enable build debugging messages
 set(BUILD_DEBUG_MSGS TRUE)
 
 include(${CMAKE_SOURCE_DIR}/cmake/cmessage.cmake)
 
 include(${CMAKE_SOURCE_DIR}/cmake/cacheVariables.cmake)
 
 cmessage(STATUS "CMAKE_INSTALL_PREFIX: \"${CMAKE_INSTALL_PREFIX}\"")
 cmessage(STATUS "CMAKE_BUILD_TYPE: \"${CMAKE_BUILD_TYPE}\"")
 
 ################################################################################
 #                            Check Dependencies
 ################################################################################
 
 ##################################  ROOT  ######################################
 include(${CMAKE_SOURCE_DIR}/cmake/ROOTSetup.cmake)
 
 ################################# InputHandler #################################
 include(${CMAKE_SOURCE_DIR}/cmake/InputHandlerSetup.cmake)
 
 #################################  Pythia6/8 ###################################
 include(${CMAKE_SOURCE_DIR}/cmake/pythia6Setup.cmake)
 
 ################################## FHICLCPP ####################################
 include(${CMAKE_SOURCE_DIR}/cmake/fhiclcppSetup.cmake)
 
 #Need this to be at the front
 LIST(REVERSE EXTRA_CXX_FLAGS)
 LIST(APPEND EXTRA_CXX_FLAGS -I${CMAKE_SOURCE_DIR}/src)
 LIST(REVERSE EXTRA_CXX_FLAGS)
 
 ################################## COMPILER ####################################
 include(${CMAKE_SOURCE_DIR}/cmake/c++CompilerSetup.cmake)
 
 ################################################################################
 
 add_subdirectory(src)
+
+configure_file(cmake/setup.sh.in
+  "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/setup.sh" @ONLY)
+install(FILES
+  "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/setup.sh" DESTINATION
+  ${CMAKE_INSTALL_PREFIX})
diff --git a/cmake/setup.sh.in b/cmake/setup.sh.in
new file mode 100644
index 0000000..44d8d3f
--- /dev/null
+++ b/cmake/setup.sh.in
@@ -0,0 +1,159 @@
+# Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
+
+################################################################################
+#    This file is part of NUISANCE.
+#
+#    NUISANCE is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    NUISANCE is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
+################################################################################
+
+#!/bin/sh
+
+### Adapted from https://unix.stackexchange.com/questions/4965/keep-duplicates-out-of-path-on-source
+function add_to_PATH () {
+  for d; do
+
+    d=$(cd -- "$d" && { pwd -P || pwd; }) 2>/dev/null  # canonicalize symbolic links
+    if [ -z "$d" ]; then continue; fi  # skip nonexistent directory
+
+    if [ "$d" == "/usr/bin" ] || [ "$d" == "/usr/bin64" ] || [ "$d" == "/usr/local/bin" ] || [ "$d" == "/usr/local/bin64" ]; then
+      case ":$PATH:" in
+        *":$d:"*) :;;
+        *) export PATH=$PATH:$d;;
+      esac
+    else
+      case ":$PATH:" in
+        *":$d:"*) :;;
+        *) export PATH=$d:$PATH;;
+      esac
+    fi
+  done
+}
+
+function add_to_LD_LIBRARY_PATH () {
+  for d; do
+
+    d=$(cd -- "$d" && { pwd -P || pwd; }) 2>/dev/null  # canonicalize symbolic links
+    if [ -z "$d" ]; then continue; fi  # skip nonexistent directory
+
+    if [ "$d" == "/usr/lib" ] || [ "$d" == "/usr/lib64" ] || [ "$d" == "/usr/local/lib" ] || [ "$d" == "/usr/local/lib64" ]; then
+      case ":$LD_LIBRARY_PATH:" in
+        *":$d:"*) :;;
+        *) export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$d;;
+      esac
+    else
+      case ":$LD_LIBRARY_PATH:" in
+        *":$d:"*) :;;
+        *) export LD_LIBRARY_PATH=$d:$LD_LIBRARY_PATH;;
+      esac
+    fi
+  done
+}
+
+if [ "@EXTRA_SETUP_SCRIPT@" ]; then
+  if [ ! -e @EXTRA_SETUP_SCRIPT@ ]; then
+      echo "[WARN]: Extra setup script \"@EXTRA_SETUP_SCRIPT@\" requested, but could not be found. Skipping..."
+  else
+    echo "[INFO]: Sourcing extra setup from \"@EXTRA_SETUP_SCRIPT@\"."
+    . @EXTRA_SETUP_SCRIPT@
+  fi
+fi
+
+add_to_PATH "@CMAKE_INSTALL_PREFIX@/bin"
+
+add_to_LD_LIBRARY_PATH "@CMAKE_INSTALL_PREFIX@/lib"
+
+if [ ! "${ROOTSYS}" ]; then
+  echo "[INFO]: Sourcing ROOT from: @CMAKE_ROOTSYS@"
+  source "@CMAKE_ROOTSYS@/bin/thisroot.sh"
+fi
+
+if [ "@USE_T2K@" != "FALSE" ]; then
+  echo "[INFO]: Adding T2K paths to the environment."
+  export T2KREWEIGHT=@T2KREWEIGHT@
+  add_to_LD_LIBRARY_PATH "@T2KREWEIGHT@/lib"
+fi
+
+if [ "@USE_NIWG@" != "FALSE" ]; then
+  echo "[INFO]: Adding NIWG paths to the environment."
+  export NIWG=@NIWG_ROOT@
+  export NIWGREWEIGHT_INPUTS=@NIWG_ROOT@/inputs
+  add_to_LD_LIBRARY_PATH "@NIWG_ROOT@"
+fi
+
+if [ "@USE_NEUT@" != "FALSE" ]; then
+  echo "[INFO]: Adding NEUT library paths to the environment."
+  export NEUT_ROOT=@NEUT_ROOT@
+  export CERN=@CERN@
+  export CERN_LEVEL=@CERN_LEVEL@
+  add_to_LD_LIBRARY_PATH "${NEUT_LIB_DIR}" "${NEUT_ROOT}/src/reweight"
+fi
+
+if [ "@USE_NuWro@" != "FALSE" ]; then
+  if [ "@NUWRO_BUILT_FROM_FILE@" == "FALSE" ]; then
+    echo "[INFO]: Adding NuWro library paths to the environment."
+    export NUWRO="@NUWRO@"
+
+    add_to_PATH "@NUWRO@/bin"
+    add_to_LD_LIBRARY_PATH "@NUWRO@/build/@CMAKE_SYSTEM_NAME@/lib"
+
+    if [ "@NUWRO_INC@" ]; then
+      export NUWRO_INC=@NUWRO_INC@
+    fi
+
+  else
+    echo "[INFO]: NuWro support included from input event file."
+  fi
+fi
+
+if [ "@NEED_PYTHIA6@" != "FALSE" ]; then
+  echo "[INFO]: Adding PYTHIA6 library paths to the environment."
+  export PYTHIA6="@PYTHIA6@"
+
+  add_to_LD_LIBRARY_PATH "@PYTHIA6@"
+fi
+
+if [ "@USE_GENIE@" != "FALSE" ]; then
+  echo "[INFO]: Adding GENIE paths to the environment."
+
+  export GENIE="@GENIE@"
+
+  export LHAPDF_LIB="@LHAPDF_LIB@"
+  export LHAPDF_INC="@LHAPDF_INC@"
+
+  export LIBXML2_LIB="@LIBXML2_LIB@"
+  export LIBXML2_INC="@LIBXML2_INC@"
+
+  export LOG4CPP_LIB="@LOG4CPP_LIB@"
+  export LOG4CPP_INC="@LOG4CPP_INC@"
+
+  if [ "@LHAPATH@" ]; then
+    export LHAPATH="@LHAPATH@"
+  fi
+
+  add_to_PATH "@GENIE@/bin"
+
+  add_to_LD_LIBRARY_PATH "@GENIE@/lib" "@LHAPDF_LIB@" "@LIBXML2_LIB@" "@LOG4CPP_LIB@"
+
+fi
+
+if [ "@BUILD_GiBUU@" != "FALSE" ]; then
+  echo "[INFO]: Sourcing GiBUU tools."
+  source @CMAKE_BINARY_DIR@/GiBUUTools/src/GiBUUTools-build/Linux/setup.sh
+fi
+
+if [ "@NUSYST_ROOT@" != "" ]; then
+  source @NUSYST_ROOT@/setup.sh
+fi
+
+export NUISANCE="@CMAKE_SOURCE_DIR@"
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 26db198..6a69ff2 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,7 +1,9 @@
 add_subdirectory(config)
 add_subdirectory(core)
 add_subdirectory(plugins)
 add_subdirectory(utility)
 add_subdirectory(generator)
 
+add_subdirectory(samples)
+
 add_subdirectory(app)
diff --git a/src/app/DumpEventInfo.cxx b/src/app/DumpEventInfo.cxx
index 3455253..b65b10c 100644
--- a/src/app/DumpEventInfo.cxx
+++ b/src/app/DumpEventInfo.cxx
@@ -1,27 +1,34 @@
 
 #include "config/GlobalConfiguration.hxx"
 
 #include "core/IInputHandler.hxx"
 #include "core/MinimalEvent.hxx"
 
+#include "samples/ISample.hxx"
+
 #include "plugins/Instantiate.hxx"
 
 #include "fhiclcpp/make_ParameterSet.h"
 
 #include <string>
 
 int main() {
   nuis::config::EnsureConfigurationRead("./nuis.global.config.fcl");
 
   fhicl::ParameterSet ps = fhicl::make_ParameterSet("./test.fcl");
 
-  nuis::plugins::plugin_traits<IInputHandler>::unique_ptr_t IH =
-      nuis::plugins::Instantiate<IInputHandler>(
-          ps.get<std::string>("sample.InputHandler"));
+  for (fhicl::ParameterSet const &samp_config :
+       ps.get<std::vector<fhicl::ParameterSet>>("samples")) {
+
+    std::cout << "[INFO]: Reading sample: "
+              << samp_config.get<std::string>("name") << std::endl;
 
-  IH->Initialize(ps.get<fhicl::ParameterSet>("sample"));
+    nuis::plugins::plugin_traits<ISample>::unique_ptr_t sample =
+        nuis::plugins::Instantiate<ISample>(
+            samp_config.get<std::string>("name"));
+            
 
-  for(IInputHandler::ev_index_t ev_it = 0; ev_it < IH->GetNEvents(); ++ev_it){
-    nuis::core::MinimalEvent const &ev = IH->GetMinimalEvent(ev_it);
+    sample->Initialize(samp_config);
+    sample->ProcessSample();
   }
 }
diff --git a/src/core/CMakeLists.txt b/src/core/CMakeLists.txt
index ad886b2..1aa7703 100644
--- a/src/core/CMakeLists.txt
+++ b/src/core/CMakeLists.txt
@@ -1,19 +1,19 @@
 set(core_implementation_files
 FullEvent.cxx
-# InputManager.cxx
+InputManager.cxx
 MinimalEvent.cxx
 Particle.cxx)
 
 set(core_header_files
 FullEvent.hxx
-# InputManager.hxx
+InputManager.hxx
 MinimalEvent.hxx
 Particle.hxx
 IInputHandler.hxx
 types.hxx)
 
 add_library(nuis_core SHARED ${core_implementation_files})
 target_link_libraries(nuis_core)
 
 install(TARGETS nuis_core DESTINATION lib)
 install(FILES ${core_header_files} DESTINATION include/core)
diff --git a/src/core/IInputHandler.hxx b/src/core/IInputHandler.hxx
index f6ee96a..94aaebf 100644
--- a/src/core/IInputHandler.hxx
+++ b/src/core/IInputHandler.hxx
@@ -1,57 +1,109 @@
 // Copyright 2018 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
 
 /*******************************************************************************
  *    This file is part of NUISANCE.
  *
  *    NUISANCE is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
  *    the Free Software Foundation, either version 3 of the License, or
  *    (at your option) any later version.
  *
  *    NUISANCE is distributed in the hope that it will be useful,
  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *    GNU General Public License for more details.
  *
  *    You should have received a copy of the GNU General Public License
  *    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
  *******************************************************************************/
 
 #ifndef CORE_IINPUTHANDLER_HXX_SEEN
 #define CORE_IINPUTHANDLER_HXX_SEEN
 
 #include "plugins/traits.hxx"
 
 #include "exception/exception.hxx"
 
+#include <iterator>
+
 namespace fhicl {
 class ParameterSet;
 }
 
 namespace nuis {
 namespace core {
 class MinimalEvent;
 class FullEvent;
 } // namespace core
 } // namespace nuis
 
 class IInputHandler {
 public:
+  struct FullEvent_const_iterator
+      : public std::iterator<
+            std::input_iterator_tag, nuis::core::FullEvent const, size_t,
+            nuis::core::FullEvent const *, nuis::core::FullEvent const &> {
+
+    FullEvent_const_iterator(size_t _idx, IInputHandler const *_ih) {
+      idx = _idx;
+      ih = _ih;
+    }
+    FullEvent_const_iterator(FullEvent_const_iterator const &other) {
+      idx = other.idx;
+      ih = other.ih;
+    }
+    FullEvent_const_iterator operator=(FullEvent_const_iterator const &other) {
+      idx = other.idx;
+      ih = other.ih;
+      return (*this);
+    }
+
+    bool operator==(FullEvent_const_iterator const &other) {
+      return (idx == other.idx);
+    }
+    bool operator!=(FullEvent_const_iterator const &other) {
+      return !(*this == other);
+    }
+    nuis::core::FullEvent const &operator*() { return ih->GetFullEvent(idx); }
+    nuis::core::FullEvent const *operator->() { return &ih->GetFullEvent(idx); }
+
+    FullEvent_const_iterator operator++() {
+      idx++;
+      return *this;
+    }
+    FullEvent_const_iterator operator++(int) {
+      FullEvent_const_iterator tmp(*this);
+      idx++;
+      return tmp;
+    }
+
+  private:
+    size_t idx;
+    IInputHandler const *ih;
+  };
 
   NEW_NUIS_EXCEPT(invalid_input_file);
   NEW_NUIS_EXCEPT(invalid_entry);
 
   typedef size_t ev_index_t;
 
   virtual void Initialize(fhicl::ParameterSet const &) = 0;
-  virtual nuis::core::MinimalEvent const &GetMinimalEvent(ev_index_t idx) = 0;
-  virtual nuis::core::FullEvent const &GetFullEvent(ev_index_t idx) = 0;
+  virtual nuis::core::MinimalEvent const &
+  GetMinimalEvent(ev_index_t idx) const = 0;
+  virtual nuis::core::FullEvent const &GetFullEvent(ev_index_t idx) const = 0;
+
+  virtual size_t GetNEvents() const = 0;
 
-  virtual size_t GetNEvents() = 0;
+  FullEvent_const_iterator begin() const {
+    return FullEvent_const_iterator(0, this);
+  }
+  FullEvent_const_iterator end() const {
+    return FullEvent_const_iterator(GetNEvents(), this);
+  }
 
-  virtual ~IInputHandler(){}
+  virtual ~IInputHandler() {}
 };
 
 DECLARE_PLUGIN_INTERFACE(IInputHandler);
 
 #endif
diff --git a/src/core/InputManager.cxx b/src/core/InputManager.cxx
index 938211f..12cfce8 100644
--- a/src/core/InputManager.cxx
+++ b/src/core/InputManager.cxx
@@ -1,22 +1,65 @@
 #include "core/InputManager.hxx"
 
+#include "plugins/Instantiate.hxx"
+
+#include "fhiclcpp/ParameterSet.h"
+
+#include <iomanip>
+
 namespace nuis {
 namespace core {
 
+InputManager *InputManager::_global_inst = nullptr;
+
+InputManager::NamedInputHandler::NamedInputHandler(
+    std::string const &file,
+    plugins::plugin_traits<IInputHandler>::unique_ptr_t &&IH) {
+  name = file;
+  handler = std::move(IH);
+}
+
+InputManager::InputManager() : Inputs() {}
+
+InputManager &InputManager::Get() {
+  if (!_global_inst) {
+    _global_inst = new InputManager();
+  }
+  return *_global_inst;
+}
+
 InputManager::Input_id_t
-InputManager::EnsureInputLoaded(std::string const &file_name) {
+InputManager::EnsureInputLoaded(fhicl::ParameterSet const &ps) {
+  std::string const &file_name = ps.get<std::string>("file");
   for (size_t i = 0; i < Inputs.size(); ++i) {
     if (Inputs[i].name == file_name) {
       return i;
     }
   }
 
-  Inputs.push_back(NamedInputHandler{
-      file_name,
-  });
+  Inputs.emplace_back(file_name,
+                      nuis::plugins::Instantiate<IInputHandler>(
+                          ps.get<std::string>("input_type") + "InputHandler"));
+  Inputs.back().handler->Initialize(ps);
+  return (Inputs.size() - 1);
 }
 InputManager::Input_id_t
-InputManager::GetInputId(std::string const &file_name) {}
-IInputHandler &InputManager::GetInputHandler(InputManager::Input_id_t id) {}
+InputManager::GetInputId(std::string const &file_name) const {
+  for (size_t i = 0; i < Inputs.size(); ++i) {
+    if (Inputs[i].name == file_name) {
+      return i;
+    }
+  }
+  throw unknown_input() << "[ERROR]: Input file " << std::quoted(file_name)
+                        << " has not been loaded.";
+}
+IInputHandler const &
+InputManager::GetInputHandler(InputManager::Input_id_t id) const {
+  if (id >= Inputs.size()) {
+    throw unknown_input() << "[ERROR]: Attempted to get input with id " << id
+                          << ", but only have " << Inputs.size()
+                          << " loaded inputs.";
+  }
+  return *Inputs[id].handler.get();
+}
 } // namespace core
 } // namespace nuis
diff --git a/src/core/InputManager.hxx b/src/core/InputManager.hxx
index f965335..c30c9cc 100644
--- a/src/core/InputManager.hxx
+++ b/src/core/InputManager.hxx
@@ -1,52 +1,64 @@
 // Copyright 2018 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
 
 /*******************************************************************************
  *    This file is part of NUISANCE.
  *
  *    NUISANCE is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
  *    the Free Software Foundation, either version 3 of the License, or
  *    (at your option) any later version.
  *
  *    NUISANCE is distributed in the hope that it will be useful,
  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *    GNU General Public License for more details.
  *
  *    You should have received a copy of the GNU General Public License
  *    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
  *******************************************************************************/
 
 #ifndef CORE_INPUTMANAGER_HXX_SEEN
 #define CORE_INPUTMANAGER_HXX_SEEN
 
-#include <memory>
+#include "core/IInputHandler.hxx"
+
+#include "plugins/traits.hxx"
+
+#include "exception/exception.hxx"
+
 #include <string>
 #include <vector>
 
-namespace nuis {
-namespace core {
-class IInputHandler;
+namespace fhicl {
+class ParameterSet;
 }
-} // namespace nuis
 
 namespace nuis {
 namespace core {
 class InputManager {
   struct NamedInputHandler {
+    NamedInputHandler(std::string const &,
+                      plugins::plugin_traits<IInputHandler>::unique_ptr_t &&);
     std::string name;
-    std::unique_ptr<IInputHandler> handler;
+    plugins::plugin_traits<IInputHandler>::unique_ptr_t handler;
   };
   std::vector<NamedInputHandler> Inputs;
 
+  InputManager();
+
+  static InputManager *_global_inst;
 public:
+
+  static InputManager &Get();
+
+  NEW_NUIS_EXCEPT(unknown_input);
   typedef size_t Input_id_t;
 
-  Input_id_t EnsureInputLoaded(std::string const &file_name);
-  Input_id_t GetInputId(std::string const &file_name);
-  IInputHandler &GetInputHandler(Input_id_t id);
+  Input_id_t EnsureInputLoaded(fhicl::ParameterSet const &);
+  Input_id_t GetInputId(std::string const &) const;
+  IInputHandler const &GetInputHandler(Input_id_t) const;
 };
 } // namespace core
 } // namespace nuis
 
 #endif
diff --git a/src/generator/CMakeLists.txt b/src/generator/CMakeLists.txt
index 85c0136..45c16fe 100644
--- a/src/generator/CMakeLists.txt
+++ b/src/generator/CMakeLists.txt
@@ -1,7 +1,6 @@
-
 if(USE_NuWro)
   add_library(InputHandlers SHARED NuWroInputHandler.cxx)
   target_link_libraries(InputHandlers nuis_core nuis_config)
 
   install(TARGETS InputHandlers DESTINATION plugins)
 endif(USE_NuWro)
diff --git a/src/generator/NuWroInputHandler.cxx b/src/generator/NuWroInputHandler.cxx
index 10b1380..9a951c6 100644
--- a/src/generator/NuWroInputHandler.cxx
+++ b/src/generator/NuWroInputHandler.cxx
@@ -1,42 +1,44 @@
 #include "NuWroInputHandler.hxx"
 
 #include "core/FullEvent.hxx"
 
 #include "utility/ROOTUtility.hxx"
 
 #include "fhiclcpp/ParameterSet.h"
 
 using namespace nuis::core;
 using namespace nuis::utility;
 
 NuWroInputHandler::NuWroInputHandler() : fInputTree(nullptr) {}
 NuWroInputHandler::NuWroInputHandler(NuWroInputHandler &&other)
     : fInputTree(std::move(other.fInputTree)),
       fReaderEvent(std::move(other.fReaderEvent)) {}
 
 void NuWroInputHandler::Initialize(fhicl::ParameterSet const &ps) {
 
   fInputTree = CheckGetTTree(ps.get<std::string>("file"), "treeout");
 
   fReaderEvent.fNuWroEvent = nullptr;
   fInputTree->tree->SetBranchAddress("e", &fReaderEvent.fNuWroEvent);
 }
-MinimalEvent const &NuWroInputHandler::GetMinimalEvent(ev_index_t idx) {
+MinimalEvent const &NuWroInputHandler::GetMinimalEvent(ev_index_t idx) const {
   if (idx >= GetNEvents()) {
     throw IInputHandler::invalid_entry()
         << "[ERROR]: Attempted to get entry " << idx
         << " from an InputHandler with only " << GetNEvents();
   }
   fInputTree->tree->GetEntry(idx);
   return fReaderEvent;
 }
 
-FullEvent const &NuWroInputHandler::GetFullEvent(ev_index_t idx) {
+FullEvent const &NuWroInputHandler::GetFullEvent(ev_index_t idx) const {
   (void)GetMinimalEvent(idx);
-  //Fill particle stack
+  // Fill particle stack
   return fReaderEvent;
 }
 
-size_t NuWroInputHandler::GetNEvents() { return fInputTree->tree->GetEntries(); }
+size_t NuWroInputHandler::GetNEvents() const {
+  return fInputTree->tree->GetEntries();
+}
 
-DECLARE_PLUGIN(IInputHandler,NuWroInputHandler);
+DECLARE_PLUGIN(IInputHandler, NuWroInputHandler);
diff --git a/src/generator/NuWroInputHandler.hxx b/src/generator/NuWroInputHandler.hxx
index 184cb96..750748a 100644
--- a/src/generator/NuWroInputHandler.hxx
+++ b/src/generator/NuWroInputHandler.hxx
@@ -1,56 +1,56 @@
 // Copyright 2018 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
 
 /*******************************************************************************
  *    This file is part of NUISANCE.
  *
  *    NUISANCE is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
  *    the Free Software Foundation, either version 3 of the License, or
  *    (at your option) any later version.
  *
  *    NUISANCE is distributed in the hope that it will be useful,
  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *    GNU General Public License for more details.
  *
  *    You should have received a copy of the GNU General Public License
  *    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
  *******************************************************************************/
 
 #ifndef GENERATOR_NUWROINPUTHANDLER_HXX_SEEN
 #define GENERATOR_NUWROINPUTHANDLER_HXX_SEEN
 
 #include "core/IInputHandler.hxx"
 #include "core/FullEvent.hxx"
 
 #include <memory>
 
 namespace fhicl {
 class ParameterSet;
 }
 
 namespace nuis {
 namespace core {
 class MinimalEvent;
 } // namespace core
 namespace utility {
 class TreeFile;
 }
 } // namespace nuis
 
 class NuWroInputHandler : public IInputHandler {
-  std::unique_ptr<nuis::utility::TreeFile> fInputTree;
-  nuis::core::FullEvent fReaderEvent;
+  mutable std::unique_ptr<nuis::utility::TreeFile> fInputTree;
+  mutable nuis::core::FullEvent fReaderEvent;
 
 public:
   NuWroInputHandler();
   NuWroInputHandler(NuWroInputHandler const &) = delete;
   NuWroInputHandler(NuWroInputHandler &&);
 
   void Initialize(fhicl::ParameterSet const &);
-  nuis::core::MinimalEvent const &GetMinimalEvent(ev_index_t idx);
-  nuis::core::FullEvent const &GetFullEvent(ev_index_t idx);
-  size_t GetNEvents();
+  nuis::core::MinimalEvent const &GetMinimalEvent(ev_index_t idx) const;
+  nuis::core::FullEvent const &GetFullEvent(ev_index_t idx) const;
+  size_t GetNEvents() const;
 };
 
 #endif
diff --git a/src/samples/CMakeLists.txt b/src/samples/CMakeLists.txt
new file mode 100644
index 0000000..98771ed
--- /dev/null
+++ b/src/samples/CMakeLists.txt
@@ -0,0 +1,6 @@
+set(samples_header_files
+ISample.hxx)
+
+install(FILES ${samples_header_files} DESTINATION include/samples)
+
+add_subdirectory(MCTools)
diff --git a/src/core/InputManager.hxx b/src/samples/IDataComparison.hxx
similarity index 59%
copy from src/core/InputManager.hxx
copy to src/samples/IDataComparison.hxx
index f965335..f73db5b 100644
--- a/src/core/InputManager.hxx
+++ b/src/samples/IDataComparison.hxx
@@ -1,52 +1,32 @@
 // Copyright 2018 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
 
 /*******************************************************************************
  *    This file is part of NUISANCE.
  *
  *    NUISANCE is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
  *    the Free Software Foundation, either version 3 of the License, or
  *    (at your option) any later version.
  *
  *    NUISANCE is distributed in the hope that it will be useful,
  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *    GNU General Public License for more details.
  *
  *    You should have received a copy of the GNU General Public License
  *    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
  *******************************************************************************/
 
-#ifndef CORE_INPUTMANAGER_HXX_SEEN
-#define CORE_INPUTMANAGER_HXX_SEEN
+#ifndef SAMPLES_IDATACOMPARISON_HXX_SEEN
+#define SAMPLES_IDATACOMPARISON_HXX_SEEN
 
-#include <memory>
-#include <string>
-#include <vector>
+#include "samples/ISample.hxx"
 
-namespace nuis {
-namespace core {
-class IInputHandler;
-}
-} // namespace nuis
+class IDataComparison : public ISample {
 
-namespace nuis {
-namespace core {
-class InputManager {
-  struct NamedInputHandler {
-    std::string name;
-    std::unique_ptr<IInputHandler> handler;
-  };
-  std::vector<NamedInputHandler> Inputs;
-
-public:
-  typedef size_t Input_id_t;
-
-  Input_id_t EnsureInputLoaded(std::string const &file_name);
-  Input_id_t GetInputId(std::string const &file_name);
-  IInputHandler &GetInputHandler(Input_id_t id);
+  double GetGOF() = 0;
 };
-} // namespace core
-} // namespace nuis
+
+DECLARE_PLUGIN_INTERFACE(IDataComparison);
 
 #endif
diff --git a/src/core/IInputHandler.hxx b/src/samples/ISample.hxx
similarity index 73%
copy from src/core/IInputHandler.hxx
copy to src/samples/ISample.hxx
index f6ee96a..2333cbd 100644
--- a/src/core/IInputHandler.hxx
+++ b/src/samples/ISample.hxx
@@ -1,57 +1,53 @@
 // Copyright 2018 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret
 
 /*******************************************************************************
  *    This file is part of NUISANCE.
  *
  *    NUISANCE is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
  *    the Free Software Foundation, either version 3 of the License, or
  *    (at your option) any later version.
  *
  *    NUISANCE is distributed in the hope that it will be useful,
  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *    GNU General Public License for more details.
  *
  *    You should have received a copy of the GNU General Public License
  *    along with NUISANCE.  If not, see <http://www.gnu.org/licenses/>.
  *******************************************************************************/
 
-#ifndef CORE_IINPUTHANDLER_HXX_SEEN
-#define CORE_IINPUTHANDLER_HXX_SEEN
+#ifndef SAMPLES_ISAMPLE_HXX_SEEN
+#define SAMPLES_ISAMPLE_HXX_SEEN
 
 #include "plugins/traits.hxx"
 
 #include "exception/exception.hxx"
 
 namespace fhicl {
 class ParameterSet;
 }
 
 namespace nuis {
 namespace core {
-class MinimalEvent;
 class FullEvent;
+class MinimalEvent;
 } // namespace core
 } // namespace nuis
 
-class IInputHandler {
+class ISample {
 public:
-
-  NEW_NUIS_EXCEPT(invalid_input_file);
-  NEW_NUIS_EXCEPT(invalid_entry);
-
-  typedef size_t ev_index_t;
+  NEW_NUIS_EXCEPT(uninitialized_ISample);
 
   virtual void Initialize(fhicl::ParameterSet const &) = 0;
-  virtual nuis::core::MinimalEvent const &GetMinimalEvent(ev_index_t idx) = 0;
-  virtual nuis::core::FullEvent const &GetFullEvent(ev_index_t idx) = 0;
 
-  virtual size_t GetNEvents() = 0;
+  virtual void ProcessSample() = 0;
+
+  virtual void Write() = 0;
 
-  virtual ~IInputHandler(){}
+  virtual ~ISample(){}
 };
 
-DECLARE_PLUGIN_INTERFACE(IInputHandler);
+DECLARE_PLUGIN_INTERFACE(ISample);
 
 #endif
diff --git a/src/samples/MCTools/CMakeLists.txt b/src/samples/MCTools/CMakeLists.txt
new file mode 100644
index 0000000..0f760ae
--- /dev/null
+++ b/src/samples/MCTools/CMakeLists.txt
@@ -0,0 +1,8 @@
+if(USE_NuWro)
+  LIST(APPEND MC_TOOL_IMPL NuisToNuWro.cxx)
+endif(USE_NuWro)
+
+add_library(MCTools SHARED ${MC_TOOL_IMPL})
+target_link_libraries(MCTools nuis_core nuis_config)
+
+install(TARGETS MCTools DESTINATION plugins)
diff --git a/src/samples/MCTools/NuisToNuWro.cxx b/src/samples/MCTools/NuisToNuWro.cxx
new file mode 100644
index 0000000..68ae343
--- /dev/null
+++ b/src/samples/MCTools/NuisToNuWro.cxx
@@ -0,0 +1,40 @@
+#include "samples/ISample.hxx"
+
+#include "core/InputManager.hxx"
+#include "core/FullEvent.hxx"
+
+#include <limits>
+#include <iostream>
+
+using namespace nuis::core;
+
+class NuisToNuWro : public ISample {
+public:
+  InputManager::Input_id_t fIH_id;
+
+  NuisToNuWro()
+      : fIH_id(std::numeric_limits<InputManager::Input_id_t>::max()) {}
+
+  void Initialize(fhicl::ParameterSet const &ps) {
+    fIH_id = InputManager::Get().EnsureInputLoaded(ps);
+  }
+
+  void Process(FullEvent const &ps) {
+    std::cout << ps.fNuWroEvent->dyn << std::endl;
+  }
+
+  void ProcessSample() {
+    if (fIH_id == std::numeric_limits<InputManager::Input_id_t>::max()) {
+      throw uninitialized_ISample();
+    }
+
+    IInputHandler const &IH = InputManager::Get().GetInputHandler(fIH_id);
+    for (auto const &fe : IH) {
+      Process(fe);
+    }
+  }
+
+  void Write() {}
+};
+
+DECLARE_PLUGIN(ISample, NuisToNuWro);