SmartPeak

SmartPeak is an application that encapsulates advanced algorithms to enable fast, accurate, and automated processing of CE-, GC- and LC-MS(/MS) data, and HPLC data for targeted and semi-targeted metabolomics, lipidomics, and fluxomics experiments. The software is based on the OpenMS toolkit.

SmartPeak provides graphical- and/or command-line-based user input validation, workflow configuration, data visualization and review, logging, and reporting. SmartPeak can be run on multiple operating systems or run on cloud infrastructures. The workflow automates all steps from peak detection and integration over calibration curve optimization, to quality control reporting.

Building from source

Windows

STEP 1: Build OpenMS dependencies

Build OpenMS-contrib by following the OpenMS wiki instructions

Download and install the pre-compiled Boost library binaries for windows

Ensure that these binaries are used both for OpenMS and SmartPeak
The only boost package required by SmartPeak is Unit Test for unit testing, however, the same version of boost must be used when compiling both OpenMS and SmartPeak

Download and install QT5 using the offline installer for windows

NOTE: only install the 5.12.1 for the relevant version of visual studios
Add the "lib" folder in the newly created qt5 directory to the system path variable so that the .dll's will be found during run-time
or add e.g. PATH=%PATH%;C:/qt/Qt5.12.1b/5.12.1/msvc2017_64/bin;C:/local/boost_1_67_0/lib64-msvc-14.1 to the environment

STEP 2: Build OpenMS

Build OpenMS following the OpenMS wiki instructions. Example cmake command on windows

cmake -DBoost_NO_SYSTEM_PATHS=ON -BOOST_INCLUDEDIR="C:/local/boost_1_67_0/boost" -DBOOST_ROOT="C:/local/boost_1_67_0" ^
-DBOOST_LIBRARYDIR="C:/local/boost_1_67_0/lib64-msvc-14.1" -DBOOST_USE_STATIC=OFF -DWITH_GUI=OFF -DPYOPENMS=OFF ^
-DOPENMS_CONTRIB_LIBS="[OpenMS directory]/contrib/build" -DCMAKE_PREFIX_PATH="C:/qt/Qt5.12.1b/5.12.1/msvc2017_64/lib/cmake" ^
-G "Visual Studio 15 2017 Win64" ..

Open "OpenMS_host" in visual studios and build only the solution for "OpenSwathAlgo" and then for "OpenMS" IN THAT ORDER
Add the "lib" folder in the openms-build directory to the system path variable so that the .dll's will be found during run-time
or add PATH=%PATH%;[OpenMS directory]/openms-build/bin/debug;C:/qt/Qt5.12.1b/5.12.1/msvc2017_64/bin;C:/local/boost_1_67_0/lib64-msvc-14.1;[SDL directory]/lib/x64 to the environment

STEP 3: Build SmartPeak dependencies

Download the latest SDL2 libraries. Add the SDL2 folder to the path environmental variable. Compile using cmake and build for "external projects" Example cmake command to download all external projects assuming that you are in the location [home directory]/smartPeak2/build_external cmake -G "Visual Studio 15 2017 Win64" -T host=x64 -DUSE_SUPERBUILD=ON .. However, many of the requirements overlap with OpenMS so for practical purposes the only libraries that will need to be download are "ImGui", "ImPlot", and "Plog"

STEP 4: Build SmartPeak

Compile using cmake. Example cmake command on windows assuming that all external dependency libraries are in the path [home directory]/smartPeak2/build_external

cmake -DEIGEN_USE_GPU=OFF -DBoost_NO_SYSTEM_PATHS=ON -BOOST_INCLUDEDIR="C:/local/boost_1_67_0/boost" -DBOOST_ROOT="C:/local/boost_1_67_0" ^
-DBOOST_LIBRARYDIR="C:/local/boost_1_67_0/lib64-msvc-14.1" -DBOOST_USE_STATIC=OFF -G "Visual Studio 15 2017 Win64" -T host=x64 -DUSE_SUPERBUILD=OFF ^
-DEIGEN3_INCLUDE_DIR=[home directory]/smartPeak2/build_external/Dependencies/Source/eigen ^
-DPLOG_INCLUDE_DIR=[home directory]/smartPeak2/build_external/Dependencies/Source/plog/include ^
-DIMGUI_DIR=[home directory]/smartPeak2/build_external/Dependencies/Source/imgui ^
-DIMPLOT_DIR=[home directory]/smartPeak2/build_external/Dependencies/Source/implot ^
-DCMAKE_PREFIX_PATH="[OpenMS directory]/openms-build";"C:/qt/Qt5.12.1b/5.12.1/msvc2017_64/lib/cmake";"[SDL directory]/SDL"; ..

Open "SmartPeak2_host" in visual studios and build the project of choice. Projects can be built using Visual Studios in the IDE by opening msbuild [build_dir]/src/SmartPeak2_host and selecting the specific target to build in the GUI or on the command line by running e.g., msbuild [build_dir]/src/smartpeak/SmartPeak.sln /verbosity:normal /maxcpucount which will build the main SmartPeak library and then running e.g., msbuild [build_dir]/examples/SmartPeak_class_examples_smartpeak.sln -target:GUI /verbosity:normal /maxcpucount which will build the SmartPeak GUI.

Linux

In the below instructions it is assumed OpenMS code resides in ~/OpenMS and SmartPeak code is in ~/SmartPeak2.

STEP 1: Build OpenMS dependencies

Build OpenMS-contrib by following the OpenMS wiki instructions.

Starting from Ubuntu 18.04, it's not necessary to manually build OpenMS' contrib. The packages available in the repositories are recent enough.

STEP 2: Build OpenMS

Build OpenMS following the OpenMS wiki instructions. Example workflow:

cd ~
mkdir OpenMS-build
cd OpenMS-build
cmake -DBOOST_USE_STATIC=OFF -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Debug -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF ~/OpenMS
make -j4 OpenMS

STEP 3: Building SmartPeak

SuperBuild helps downloading the dependencies for SmartPeak.

cd ~
mkdir SmartPeak2_superbuild SmartPeak2_build
cd SmartPeak2_superbuild
cmake -DUSE_SUPERBUILD=ON -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Debug ~/SmartPeak2
make -j4
cd ~/SmartPeak2_build
cmake -DEIGEN_USE_GPU=OFF -DUSE_SUPERBUILD=OFF -DBOOST_USE_STATIC=OFF -G "Unix Makefiles" -DCMAKE_PREFIX_PATH=$HOME/OpenMS-build/ -DPLOG_INCLUDE_DIR=$HOME/SmartPeak2_superbuild/Dependencies/Source/plog/include -DIMGUI_DIR=$HOME/SmartPeak2_superbuild/Dependencies/Source/imgui -DIMPLOT_DIR=$HOME/SmartPeak2_superbuild/Dependencies/Source/implot -DCMAKE_BUILD_TYPE=Debug ~/SmartPeak2
make -j4

Some dependencies one might have to install:

sudo apt install qt5-default libboost-dev libeigen3-dev libxerces-c-dev coinor-libcbc-dev libsvm-dev libboost-iostreams-dev libboost-date-time-dev libboost-math-dev libwildmagic-dev libsqlite3-dev libglpk-dev seqan-dev libhdf5-dev

Running the tests

The tests are run with ctest command.

ctest

In order to run a specific test, use -R option and the test class name (without .cpp extension)

ctest -R Utilities_test

Running the examples

The collection of examples is located at src/example/data directory of the SmartPeak source code. The directory contains examples of different kinds of data in .mzML format and their corresponding configuration files.

Using GUI

To start the GUI, from the build directory run

./bin/GUI

for Mac and Linux, or

./bin/[Debug or Release]/GUI

for Windows. or double-click GUI executable in the file browser of your OS.

Start the session with File | Load session from sequence
Choose the corresponding directory with Change dir. The path to example folder can be shortened to f.e. /data/GCMS_SIM_Unknowns
Select the sequence file
The integrity of the loaded data can be checked with Actions | Integrity checks. The results of the integrity checks can be viewed with View | Info.
Edit the workflow with Edit | Workflow. You have an option to cherry pick the custom workflow or to choose the predefined set of operations. For example, the workflow steps for GC-MS SIM Unknowns are the following:
View and verify the workflow steps and input files with View | [table].
The explorer panes can be used to filter the table views with View | Injections or Transitions. Click on the checkbox under plot or table to include or exclude the injection or tansition from the view.
Changes to any of the input files can be made by reloading a modified .csv version of the file with File | Import File.
Run the workflow with Actions | Run workflow. Verify or change the data input/output directories before running the workflow.
The status of the workflow can be monitored with View | info.
Alternatively, a more detailed status can be obtained with View | log which will display the most recent SmartPeak log information.
After the workflow has finished, the results can be viewed in a tabular form as a large data table with View | features (table). The feature metavalues shown can be added or removed with View | Features and clicking on the checkboxes under plot or table. For performance reasons, the amount of data that one can view is limited to 5000 entries.
The results can be viewed in a graphical form as a line plot or as a heatmap with View | features (line). or View | features (heatmap)
The underlying data can also be displayed as a table matrix with View | features (matrix). Samples, transitions, or feature metavalues can be included or excluded from any of the views using the explorer panes.
The results of calibration curve fitting can be inspected with View | Workflow settings | Quant Methods.
A detailed look at the calibration fitted model and selected points for the model can be seen with View | Calibrators.
For debugging problematic peaks, the raw chromatographic data and the picked and selected peaks can be viewed graphically with View | Chromatograms. For performance reasons, the amount of data that one can view is limited to 9000 points.
Export the results with Actions | Report. There is an option to choose the set of variables of interest
The results will be exported to PivotTable.csv in the same folder