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Whole Cell Simulator

A whole cell model (WCM) is a comprehensive multi-scale computational model representing all the known biochemical processes in a cell. It relies on a variety of intracellular pathway models and omics data.

This computational framework enables seamless integration of diverse simulation methods used in WCM such as stochastic simulation algorithm (SSA), ordinary differential equations (ODE), flux balance analysis (FBA), and logic-based approaches. These methods run simultaneously, not only for whole pathways but also for subsets of reactions. Furthermore, we aim to enable switching dynamically between the methods when beneficial.

Current Requirements:

• c++ compiler that supports c++17 e.g., clang++ 5.0 or later, g++ 7.1 or later, and icpc 19.0.1 or later

• GNU Boost library The particular boost libraries used are graph, filesystem, regex and system. To build with other pre-existing installation of boost, set the environment variable BOOST_ROOT or pass -DBOOST_ROOT=<path-to-boost> to cmake. An example path to boost on LC is /usr/tce/packages/boost/boost-1.69.0-mvapich2-2.3-gcc-8.1.0. To run the executable, add ${BOOST_ROOT}/lib to the LD_LIBRARY_PATH as needed

• Guide specific to using clang on Livermore Computing (LC) platforms Currently, to use clang on Livermore Computing (LC) platforms with the libraries compiled with gcc, make sure the c++ standard library is compatible. On LC, clang by default is paired with c++ standard library from gcc/4.9.3. To avoid incompatibility issue,

  0. Use the user libraries compiled with the system default compiler. On many of LC platforms, it is currently gcc/4.9.3. On others, it depends on how clang is configure there.
  1. Make clang use the c++ standard library from the same version of gcc as that used for building user libraries to link. e.g., clang++ --gcc-toolchain=/usr/tce/packages/gcc/gcc-8.1.0/ ...
  2. Use clang's c++ standard library. Recompile user libraries in the same way as needed. i.e., clang++ --stdlib=libc++ ...

  Choose either USE_GCC_LIBCXX for option 1 or USE_CLANG_LIBCXX for option 2 if needed. Usually, option 1 works best. Option 0 does not work well especially with Catch2 due to the incomplete support for C++17. If neither is chosen, the build relies on the system default, which is, on LC, with USE_GCC_LIBCXX on and GCC_TOOLCHAIN_VER set to "4.9.3". If both are on, USE_GCC_LIBCXX is turned off. When USE_GCC_LIBCXX is on, GCC_TOOLCHAIN_VER can be set accordingly (e.g., "8.1.0").

• cmake 3.12 or later This requirement mostly comes from the compatibility between the cmake module find_package(), and the version of boost used. An older version might still work with some warnings.

• Cereal We rely on Cereal serialization library to enable state packing and unpacking of which needs arises under various circumstances including messaging, rollback, migration, and checkpointing. Cereal is a c++ header-only library. No pre-installation is required as it is automatically downloaded and made available.

Getting started:

git clone https://github.com/llnl/wcs.git
mkdir build; cd build
cmake -DBOOST_ROOT:PATH=<PathToYourBoostDev> -DCMAKE_INSTALL_PREFIX:PATH=<YourInstallPath> ../wcs
make
make install

Future requirements:

• Charm++ and Charades (ROSS over Charm++)
• Sundial CVODE For linking with CVODES of Sundials package, use -DWCS_WITH_SUNDIALS:BOOL=ON and -DSUNDIALS_ROOT:FILEPATH=<path-to-sundials>. Make sure that Sundials is built with the cmake option -DBUILD_CVODE:BOOL=ON.

Optional requirements:

• libSBML C++ API
• ExprTK

We currently rely on ExprTk to ingest problem inputs, and moving toward utilizing libSBML. Until the latter replaces the former, the former is used to parse the formula of the reaction rate annotated to each reaction vertex in the GraphML-formatted description of the reaction network. Without either, reaction rate simply computes as the multiplication of the counts of all the input species and the reaction coefficient. As the integraton of libSBML completes, it will no longer be optional. To enable one of the optional components, either set the environment variable WCS_WITH_SBML or WCS_WITH_EXPRTK, or invoke cmake with the option -DWCS_WITH_SBML:BOOL=ON or -DWCS_WITH_EXPRTK:BOOL=ON respectively for libSBML or ExprTk. To use a pre-installed libSBML, either set the environment variable SBML_ROOT or invoke cmake with the option -DSBML_ROOT=<path-to-libsbml>. For ExprTk, no pre-installation is required as it will automatically download it during the build if the presence is not detected. To use a pre-installed copy, use the variable EXPRTK_ROOT.

Unit testing:

• Catch2 We rely on Catch2 for unit testing. To enable testing for development, set the environment variable WCS_WITH_UNIT_TESTING or invoke cmake with the option -DWCS_WITH_UNIT_TESTING=ON. No pre-installation of Catch2 is required as it is automatically downloaded and made available. To use a pre-installed copy, use the variable CATCH2_ROOT.

Authors:

Many thanks go to WCS's contributors.

• Jae-Seung Yeom
• Giorgis Georgakoudis
• Robert Blake
• Ali Navid

Release:

Whole cell simulator is distributed under the terms of the MIT license. All new contributions must be made under this license. See LICENSE and NOTICE for details.

• SPDX-License-Identifier: MIT
• LLNL-CODE-809742

Contributing:

Please submit any bugfixes or feature improvements as pull requests.