Package: atlas-rbm
Atlas RBMAutomatic rule-based modeling of metabolism, protein-protein interactions, and regulation of gene expressionAuthors: Rodrigo Santibáñez[1,2], Daniel Garrido[2], and Alberto Martín[1]Date: August 2020Affiliations:Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, 8580745, Chile.Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, 7820436, ChilePrerequisitesPathwayTools must be installed and running to obtain data from the BioCyc databases. Please, runpathway-tools -lisp -python-local-onlybefore to obtain any data.(Optional) The PathwayTools software could be executed in the background, with help ofnohup pathway-tools -lisp -python-local-only > /dev/null 2> /dev/null &.Please follow instructions athttp://pathwaytools.org/to obtain a licensed copy of the software fromhttps://biocyc.org/download-bundle.shtml. However, data could be manually formatted using a text-based editor or a spreadsheet software.Note: If you ran into thepathway-tools/ptools/24.0/exe/aclssl.so: undefined symbol: CRYPTO_set_locking_callbackerror, please follow instructions here:https://github.com/glucksfall/atlas/tree/master/PTools-Docker. Instructions will guide you to install a docker image that is able to run pathway tools, but does not include it, so you still need to obtain the software with a valid license.(Highly recommended) Install Docker. Please follow instructions for a supported Operating Systemhttps://docs.docker.com/engine/install/:On Ubuntu, install it withapt-get install docker.io.On Win10, install Docker Desktop with WSL2 supporthttps://docs.docker.com/docker-for-windows/wsl/.On MacOS, install Docker Desktophttps://docs.docker.com/docker-for-mac/install/.The Dockernetworkbiolab/pleiadesinstalls the python packages, the jupyter server, and the stochastic simulators.(Recommended) Jupyter notebook. We recommend the use of Anaconda3https://www.anaconda.com/products/individualbecause of the easier installation of the stochastic simulators fromhttps://anaconda.org/alubbock.(Optional) A stochastic simulator, supported by the pySB python package (BNG2,NFsim,KaSimorStochkit). pySB requires BNG2 to simulate models with NFsim.(Optional) Cytoscape to visualize metabolic networks and others.(Optional) A deterministic simulator: pySB supports ODE integration via scipy.integrate.ode, BioNetGen ODE integration, and CUDA-accelerated ODE integration with Marco S. Nobile's cupSODA software (https://github.com/aresio/cupSODA). If the user feel comfortable with SBML models, pySB could export to SBML and deterministic simulation done with libRoadRunner (http://libroadrunner.org/), Tellurium (http://tellurium.analogmachine.org/), COPASI (http://copasi.org/), etc.InstallationTo install, please follow one of the following steps:Install the docker image "pleiades" usingdocker pull networkbiolab/pleiades. The container is based on the Anaconda3 software and it installs Atlas, and the stochastic simulators BNG2, NFsim, KaSim, and Stochkit. After building the image, please run the container withdocker run --detach --publish 10000:8888 networkbiolab/pleiades, and go tolocalhost:10000in your preferred browser. The required password ispleiades.Download or clone the Github repository fromhttps://github.com/networkbiolab/pleiadeswithgit clone https://github.com/networkbiolab/pleiades foo(wherefoois an absolute or relative path). Then, you could build the docker image withdocker build foo --tag pleiadesand run it withdocker run --detach --publish 10000:8888 pleiades. Finally, go tolocalhost:10000in your preferred browser. The required password ispleiades.Install with pip3:sudo -H python3 -m pip install pleiadesorpython3 -m pip install pleiades --user. Pleiades is a meta-package that install Atlas (the rule-based modeller), Pleione (a genetic algorithm for parameter calibration of RBMs, compatible with SLURM), Alcyone (to perform identifiability analysis of parameters), and Sterope (to perform sensitivity analysis of parameters in kappa RBMs, compatible with SLURM).You should install, configure, and run the jupyter notebook on your own: examplesudo -H pip3 install jupyter && nohup python3 -m jupyter notebook --port=8888 --no-browser --port-retries=0 > /dev/null 2> /dev/null &.Download or clone the Github repository fromhttps://github.com/networkbiolab/atlaswithgit clone https://github.com/networkbiolab/atlas foo(wherefoois an absolute or relative path). Requisites must be fulfilled manually with pip3:sudo -H python3 -m pip install pandas pysb pythoncyc jupyter seabornorpython3 -m pip install pandas pysb pythoncyc jupyter seaborn --user.