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ig13470
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‎models/ecoli/processes/metabolism_new_pathway.py

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@@ -29,7 +29,7 @@ def initialize(self, sim, sim_data):
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# Get constants
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self.nAvogadro = sim_data.constants.n_avogadro.asNumber(1 / units.mmol)
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self.cellDensity = sim_data.constants.cell_density.asNumber(units.g / units.L)
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print(sim_data.process.metabolism_new_pathway.__dir__())
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#check if there is a new metabolic pathway to be added
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if hasattr(sim_data.process.metabolism_new_pathway, 'molecule_names'):
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self.new_pathway = True

‎reconstruction/ecoli/dataclasses/process/metabolism_new_pathway.py

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‎reconstruction/ecoli/flat/new_gene_data/vioAE_meta/metabolic_reactions_new.tsv

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"id" "stoichiometry" "direction" "catalyzed_by" "forward_rate" "reverse_rate" "kcat" "km"
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"rxnvio1" {"OXYGEN-MOLECULE[CCO-CYTOSOL]": -1, "TRP[CCO-CYTOSOL]": -1, "CPD-11890[CCO-CYTOSOL]": 1, "HYDROGEN-PEROXIDE[CCO-CYTOSOL]": 1, "PROTON[CCO-CYTOSOL]": 1} "L2R" ["NG-VioA-MONOMER"] 3000000 0 3.38 31
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"rxnvio1" {"TRP[CCO-CYTOSOL]": -1, "OXYGEN-MOLECULE[CCO-CYTOSOL]": -1, "CPD-11890[CCO-CYTOSOL]": 1, "HYDROGEN-PEROXIDE[CCO-CYTOSOL]": 1, "PROTON[CCO-CYTOSOL]": 1} "L2R" ["NG-VioA-MONOMER"] 3000000 0 3.38 31

‎runscripts/fireworks/fw_queue.py

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print(message)
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OUT_DIRECTORY = filepath.makedirs(filepath.ROOT_PATH, "out")
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OUT_DIRECTORY = filepath.makedirs("/user/work/ig13470/out/vioAE")
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CACHED_SIM_DATA_DIRECTORY = os.path.join(filepath.ROOT_PATH, "cached")
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SUBMISSION_TIME = filepath.timestamp()
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‎runscripts/fireworks/vioae.sh

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# Author: Joshua Rees, [email protected]
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# Affiliation: Genome Design Group, Life Sciences, University of Bristol
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# Run Using: BlueCrystal Supercomputer and the PBS Queue System
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# Last Updated: 2019-12-10
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# Experiment - Testing qadapter settings, and WildType analysis of single and multi-generation simulations
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# See https://github.com/CovertLab/WholeCellEcoliRelease/tree/master/runscripts/paper for other options
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# UPDATE - using scripts from https://github.com/CovertLab/WholeCellEcoliRelease/tree/master/runscripts/jenkins
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## To Run
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# chmod u+x FireWorksBox_1.sh
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# ./FireWorksBox_1.sh
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## Initialise the Database (is this really the only way to do this?)
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cd /user/home/ig13470/wcm_2023_vio/wcEcoli/wholecell/fireworks
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lpad -l my_launchpad.yaml reset
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## Pre Simulation Requirements
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cd /user/home/ig13470/wcm_2023_vio/wcEcoli
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##Compile Cython code
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make clean compile
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# Set the $PYTHONPATH:
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export PYTHONPATH="/user/home/ig13470/wcm_2023_vio/wcEcoli"
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## Create and Add FireWorks to the Launchpad
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cd /user/home/ig13470/wcm_2023_vio/wcEcoli/wholecell/fireworks/
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# Set the $PYTHONPATH:
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# export PYTHONPATH="$PWD:$PYTHONPATH"
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# export PYTHONPATH=.
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DESC="new_gene_expression" PLOTS="aaCounts" \
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VARIANT="new_gene_expression" FIRST_VARIANT_INDEX=2 LAST_VARIANT_INDEX=8 \
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CACHED_SIM_DATA=0 PARALLEL_PARCA=1 SEED=0 \
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SINGLE_DAUGHTERS=0 N_GENS=2 N_INIT_SIMS=1 \
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NEW_GENES="vioAE_meta" \
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LAUNCHPAD_FILE='/user/home/ig13470/wcm_2023_vio/wcEcoli/wholecell/fireworks/my_launchpad.yaml' \
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python /user/home/ig13470/wcm_2023_vio/wcEcoli/runscripts/fireworks/fw_queue.py
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DESC="new_gene_expression" PLOTS="aaCounts" \
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VARIANT="new_gene_expression" FIRST_VARIANT_INDEX=2 LAST_VARIANT_INDEX=8 \
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CACHED_SIM_DATA=0 PARALLEL_PARCA=1 SEED=0 \
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SINGLE_DAUGHTERS=0 N_GENS=2 N_INIT_SIMS=1 \
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NEW_GENES="vioAE" \
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LAUNCHPAD_FILE='/user/home/ig13470/wcm_2023_vio/wcEcoli/wholecell/fireworks/my_launchpad.yaml' \
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python /user/home/ig13470/wcm_2023_vio/wcEcoli/runscripts/fireworks/fw_queue.py
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## Launch Rockets to collect the FireWorks (created by fw_queue.py) from the Launchpad (MongoDB hosted on MLab via Heroku) and run them on the Queue (BlueCrystal)
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nohup qlaunch -r -l my_launchpad.yaml -w my_fworker.yaml -q my_qadapter.yaml rapidfire --nlaunches infinite --sleep 30 --maxjobs_queue 100

‎wholecell/fireworks/my_launchpad.yaml

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logdir: '/user/home/ig13470/wcm_2023_vio/fw'
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authsource: admin
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host: mongodb+srv://ioana:[email protected]/?retryWrites=true&w=majority
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name: 'fireworks'
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ssl: True
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username: 'ioana'
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password: '3dHgK7Va72mCcoqP'
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port: 27017

‎wholecell/fireworks/my_qadapter.yaml

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logdir: /user/home/ig13470/wcm_2023_vio/fw/logs
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_fw_name: CommonAdapter
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_fw_q_type: SLURM
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rocket_launch: rlaunch -w /user/home/ig13470/wcm_2023_vio/wcEcoli/wholecell/fireworks/my_fworker.yaml -l /user/home/ig13470/wcm_2023_vio/wcEcoli/wholecell/fireworks/my_launchpad.yaml singleshot
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job_name: 'wcEcoli'
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walltime: '01:00:00'
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account: 'EMAT022602'
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mail_user: '[email protected]'
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mail_type: FAIL # Warning, this will generate a LOT of emails. I'd suggest setting up a filter, e.g. if you use Outlook select one and tag "Always move to Other"
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ntasks: 1
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nodes: 2
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#cpus_per_task: 1
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mem_per_cpu: 5G # You need to set a memory limit on BC4 or your job will be rejected. 4G is recommended in the model docs for running in Docker containers
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pre_rocket: null
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post_rocket: null
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#logdir: /user/home/ig13470/fw/logs/qadapter
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#_fw_name: CommonAdapter
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#_fw_q_type: SLURM
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#rocket_launch: rlaunch -w /user/home/ig13470/wholecell3/wcEcoli/wholecell/fireworks/my_fworker.yaml -l /user/home/ig13470/wholecell3/wcEcoli/wholecell/fireworks/my_launchpad.yaml singleshot
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#queue: serial
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#account: null
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#job-name: 'wcecoli'
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#time: '06:00:00'
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#mem: 4500
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#mail_user: '[email protected]'
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#mail_type: ALL
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#ntasks: 1
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#cpus-per-task: 1
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#SBATCH --nodes=$${nodes}
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##SBATCH --ntasks=$${ntasks}
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##SBATCH --ntasks-per-node=$${ntasks_per_node}
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##SBATCH --ntasks-per-core=$${ntasks_per_core}
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##SBATCH --core-spec=$${core_spec}
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##SBATCH --exclude=$${exclude_nodes}
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##SBATCH --cpus-per-task=$${cpus_per_task}
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##SBATCH --gres=$${gres}
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##SBATCH --qos=$${qos}
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##SBATCH --time=$${walltime}
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##SBATCH --time-min=$${time_min}
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##SBATCH --partition=$${queue}
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##SBATCH --account=$${account}
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##SBATCH --job-name=$${job_name}
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##SBATCH --license=$${license}
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##SBATCH --output=$${job_name}-%j.out
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##SBATCH --error=$${job_name}-%j.error
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##SBATCH --constraint=$${constraint}
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##SBATCH --signal=$${signal}
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##SBATCH --mem=$${mem}
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##SBATCH --mem-per-cpu=$${mem_per_cpu}
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##SBATCH --mail-type=$${mail_type}
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##SBATCH --mail-user=$${mail_user}
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#

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