From 9c1a43b00687c25cdb246fd54d273714963ad66e Mon Sep 17 00:00:00 2001 From: chris-krenz Date: Fri, 26 Apr 2024 05:17:32 -0400 Subject: [PATCH] template files, bin script, cli options re-enabled, etc. --- app/cli.py | 44 +- bin/designs_to_outputs.py | 445 +- core_algorithm/celloAlgo.py | 66 +- core_algorithm/utils/gate_assignment.py | 27 +- library/templates/Eco1C1G1T1.UCF.json | 135425 +++++++++++++++ library/templates/Eco1C1G1T1.input.json | 265 + library/templates/Eco1C1G1T1.output.json | 217 + .../cello_verilog_template.v | 0 8 files changed, 136358 insertions(+), 131 deletions(-) create mode 100644 library/templates/Eco1C1G1T1.UCF.json create mode 100644 library/templates/Eco1C1G1T1.input.json create mode 100644 library/templates/Eco1C1G1T1.output.json rename library/{verilogs => templates}/cello_verilog_template.v (100%) diff --git a/app/cli.py b/app/cli.py index 280a67c..b85c0f4 100644 --- a/app/cli.py +++ b/app/cli.py @@ -143,29 +143,29 @@ def start_cli(): f'Output File Name: ')) options = '' - # log.cf.info(options := input( - # f'\n\nIf you want any additional options set, type the space-separated strings below...\n' - # f'Available Settings:\n' - # f' - (v) Verbose: {verbose} \n' - # f' Include \'v\' to print more details to both console and the log file\n' - # f' - (o) Log overwrite: {log_overwrite} \n' - # f' Include \'o\' to overwrite an old log when a new log is run; removes dates from log name\n' - # f' - (pi) Print all iterations: {print_iters} \n' - # f' Include \'pi\' to print info on all iterations (copious output)\n' - # f' - (ex) Exhaustive: {exhaustive} \n' - # f' Include \'ex\' to test *all* possible permutations to get global optimum \n' - # f' May take *long* time; normally uses simulated annealing to efficiently find good solution\n' - # f'Otherwise, just press Enter to proceed with default settings...\n\n' - # f'Options (if any): ')) + log.cf.info(options := input( + f'\n\nIf you want any additional options set, type the space-separated strings below...\n' + f'Available Settings:\n' + f' - (v) Verbose: {verbose} \n' + f' Include \'v\' to print more details to both console and the log file\n' + f' - (o) Log overwrite: {log_overwrite} \n' + f' Include \'o\' to overwrite an old log when a new log is run; removes dates from log name\n' + f' - (pi) Print all iterations: {print_iters} \n' + f' Include \'pi\' to print info on all iterations (copious output)\n' + f' - (ex) Exhaustive: {exhaustive} \n' + f' Include \'ex\' to test *all* possible permutations to get global optimum \n' + f' May take *long* time; normally uses simulated annealing to efficiently find good solution\n' + f'Otherwise, just press Enter to proceed with default settings...\n\n' + f'Options (if any): ')) options_list = options.split() - # if 'v' in options_list: - # verbose = True - # if 'o' in options_list: - # log_overwrite = True - # if 'pi' in options_list: - # print_iters = True - # if 'ex' in options_list: - # exhaustive = True + if 'v' in options_list: + verbose = True + if 'o' in options_list: + log_overwrite = True + if 'pi' in options_list: + print_iters = True + if 'ex' in options_list: + exhaustive = True result = cello_initializer(v_name_, ucf_name_, in_name_, out_name_, in_path_, out_path_, options={'yosys_cmd_choice': yosys_cmd_choice, diff --git a/bin/designs_to_outputs.py b/bin/designs_to_outputs.py index 8453376..5e3e9a1 100644 --- a/bin/designs_to_outputs.py +++ b/bin/designs_to_outputs.py @@ -1,101 +1,376 @@ #!/usr/bin/env python3 # -*- coding: utf-8 -*- """ -Script to take in a CSV with pre-generated design options (i.e. part orders), rather than a Verilog file, and -score each design option, returning the normal results/outputs that Cello generates. -TODO: For only the best design option? -TODO: Only on command line ok? -TODO: What outputs need to be generated? Just score? -TODO: It still needs on vs. off designations, or can it just run every such combination? +Script to take in a CSV with pre-generated design options (i.e. part orders), rather than Verilog, +and scores each design option, returning just the scores for each. @author: chris-krenz - """ -import json import csv -import argparse -from pathlib import Path -import os -import sys -from textwrap import dedent +import statistics as stat +# from dataclasses import dataclass + +from ucf_class import UCF +# from gate_assignment import * + +# Global config vars +ucf_file = 'Bsup' # to mix-and-match, change below in main... +csv_file = './2-gate.csv' # 2-gate, 3-gate +verbose = False +design_cnt = 0 # 0 for no restriction + + +def convert_part_names(design: list[str]) -> list[str]: + new_list = [] + part_types = [] + suffixes = {} + bases = { + 'A': 'AmtR', + 'B': 'BM3R1', + 'H': 'HlyIIR', + 'P': 'PhlF', + 'S': 'SrpR' + } + + for part in design: + length = len(part) + + if length == 3 and part.startswith('P'): + part_types.append('Promoter') + suffixes[part[1]] = part[2] + elif length == 4 and 'In' in part: + part_types.append('Input') + elif part == 'Y': + part_types.append('Output') + else: + part_types.append('Gate') + + for i, type in enumerate(part_types): + name = design[i] + if type == 'Promoter': + new_list.append(name) + elif type == 'Input': + if name == 'PIn1': + new_list.append('Xyl_sensor') + else: + new_list.append('Xyl-tetO_sensor') + elif type == 'Output': + new_list.append('GFP_reporter') + else: + suffix = suffixes[name[0]] + base = bases[name[0]] + new_list.append(name + '-' + suffix + '_' + base) + + return new_list + + +def collection_list_to_dict(collection_list): + collection_dict = {} + for collection in collection_list: + collection_dict[collection['name']] = collection + return collection_dict -from core_algorithm.celloAlgo import cello_initializer -from config import LIBRARY_DIR, VERILOGS_DIR, CONSTRAINTS_DIR, TEMP_OUTPUTS_DIR -from core_algorithm.utils import log -from core_algorithm.utils.config_tester import test_all_configs -from core_algorithm.utils.cello_helpers import * -from core_algorithm.utils.gate_assignment import * -from core_algorithm.celloAlgo import * + +# @dataclass +class Node: + + def __init__(self, name, type, inputs=[], output=None, params=None): + self.name = name + self.type = type + self.inputs = inputs + self.output = output + self.params = params + + self.root_input = None # TODO: Rolling values, changing in main loop + + # if verbose: print(self.name, self.type, self.inputs, self.output, self.params, self.root_input) + + def calc_score(self): + if self.type == 'input': + if self.root_input == 'hi': + return self.params['ymax'], 1 + elif self.root_input == 'lo': + return self.params['ymin'], 0 + else: + raise ValueError('Unknown root_input (should be "hi" or "lo")') + elif self.type == 'promoter': + if len(self.inputs) > 1: + # Need to sum inputs, run sum through each of the equations, and then average result + x = 0 + bin = 0 + for input in self.inputs: + result = input.calc_score()[0] # take raw score (to combine into NOR gate) + x += result[0] + bin += result[1] + partial_results = [] + for input in self.inputs: + ymax = input.params['ymax'] + ymin = input.params['ymin'] + K = input.params['K'] + n = input.params['n'] + partial_results.append(ymin + (ymax - ymin) * (K**n) / ((x**n) + (K**n))) + # if verbose: print('partial_results: ', partial_results) + cell_score = stat.mean(partial_results) + binary = 1 if bin == 0 else 0 # acts as either NOR or NOT gate + if verbose: print(self.name, len(self.inputs), cell_score, binary) + return cell_score, binary + # raise ValueError('Promoter inputs are already summed in the calculations of the antecedents; promoter should have a single node as input.') + else: + cell_score, binary = self.inputs[0].calc_score()[1] # take NOT gate result + if verbose: print(self.name, len(self.inputs), cell_score, binary) + return cell_score, binary + elif self.type == 'output': + row_score, binary = self.inputs[0].calc_score() + if verbose: print(row_score, self.name, binary) + return row_score, binary + elif self.type == 'gate': # TODO: Check for actual equation + ymax = self.params['ymax'] + ymin = self.params['ymin'] + K = self.params['K'] + n = self.params['n'] + x = 0 + bin = 0 + for input in self.inputs: + result = input.calc_score() + x += result[0] + bin += result[1] + cell_score = ymin + (ymax - ymin) * (K ** n) / ((x ** n) + (K ** n)) + binary = 1 if bin == 0 else 0 # acts as either NOR or NOT gate + if verbose: print(self.name, len(self.inputs), cell_score, binary) + if len(self.inputs) == 1: + return self.inputs[0].calc_score(), (cell_score, binary) + else: + return (cell_score, binary), (cell_score, binary) # TODO: Messy, fix logic! + else: + raise ValueError('Unknown node type') + + def __repr__(self): + return f"{self.name}, {self.type}, {self.inputs}, {self.output}, {self.params}, {self.root_input}" def main(): - in_path_ = LIBRARY_DIR - ucf_path = CONSTRAINTS_DIR - out_path_ = TEMP_OUTPUTS_DIR - ucf_name_ = '' - in_name_ = '' - out_name_ = '' - designs_given = True - verbose = False - print_iters = False - - print(csv_filepath := input( - f'\n\nFor which CSV file of pre-generated design options do you want Cello output generated?\n' - f'(Hint: See the design_options_template.csv file in the bin folder as an example...)\n\n' - f'Design Options CSV Filepath: ')) - - ucf_list = ['Bth1C1G1T1', 'Eco1C1G1T1', 'Eco1C2G2T2', 'Eco2C1G3T1', 'Eco2C1G5T1', 'Eco2C1G6T1', 'SC1C1G1T1'] - log.cf.info(name := input( - f'\n\nIf you want to use a built-in UCF (User Constrain File) and associated Input & Output files, ' - f'which of the following do you want to use? \n' - f'Options: {list(zip(range(len(ucf_list)), ucf_list))} \n\n' - f'Alternatively, just hit Enter if you want to specify your own UCF, Input, and Output files...\n\n' - f'Index of built-in UCF (or leave blank for custom): ')) - if name: - try: - ucf_name_ = ucf_list[int(name)] + '.UCF' - in_name_ = ucf_list[int(name)] + '.input' - out_name_ = ucf_list[int(name)] + '.output' - except Exception as e: - log.cf.info( - 'Cello was unable to identify the UCF you specified...') - log.cf.info(e) - else: - os.system('') - label = "\u001b[4m" + ' .UCF' + "\u001b[0m" - log.cf.info(ucf_name_ := input( - f'\n\nPlease specify the name of the UCF file you want to use...\n' - f'(Hint: {label}.json, with the .UCF but not the .json, from the' - f' {ucf_path[:-1]} folder.)\n\n' - f'UCF File Name: ')) - label = "\u001b[4m" + ' .input' + "\u001b[0m" - log.cf.info(in_name_ := input( - f'\n\nPlease specify the name of the Input file you want to use...\n' - f'(Hint: {label}.json, with the .input but not the .json, from the {ucf_path[:-1]} folder.)\n\n' - f'Input File Name: ')) - label = "\u001b[4m" + ' .output' + "\u001b[0m" - log.cf.info(out_name_ := input( - f'\n\nPlease specify the name of the Output file you want to use...\n' - f'(Hint: {label}.json, with the .output but not the .json, from the {ucf_path[:-1]} folder.)\n\n' - f'Output File Name: ')) - - # result = cello_initializer('No Verilog', ucf_name_, in_name_, out_name_, 'No Verilog Path', ucf_path, out_path_, - # options={'designs_given': True, 'verbose': False, 'print_iters': False}) - - with open(csv_filepath, 'r') as csv_file: - csv_reader = csv.reader(csv_file) - # TODO: Easier to construct netgraph and pass to prep_assign_for_scoring or to adjust how score_circuit works? - # TODO: Can just trace outputs in UCF to reconstruct the graph... - - for design_option in csv_reader: - - print('test') - - # score_circuit() - - print('\nExisting script...\n') + + # csv_file = input('Where is the csv of design options?\n') + # ucf_file = input('Where is the UCF file you want to use?\n') + # ins_file = ucf_file.replace('UCF.json', 'input.json') + # out_file = ucf_file.replace('UCF.json', 'output.json') + # Xyl-tetO_sensor,B2-1_BM3R1,Xyl_sensor,B2-1_BM3R1,PB1,GFP_reporter + + ucf = UCF('./', f'{ucf_file}.UCF', f'{ucf_file}.input', f'{ucf_file}.output') + + with open(csv_file, 'r') as f: + csv_reader = csv.reader(f) + print("File found, script starting...\n") + + u_gates = collection_list_to_dict(ucf.query_top_level_collection(ucf.UCFmain, 'gates')) + u_models = collection_list_to_dict(ucf.query_top_level_collection(ucf.UCFmain, 'models')) + u_structures = collection_list_to_dict(ucf.query_top_level_collection(ucf.UCFmain, 'structures')) + u_functions = collection_list_to_dict(ucf.query_top_level_collection(ucf.UCFmain, 'functions')) + + i_gates = collection_list_to_dict(ucf.query_top_level_collection(ucf.UCFin, 'input_sensors')) + i_models = collection_list_to_dict(ucf.query_top_level_collection(ucf.UCFin, 'models')) + i_structures = collection_list_to_dict(ucf.query_top_level_collection(ucf.UCFin, 'structures')) + i_functions = collection_list_to_dict(ucf.query_top_level_collection(ucf.UCFin, 'functions')) + + o_gates = collection_list_to_dict(ucf.query_top_level_collection(ucf.UCFout, 'output_devices')) + o_models = collection_list_to_dict(ucf.query_top_level_collection(ucf.UCFout, 'models')) + o_structures = collection_list_to_dict(ucf.query_top_level_collection(ucf.UCFout, 'structures')) + o_functions = collection_list_to_dict(ucf.query_top_level_collection(ucf.UCFout, 'functions')) + + if verbose: + print('\nu_gates: ', u_gates) + print('\ni_gates: ', i_gates) + print('\no_gates: ', o_gates) + + csv_rows = [] + for i, row in enumerate(csv_reader): + if 'design' in row[0]: + continue + if design_cnt and i == design_cnt + 1: + break + + if verbose: print(row) + + try: + design_option = convert_part_names(row) + # print('Input csv appears to be raw Knox output; parts converted to UCF names...') + except Exception: + design_option = row + # print('Input csv appears to already have parts converted to UCF names...') + pass + + # Construct the parts graph + nodes, gates, inputs, outputs, promoters = [], [], [], [], [] + prev_promoter = [] + for part in design_option: + + # Gates + if part in u_gates.keys(): + struct_name = u_gates[part]['structure'] + model_name = u_gates[part]['model'] + parameters = u_models[model_name]['parameters'] + params = {} + for param in parameters: + params[param['name']] = param['value'] + + existing_node = None # Check if gate already exists + for gate in gates: + if gate.name == part: + existing_node = gate + break + if existing_node: + gate.inputs.extend(prev_promoter if prev_promoter else []) + else: + node = Node(part, 'gate', prev_promoter if prev_promoter else [], + u_structures[struct_name]['outputs'][0], params) # should only be 1 output + gates.append(node) + + for promoter in prev_promoter: + promoter.output = part + prev_promoter = [] + + # Inputs + elif part in i_gates.keys(): + struct_name = i_gates[part]['structure'] # input actually has the name of its output promoter + model_name = i_gates[part]['model'] + parameters = i_models[model_name]['parameters'] + params = {} + for param in parameters: + params[param['name']] = param['value'] + node = Node(i_structures[struct_name]['outputs'][0], 'input', [], None, params) # output set on next round + inputs.append(node) + prev_promoter.append(node) + + # Outputs + elif part in o_gates.keys(): + node = Node(part, 'output', prev_promoter if prev_promoter else [], None, None) + outputs.append(node) + for promoter in prev_promoter: + promoter.output = part + prev_promoter = [] + + # Promoters + else: + node = Node(part, 'promoter', [], None, None) # output set on next round + promoters.append(node) + prev_promoter.append(node) + + nodes.append(node) + + # Add inputs to promoters (and promoters as nodes to gate outputs) + for promoter in promoters: + for node in nodes: + if promoter.name == node.output: + node.output = promoter + promoter.inputs.append(node) + + if verbose: + for input in inputs: + print('input: ', input) + for gate in gates: + print('gate: ', gate) + for output in outputs: + print('output: ', output) + for promoter in promoters: + print('promoter: ', promoter) + + # Calculate output scores + scores = [] + output_scores = [] + output_truths = [] + gate_scores = {'lolo': [], 'lohi': [], 'hilo': [], 'hihi': []} + input_permutes = [('lo', 'lo'), # TODO: Accommodate more than 2 inputs! + ('lo', 'hi'), + ('hi', 'lo'), + ('hi', 'hi')] + for permute in input_permutes: + # print('PERMUTATION...') + row_scores = [] + row_truths = [] + for i, input in enumerate(inputs): + input.root_input = permute[i] + for output in outputs: + result = output.calc_score() + row_scores.append(result[0]) + row_truths.append(result[1]) + output_scores.append(row_scores) + output_truths.append(row_truths) + gate_scores[''.join(permute)].append(row_scores[0]) + # print(permute, output_scores, output_truths) + + # Calculate final score + # for output in outputs: # TODO: Add for multiple outputs... + lowest_hi = min(v[0] for i, v in enumerate(output_scores) if output_truths[i][0] == 1) + highest_lo = max(v[0] for i, v in enumerate(output_scores) if output_truths[i][0] == 0) + score = lowest_hi / highest_lo + scores.append(score) + first = inputs[0].name + second = inputs[1].name + csv_row = [score, f'{first};{second}', *[v[0] for v in (g for g in gate_scores.values())], *design_option] + for i, cell in enumerate(csv_row): # request from Bipoc to change these names + if cell == 'PIn1': + csv_row[i] = 'Pxyl' + elif cell == 'PIn2': + csv_row[i] = 'Pxyl-tetO' + csv_rows.append(csv_row) + print(','.join(str(v) for v in csv_row)) + + with open((csv_loc := '-'.join([csv_file[:-4], ucf_file, 'output.csv'])), 'w') as file: + file = csv.writer(file) + file.writerow(['score', 'input_order', '0;0', '0;1', '1;0', '1;1', 'design']) + file.writerows(csv_rows) + print(f'\n{len(scores)} scores generated. CSV generated at {csv_loc}. Script completed.') if __name__ == '__main__': main() + + +# Example 2-gate output... +# 44.308928339334244,0.6675408966203453,0.014523068884012105,0.015065606902249338,0.0145048481526393,Pxyl,B1,Pxyl-tetO,B1,PB1,Y +# 32.34116996224632,0.9279142043976469,0.019574656547713103,0.02869142351624427,0.01906796034088929,Pxyl,B2,Pxyl-tetO,B1,PB1,Y +# 32.34116996224632,0.9279142043976469,0.019574656547713103,0.02869142351624427,0.01906796034088929,Pxyl,B1,Pxyl-tetO,B2,PB1,Y +# 28.080458662185247,1.1882875121749485,0.0246262442114141,0.0423172401302392,0.023631072529139284,Pxyl,B2,Pxyl-tetO,B2,PB1,Y +# 44.23033871055055,0.49056611451091126,0.011056506303518555,0.011091167936136409,0.011055893761221545,Pxyl,B1,Pxyl-tetO,B1,PB2,Y +# 49.999736912975216,0.7727404031179309,0.014700422090613475,0.015454889381975936,0.014679184628406353,Pxyl,B2,Pxyl-tetO,B1,PB2,Y +# 49.999736912975216,0.7727404031179309,0.014700422090613475,0.015454889381975936,0.014679184628406353,Pxyl,B1,Pxyl-tetO,B2,PB2,Y +# 53.228488156413846,1.0549146917249506,0.018344337877708394,0.019818610827815462,0.01830247549559116,Pxyl,B2,Pxyl-tetO,B2,PB2,Y +# 1.000025220730539,5.807309588,0.12382792989932026,5.807163127103576,0.12380970723865821,Pxyl,S1,Pxyl-tetO,S1,PS1,Y +# 14.247966106900305,3.196816181886522,0.22437000185860215,0.17199424360757387,0.17036253873397048,Pxyl-tetO,H2,Pxyl,H2,PH1,Y +# 14.444870331017666,2.6996526126466254,0.18689351657588954,0.1602744010570372,0.15944800307260665,Pxyl-tetO,H1,Pxyl,H2,PH1,Y +# 14.444870331017666,2.6996526126466254,0.18689351657588954,0.1602744010570372,0.15944800307260665,Pxyl-tetO,H2,Pxyl,H1,PH1,Y +# 14.740548813910905,2.2024890434067284,0.14941703129317696,0.1485545585065005,0.1485334674112428,Pxyl-tetO,H1,Pxyl,H1,PH1,Y +# 14.247966106900305,3.196816181886522,0.17199424360757387,0.22437000185860215,0.17036253873397048,Pxyl,H2,Pxyl-tetO,H2,PH1,Y +# 14.444870331017666,2.6996526126466254,0.1602744010570372,0.18689351657588954,0.15944800307260665,Pxyl,H1,Pxyl-tetO,H2,PH1,Y +# 14.444870331017666,2.6996526126466254,0.1602744010570372,0.18689351657588954,0.15944800307260665,Pxyl,H2,Pxyl-tetO,H1,PH1,Y +# 14.740548813910905,2.2024890434067284,0.1485545585065005,0.14941703129317696,0.1485334674112428,Pxyl,H1,Pxyl-tetO,H1,PH1,Y +# 1.0000451953445197,4.768509838,0.31567039918950396,4.768294333294835,0.31566279747794956,Pxyl,P2,Pxyl-tetO,P2,PP1,Y +# 1.9418270449412387,5.312207546910235,0.219641248970257,2.7356749205596667,0.21502468337494135,Pxyl,P1,Pxyl-tetO,P2,PP1,Y +# 1.9418270449412387,5.312207546910235,0.219641248970257,2.7356749205596667,0.21502468337494135,Pxyl,P2,Pxyl-tetO,P1,PP1,Y +# 8.329221790667297,5.855905255820471,0.12361209875101001,0.703055507824498,0.11438656927193315,Pxyl,P1,Pxyl-tetO,P1,PP1,Y +# 1.000063799270972,2.979821511,0.12211029127968986,2.9796314126881054,0.12210674196572506,Pxyl,P2,Pxyl-tetO,P2,PP2,Y +# 1.0000663435285375,2.980415522,0.1001363619681919,2.980217803835083,0.10013289206377349,Pxyl,P1,Pxyl-tetO,P2,PP2,Y +# 1.0000663435285375,2.980415522,0.1001363619681919,2.980217803835083,0.10013289206377349,Pxyl,P2,Pxyl-tetO,P1,PP2,Y +# 1.000068886785078,2.981009533,0.07816243265669393,2.9808041949820607,0.0781590421618219,Pxyl,P1,Pxyl-tetO,P1,PP2,Y +# 19.84316315651205,0.9305500725178698,0.0468952487654412,0.025609589722490493,0.024283962986096287,Pxyl-tetO,A1,Pxyl,A1,PA2,Y +# 12.416881503678193,1.076345723552596,0.08668406179391784,0.037375864686983645,0.034446998445008856,Pxyl-tetO,A1,Pxyl,A1,PA1,Y +# 1.0000451953445197,4.768509838,4.768294333294835,0.31567039918950396,0.31566279747794956,Pxyl-tetO,P2,Pxyl,P2,PP1,Y +# 1.9418270449412387,5.312207546910235,2.7356749205596667,0.219641248970257,0.21502468337494135,Pxyl-tetO,P1,Pxyl,P2,PP1,Y +# 1.9418270449412387,5.312207546910235,2.7356749205596667,0.219641248970257,0.21502468337494135,Pxyl-tetO,P2,Pxyl,P1,PP1,Y +# 8.329221790667297,5.855905255820471,0.703055507824498,0.12361209875101001,0.11438656927193315,Pxyl-tetO,P1,Pxyl,P1,PP1,Y +# 1.000063799270972,2.979821511,2.9796314126881054,0.12211029127968986,0.12210674196572506,Pxyl-tetO,P2,Pxyl,P2,PP2,Y +# 1.0000663435285375,2.980415522,2.980217803835083,0.1001363619681919,0.10013289206377349,Pxyl-tetO,P1,Pxyl,P2,PP2,Y +# 1.0000663435285375,2.980415522,2.980217803835083,0.1001363619681919,0.10013289206377349,Pxyl-tetO,P2,Pxyl,P1,PP2,Y +# 1.000068886785078,2.981009533,2.9808041949820607,0.07816243265669393,0.0781590421618219,Pxyl-tetO,P1,Pxyl,P1,PP2,Y +# 1.000025220730539,5.807309588,5.807163127103576,0.12382792989932026,0.12380970723865821,Pxyl-tetO,S1,Pxyl,S1,PS1,Y +# 44.308928339334244,0.6675408966203453,0.015065606902249338,0.014523068884012105,0.0145048481526393,Pxyl-tetO,B1,Pxyl,B1,PB1,Y +# 32.34116996224632,0.9279142043976469,0.02869142351624427,0.019574656547713103,0.01906796034088929,Pxyl-tetO,B2,Pxyl,B1,PB1,Y +# 32.34116996224632,0.9279142043976469,0.02869142351624427,0.019574656547713103,0.01906796034088929,Pxyl-tetO,B1,Pxyl,B2,PB1,Y +# 28.080458662185247,1.1882875121749485,0.0423172401302392,0.0246262442114141,0.023631072529139284,Pxyl-tetO,B2,Pxyl,B2,PB1,Y +# 44.23033871055055,0.49056611451091126,0.011091167936136409,0.011056506303518555,0.011055893761221545,Pxyl-tetO,B1,Pxyl,B1,PB2,Y +# 49.999736912975216,0.7727404031179309,0.015454889381975936,0.014700422090613475,0.014679184628406353,Pxyl-tetO,B2,Pxyl,B1,PB2,Y +# 49.999736912975216,0.7727404031179309,0.015454889381975936,0.014700422090613475,0.014679184628406353,Pxyl-tetO,B1,Pxyl,B2,PB2,Y +# 53.228488156413846,1.0549146917249506,0.019818610827815462,0.018344337877708394,0.01830247549559116,Pxyl-tetO,B2,Pxyl,B2,PB2,Y +# 19.84316315651205,0.9305500725178698,0.025609589722490493,0.0468952487654412,0.024283962986096287,Pxyl,A1,Pxyl-tetO,A1,PA2,Y +# 12.416881503678193,1.076345723552596,0.037375864686983645,0.08668406179391784,0.034446998445008856,Pxyl,A1,Pxyl-tetO,A1,PA1,Y diff --git a/core_algorithm/celloAlgo.py b/core_algorithm/celloAlgo.py index 691bb9e..3f9f227 100644 --- a/core_algorithm/celloAlgo.py +++ b/core_algorithm/celloAlgo.py @@ -118,7 +118,7 @@ def __init__(self, v_name, ucf_name, in_name, out_name, verilogs_path, constrain self.best_score = 0 self.best_graphs = [] self.units = 'Unknown_Units' - + self.filepath = os.path.join(out_path, self.verilog_name, f'{self.verilog_name}_{self.ucf_name[:-4]}') # Loggers log.config_logger(self.verilog_name, self.ucf_name, self.log_overwrite) log.reset_logs() @@ -226,7 +226,6 @@ def __init__(self, v_name, ucf_name, in_name, out_name, verilogs_path, constrain for rnl_out, g_out in graph_outputs_for_printing: log.cf.info(f' - {rnl_out} {str(g_out)}') out_labels[rnl_out[0]] = g_out.name - tech_diagram_filepath = os.path.join(self.out_path, v_name, f'{self.verilog_name}_{self.ucf_name[:-4]}') replace_techmap_diagram_labels(tech_diagram_filepath, gate_labels, in_labels, out_labels) except Exception as e: @@ -248,7 +247,8 @@ def __init__(self, v_name, ucf_name, in_name, out_name, verilogs_path, constrain print('(See log for more precision)') # Now write the CSV file - with open(f'{filepath}_activity-table.csv', 'w', newline='') as csvfile: + fullpath = os.path.join(os.path.dirname(filepath), f"{os.path.basename(filepath)}_activity-table.csv") + with open(fullpath, 'w', newline='') as csvfile: csv_writer = csv.writer(csvfile) csv_writer.writerow(['Scores...']) csv_writer.writerows(zip(*[["{:.2e}".format(float(c)) if i > 0 else c for i, c in enumerate(row)] @@ -647,15 +647,29 @@ def exhaustive_assign(self, i_list: list, o_list: list, g_list: list, i: int, o: for I_perm in itertools.permutations(i_list, i): for O_perm in itertools.permutations(o_list, o): for G_perm in itertools.permutations(g_list, g): - self.prep_assign_for_scoring( - (I_perm, O_perm, G_perm), (None, None, None, netgraph, i, o, g, iter_)) - + self.prep_assign_for_scoring((I_perm, O_perm, G_perm), + (None, None, None, netgraph, i, o, g, iter_)) if not self.verbose: log.cf.info('\n') log.cf.info(f'\nDONE!\nCounted: {self.iter_count:,} iterations') return self.best_graphs + # def user_specified_assign(self, i_list: list, o_list: list, g_list: list, i: int, o: int, g: int, + # netgraph: GraphParser, iter_: int) -> list: + # """ + # + # """ + # print_centered('Running USER-SPECIFIED gate-assignment algorithm...') + # log.cf.info('Scoring potential gate assignments...') + # + # for perm in perms: + # self.prep_assign_for_scoring() + # + # self.prep_assign_for_scoring() + # + # return self.best_graphs + def prep_assign_for_scoring(self, x, args): """ Prepares a specific iteration/configuration to be scored by score_circuit. @@ -686,19 +700,23 @@ def prep_assign_for_scoring(self, x, args): o_perm = o_perms[math.floor(o_perm)] g_perm = g_perms[math.floor(g_perm)] + # print('\ni_perm: \n', i_perm) + # print('g_perm: \n', g_perm) + # print('o_perm: \n', o_perm) + # Ignore invalid cases where a type of CM is both an input and output (would create feedback) case_invalid = False - inputs = [] - for input in i_perms[math.floor(x[0])]: - input_short = input.removesuffix('_in') - input_short = input_short.removesuffix('_input') - inputs.append(input_short) - for output in o_perms[math.floor(x[1])]: - output_short = output.removesuffix('_out') - output_short = output_short.removesuffix('_output') - if output_short in inputs: - case_invalid = True - break + # inputs = [] + # for input in i_perms[math.floor(x[0])]: + # input_short = input.removesuffix('_in') + # input_short = input_short.removesuffix('_input') + # inputs.append(input_short) + # for output in o_perms[math.floor(x[1])]: + # output_short = output.removesuffix('_out') + # output_short = output_short.removesuffix('_output') + # if output_short in inputs: + # case_invalid = True + # break # Check if inputs, outputs, and gates are unique and the correct number if len(set(i_perm + o_perm + g_perm)) == i + o + g: @@ -739,6 +757,14 @@ def map_helper(l, c): print_centered(f'end of iteration {self.iter_count} : intermediate circuit score = {circuit_score}', also_logfile=False) + # # Now write the CSV file if verbose + # if self.verbose: + # with open((fp := f'{self.filepath}_all_scores.csv'), 'a+') as csvfile: + # csv_writer = csv.writer(csvfile) + # if os.stat(fp).st_size == 0: + # csv_writer.writerow(['Scores', 'Designs...']) + # csv_writer.writerow([circuit_score, graph]) + if circuit_score > self.best_score: self.best_score = circuit_score self.best_graphs = [(circuit_score, graph, tb, tb_labels)] @@ -750,6 +776,7 @@ def map_helper(l, c): self.best_graphs.append((circuit_score, graph, tb, tb_labels)) # Inverted because Dual Annealing designed to find minimum; should ONLY return score + return -self.best_score def score_circuit(self, graph: AssignGraph): @@ -1017,7 +1044,10 @@ def fill_truth_table_IO(graph_node): output_name = graph_output.name graph_output_idx = truth_table_labels.index(output_name) if truth_table[r][graph_output_idx] is None: - output_score = graph.get_score(graph_output, verbose=self.verbose)[0] + output_score = graph.get_score(graph_output, verbose=self.verbose, + table_info={'table': truth_table, + 'labels': truth_table_labels, + 'r': r})[0] truth_table[r][graph_output_idx] = output_score circuit_scores.append((output_score, output_name)) diff --git a/core_algorithm/utils/gate_assignment.py b/core_algorithm/utils/gate_assignment.py index f3076e1..dc9e3ae 100644 --- a/core_algorithm/utils/gate_assignment.py +++ b/core_algorithm/utils/gate_assignment.py @@ -237,7 +237,7 @@ def add_eval_params(self, gate_funcs, g_name, params): # self.input_comp = input_composition self.gate_params[g_name] = params - def eval_gates(self, in_comp): + def eval_gates(self, in_comp, io_gate_val): """ Returns the best gate assignment from gate group. @@ -252,6 +252,14 @@ def eval_gates(self, in_comp): scores.append(self.eval_gate(gname, in_comp)) # NOTE: this eval function needs to be modified best_score = max(scores) + # print(best_score) + # if io_gate_val == 1: + # best_score = max(scores) + # elif io_gate_val == 0: + # best_score = min(scores) + # else: + # print('ERROR') + # TODO: CK: Correct this ^ to replace simplistic max func self.best_score = best_score[0] self.gate_in_use = best_score[1] self.tandem_score = best_score[2] @@ -272,6 +280,7 @@ def eval_gate(self, gate_name, in_comp): tandem = 0 if self.tandem_factor_func: tandem = eval(self.tandem_factor_func) + # print(gate_name, result) return result, gate_name, tandem def __str__(self): @@ -363,13 +372,14 @@ def find_prev(self, node): return ValueError() # NOTE: needs modification - def get_score(self, node, verbose=False): + def get_score(self, node, verbose=False, table_info={}): """ :param node: :param verbose: :return: """ + if type(node) == Input: if node.score_in_use is not None: # if verbose: @@ -379,17 +389,22 @@ def get_score(self, node, verbose=False): log.cf.warning('this should not happen') return max(node.out_scores.values()), node.tandem_scores[node.score_in_use] elif type(node) == Output: - input_score = self.get_score(self.find_prev(node))[0] + input_score = self.get_score(self.find_prev(node), table_info=table_info)[0] output_score = node.eval_output(input_score=input_score) # if verbose: # print(f'{node.name} {output_score}') return output_score, 0 elif type(node) == Gate: + if table_info: + table, labels, r = table_info['table'], table_info['labels'], table_info['r'] + c = labels.index(node.name + '_I/O') + io_gate_val = table[r][c] + # print(node.name, io_gate_val) if node.gate_type == 'NOT': # has single input - input_score = self.get_score(self.find_prev(node))[0] + input_score = self.get_score(self.find_prev(node), table_info=table_info)[0] x = input_score elif node.gate_type == 'NOR': # has two inputs - scores = [self.get_score(x) for x in self.find_prev(node)] + scores = [self.get_score(x, table_info=table_info) for x in self.find_prev(node)] x1 = scores[0][0] x2 = scores[1][0] t1 = scores[0][1] @@ -403,7 +418,7 @@ def get_score(self, node, verbose=False): # there shouldn't be gates other than NOR/NOT raise Exception # below tries to calculate scores for a gate (the best gate choice in this case) - gate_score, tandem_score = node.eval_gates(x) + gate_score, tandem_score = node.eval_gates(x, io_gate_val) # if verbose: # print(f'{node.gate_in_use} {gate_score}') return gate_score, tandem_score # CRIT: Fix tandem scoring... diff --git a/library/templates/Eco1C1G1T1.UCF.json b/library/templates/Eco1C1G1T1.UCF.json new file mode 100644 index 0000000..9c0fcb4 --- /dev/null +++ b/library/templates/Eco1C1G1T1.UCF.json @@ -0,0 +1,135425 @@ +[ + { + "collection": "header", + "description": "TetR homologs: PhlF, SrpR, BM3R1, HlyIIR, BetI, AmtR, AmeR, QacR, IcaRA, LitR, PsrA, LmrA", + "version": "Eco1C1G1T1", + "date": "Thu Dec 24 00:56:10 EST 2015", + "author": [ + "Bryan Der", + "Timothy Jones" + ], + "organism": "Escherichia coli NEB 10-beta", + "genome": "NEB 10 \u2206(ara-leu) 7697 araD139 fhuA \u2206lacX74 galK16 galE15 e14- \u03c680dlacZ\u2206M15 recA1 relA1 endA1 nupG rpsL (StrR) rph spoT1 \u2206(mrr-hsdRMS-mcrBC)", + "media": "M9 minimal media composed of M9 media salts (6.78 g/L Na2HPO4, 3 g/L KH2PO4, 1 g/L NH4Cl, 0.5 g/L NaCl, 0.34 g/L thiamine hydrochloride, 0.4% D-glucose, 0.2% Casamino acids, 2 mM MgSO4, and 0.1 mM CaCl2; kanamycin (50 ug/ml), spectinomycin (50 ug/ml)", + "temperature": "37", + "growth": "Inoculation: Individual colonies into M9 media, 16 hours overnight in plate shaker. Dilution: Next day, cells dilute ~200-fold into M9 media with antibiotics, growth for 3 hours. Induction: Cells diluted ~650-fold into M9 media with antibiotics. Growth: shaking incubator for 5 hours. Arrest protein production: PBS and 2mg/ml kanamycin. Measurement: flow cytometry, data processing for RPU normalization." + }, + { + "collection": "measurement_std", + "signal_carrier_units": "RPUG", + "normalization_instructions": "The following equation converts the median YFP fluorescence to RPU. RPU = (YFP - YFP0)/(YFPRPUG - YFP0), where YFP is the median fluorescence of the cells of interest, YFP0 is the median fluorescence of the cells containing full sensor array with two other landing pads empty, and YFPRPUG is the median fluorescence of the cells containing the measurement standard on the genome landing pad", + "plasmid_description": "p15A plasmid backbone with kanamycin resistance and a YFP expression cassette. Upstream isulation by terminator L3S3P21\nand a 5\u2019-promoter spacer. Promoter BBa_J23101, ribozyme RiboJ, RBS BBa_B0064 drives constitutive YFP expression, with transcriptional termination by L3S3P21.", + "plasmid_sequence": [ + "LOCUS pAN801star__LacI 2853 bp ds-DNA circular 27-MAR-2015", + "SOURCE ", + " ORGANISM ", + "COMMENT ", + "COMMENT ", + "COMMENT ApEinfo:methylated:1", + "FEATURES Location/Qualifiers", + " misc_feature 160..879", + " /label=YFP 3snp", + " /ApEinfo_fwdcolor=#ffff00", + " /ApEinfo_revcolor=#ffff00", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature join(61..64,66..133)", + " /label=RiboJ spacer", + " /ApEinfo_fwdcolor=#808040", + " /ApEinfo_revcolor=#808040", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 59..133", + " /label=RiboJ", + " /ApEinfo_fwdcolor=#ffff80", + " /ApEinfo_revcolor=#ffff80", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(214..243)", + " /label=AAKN 37 primer binding site", + " /ApEinfo_fwdcolor=#804040", + " /ApEinfo_revcolor=#804040", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 134..139", + " /label=SCAR", + " /ApEinfo_fwdcolor=#c0c0c0", + " /ApEinfo_revcolor=#c0c0c0", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 154..159", + " /label=SCAR(1)", + " /ApEinfo_label=SCAR", + " /ApEinfo_fwdcolor=#c0c0c0", + " /ApEinfo_revcolor=#c0c0c0", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 142..153", + " /label=B0064", + " /ApEinfo_fwdcolor=#ff8040", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 134..141", + " /label=SCAR(2)", + " /ApEinfo_label=SCAR", + " /ApEinfo_fwdcolor=#c0c0c0", + " /ApEinfo_revcolor=#c0c0c0", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " rep_origin complement(1251..1251)", + " /vntifkey=\"33\"", + " /label=origin", + " /ApEinfo_fwdcolor=pink", + " /ApEinfo_revcolor=pink", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " rep_origin 978..1813", + " /vntifkey=\"33\"", + " /label=more\\stringent\\p15A", + " /ApEinfo_fwdcolor=pink", + " /ApEinfo_revcolor=pink", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " CDS complement(1885..2700)", + " /vntifkey=\"4\"", + " /label=Kanamycin\\phosphotransferase", + " /ApEinfo_fwdcolor=pink", + " /ApEinfo_revcolor=pink", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 880..940", + " /label=terminator (L3S2P21)", + " /ApEinfo_fwdcolor=#ff0000", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(988..1015)", + " /label=pMJS02 seq R v2", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=cyan", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 2801..2853", + " /label=L3S3P21", + " /ApEinfo_fwdcolor=#ff0000", + " /ApEinfo_revcolor=#ff0000", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 20..54", + " /label=J23101", + " /ApEinfo_fwdcolor=#00ff00", + " /ApEinfo_revcolor=#00ff00", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 20..39", + " /label=spacer:J23101", + " /ApEinfo_fwdcolor=#ff8040", + " /ApEinfo_revcolor=#804040", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(29..48)", + " /label=spacer:A23001-2", + " /ApEinfo_fwdcolor=#800000", + " /ApEinfo_revcolor=#ff8000", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 5..19", + " /label=pre-J23101 random DNA", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=cyan", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + "ORIGIN", + " 1 gcttGATAAG TCCCTAACTT TTACAGCTAG CTCAGTCCTA GGTATTATGC TAGCCTGAAG", + " 61 CTGTCACCGG ATGTGCTTTC CGGTCTGATG AGTCCGTGAG GACGAAACAG CCTCTACAAA", + " 121 TAATTTTGTT TAATACTAGA GAAAGAGGGG AAATACTAGA TGGTGAGCAA GGGCGAGGAG", + " 181 CTGTTCACCG GGGTGGTGCC CATCCTGGTC GAGCTGGACG GCGACGTAAA CGGCCACAAG", + " 241 TTCAGCGTGT CCGGCGAGGG CGAGGGCGAT GCCACCTACG GCAAGCTGAC CCTGAAGTTC", + " 301 ATCTGCACCA CAGGCAAGCT GCCCGTGCCC TGGCCCACCC TCGTGACCAC CTTCGGCTAC", + " 361 GGCCTGCAAT GCTTCGCCCG CTACCCCGAC CACATGAAGC TGCACGACTT CTTCAAGTCC", + " 421 GCCATGCCCG AAGGCTACGT CCAGGAGCGC ACCATCTTCT TCAAGGACGA CGGCAACTAC", + " 481 AAGACCCGCG CCGAGGTGAA GTTCGAGGGC GACACCCTGG TGAACCGCAT CGAGCTGAAG", + " 541 GGCATCGACT TCAAGGAGGA CGGCAACATC CTGGGGCACA AGCTGGAGTA CAACTACAAC", + " 601 AGCCACAACG TCTATATCAT GGCCGACAAG CAGAAGAACG GCATCAAGGT GAACTTCAAG", + " 661 ATCCGCCACA ACATCGAGGA CGGCAGCGTG CAGCTCGCCG ACCACTACCA GCAGAACACC", + " 721 CCAATCGGCG ACGGCCCCGT GCTGCTGCCC GACAACCACT ACCTTAGCTA CCAGTCCGCC", + " 781 CTGAGCAAAG ACCCCAACGA GAAGCGCGAT CACATGGTCC TGCTGGAGTT CGTGACCGCC", + " 841 GCCGGGATCA CTCTCGGCAT GGACGAGCTG TACAAGTAAC TCGGTACCAA ATTCCAGAAA", + " 901 AGAGGCCTCC CGAAAGGGGG GCCTTTTTTC GTTTTGGTCC AGGTGCTTCC TCGCTCACTG", + " 961 ACTCGCTGCA CGAGGCAGAC CTCAGCGCTA GCGGAGTGTA TACTGGCTTA CTATGTTGGC", + " 1021 ACTGATGAGG GTGTCAGTGA AGTGCTTCAT GTGGCAGGAG AAAAAAGGCT GCACCGGTGC", + " 1081 GTCAGCAGAA TATGTGATAC AGGATATATT CCGCTTCCTC GCTCACTGAC TCGCTACGCT", + " 1141 CGGTCGTTCG ACTGCGGCGA GCGGAAATGG CTTACGAACG GGGCGGAGAT TTCCTGGAAG", + " 1201 ATGCCAGGAA GATACTTAAC AGGGAAGTGA GAGGGCCGCG GCAAAGCCGT TTTTCCATAG", + " 1261 GCTCCGCCCC CCTGACAAGC ATCACGAAAT CTGACGCTCA AATCAGTGGT GGCGAAACCC", + " 1321 GACAGGACTA TAAAGATACC AGGCGTTTCC CCTGGCGGCT CCCTCGTGCG CTCTCCTGTT", + " 1381 CCTGCCTTTC GGTTTACCGG TGTCATTCCG CTGTTATGGC CGCGTTTGTC TCATTCCACG", + " 1441 CCTGACACTC AGTTCCGGGT AGGCAGTTCG CTCCAAGCTG GACTGTATGC ACGAACCCCC", + " 1501 CGTTCAGTCC GACCGCTGCG CCTTATCCGG TAACTATCGT CTTGAGTCCA ACCCGGAAAG", + " 1561 ACATGCAAAA GCACCACTGG CAGCAGCCAC TGGTAATTGA TTTAGAGGAG TTAGTCTTGA", + " 1621 AGTCATGCGC CGGTTAAGGC TAAACTGAAA GGACAAGTTT TGGTGACTGC GCTCCTCCAA", + " 1681 GCCAGTTACC TCGGTTCAAA GAGTTGGTAG CTCAGAGAAC CTTCGAAAAA CCGCCCTGCA", + " 1741 AGGCGGTTTT TTCGTTTTCA GAGCAAGAGA TTACGCGCAG ACCAAAACGA TCTCAAGAAG", + " 1801 ATCATCTTAT TAAGGGGTCT GACGCTCAGT GGAACGAAAA ATCAATCTAA AGTATATATG", + " 1861 AGTAAACTTG GTCTGACAGT TACCTTAGAA AAACTCATCG AGCATCAAAT GAAACTGCAA", + " 1921 TTTATTCATA TCAGGATTAT CAATACCATA TTTTTGAAAA AGCCGTTTCT GTAATGAAGG", + " 1981 AGAAAACTCA CCGAGGCAGT TCCATAGGAT GGCAAGATCC TGGTATCGGT CTGCGATTCC", + " 2041 GACTCGTCCA ACATCAATAC AACCTATTAA TTTCCCCTCG TCAAAAATAA GGTTATCAAG", + " 2101 TGAGAAATCA CCATGAGTGA CGACTGAATC CGGTGAGAAT GGCAAAAGCT TATGCATTTC", + " 2161 TTTCCAGACT TGTTCAACAG GCCAGCCATT ACGCTCGTCA TCAAAATCAC TCGCATCAAC", + " 2221 CAAACCGTTA TTCATTCGTG ATTGCGCCTG AGCGAGACGA AATACGCGAT CGCTGTTAAA", + " 2281 AGGACAATTA CAAACAGGAA TCGAATGCAA CCGGCGCAGG AACACTGCCA GCGCATCAAC", + " 2341 AATATTTTCA CCTGAATCAG GATATTCTTC TAATACCTGG AATGCTGTTT TCCCGGGGAT", + " 2401 CGCAGTGGTG AGTAACCATG CATCATCAGG AGTACGGATA AAATGCTTGA TGGTCGGAAG", + " 2461 AGGCATAAAT TCCGTCAGCC AGTTTAGTCT GACCATCTCA TCTGTAACAT CATTGGCAAC", + " 2521 GCTACCTTTG CCATGTTTCA GAAACAACTC TGGCGCATCG GGCTTCCCAT ACAATCGATA", + " 2581 GATTGTCGCA CCTGATTGCC CGACATTATC GCGAGCCCAT TTATACCCAT ATAAATCAGC", + " 2641 ATCCATGTTG GAATTTAATC GCGGCCTCGA GCAAGACGTT TCCCGTTGAA TATGGCTCAT", + " 2701 AACACCCCTT GTATTACTGT TTATGTAAGC AGACAGTTTT ATTGTTCATG ATGATATATT", + " 2761 TTTATCTTGT GCAATGTACA TCAGAGATTT TGAGACACAA CCAATTATTG AAGGCCTCCC", + " 2821 TAACGGGGGG CCTTTTTTTG TTTCTGGTCT CCC ", + "//" + ] + }, + { + "collection": "logic_constraints", + "available_gates": [ + { + "type": "NOR", + "max_instances": 12 + }, + { + "type": "OUTPUT_OR", + "max_instances": true + } + 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"map": "#//model/functions/input_composition" + } + ], + "parameters": [ + { + "name": "ymax", + "map": "#//model/parameters/ymax" + }, + { + "name": "ymin", + "map": "#//model/parameters/ymin" + }, + { + "name": "K", + "map": "#//model/parameters/K" + }, + { + "name": "n", + "map": "#//model/parameters/n" + } + ] + }, + { + "collection": "functions", + "name": "linear_input_composition", + "equation": "x2 + x1", + "variables": [ + { + "name": "x1", + "map": "#//structure/inputs/in1/model/functions/response_function" + }, + { + "name": "x2", + "map": "#//structure/inputs/in2/model/functions/response_function" + } + ] + }, + { + "collection": "parts", + "type": "ribozyme", + "name": "BydvJ", + "dnasequence": "CTGAagGGTGTCTCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCcctctacaaataattttgtttaa", + "parameters": [ + { + "name": "ribozyme_efficiency", + "value": 0.95 + } + ] + }, + { + "collection": "parts", + "type": "rbs", + "name": "A1", + "dnasequence": "AATGTTCCCTAATAATCAGCAAAGAGGTTACTAG" + }, + { + "collection": "parts", + "type": "cds", + "name": "AmtR", + "dnasequence": "ATGGCAGGCGCAGTTGGTCGTCCGCGTCGTAGTGCACCGCGTCGTGCAGGTAAAAATCCGCGTGAAGAAATTCTGGATGCAAGCGCAGAACTGTTTACCCGTCAGGGTTTTGCAACCACCAGTACCCATCAGATTGCAGATGCAGTTGGTATTCGTCAGGCAAGCCTGTATTATCATTTTCCGAGCAAAACCGAAATCTTTCTGACCCTGCTGAAAAGCACCGTTGAACCGAGCACCGTTCTGGCAGAAGATCTGAGCACCCTGGATGCAGGTCCGGAAATGCGTCTGTGGGCAATTGTTGCAAGCGAAGTTCGTCTGCTGCTGAGCACCAAATGGAATGTTGGTCGTCTGTATCAGCTGCCGATTGTTGGTAGCGAAGAATTTGCAGAATATCATAGCCAGCGTGAAGCACTGACCAATGTTTTTCGTGATCTGGCAACCGAAATTGTTGGTGATGATCCGCGTGCAGAACTGCCGTTTCATATTACCATGAGCGTTATTGAAATGCGTCGCAATGATGGTAAAATTCCGAGTCCGCTGAGCGCAGATAGCCTGCCGGAAACCGCAATTATGCTGGCAGATGCAAGCCTGGCAGTTCTGGGTGCACCGCTGCCTGCAGATCGTGTTGAAAAAACCCTGGAACTGATTAAACAGGCAGATGCAAAATAA" + }, + { + "collection": "parts", + "type": "terminator", + "name": "L3S2P55", + "dnasequence": "CTCGGTACCAAAGACGAACAATAAGACGCTGAAAAGCGTCTTTTTTCGTTTTGGTCC", + "parameters": [ + { + "name": "terminator_strength", + "value": 255.66 + } + ] + }, + { + "collection": "parts", + "type": "promoter", + "name": "pAmtR", + "dnasequence": "CTTGTCCAACCAAATGATTCGTTACCAATTGACAGTTTCTATCGATCTATAGATAATGCTAGC" + }, + { + "collection": "parts", + "type": "ribozyme", + "name": "SarJ", + "dnasequence": "CTGAGACTGTCGCCGGATGTGTATCCGACCTGACGATGGCCCAAAAGGGCCGAAACAGTCCTCTACAAATAATTTTGTTTAA", + "parameters": [ + { + "name": "ribozyme_efficiency", + "value": 0.95 + } + ] + }, + { + "collection": "parts", + "type": "rbs", + "name": "B1", + "dnasequence": "CTATGGACTATGTTTTAACTACTAG" + }, + { + "collection": "parts", + "type": "cds", + "name": "BM3R1", + "dnasequence": "ATGGAAAGCACCCCGACCAAACAGAAAGCAATTTTTAGCGCAAGCCTGCTGCTGTTTGCAGAACGTGGTTTTGATGCAACCACCATGCCGATGATTGCAGAAAATGCAAAAGTTGGTGCAGGCACCATTTATCGCTATTTCAAAAACAAAGAAAGCCTGGTGAACGAACTGTTTCAGCAGCATGTTAATGAATTTCTGCAGTGTATTGAAAGCGGTCTGGCAAATGAACGTGATGGTTATCGTGATGGCTTTCATCACATTTTTGAAGGTATGGTGACCTTTACCAAAAATCATCCGCGTGCACTGGGTTTTATCAAAACCCATAGCCAGGGCACCTTTCTGACCGAAGAAAGCCGTCTGGCATATCAGAAACTGGTTGAATTTGTGTGCACCTTTTTTCGTGAAGGTCAGAAACAGGGTGTGATTCGTAATCTGCCGGAAAATGCACTGATTGCAATTCTGTTTGGCAGCTTTATGGAAGTGTATGAAATGATCGAGAACGATTATCTGAGCCTGACCGATGAACTGCTGACCGGTGTTGAAGAAAGCCTGTGGGCAGCACTGAGCCGTCAGAGCTAA" + }, + { + "collection": "parts", + "type": "terminator", + "name": "L3S2P11", + "dnasequence": "CTCGGTACCAAATTCCAGAAAAGAGACGCTTTCGAGCGTCTTTTTTCGTTTTGGTCC", + "parameters": [ + { + "name": "terminator_strength", + "value": 261.55 + } + ] + }, + { + "collection": "parts", + "type": "promoter", + "name": "pBM3R1", + "dnasequence": "AATCCGCGTGATAGGTCTGATTCGTTACCAATTGACGGAATGAACGTTCATTCCGATAATGCTAGC" + }, + { + "collection": "parts", + "type": "rbs", + "name": "B2", + "dnasequence": "CTATGGACTATGTTTTTCAAAGACGAAAAACTACTAG" + }, + { + "collection": "parts", + "type": "rbs", + "name": "B3", + "dnasequence": "CCAAACGAGGCCGGGAGG" + }, + { + "collection": "parts", + "type": "ribozyme", + "name": "RiboJ57", + "dnasequence": "CTGAAGAAGTCAATTAATGTGCTTTTAATTCTGATGAGTCGGTGACGACGAAACTTCCTCTACAAATAATTTTGTTTAA", + "parameters": [ + { + "name": "ribozyme_efficiency", + "value": 0.95 + } + ] + }, + { + "collection": "parts", + "type": "rbs", + "name": "E1", + "dnasequence": "CCCCCCGAGGAGTAGCAC" + }, + { + "collection": "parts", + "type": "cds", + "name": "BetI", + "dnasequence": "ATGCCGAAACTGGGTATGCAGAGCATTCGTCGTCGTCAGCTGATTGATGCAACCCTGGAAGCAATTAATGAAGTTGGTATGCATGATGCAACCATTGCACAGATTGCACGTCGTGCCGGTGTTAGCACCGGTATTATTAGCCATTATTTCCGCGATAAAAACGGTCTGCTGGAAGCAACCATGCGTGATATTACCAGCCAGCTGCGTGATGCAGTTCTGAATCGTCTGCATGCACTGCCGCAGGGTAGCGCAGAACAGCGTCTGCAGGCAATTGTTGGTGGTAATTTTGATGAAACCCAGGTTAGCAGCGCAGCAATGAAAGCATGGCTGGCATTTTGGGCAAGCAGCATGCATCAGCCGATGCTGTATCGTCTGCAGCAGGTTAGCAGTCGTCGTCTGCTGAGCAATCTGGTTAGCGAATTTCGTCGTGAACTGCCTCGTGAACAGGCACAAGAGGCAGGTTATGGTCTGGCAGCACTGATTGATGGTCTGTGGCTGCGTGCAGCACTGAGCGGTAAACCGCTGGATAAAACCCGTGCAAATAGCCTGACCCGTCATTTTATCACCCAGCATCTGCCGACCGATTAA" + }, + { + "collection": "parts", + "type": "terminator", + "name": "L3S3P11", + "dnasequence": "CCAATTATTGAACACCCTTCGGGGTGTTTTTTTGTTTCTGGTCTACC", + "parameters": [ + { + "name": "terminator_strength", + "value": 172.6 + } + ] + }, + { + "collection": "parts", + "type": "promoter", + "name": "pBetI", + "dnasequence": "AGCGCGGGTGAGAGGGATTCGTTACCAATTGACAATTGATTGGACGTTCAATATAATGCTAGC" + }, + { + "collection": "parts", + "type": "ribozyme", + "name": "RiboJ54", + "dnasequence": "CTGAAGGGGTCAGTTGATGTGCTTTCAACTCTGATGAGTCAGTGATGACGAAACCCCCTCTACAAATAATTTTGTTTAA", + "parameters": [ + { + "name": "ribozyme_efficiency", + "value": 0.95 + } + ] + }, + { + "collection": "parts", + "type": "rbs", + "name": "F1", + "dnasequence": "CTATGGACTATGTTTTCACATACGAGGGGGATTAG" + }, + { + "collection": "parts", + "type": "cds", + "name": "AmeR", + "dnasequence": "ATGAACAAAACCATTGATCAGGTGCGTAAAGGTGATCGTAAAAGCGATCTGCCGGTTCGTCGTCGTCCGCGTCGTAGTGCCGAAGAAACCCGTCGTGATATTCTGGCAAAAGCCGAAGAACTGTTTCGTGAACGTGGTTTTAATGCAGTTGCCATTGCAGATATTGCAAGCGCACTGAATATGAGTCCGGCAAATGTGTTTAAACATTTTAGCAGCAAAAACGCACTGGTTGATGCAATTGGTTTTGGTCAGATTGGTGTTTTTGAACGTCAGATTTGTCCGCTGGATAAAAGCCATGCACCGCTGGATCGTCTGCGTCATCTGGCACGTAATCTGATGGAACAGCATCATCAGGATCATTTCAAACACATACGGGTTTTTATTCAGATCCTGATGACCGCCAAACAGGATATGAAATGTGGCGATTATTACAAAAGCGTGATTGCAAAACTGCTGGCCGAAATTATTCGTGATGGTGTTGAAGCAGGTCTGTATATTGCAACCGATATTCCGGTTCTGGCAGAAACCGTTCTGCATGCACTGACCAGCGTTATTCATCCGGTTCTGATTGCACAAGAAGATATTGGTAATCTGGCAACCCGTTGTGATCAGCTGGTTGATCTGATTGATGCAGGTCTGCGTAATCCGCTGGCAAAATAA" + }, + { + "collection": "parts", + "type": "terminator", + "name": "L3S3P31", + "dnasequence": "CCAATTATTGAACACCCTAACGGGTGTTTTTTTTTTTTTGGTCTACC", + "parameters": [ + { + "name": "terminator_strength", + "value": 113.76 + } + ] + }, + { + "collection": "parts", + "type": "promoter", + "name": "pAmeR", + "dnasequence": "TCGTCACTAGAGGGCGATAGTGACAAACTTGACAACTCATCACTTCCTAGGTATAATGCTAGC" + }, + { + "collection": "parts", + "type": "ribozyme", + "name": "RiboJ51", + "dnasequence": "CTGAAGTAGTCACCGGCTGTGCTTGCCGGTCTGATGAGCCTGTGAAGGCGAAACTACCTCTACAAATAATTTTGTTTAA", + "parameters": [ + { + "name": "ribozyme_efficiency", + "value": 0.95 + } + ] + }, + { + "collection": "parts", + "type": "rbs", + "name": "H1", + "dnasequence": "ACCCCCGAG" + }, + { + "collection": "parts", + "type": "cds", + "name": "HlyIIR", + "dnasequence": "ATGAAATACATCCTGTTTGAGGTGTGCGAAATGGGTAAAAGCCGTGAACAGACCATGGAAAATATTCTGAAAGCAGCCAAAAAGAAATTCGGCGAACGTGGTTATGAAGGCACCAGCATTCAAGAAATTACCAAAGAAGCCAAAGTTAACGTTGCAATGGCCAGCTATTACTTTAATGGCAAAGAGAACCTGTACTACGAGGTGTTCAAAAAATACGGTCTGGCAAATGAACTGCCGAACTTTCTGGAAAAAAACCAGTTTAATCCGATTAATGCCCTGCGTGAATATCTGACCGTTTTTACCACCCACATTAAAGAAAATCCGGAAATTGGCACCCTGGCCTATGAAGAAATTATCAAAGAAAGCGCACGCCTGGAAAAAATCAAACCGTATTTTATCGGCAGCTTCGAACAGCTGAAAGAAATTCTGCAAGAGGGTGAAAAACAGGGTGTGTTTCACTTTTTTAGCATCAACCATACCATCCATTGGATTACCAGCATTGTTCTGTTTCCGAAATTCAAAAAATTCATCGATAGCCTGGGTCCGAATGAAACCAATGATACCAATCATGAATGGATGCCGGAAGATCTGGTTAGCCGTATTATTAGCGCACTGACCGATAAACCGAACATTTAA" + }, + { + "collection": "parts", + "type": "terminator", + "name": "ECK120033736", + "dnasequence": "aacgcatgagAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTtttattgcgc", + "parameters": [ + { + "name": "terminator_strength", + "value": 164.6 + } + ] + }, + { + "collection": "parts", + "type": "promoter", + "name": "pHlyIIR", + "dnasequence": "ACCAGGAATCTGAACGATTCGTTACCAATTGACATATTTAAAATTCTTGTTTAAAatgctagc" + }, + { + "collection": "parts", + "type": "ribozyme", + "name": "ElvJ", + "dnasequence": "CTGAagCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGACGAAATGGGGcctctacaaataattttgtttaa", + "parameters": [ + { + "name": "ribozyme_efficiency", + "value": 0.95 + } + ] + }, + { + "collection": "parts", + "type": "rbs", + "name": "I1", + "dnasequence": "ATTGCTATGGACTATGTTTCAAAGTGAGAATACTAG" + }, + { + "collection": "parts", + "type": "cds", + "name": "IcaRA", + "dnasequence": "GTGAAAGACAAAATTATCGATAACGCCATCACCCTGTTTAGCGAAAAAGGTTATGACGGCACCACCCTGGATGATATTGCAAAAAGCGTGAACATCAAAAAAGCCAGCCTGTATTATCACTTTGATAGCAAAAAAAGCATCTACGAGCAGAGCGTTAAATGCTGTTTCGATTATCTGAACAACATCATCATGATGAACCAGAACAAAAGCAACTATAGCATCGATGCCCTGTATCAGTTTCTGTTTGAGTTCATCTTCGATATCGAGGAACGCTATATTCGTATGTATGTTCAGCTGAGCAACACACCGGAAGAATTTTCAGGTAACATTTATGGCCAGATCCAGGATCTGAATCAGAGCCTGAGCAAAGAAATCGCCAAATTCTATGACGAAAGCAAAATCAAAATGACCAAAGAGGACTTCCAGAATCTGATTCTGCTGTTTCTGGAAAGCTGGTATCTGAAAGCCAGCTTTAGCCAGAAATTTGGTGCAGTTGAAGAAAGCAAAAGCCAGTTTAAAGATGAGGTTTATAGCCTGCTGAACATCTTTCTGAAGAAATAA" + }, + { + "collection": "parts", + "type": "terminator", + "name": "ECK120016170", + "dnasequence": "ACAATTTTCGAAAAAACCCGCTTCGGCGGGTTTTTTTATAGCTAAAA", + "parameters": [ + { + "name": "terminator_strength", + "value": 85.78 + } + ] + }, + { + "collection": "parts", + "type": "promoter", + "name": "pIcaRA", + "dnasequence": "GTCAACTCATAAGATtctgattcgttaccaattgacaaTTCACCTACCTTTCGTTAGgTTAGGTTGT" + }, + { + "collection": "parts", + "type": "ribozyme", + "name": "PlmJ", + "dnasequence": "CTGAAGTCATAAGTCTGGGCTAAGCCCACTGATGAGTCGCTGAAATGCGACGAAACTTATGACCTCTACAAATAATTTTGTTTAA", + "parameters": [ + { + "name": "ribozyme_efficiency", + "value": 0.95 + } + ] + }, + { + "collection": "parts", + "type": "rbs", + "name": "L1", + "dnasequence": "GTCCTATGGACTTTTTCATACAGGAGAACCCTCG" + }, + { + "collection": "parts", + "type": "cds", + "name": "LitR", + "dnasequence": "ATGGATACCATTCAGAAACGTCCGCGTACCCGTCTGAGTCCGGAAAAACGTAAAGAACAGCTGCTGGATATTGCCATTGAAGTTTTTAGCCAGCGTGGTATTGGTCGTGGTGGTCATGCAGATATTGCAGAAATTGCACAGGTTAGCGTTGCAACCGTGTTTAACTATTTTCCGACCCGTGAAGATCTGGTTGATGATGTTCTGAACAAAGTGGAAAACGAGTTTCACCAGTTCATCAATAACAGCATTAGCCTGGATCTGGATGTTCGTAGCAATCTGAATACCCTGCTGCTGAACATTATTGATAGCGTTCAGACCGGCAACAAATGGATTAAAGTTTGGTTTGAATGGTCAACCAGCACCCGTGATGAAGTTTGGCCTCTGTTTCTGAGCACCCATAGCAATACCAATCAGGTGATCAAAACCATGTTTGAAGAGGGTATTGAACGCAATGAAGTGTGCAATGATCATACACCGGAAAATCTGACCAAAATGCTGCATGGTATTTGCTATAGCGTGTTTATTCAGGCCAATCGTAATAGCAGCAGCGAAGAAATGGAAGAAACCGCAAATTGCTTTCTGAATATGCTGTGCATCTACAAATAA" + }, + { + "collection": "parts", + "type": "terminator", + "name": "L3S2P24", + "dnasequence": "CTCGGTACCAAATTCCAGAAAAGACACCCGAAAGGGTGTTTTTTCGTTTTGGTCC", + "parameters": [ + { + "name": "terminator_strength", + "value": 151.16 + } + ] + }, + { + "collection": "parts", + "type": "promoter", + "name": "pLitR", + "dnasequence": "CGAGCGTAGAGCTTAgattcgttaccaatTGACAAATTTATAAATTGTCAgtacagtcctagc" + }, + { + "collection": "parts", + "type": "ribozyme", + "name": "RiboJ64", + "dnasequence": "AGGAGTCAATTAATGTGCTTTTAATTCTGATGAGACGGTGACGTCGAAACTCCCTCTACAAATAATTTTGTTTAA", + "parameters": [ + { + "name": "ribozyme_efficiency", + "value": 0.95 + } + ] + }, + { + "collection": "parts", + "type": "rbs", + "name": "N1", + "dnasequence": "TACGCTATGGACTATGTTTTCTGCTATGGACTATGTTTTCACACACGAGATGCCTCG" + }, + { + "collection": "parts", + "type": "cds", + "name": "LmrA", + "dnasequence": "ATGAGCTATGGTGATAGCCGTGAAAAAATTCTGAGCGCAGCAACCCGTCTGTTTCAGCTGCAGGGTTATTATGGCACCGGTCTGAATCAGATTATCAAAGAAAGCGGTGCACCGAAAGGTAGCCTGTATTATCATTTTCCGGGTGGTAAAGAACAGCTGGCAATTGAAGCAGTGAACGAAATGAAAGAATATATCCGCCAGAAAATCGCCGATTGTATGGAAGCATGTACCGATCCGGCAGAAGGTATTCAGGCATTTCTGAAAGAACTGAGCTGTCAGTTTAGCTGTACCGAAGATATTGAAGGTCTGCCGGTTGGTCTGCTGGCAGCAGAAACCAGCCTGAAAAGCGAACCGCTGCGTGAAGCATGTCATGAAGCATATAAAGAATGGGCCAGCGTGTATGAAGAAAAACTGCGTCAGACCGGTTGTAGCGAAAGCCGTGCAAAAGAAGCAAGCACCGTTGTTAATGCAATGATTGAAGGTGGTATTCTGCTGAGCCTGACCGCAAAAAATAGCACACCGCTGCTGCATATTAGCAGCTGTATTCCGGATCTGCTGAAACGTTAA" + }, + { + "collection": "parts", + "type": "terminator", + "name": "ECK120010876", + "dnasequence": "taaggttgaaAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTgacggtggta", + "parameters": [ + { + "name": "terminator_strength", + "value": 97.42 + } + ] + }, + { + "collection": "parts", + "type": "promoter", + "name": "pLmrA", + "dnasequence": "CGCTCATTCACTAGGTCTGATTCGTTACCAATTGACAACTGGTGGTCGAATCAAGATAATAGACCAGTCACTATATTT" + }, + { + "collection": "parts", + "type": "ribozyme", + "name": "RiboJ53", + "dnasequence": "CTGAAGCGGTCAACGCATGTGCTTTGCGTTCTGATGAGACAGTGATGTCGAAACCGCCTCTACAAATAATTTTGTTTAA", + "parameters": [ + { + "name": "ribozyme_efficiency", + "value": 0.95 + } + ] + }, + { + "collection": "parts", + "type": "rbs", + "name": "P1", + "dnasequence": "CTATGGACTATGTTTGAAAGGGAGAAATACTAG" + }, + { + "collection": "parts", + "type": "cds", + "name": "PhlF", + "dnasequence": "ATGGCACGTACCCCGAGCCGTAGCAGCATTGGTAGCCTGCGTAGTCCGCATACCCATAAAGCAATTCTGACCAGCACCATTGAAATCCTGAAAGAATGTGGTTATAGCGGTCTGAGCATTGAAAGCGTTGCACGTCGTGCCGGTGCAAGCAAACCGACCATTTATCGTTGGTGGACCAATAAAGCAGCACTGATTGCCGAAGTGTATGAAAATGAAAGCGAACAGGTGCGTAAATTTCCGGATCTGGGTAGCTTTAAAGCCGATCTGGATTTTCTGCTGCGTAATCTGTGGAAAGTTTGGCGTGAAACCATTTGTGGTGAAGCATTTCGTTGTGTTATTGCAGAAGCACAGCTGGACCCTGCAACCCTGACCCAGCTGAAAGATCAGTTTATGGAACGTCGTCGTGAGATGCCGAAAAAACTGGTTGAAAATGCCATTAGCAATGGTGAACTGCCGAAAGATACCAATCGTGAACTGCTGCTGGATATGATTTTTGGTTTTTGTTGGTATCGCCTGCTGACCGAACAGCTGACCGTTGAACAGGATATTGAAGAATTTACCTTCCTGCTGATTAATGGTGTTTGTCCGGGTACACAGCGTTAA" + }, + { + "collection": "parts", + "type": "terminator", + "name": "ECK120033737", + "dnasequence": "GGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGG", + "parameters": [ + { + "name": "terminator_strength", + "value": 312.5 + } + ] + }, + { + "collection": "parts", + "type": "promoter", + "name": "pPhlF", + "dnasequence": "CGACGTACGGTGGAATCTGATTCGTTACCAATTGACATGATACGAAACGTACCGTATCGTTAAGGT" + }, + { + "collection": "parts", + "type": "rbs", + "name": "P2", + "dnasequence": "GGAGCTATGGACTATGTTTGAAAGGCTGAAATACTAG" + }, + { + "collection": "parts", + "type": "rbs", + "name": "P3", + "dnasequence": "CTTTACGAGGGCGATCCT" + }, + { + "collection": "parts", + "type": "ribozyme", + "name": "RiboJ60", + "dnasequence": "CTGAAGTCGTCAAGTGCTGTGCTTGCACTTCTGATGAGGCAGTGATGCCGAAACGACCTCTACAAATAATTTTGTTTAA", + "parameters": [ + { + "name": "ribozyme_efficiency", + "value": 0.95 + } + ] + }, + { + "collection": "parts", + "type": "rbs", + "name": "Q1", + "dnasequence": "GTAAGCCATGCCATTGGCTTTTGATAGAGGATAACTACTAG" + }, + { + "collection": "parts", + "type": "cds", + "name": "QacR", + "dnasequence": 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+ "pQacR BEFORE pLmrA", + "pQacR BEFORE pPsrA", + "pQacR BEFORE pAmtR", + "pQacR BEFORE pIcaRA", + "ALL_FORWARD" + ] + } + }, + { + "collection": "circuit_rules", + "rules": { + "function": "AND", + "rules": [ + "STARTSWITH Loc1", + "Loc2 NEXTTO Loc1", + "P1_PhlF BEFORE S1_SrpR", + "P1_PhlF BEFORE S2_SrpR", + "P1_PhlF BEFORE S3_SrpR", + "P1_PhlF BEFORE S4_SrpR", + "P1_PhlF BEFORE B1_BM3R1", + "P1_PhlF BEFORE B2_BM3R1", + "P1_PhlF BEFORE B3_BM3R1", + "P1_PhlF BEFORE E1_BetI", + "P1_PhlF BEFORE F1_AmeR", + "P1_PhlF BEFORE L1_LitR", + "P1_PhlF BEFORE I1_IcaRA", + "P1_PhlF BEFORE Q1_QacR", + "P1_PhlF BEFORE Q2_QacR", + "P1_PhlF BEFORE R1_PsrA", + "P1_PhlF BEFORE N1_LmrA", + "P1_PhlF BEFORE H1_HlyIIR", + "P1_PhlF BEFORE A1_AmtR", + "P2_PhlF BEFORE S1_SrpR", + "P2_PhlF BEFORE S2_SrpR", + "P2_PhlF BEFORE S3_SrpR", + "P2_PhlF BEFORE S4_SrpR", + "P2_PhlF BEFORE B1_BM3R1", + "P2_PhlF BEFORE B2_BM3R1", + "P2_PhlF BEFORE B3_BM3R1", + "P2_PhlF BEFORE E1_BetI", + "P2_PhlF BEFORE F1_AmeR", + "P2_PhlF BEFORE L1_LitR", + "P2_PhlF BEFORE I1_IcaRA", + "P2_PhlF BEFORE Q1_QacR", + "P2_PhlF BEFORE Q2_QacR", + "P2_PhlF BEFORE R1_PsrA", + "P2_PhlF BEFORE N1_LmrA", + "P2_PhlF BEFORE H1_HlyIIR", + "P2_PhlF BEFORE A1_AmtR", + "P3_PhlF BEFORE S1_SrpR", + "P3_PhlF BEFORE S2_SrpR", + "P3_PhlF BEFORE S3_SrpR", + "P3_PhlF BEFORE S4_SrpR", + "P3_PhlF BEFORE B1_BM3R1", + "P3_PhlF BEFORE B2_BM3R1", + "P3_PhlF BEFORE B3_BM3R1", + "P3_PhlF BEFORE E1_BetI", + "P3_PhlF BEFORE F1_AmeR", + "P3_PhlF BEFORE L1_LitR", + "P3_PhlF BEFORE I1_IcaRA", + "P3_PhlF BEFORE Q1_QacR", + "P3_PhlF BEFORE Q2_QacR", + "P3_PhlF BEFORE R1_PsrA", + "P3_PhlF BEFORE N1_LmrA", + "P3_PhlF BEFORE H1_HlyIIR", + "P3_PhlF BEFORE A1_AmtR", + "S1_SrpR BEFORE B1_BM3R1", + "S1_SrpR BEFORE B2_BM3R1", + "S1_SrpR BEFORE B3_BM3R1", + "S1_SrpR BEFORE E1_BetI", + "S1_SrpR BEFORE F1_AmeR", + "S1_SrpR BEFORE L1_LitR", + "S1_SrpR BEFORE I1_IcaRA", + "S1_SrpR BEFORE Q1_QacR", + "S1_SrpR BEFORE Q2_QacR", + "S1_SrpR BEFORE R1_PsrA", + "S1_SrpR BEFORE N1_LmrA", + "S1_SrpR BEFORE H1_HlyIIR", + "S1_SrpR BEFORE A1_AmtR", + "S2_SrpR BEFORE B1_BM3R1", + "S2_SrpR BEFORE B2_BM3R1", + "S2_SrpR BEFORE B3_BM3R1", + "S2_SrpR BEFORE E1_BetI", + "S2_SrpR BEFORE F1_AmeR", + "S2_SrpR BEFORE L1_LitR", + "S2_SrpR BEFORE I1_IcaRA", + "S2_SrpR BEFORE Q1_QacR", + "S2_SrpR BEFORE Q2_QacR", + "S2_SrpR BEFORE R1_PsrA", + "S2_SrpR BEFORE N1_LmrA", + "S2_SrpR BEFORE H1_HlyIIR", + "S2_SrpR BEFORE A1_AmtR", + "S3_SrpR BEFORE B1_BM3R1", + "S3_SrpR BEFORE B2_BM3R1", + "S3_SrpR BEFORE B3_BM3R1", + "S3_SrpR BEFORE E1_BetI", + "S3_SrpR BEFORE F1_AmeR", + "S3_SrpR BEFORE L1_LitR", + "S3_SrpR BEFORE I1_IcaRA", + "S3_SrpR BEFORE Q1_QacR", + "S3_SrpR BEFORE Q2_QacR", + "S3_SrpR BEFORE R1_PsrA", + "S3_SrpR BEFORE N1_LmrA", + "S3_SrpR BEFORE H1_HlyIIR", + "S3_SrpR BEFORE A1_AmtR", + "S4_SrpR BEFORE B1_BM3R1", + "S4_SrpR BEFORE B2_BM3R1", + "S4_SrpR BEFORE B3_BM3R1", + "S4_SrpR BEFORE E1_BetI", + "S4_SrpR BEFORE F1_AmeR", + "S4_SrpR BEFORE L1_LitR", + "S4_SrpR BEFORE I1_IcaRA", + "S4_SrpR BEFORE Q1_QacR", + "S4_SrpR BEFORE Q2_QacR", + "S4_SrpR BEFORE R1_PsrA", + "S4_SrpR BEFORE N1_LmrA", + "S4_SrpR BEFORE H1_HlyIIR", + "S4_SrpR BEFORE A1_AmtR", + "B1_BM3R1 BEFORE E1_BetI", + "B1_BM3R1 BEFORE F1_AmeR", + "B1_BM3R1 BEFORE I1_IcaRA", + "B1_BM3R1 BEFORE L1_LitR", + "B1_BM3R1 BEFORE N1_LmrA", + "B1_BM3R1 BEFORE Q1_QacR", + "B1_BM3R1 BEFORE Q2_QacR", + "B1_BM3R1 BEFORE R1_PsrA", + "B1_BM3R1 BEFORE H1_HlyIIR", + "B1_BM3R1 BEFORE A1_AmtR", + "B2_BM3R1 BEFORE E1_BetI", + "B2_BM3R1 BEFORE F1_AmeR", + "B2_BM3R1 BEFORE I1_IcaRA", + "B2_BM3R1 BEFORE L1_LitR", + "B2_BM3R1 BEFORE N1_LmrA", + "B2_BM3R1 BEFORE Q1_QacR", + "B2_BM3R1 BEFORE Q2_QacR", + "B2_BM3R1 BEFORE R1_PsrA", + "B2_BM3R1 BEFORE H1_HlyIIR", + "B2_BM3R1 BEFORE A1_AmtR", + "B3_BM3R1 BEFORE E1_BetI", + "B3_BM3R1 BEFORE F1_AmeR", + "B3_BM3R1 BEFORE I1_IcaRA", + "B3_BM3R1 BEFORE L1_LitR", + "B3_BM3R1 BEFORE N1_LmrA", + "B3_BM3R1 BEFORE Q1_QacR", + "B3_BM3R1 BEFORE Q2_QacR", + "B3_BM3R1 BEFORE R1_PsrA", + "B3_BM3R1 BEFORE H1_HlyIIR", + "B3_BM3R1 BEFORE A1_AmtR", + "E1_BetI BEFORE F1_AmeR", + "E1_BetI BEFORE L1_LitR", + "E1_BetI BEFORE I1_IcaRA", + "E1_BetI BEFORE Q1_QacR", + "E1_BetI BEFORE Q2_QacR", + "E1_BetI BEFORE R1_PsrA", + "E1_BetI BEFORE N1_LmrA", + "E1_BetI BEFORE H1_HlyIIR", + "E1_BetI BEFORE A1_AmtR", + "F1_AmeR BEFORE L1_LitR", + "F1_AmeR BEFORE I1_IcaRA", + "F1_AmeR BEFORE Q1_QacR", + "F1_AmeR BEFORE Q2_QacR", + "F1_AmeR BEFORE R1_PsrA", + "F1_AmeR BEFORE N1_LmrA", + "F1_AmeR BEFORE H1_HlyIIR", + "F1_AmeR BEFORE A1_AmtR", + "L1_LitR BEFORE I1_IcaRA", + "L1_LitR BEFORE Q1_QacR", + "L1_LitR BEFORE Q2_QacR", + "L1_LitR BEFORE R1_PsrA", + "L1_LitR BEFORE N1_LmrA", + "L1_LitR BEFORE H1_HlyIIR", + "L1_LitR BEFORE A1_AmtR", + "I1_IcaRA BEFORE Q1_QacR", + "I1_IcaRA BEFORE Q2_QacR", + "I1_IcaRA BEFORE R1_PsrA", + "I1_IcaRA BEFORE N1_LmrA", + "I1_IcaRA BEFORE H1_HlyIIR", + "I1_IcaRA BEFORE A1_AmtR", + "Q1_QacR BEFORE R1_PsrA", + "Q1_QacR BEFORE N1_LmrA", + "Q1_QacR BEFORE H1_HlyIIR", + "Q1_QacR BEFORE A1_AmtR", + "Q2_QacR BEFORE R1_PsrA", + "Q2_QacR BEFORE N1_LmrA", + "Q2_QacR BEFORE H1_HlyIIR", + "Q2_QacR BEFORE A1_AmtR", + "R1_PsrA BEFORE N1_LmrA", + "R1_PsrA BEFORE H1_HlyIIR", + "R1_PsrA BEFORE A1_AmtR", + "N1_LmrA BEFORE H1_HlyIIR", + "N1_LmrA BEFORE A1_AmtR", + "H1_HlyIIR BEFORE A1_AmtR", + "P1_PhlF AFTER Loc2", + "P2_PhlF AFTER Loc2", + "P3_PhlF AFTER Loc2", + "S1_SrpR AFTER Loc2", + "S2_SrpR AFTER Loc2", + "S3_SrpR AFTER Loc2", + "S4_SrpR AFTER Loc2", + "B1_BM3R1 AFTER Loc2", + "B2_BM3R1 AFTER Loc2", + "B3_BM3R1 AFTER Loc2", + "E1_BetI AFTER Loc2", + "F1_AmeR AFTER Loc2", + "L1_LitR AFTER Loc2", + "I1_IcaRA AFTER Loc2", + "Q1_QacR AFTER Loc2", + "Q2_QacR AFTER Loc2", + "R1_PsrA AFTER Loc2", + "N1_LmrA AFTER Loc2", + "H1_HlyIIR AFTER Loc2", + "A1_AmtR AFTER Loc2", + "P1_PhlF BEFORE Loc3", + "P2_PhlF BEFORE Loc3", + "P3_PhlF BEFORE Loc3", + "S1_SrpR BEFORE Loc3", + "S2_SrpR BEFORE Loc3", + "S3_SrpR BEFORE Loc3", + "S4_SrpR BEFORE Loc3", + "B1_BM3R1 BEFORE Loc3", + "B2_BM3R1 BEFORE Loc3", + "B3_BM3R1 BEFORE Loc3", + "E1_BetI BEFORE Loc3", + "F1_AmeR BEFORE Loc3", + "L1_LitR BEFORE Loc3", + "I1_IcaRA BEFORE Loc3", + "Q1_QacR BEFORE Loc3", + "Q2_QacR BEFORE Loc3", + "R1_PsrA BEFORE Loc3", + "N1_LmrA BEFORE Loc3", + "H1_HlyIIR BEFORE Loc3", + "A1_AmtR BEFORE Loc3", + "YFP_reporter NEXTTO Loc3", + "YFP_reporter AFTER Loc3", + "ALL_FORWARD" + ] + } + }, + { + "collection": "genetic_locations", + "locations": [ + { + "symbol": "Loc1", + "description": "Input sensors location", + "locus": { + "start": 560, + "end": 560 + }, + "sequence": { + "type": "file", + "ref": "pAN1201" + } + }, + { + "symbol": "Loc2", + "description": "Logic gates location", + "locus": { + "start": 54, + "end": 560 + }, + "sequence": { + "type": "file", + "ref": "pCello_circuit" + } + }, + { + "symbol": "Loc3", + "description": "Output devices location", + "locus": { + "start": 953, + "end": 953 + }, + "unit_conversion": 0.4, + "sequence": { + "type": "file", + "ref": "pAN4020" + } + } + ], + "sequences": [ + { + "name": "pAN1201", + "type": "file", + "data": [ + "LOCUS pCello_circuit 2419 bp ds-DNA circular 19-MAR-2015", + "SOURCE ", + " ORGANISM ", + "COMMENT ", + "COMMENT ", + "COMMENT ApEinfo:methylated:1", + "FEATURES Location/Qualifiers", + " misc_feature complement(450..464)", + " /vntifkey=\"21\"", + " /label=CAP\\site", + " /ApEinfo_fwdcolor=#ff0080", + " /ApEinfo_revcolor=#ff0080", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(178..183)", + " /vntifkey=\"21\"", + " /label=<-- EarI site", + " /ApEinfo_fwdcolor=#ff0000", + " /ApEinfo_revcolor=#ff0000", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " CDS complement(join(127..177,184..195))", + " /vntifkey=\"4\"", + " /label=LacZ\\alpha", + " /ApEinfo_fwdcolor=#6495ed", + " /ApEinfo_revcolor=#6495ed", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(480..487)", + " /vntifkey=\"21\"", + " /label=LacI", + " /ApEinfo_fwdcolor=#ff8080", + " /ApEinfo_revcolor=#ff8080", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 556..559", + " /label=cc", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 548..555", + " /vntifkey=\"21\"", + " /label=Linker\\2", + " /ApEinfo_fwdcolor=#0080ff", + " /ApEinfo_revcolor=#00ff00", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 58..65", + " /vntifkey=\"21\"", + " /label=Linker\\1", + " /ApEinfo_fwdcolor=#0080ff", + " /ApEinfo_revcolor=#00ff00", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(426..431)", + " /vntifkey=\"21\"", + " /label=pLac\\-35\\box", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=cyan", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(467..487)", + " /vntifkey=\"21\"", + " /label=LacO3", + " /ApEinfo_fwdcolor=#8080ff", + " /ApEinfo_revcolor=#8080ff", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(400..429)", + " /vntifkey=\"21\"", + " /label=3'\\lacI\\KO\\check\\-\\R\\(580bp)", + " /ApEinfo_fwdcolor=#0080ff", + " /ApEinfo_revcolor=#0080ff", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(402..407)", + " /vntifkey=\"21\"", + " /label=pLac\\-10\\box", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(477..477)", + " /vntifkey=\"21\"", + " /label=Center\\LacO3", + " /ApEinfo_fwdcolor=#ffff00", + " /ApEinfo_revcolor=#ffff00", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " rep_origin complement(870..870)", + " /vntifkey=\"33\"", + " /label=origin", + " /ApEinfo_fwdcolor=pink", + " /ApEinfo_revcolor=pink", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " rep_origin 597..1432", + " /vntifkey=\"33\"", + " /label=more\\stringent\\p15A", + " /ApEinfo_fwdcolor=pink", + " /ApEinfo_revcolor=pink", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " CDS complement(1504..2319)", + " /vntifkey=\"4\"", + " /label=Kanamycin\\phosphotransferase", + " /ApEinfo_fwdcolor=pink", + " /ApEinfo_revcolor=pink", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " primer_bind 266..283", + " /label=M13-fwd", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " primer_bind complement(349..369)", + " /label=M13-rev", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " CDS complement(127..195)", + " /label=LacZ alpha", + " /ApEinfo_fwdcolor=#6495ed", + " /ApEinfo_revcolor=#6495ed", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_binding complement(375..397)", + " /label=LacO", + " /ApEinfo_fwdcolor=#6495ed", + " /ApEinfo_revcolor=#6495ed", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(607..634)", + " /label=pMJS02 seq R v2", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=cyan", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 154..173", + " /label=spacer:lacZ", + " /ApEinfo_fwdcolor=#ff8080", + " /ApEinfo_revcolor=#ff8080", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(1504..2319)", + " /label=KanR", + " /ApEinfo_fwdcolor=#ff8080", + " /ApEinfo_revcolor=#ff8080", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 597..1432", + " /label=p15A", + " /ApEinfo_fwdcolor=#ff00ff", + " /ApEinfo_revcolor=#ff00ff", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 1..53", + " /label=L3S3P21", + " /ApEinfo_fwdcolor=#ff0000", + " /ApEinfo_revcolor=#ff0000", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + "ORIGIN", + " 1 CCAATTATTG AAGGCCTCCC TAACGGGGGG CCTTTTTTTG TTTCTGGTCT CCCgcttctg", + " 61 tcttctgcac catatgcggt gtgaaatacc gcacagatgc gtaaggagaa aataccgcat", + " 121 caggcgccat tcgccattca ggctgcgcaa ctgttgggaa gggcgatcgg tgcgggcctc", + " 181 ttcgctatta cgccagctgg cgaaaggggg atgtgctgca aggcgattaa gttgggtaac", + " 241 gccagggttt tcccagtcac gacgttgtaa aacgacggcc agtgaattcg agctcggtac", + " 301 ccggggatcc tctagagtcg acctgcaggc atgcaagctt ggcgtaatca tggtcatagc", + " 361 tgtttcctgt gtgaaattgt tatccgctca caattccaca caacatacga gccggaagca", + " 421 taaagtgtaa agcctggggt gcctaatgag tgagctaact cacattaatt gcgttgcgct", + " 481 cactgcccgc tttccagtcg ggaaacctgt cgtgccagct gcattaatga atcggccaac", + " 541 gcgcggggaa gacagaatgA GGTGCTTCCT CGCTCACTGA CTCGCTGCAC GAGGCAGACC", + " 601 TCAGCGCTAG CGGAGTGTAT ACTGGCTTAC TATGTTGGCA CTGATGAGGG TGTCAGTGAA", + " 661 GTGCTTCATG TGGCAGGAGA AAAAAGGCTG CACCGGTGCG TCAGCAGAAT ATGTGATACA", + " 721 GGATATATTC CGCTTCCTCG CTCACTGACT CGCTACGCTC GGTCGTTCGA CTGCGGCGAG", + " 781 CGGAAATGGC TTACGAACGG GGCGGAGATT TCCTGGAAGA TGCCAGGAAG ATACTTAACA", + " 841 GGGAAGTGAG AGGGCCGCGG CAAAGCCGTT TTTCCATAGG CTCCGCCCCC CTGACAAGCA", + " 901 TCACGAAATC TGACGCTCAA ATCAGTGGTG GCGAAACCCG ACAGGACTAT AAAGATACCA", + " 961 GGCGTTTCCC CTGGCGGCTC CCTCGTGCGC TCTCCTGTTC CTGCCTTTCG GTTTACCGGT", + " 1021 GTCATTCCGC TGTTATGGCC GCGTTTGTCT CATTCCACGC CTGACACTCA GTTCCGGGTA", + " 1081 GGCAGTTCGC TCCAAGCTGG ACTGTATGCA CGAACCCCCC GTTCAGTCCG ACCGCTGCGC", + " 1141 CTTATCCGGT AACTATCGTC TTGAGTCCAA CCCGGAAAGA CATGCAAAAG CACCACTGGC", + " 1201 AGCAGCCACT GGTAATTGAT TTAGAGGAGT TAGTCTTGAA GTCATGCGCC GGTTAAGGCT", + " 1261 AAACTGAAAG GACAAGTTTT GGTGACTGCG CTCCTCCAAG CCAGTTACCT CGGTTCAAAG", + " 1321 AGTTGGTAGC TCAGAGAACC TTCGAAAAAC CGCCCTGCAA GGCGGTTTTT TCGTTTTCAG", + " 1381 AGCAAGAGAT TACGCGCAGA CCAAAACGAT CTCAAGAAGA TCATCTTATT AAGGGGTCTG", + " 1441 ACGCTCAGTG GAACGAAAAA TCAATCTAAA GTATATATGA GTAAACTTGG TCTGACAGTT", + " 1501 ACCTTAGAAA AACTCATCGA GCATCAAATG AAACTGCAAT TTATTCATAT CAGGATTATC", + " 1561 AATACCATAT TTTTGAAAAA GCCGTTTCTG TAATGAAGGA GAAAACTCAC CGAGGCAGTT", + " 1621 CCATAGGATG GCAAGATCCT GGTATCGGTC TGCGATTCCG ACTCGTCCAA CATCAATACA", + " 1681 ACCTATTAAT TTCCCCTCGT CAAAAATAAG GTTATCAAGT GAGAAATCAC CATGAGTGAC", + " 1741 GACTGAATCC GGTGAGAATG GCAAAAGCTT ATGCATTTCT TTCCAGACTT GTTCAACAGG", + " 1801 CCAGCCATTA CGCTCGTCAT CAAAATCACT CGCATCAACC AAACCGTTAT TCATTCGTGA", + " 1861 TTGCGCCTGA GCGAGACGAA ATACGCGATC GCTGTTAAAA GGACAATTAC AAACAGGAAT", + " 1921 CGAATGCAAC CGGCGCAGGA ACACTGCCAG CGCATCAACA ATATTTTCAC CTGAATCAGG", + " 1981 ATATTCTTCT AATACCTGGA ATGCTGTTTT CCCGGGGATC GCAGTGGTGA GTAACCATGC", + " 2041 ATCATCAGGA GTACGGATAA AATGCTTGAT GGTCGGAAGA GGCATAAATT CCGTCAGCCA", + " 2101 GTTTAGTCTG ACCATCTCAT CTGTAACATC ATTGGCAACG CTACCTTTGC CATGTTTCAG", + " 2161 AAACAACTCT GGCGCATCGG GCTTCCCATA CAATCGATAG ATTGTCGCAC CTGATTGCCC", + " 2221 GACATTATCG CGAGCCCATT TATACCCATA TAAATCAGCA TCCATGTTGG AATTTAATCG", + " 2281 CGGCCTCGAG CAAGACGTTT CCCGTTGAAT ATGGCTCATA ACACCCCTTG TATTACTGTT", + " 2341 TATGTAAGCA GACAGTTTTA TTGTTCATGA TGATATATTT TTATCTTGTG CAATGTACAT", + " 2401 CAGAGATTTT GAGACACAA ", + "//" + ] + }, + { + "name": "pAN1201", + "type": "file", + "data": [ + "LOCUS pCello_output 3363 bp ds-DNA linear 19-MAR-2015", + "DEFINITION .", + "ACCESSION ", + "VERSION ", + "SOURCE .", + " ORGANISM .", + "COMMENT ", + "COMMENT ", + "COMMENT ApEinfo:methylated:1", + "FEATURES Location/Qualifiers", + " misc_feature complement(957..973)", + " /label=VR", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 3132..3146", + " /label=beta-lactamase (ampR; rev)", + " /ApEinfo_fwdcolor=#8080ff", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 3141..3146", + " /label=HindIII", + " /ApEinfo_fwdcolor=#ff0000", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 3244..3267", + " /label=pMB1 rev", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 3298..3320", + " /label=AG_s29 rev", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 1058..3094", + " /label=pSC101", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 872..891", + " /label=Primer AG14 VF2", + " /ApEinfo_fwdcolor=#ff8040", + " /ApEinfo_revcolor=#00ff00", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " Part 1..792", + " /label=tac-377", + " /ApEinfo_fwdcolor=#41507E", + " /ApEinfo_revcolor=#767061", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 352..371", + " /label=1658", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 1..792", + " /label=Strep Resistance", + " /ApEinfo_fwdcolor=#ff80ff", + " /ApEinfo_revcolor=#ff80ff", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 253..292", + " /label=seam", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 762..781", + " /label=strep forward", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(1532..1542)", + " /label=DR5", + " /ApEinfo_fwdcolor=#0000ff", + " /ApEinfo_revcolor=#0000ff", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 3250..3257", + " /label=SCAR", + " /ApEinfo_fwdcolor=#c0c0c0", + " /ApEinfo_revcolor=#c0c0c0", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 793..798", + " /label=SCAR(1)", + " /ApEinfo_label=SCAR", + " /ApEinfo_fwdcolor=#c0c0c0", + " /ApEinfo_revcolor=#c0c0c0", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 3250..3255", + " /label=SCAR(2)", + " /ApEinfo_label=SCAR", + " /ApEinfo_fwdcolor=#c0c0c0", + " /ApEinfo_revcolor=#c0c0c0", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature complement(957..976)", + " /label=VR(1)", + " /ApEinfo_label=VR", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=cyan", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 872..891", + " /label=VF2", + " /ApEinfo_fwdcolor=cyan", + " /ApEinfo_revcolor=green", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + " misc_feature 892..948", + " /label=L3S2P44", + " /ApEinfo_fwdcolor=#ff0000", + " /ApEinfo_revcolor=#ff0000", + " /ApEinfo_graphicformat=arrow_data {{0 1 2 0 0 -1} {} 0}", + " width 5 offset 0", + "ORIGIN", + " 1 atgagggaag cggtgatcgc cgaagtatcg actcaactat cagaggtagt tggcgtcatc", + " 61 gagcgccatc tcgaaccgac gttgctggcc gtacatttgt acggctccgc agtggatggc", + " 121 ggcctgaagc cacacagtga tattgatttg ctggttacgg tgaccgtaag gcttgatgaa", + " 181 acaacgcggc gagctttgat caacgacctt ttggaaactt cggcttcccc tggagagagc", + " 241 gagattctcc gcgctgtaga agtcaccatt gttgtgcacg acgacatcat tccgtggcgt", + " 301 tatccagcta agcgcgaact gcaatttgga gaatggcagc gcaatgacat tcttgcaggt", + " 361 atcttcgagc cagccacgat cgacattgat ctggctatct tgctgacaaa agcaagagaa", + " 421 catagcgttg ccttggtagg tccagcggcg gaggaactct ttgatccggt tcctgaacag", + " 481 gatctatttg aggcgctaaa tgaaacctta acgctatgga actcgccgcc cgactgggct", + " 541 ggcgatgagc gaaatgtagt gcttacgttg tcccgcattt ggtacagcgc agtaaccggc", + " 601 aaaatcgcgc cgaaggatgt cgctgccgac tgggcaatgg agcgcctgcc ggcccagtat", + " 661 cagcccgtca tacttgaagc tagacaggct tatcttggac aagaagaaga tcgcttggcc", + " 721 tcgcgcgcag atcagttgga agaatttgtc cactacgtga aaggcgagat caccaaggta", + " 781 gtcggcaaat aatactagct ccggcaaaaa aacgggcaag gtgtcaccac cctgcccttt", + " 841 ttctttaaaa ccgaaaagat tacttcgcgt ttgccacctg acgtctaaga aCTCGGTACC", + " 901 AAACCAATTA TTGAAGACGC TGAAAAGCGT CTTTTTTTGT TTCGGTCCGC TTAATGgctc", + " 961 actcaaaggc ggtaatacgg ttatccacag aatcagggga taacgcagga aagaacatgt", + " 1021 gagcaaaagg ccagcaaaag gccaggaacc gtaaaaactg tcagaccaag tttacgagct", + " 1081 cgcttggact cctgttgata gatccagtaa tgacctcaga actccatctg gatttgttca", + " 1141 gaacgctcgg ttgccgccgg gcgtttttta ttggtgagaa tccaagcact agggacagta", + " 1201 agacgggtaa gcctgttgat gataccgctg ccttactggg tgcattagcc agtctgaatg", + " 1261 acctgtcacg ggataatccg aagtggtcag actggaaaat cagagggcag gaactgctga", + " 1321 acagcaaaaa gtcagatagc accacatagc agacccgcca taaaacgccc tgagaagccc", + " 1381 gtgacgggct tttcttgtat tatgggtagt ttccttgcat gaatccataa aaggcgcctg", + " 1441 tagtgccatt tacccccatt cactgccaga gccgtgagcg cagcgaactg aatgtcacga", + " 1501 aaaagacagc gactcaggtg cctgatggtc ggagacaaaa ggaatattca gcgatttgcc", + " 1561 cgagcttgcg agggtgctac ttaagccttt agggttttaa ggtctgtttt gtagaggagc", + " 1621 aaacagcgtt tgcgacatcc ttttgtaata ctgcggaact gactaaagta gtgagttata", + " 1681 cacagggctg ggatctattc tttttatctt tttttattct ttctttattc tataaattat", + " 1741 aaccacttga atataaacaa aaaaaacaca caaaggtcta gcggaattta cagagggtct", + " 1801 agcagaattt acaagttttc cagcaaaggt ctagcagaat ttacagatac ccacaactca", + " 1861 aaggaaaagg acatgtaatt atcattgact agcccatctc aattggtata gtgattaaaa", + " 1921 tcacctagac caattgagat gtatgtctga attagttgtt ttcaaagcaa atgaactagc", + " 1981 gattagtcgc tatgacttaa cggagcatga aaccaagcta attttatgct gtgtggcact", + " 2041 actcaacccc acgattgaaa accctacaag gaaagaacgg acggtatcgt tcacttataa", + " 2101 ccaatacgct cagatgatga acatcagtag ggaaaatgct tatggtgtat tagctaaagc", + " 2161 aaccagagag ctgatgacga gaactgtgga aatcaggaat cctttggtta aaggctttga", + " 2221 gattttccag tggacaaact atgccaagtt ctcaagcgaa aaattagaat tagtttttag", + " 2281 tgaagagata ttgccttatc ttttccagtt aaaaaaattc ataaaatata atctggaaca", + " 2341 tgttaagtct tttgaaaaca aatactctat gaggatttat gagtggttat taaaagaact", + " 2401 aacacaaaag aaaactcaca aggcaaatat agagattagc cttgatgaat ttaagttcat", + " 2461 gttaatgctt gaaaataact accatgagtt taaaaggctt aaccaatggg ttttgaaacc", + " 2521 aataagtaaa gatttaaaca cttacagcaa tatgaaattg gtggttgata agcgaggccg", + " 2581 cccgactgat acgttgattt tccaagttga actagataga caaatggatc tcgtaaccga", + " 2641 acttgagaac aaccagataa aaatgaatgg tgacaaaata ccaacaacca ttacatcaga", + " 2701 ttcctaccta cgtaacggac taagaaaaac actacacgat gctttaactg caaaaattca", + " 2761 gctcaccagt tttgaggcaa aatttttgag tgacatgcaa agtaagcatg atctcaatgg", + " 2821 ttcgttctca tggctcacgc aaaaacaacg aaccacacta gagaacatac tggctaaata", + " 2881 cggaaggatc tgaggttctt atggctcttg tatctatcag tgaagcatca agactaacaa", + " 2941 acaaaagtag aacaactgtt caccgttaga tatcaaaggg aaaactgtcc atatgcacag", + " 3001 atgaaaacgg tgtaaaaaag atagatacat cagagctttt acgagttttt ggtgcattta", + " 3061 aagctgttca ccatgaacag atcgacaatg taacgattat caaaaaggat cttcacctag", + " 3121 atccttttaa attaaaaatg aagcttcgtt gtgtctcaaa atctctgatg ttacattgca", + " 3181 caagataaaa atatatcatc atgaacaata aaactgtctg cttacataaa cagtaataca", + " 3241 aggggtgttt actagaggtt gatcgggcac gtaagaggtt ccaactttca ccataatgaa", + " 3301 ataagatcac taccgggcgt attttttgag ttatcgagat tttcaggagc taaggaagct", + " 3361 aaa ", + "//" + ] + } + ] + } +] diff --git a/library/templates/Eco1C1G1T1.input.json b/library/templates/Eco1C1G1T1.input.json new file mode 100644 index 0000000..60218eb --- /dev/null +++ b/library/templates/Eco1C1G1T1.input.json @@ -0,0 +1,265 @@ +[ + { + "collection": "input_sensors", + "name": "LacI_sensor", + "model": "LacI_sensor_model", + "structure": "LacI_sensor_structure" + }, + { + "collection": "models", + "name": "LacI_sensor_model", + "functions": { + "response_function": "sensor_response" + }, + "parameters": [ + { + "name": "ymax", + "value": 2.8, + "description": "Maximal transcription" + }, + { + "name": "ymin", + "value": 0.0034, + "description": "Minimal transcription" + }, + { + "name": "alpha", + "value": 0.73, + "description": "Tandem parameter" + }, + { + "name": "beta", + "value": 0.04, + "description": "Tandem parameter" + } + ] + }, + { + "collection": "structures", + "name": "LacI_sensor_structure", + "outputs": [ + "pTac" + ] + }, + { + "collection": "input_sensors", + "name": "TetR_sensor", + "model": "TetR_sensor_model", + "structure": "TetR_sensor_structure" + }, + { + "collection": "models", + "name": "TetR_sensor_model", + "functions": { + "response_function": "sensor_response" + }, + "parameters": [ + { + "name": "ymax", + "value": 4.4, + "description": "Maximal transcription" + }, + { + "name": "ymin", + "value": 0.0013, + "description": "Minimal transcription" + }, + { + "name": "alpha", + "value": 0.69, + "description": "Tandem parameter" + }, + { + "name": "beta", + "value": 1.0, + "description": "Tandem parameter" + } + ] + }, + { + "collection": "structures", + "name": "TetR_sensor_structure", + "outputs": [ + "pTet" + ] + }, + { + "collection": "input_sensors", + "name": "AraC_sensor", + "model": "AraC_sensor_model", + "structure": "AraC_sensor_structure" + }, + { + "collection": "models", + "name": "AraC_sensor_model", + "functions": { + "response_function": "sensor_response" + }, + "parameters": [ + { + "name": "ymax", + "value": 2.5, + "description": "Maximal transcription" + }, + { + "name": "ymin", + "value": 0.0082, + "description": "Minimal transcription" + }, + { + "name": "alpha", + "value": 0.01, + "description": "Tandem parameter" + }, + { + "name": "beta", + "value": 0.99, + "description": "Tandem parameter" + } + ] + }, + { + "collection": "structures", + "name": "AraC_sensor_structure", + "outputs": [ + "pBAD" + ] + }, + { + "collection": "input_sensors", + "name": "LuxR_sensor", + "model": "LuxR_sensor_model", + "structure": "LuxR_sensor_structure" + }, + { + "collection": "models", + "name": "LuxR_sensor_model", + "functions": { + "response_function": "sensor_response" + }, + "parameters": [ + { + "name": "ymax", + "value": 0.31, + "description": "Maximal transcription" + }, + { + "name": "ymin", + "value": 0.025, + "description": "Minimal transcription" + }, + { + "name": "alpha", + "value": 0.8, + "description": "Tandem parameter" + }, + { + "name": "beta", + "value": 1.0, + "description": "Tandem parameter" + } + ] + }, + { + "collection": "structures", + "name": "LuxR_sensor_structure", + "outputs": [ + "pLuxStar" + ] + }, + { + "collection": "functions", + "name": "sensor_response", + "equation": "$STATE * (ymax - ymin) + ymin", + "parameters": [ + { + "name": "ymax", + "map": "#//model/parameters/ymax" + }, + { + "name": "ymin", + "map": "#//model/parameters/ymin" + } + ] + }, + { + "collection": "parts", + "type": "promoter", + "name": "pTac", + "dnasequence": "AACGATCGTTGGCTGTGTTGACAATTAATCATCGGCTCGTATAATGTGTGGAATTGTGAGCGCTCACAATT" + }, + { + "collection": "parts", + "type": "promoter", + "name": "pTet", + "dnasequence": "TACTCCACCGTTGGCTTTTTTCCCTATCAGTGATAGAGATTGACATCCCTATCAGTGATAGAGATAATGAGCAC" + }, + { + "collection": "parts", + "type": "promoter", + "name": "pBAD", + "dnasequence": "ACTTTTCATACTCCCGCCATTCAGAGAAGAAACCAATTGTCCATATTGCATCAGACATTGCCGTCACTGCGTCTTTTACTGGCTCTTCTCGCTAACCAAACCGGTAACCCCGCTTATTAAAAGCATTCTGTAACAAAGCGGGACCAAAGCCATGACAAAAACGCGTAACAAAAGTGTCTATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCACACTTTGCTATGCCATAGCATTTTTATCCATAAGATTAGCGGATCCTACCTGACGCTTTTTATCGCAACTCTCTACTGTTTCTCCATACCCGTTTTTTTGGGCTAGC" + }, + { + "collection": "parts", + "type": "promoter", + "name": "pLuxStar", + "dnasequence": "ATAGCTTCTTACCGGACCTGTAGGATCGTACAGGTTTACGCAAGAAAATGGTTTGTTACTTTCGAATAAA" + }, + + + + + + + { + "collection": "device_rules", + "rules": { + "function": "AND", + "rules": [ + "STARTSWITH pTac", + "STARTSWITH pBAD", + "pSrpR BEFORE pTet", + "pBAD BEFORE pSrpR", + "pBAD BEFORE pAmeR", + "pBAD BEFORE pBetI", + "pBAD BEFORE pLitR", + "pBAD BEFORE pTet", + "pBAD BEFORE pHlyIIR", + "pBAD BEFORE pLmrA", + "pBAD BEFORE pPhlF", + "pBAD BEFORE pPsrA", + "pBAD BEFORE pBM3R1", + "pBAD BEFORE pAmtR", + "pBAD BEFORE pIcaRA", + "pBAD BEFORE pQacR", + "pTet BEFORE pAmeR", + "pTet BEFORE pBetI", + "pTet BEFORE pLitR", + "pTet BEFORE pHlyIIR", + "pTet BEFORE pLmrA", + "pTet BEFORE pPsrA", + "pTet BEFORE pAmtR", + "pTet BEFORE pIcaRA", + "pTac BEFORE pSrpR", + "pTac BEFORE pAmeR", + "pTac BEFORE pBetI", + "pTac BEFORE pLitR", + "pTac BEFORE pBAD", + "pTac BEFORE pTet", + "pTac BEFORE pHlyIIR", + "pTac BEFORE pLmrA", + "pTac BEFORE pPhlF", + "pTac BEFORE pPsrA", + "pTac BEFORE pBM3R1", + "pTac BEFORE pAmtR", + "pTac BEFORE pIcaRA", + "pTac BEFORE pQacR", + "pPhlF BEFORE pTet", + "pBM3R1 BEFORE pTet", + "pQacR BEFORE pTet", + "ALL_FORWARD" + ] + } + } +] diff --git a/library/templates/Eco1C1G1T1.output.json b/library/templates/Eco1C1G1T1.output.json new file mode 100644 index 0000000..cc3bb79 --- /dev/null +++ b/library/templates/Eco1C1G1T1.output.json @@ -0,0 +1,217 @@ +[ + { + "collection": "measurement_std", + "signal_carrier_units": "RNAP/s", + "normalization_instructions": "Starting with a base conversion of 0.4, the values are then converted from RPUG (from the Bth1C1G1T1 UCF) to RNAP/s (with a conversion of 1 RPU = 0.019 RNAP/s, see 10.15252/msb.20209584), for a final conversion factor of 0.0076. Note: change unit conversion factors accordingly if using a different or modified UCF." + }, + + + + + + { + "collection": "output_devices", + "name": "YFP_reporter", + "model": "YFP_reporter_model", + "structure": "YFP_reporter_structure" + }, + { + "collection": "models", + "name": "YFP_reporter_model", + "functions": { + "response_function": "linear_response", + "input_composition": "linear_input_composition" + }, + "parameters": [ + { + "name": "unit_conversion", + "value": 0.0076 + } + ] + }, + { + "collection": "structures", + "name": "YFP_reporter_structure", + "inputs": [ + { + "name": "in1", + "part_type": "promoter" + }, + { + "name": "in2", + "part_type": "promoter" + } + ], + "devices": [ + { + "name": "YFP_reporter", + "components": [ + "#in1", + "#in2", + "YFP_cassette" + ] + } + ] + }, + { + "collection": "parts", + "type": "cassette", + "name": "YFP_cassette", + "dnasequence": "CTGAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAGAAAGAGGGGAAATACTAGATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACAGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCCTGCAATGCTTCGCCCGCTACCCCGACCACATGAAGCTGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCAATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTTAGCTACCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTCGGTACCAAATTCCAGAAAAGAGGCCTCCCGAAAGGGGGGCCTTTTTTCGTTTTGGTCC" + }, + + + + + + { + "collection": "output_devices", + "name": "YFP_reporter_2", + "model": "YFP_reporter_2_model", + "structure": "YFP_reporter_2_structure" + }, + { + "collection": "models", + "name": "YFP_reporter_2_model", + "functions": { + "response_function": "linear_response", + "input_composition": "linear_input_composition" + }, + "parameters": [ + { + "name": "unit_conversion", + "value": 0.0076 + } + ] + }, + { + "collection": "structures", + "name": "YFP_reporter_2_structure", + "inputs": [ + { + "name": "in1", + "part_type": "promoter" + }, + { + "name": "in2", + "part_type": "promoter" + } + ], + "devices": [ + { + "name": "YFP_reporter_2", + "components": [ + "#in1", + "#in2", + "YFP_cassette" + ] + } + ] + }, + { + "collection": "parts", + "type": "cassette", + "name": "YFP_cassette", + "dnasequence": "CTGAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAGAAAGAGGGGAAATACTAGATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACAGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCCTGCAATGCTTCGCCCGCTACCCCGACCACATGAAGCTGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCAATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTTAGCTACCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTCGGTACCAAATTCCAGAAAAGAGGCCTCCCGAAAGGGGGGCCTTTTTTCGTTTTGGTCC" + }, + + + + + { + "collection": "output_devices", + "name": "YFP_reporter_3", + "model": "YFP_reporter_3_model", + "structure": "YFP_reporter_3_structure" + }, + { + "collection": "models", + "name": "YFP_reporter_3_model", + "functions": { + "response_function": "linear_response", + "input_composition": "linear_input_composition" + }, + "parameters": [ + { + "name": "unit_conversion", + "value": 0.0076 + } + ] + }, + { + "collection": "structures", + "name": "YFP_reporter_3_structure", + "inputs": [ + { + "name": "in1", + "part_type": "promoter" + }, + { + "name": "in2", + "part_type": "promoter" + } + ], + "devices": [ + { + "name": "YFP_reporter_3", + "components": [ + "#in1", + "#in2", + "YFP_cassette" + ] + } + ] + }, + { + "collection": "parts", + "type": "cassette", + "name": "YFP_cassette", + "dnasequence": "CTGAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAGAAAGAGGGGAAATACTAGATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACAGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCCTGCAATGCTTCGCCCGCTACCCCGACCACATGAAGCTGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCAATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTTAGCTACCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTCGGTACCAAATTCCAGAAAAGAGGCCTCCCGAAAGGGGGGCCTTTTTTCGTTTTGGTCC" + }, + + + + + + { + "collection": "functions", + "name": "linear_response", + "equation": "c * x", + "variables": [ + { + "name": "x", + "map": "#//model/functions/input_composition" + } + ], + "parameters": [ + { + "name": "c", + "map": "#//model/parameters/unit_conversion" + } + ] + }, + + + + + + { + "collection": "circuit_rules", + "rules": { + "function": "AND", + "rules": [ + "YFP_reporter NEXTTO Loc3", + "YFP_reporter AFTER Loc3" + ] + } + }, + { + "collection": "device_rules", + "rules": { + "function": "AND", + "rules": [ + "ALL_FORWARD" + ] + } + } +] diff --git a/library/verilogs/cello_verilog_template.v b/library/templates/cello_verilog_template.v similarity index 100% rename from library/verilogs/cello_verilog_template.v rename to library/templates/cello_verilog_template.v