Featured Application: David N. Carruthers, Jinho Kim, Daniel Mendez-Perez, Eric Monroe, Nick Myllenbeck, Yuzhong Liu, Ryan W. Davis, Eric Sundstrom & Taek Soon Lee. (2023) Microbial production of high octane and high sensitivity olefinic ester biofuels. Biotechnology for Biofuels and Bioproducts. v16(60)

Operon Calculator

Predict Expression Levels in Bacterial Operons

Latest version: 1.0

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Articles to Cite

LaFleur, T.L., Hossain, A., & Salis, H.M. (2022). Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria. Nature communications, 13(1), 1-15.

Cetnar, D.P. & Salis, H.M. (2021). Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons. ACS Synthetic Biology, 10(2), 318-332.

Reis, A.C. & Salis, H.M. (2020). An automated model test system for systematic development and improvement of gene expression models. ACS Synthetic Biology, 9(11), 3145-3156.

Halper, S. M., Hossain, A., & Salis, H.M. (2020). Synthesis Success Calculator: predicting the rapid synthesis of DNA fragments with machine learning. ACS Synthetic Biology, 9(7), 1563-1571.

Farasat, I., Kushwaha, M., Collens, J., Easterbrook, M., Guido, M., & Salis, H.M. (2014). Efficient search, mapping, and optimization of multi‐protein genetic systems in diverse bacteria. Molecular systems biology, 10(6), 731.

Ng, C. Y., Farasat, I., Maranas, C.D., & Salis, H.M. (2015). Rational design of a synthetic Entner–Doudoroff pathway for improved and controllable NADPH regeneration. Metabolic engineering, 29, 86-96.
API Power Mode Documentation.

#!/usr/bin/python import requests, json, hmac, hashlib, datetime #Create an input parameter dictionary params['title'] = '' params['promoter_name'] = '' params['promoter_sequence'] = '' params['mRNA'] = 'undefined' params['RBS_sequence_list'] = ',,' params['CDS_name_list'] = 'no name,no name,no name' params['CDS_sequence_list'] = ',,' params['terminator_name'] = '' params['terminator_sequence'] = '' params['16S_rRNA'] = 'undefined' params['organism'] = 'undefined' params['algorithm'] = 'OperonCalculator_EvaluateAnnotatedOperonMode' params['RBS_Calculator_version'] = 'v2.1.1' #Send it to https://api.denovodna.com/ using a HTTPS POST params['publicConsumerToken'] = 'test' params['privateConsumerToken'] = 'private key' params['timestamp'] = datetime.datetime.utcnow().isoformat() message = params[publicConsumerToken'] + params['timestamp'] + 'OperonCalculator_EvaluateAnnotatedOperonMode' params['signature'] = hmac.new('private key', message, hashlib.sha1).hexdigest() headers = {'Content-type': u'application/json', 'Accept': u'application/json'} r = requests.post('https://api.denovodna.com/OperonCalculator_EvaluateAnnotatedOperonMode', data=json.dumps(params), headers=headers) output = r.json() #Retrieve the result after the calculation has completed. id = output['JobInfo']['id'] result = sendGet('Result',{'id' : id})