DESHARKY: automatic design of metabolic pathways for optimal cell growth

Abstract

Software, a tutorial and examples are freely available and open source at http://soft.synth-bio.org/desharky.html

The Logic of Decision Making in Environmental Bacteria

“…Yet, the ultimate agenda of these endeavors, in particular implementation of Boolean tools, is not only their understanding but also their biotechnological action. Logic networks of the type discussed above share many of the qualities of the electronic processors: for example, they execute computation of signals into responses [104][105][106]. The notion that bacteria behave to an extent as computers making computers has been even entertained in the recent literature [107].…”

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

“…The most common in silico pathway prediction tools offer the enumeration of pathways in two ways: either they effectively combine known reactions from databases that lead to the production of a desired compound from different organisms (heterologous pathways) [23,[27][28][29] or they construct de novo pathways that include not only known reactions but also hypothetical steps whose corresponding enzymes might not actually exist in nature [11,18,19,22,24 ,25 ,30]. A comprehensive algorithm for the in silico prediction of de novo pathways is a significant driver for the success of retrobiosynthetic analyses, and a variety of such tools have been developed in the past decade ( Table 1).…”

Applications of genome-scale metabolic network model in metabolic engineering

“…OptStrain [67], OptReg [68], OptForce [72], k-OptForce [16], OptORF [44], CosMos [20] Omics data integration Transcriptome GIMME [5], iMAT [82], GIM 3 E [76], E-Flux [18], PROM [13], MADE [38], tFBA [90], RELATCH [45], TEAM [19], AdaM [89], GX-FBA [60], mCADRE [92], FCGs [43], EXAMO [75], TIGER [37] Proteome GIMMEp [6] Pathway prediction BNICE [29], Cho et al [14], RetroPath [11], PathPred [59], DESHARKY [74], BioPath [94], XTMS [12], GEM-Path [56] phenotype and gene essentiality [24]. Even further, taking advantage of a large set of genome sequences available for various E. coli strains, the GEMs for 55 E. coli strains were used to investigate the variations in gene, reaction and metabolite contents, and the capabilities to adapt to different nutritional environments among the strains [40].…”

“…BNICE also takes into account reaction thermodynamics and the entries in BNICE are not limited to the chemicals from a specific database such as KEGG LIGAND facilitating the prediction of novel synthetic pathways. Various prediction algorithms, including the pathway prediction system developed by Cho et al [14], RetroPath [11], PathPred [59], DESHARKY [74] and Biopathway Predictor (BioPath), have been developed using their own reaction rules and the heuristics for ranking and pathway search algorithms (Table 1) [94].…”