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FindPath specifications

Information


Unique identifier OMICS_04876
Name FindPath
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Stéphanie Heux <>

Publication for FindPath

FindPath in publications

 (7)
PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] method used to rank pathways is by the number of reaction steps, as this can be easily translated into an objective function in a number of methods (e.g., optstoic , cfp , and k-shortest efm , findpath ) to find the shortest pathway or pathway with the least total flux. the shortest pathway also implies fewest reaction steps or minimal enzyme requirement, thereby reducing […]

PMCID: 5657077
PMID: 29072147
DOI: 10.1186/s12859-017-1823-5

[…] until one reaches structures within the already explored energy band. this approach seems to be more adequate in the context of a gradient basin coarse graining than a direct path heuristic (e. g. findpath [])., in step 2a, we compute the gradient basins and rates for the monomer landscape from the list of input structures using barriers [] (with minh heuristic). for step 2b, a list […]

PMCID: 5492299
PMID: 28587084
DOI: 10.3390/s17061208

[…] propose a bounded approximation algorithm 1, named the minimum vertices maximum flow algorithm (mvmfa). the key insight of mvmfa is that each augmenting path picked out by the pivotal algorithm 2 findpath has more flow and few inactive sensors. this means that a sensor with a high detection probability, but passing few relaying sensors by, will be activated firstly. our main contributions […]

PMCID: 4559319
PMID: 26335276
DOI: 10.1186/s12859-015-0706-x

[…] ensemble defect; cont: gc content. the str. column indicates whether the method assigns a predicted structure to each individual or not arnafold with option -p bwe use accessfindpath.py [] for the findpath.c [] in the vienna rna package cthe secondary structure of all nucleotide positions is constrained to obtain the free energy of a specified secondary structure like rnaeval dfree energy […]

PMCID: 3311099
PMID: 22536898
DOI: 10.1186/1471-2105-13-S3-S14

[…] this way, we use the cpe code to recursively reconstruct all the non-tree paths. figure is the pseudo-code algorithm., example 4: let's take the node p6 in figure as an example and show how to use findpath algorithm in figure to find all paths from p1 to p6., p e t ( p 1 ) : 1 , c p e ( p 6 ) : 1 , 1 . $ 0 . 0 , 0 . $ 1 , 1 . # 1 , # 0 . 0 , # 1 , 0 . # 0 . 0 […]


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FindPath institution(s)
Université de Toulouse, Toulouse, France

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