• GXL

  • Referenced in 18 articles [sw16479]
  • graph-based standard exchange format for reengineering. GXL (Graph eXchange Language) is an XML-based ... sharing data between tools. Formally, GXL represents typed, attributed, directed, ordered graphs which are extended ... graphs. An advantage of GXL is that it can be used to exchange instance graphs ... used to provide interoperability of graph-based tools. GXL has been ratified by reengineering...
  • REforDI

  • Referenced in 2 articles [sw20284]
  • Graph-based tools for re-engineering. Maintenance of legacy systems is a challenging task. Often ... REforDI (REengineering for DIstribution) is a graph-based environment supporting this task. REforDI provides integrated ... thus to enhance adaptability. In particular, graph-based tools for re-engineering are generated from...
  • GOLEM

  • Referenced in 4 articles [sw20340]
  • GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BACKGROUND: The Gene Ontology ... become an extremely useful tool for the analysis of genomic data and structuring of biological ... knowledge. Several excellent software tools for navigating the gene ontology have been developed. However ... expandable graph-based view of the gene ontology hierarchy. Furthermore, most existing tools...
  • GraCAD

  • Referenced in 1 article [sw01758]
  • GraCAD -- graph-based tool for conceptual design. This paper proposes a new methodology for computer ... program ArchiCAD. This design tool has been realized using graph-based knowledge representation techniques...
  • Predator

  • Referenced in 18 articles [sw07396]
  • list manipulation. (Competition contribution). Predator is a tool for automated formal verification of sequential ... predicates, but they are now purely graph-based and significantly extended to support various forms...
  • Grail

  • Referenced in 7 articles [sw24229]
  • grammar logics. The Grail system is a tool for the development and prototyping of grammar ... automated theorem prover based on proof nets, a graph-based representation of proofs, and labeled...
  • MotifClick

  • Referenced in 2 articles [sw29728]
  • missed by these tools. Results: Here, we present a graph-based polynomial-time algorithm, MotifClick ... sites with length k, we construct a graph using some 2(k-1)-mers ... eukaryotes, MotifClick outperforms existing leading motif-finding tools for prediction accuracy and balancing the prediction...
  • pkgDepTools

  • Referenced in 1 article [sw38838]
  • packages. It provides tools for building a graph-based representation of the dependencies among...
  • GRAPPA

  • Referenced in 7 articles [sw20931]
  • GRAPPA: a semantical framework for graph-based argument processing. Graphical models are widely used ... intuitive meaning of the links in the graphs is typically expressed using labels of various ... assigning a precise meaning to labelled argument graphs which makes them suitable for automatic evaluation ... argument graphs can be compiled to ADFs, thus providing an automatic evaluation tool via existing...
  • BrainNet Viewer

  • Referenced in 11 articles [sw26512]
  • BrainNet Viewer: a network visualization tool for human brain connectomics. The human brain ... characterized using sophisticated analytic strategies, such as graph theory. These methods reveal the intriguing topological ... complexity of this methodology, toolboxes for graph-based network visualization are still lacking. Here, using...
  • Grouper

  • Referenced in 1 article [sw28783]
  • graph-based clustering and annotation for improved de novo transcriptome analysis. Grouper is a tool...
  • MimoPro

  • Referenced in 1 article [sw33284]
  • MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries. Conclusions ... search algorithm designed for processing well constructed graphs using an ADT regulated ... sensitive and significantly faster than other graph-based approaches in epitope prediction. MimoPro...
  • RepeatExplorer

  • Referenced in 1 article [sw23829]
  • RepeatExplorer: a galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from ... hampered by the lack of specialized bioinformatics tools and appropriate computational resources that would enable ... present RepeatExplorer, a collection of software tools for characterization of repetitive elements, which is accessible ... computational pipeline using a graph-based sequence clustering algorithm to facilitate de novo repeat identification...
  • Olena

  • Referenced in 1 article [sw18719]
  • fast, safe, reusable and extensible image processing tool chains. The library provides many ready ... structures (regular 1D, 2D, 3D images, graph-based images, etc.) and algorithms. Milena’s algorithms...
  • ProClust

  • Referenced in 6 articles [sw35761]
  • graph-based clustering algorithm which uses an asymmetric distance measure, scaling similarity values based ... algorithm. Post-processing, to merge further clusters based on profile HMMs is proposed. SCOP sequences ... which is probably the most widely-used tool for finding remote homologues. We demonstrate that...
  • GenomeTools

  • Referenced in 0 articles [sw37843]
  • software tools for developing bioinformatics software intended to create, process or convert annotation graphs ... strictly follow the annotation graph approach, offering a unified graph-based representation. This gives ... immediate access to genomic features and tools for their manipulation. To process large annotation sets...
  • NeAT

  • Referenced in 1 article [sw21914]
  • tools supports basic operations on graphs (comparison between two graphs, neighborhood ... graph randomization). Another set of programs makes the connection between networks and clusters (graph-based ... questions about networks of interest. Each tool can also be used separately by entering custom...
  • CyGraph

  • Referenced in 1 article [sw22314]
  • critical assets. CyGraph adopts a unified graph-based cybersecurity model relevant to potential and actual ... context of mission assurance. The resulting knowledge graph captures the complex relationships among entities ... separation of graph models into interdependent layers. For time-dependent graph models, it provides dynamic ... visualization of evolving graph state. CyGraph also integrates with third-party tools for visualizing graph...
  • GNNExplainer

  • Referenced in 2 articles [sw37864]
  • powerful tool for machine learning on graphs.GNNs combine node feature information with the graph structure ... along edges of the input graph. However, incorporating both graph structure and feature information leads ... predictions of any GNN-based model on any graph-based machine learning task. Given...
  • HaploMerger

  • Referenced in 1 article [sw19476]
  • ChainNet alignment approach with a novel graph-based structure, which helps to untangle allelic relationships ... have demonstrated that HaploMerger is an effective tool for analyzing and exploiting polymorphic genome assemblies...