## Designed to be used with Eclipse 3.1 (2005)

### BibTeX

@MISC{Sabri05designedto,

author = {Skhiri Dit Gabouje Sabri},

title = {Designed to be used with Eclipse 3.1},

year = {2005}

}

### OpenURL

### Abstract

### Citations

3741 | Optimization by simulated annealing
- Gelatt, Vecchi
- 1983
(Show Context)
Citation Context ...ithm oscillates between -1 and 1, and never identify the two zero points +2.7335, -2.7335. We have to protect our algorithm to a non-terminating program. Simon proposes to use the simulated annealing =-=[12]-=-(SA). It uses an analogy with thermodynamics 71sand most particularly the process of metals cooling and annealing. The principle is quite simple, at high temperature the molecules of liquid metal move... |

1035 | Depth First Search and Linear Graph Algorithms - Tarjan - 1972 |

525 | A heuristic for graph drawing
- Eades
- 1984
(Show Context)
Citation Context ...nimize it by moving nodes in an optimal position. But the global optimization of the energy is an NP-complete problem. The most popular heuristic is the spring embedder algorithm. First introduced by =-=[3]-=- and [16], this algorithm simulates a mechanical system in which graph’s edges are replaced by springs and nodes are replaced by rings connecting edges incident on a node. From the initial configurati... |

492 | An algorithm for drawing general undirected graphs
- Kamada, Kawai
- 1989
(Show Context)
Citation Context ...een u and v such that the spring force between them is proportional to the difference between the distance(u, v) and the natural length of the spring. Kamada et al. describe an interesting variant in =-=[10]-=-. These authors associate a potential energy to each node pair, that are not adjacent, . The consequence is that we consider a graph in which all nodes are connected by springs, the important paramete... |

449 | Graph drawing by force-directed placement
- Fruchterman, Reingold
- 1991
(Show Context)
Citation Context ... the algorithm stops, we know all shortest paths from v to all other nodes. We have to run this algorithm for all nodes of V . 10.3 Force-directed algorithm: Spring with repulsion forces Some authors =-=[6, 8]-=- add a repulsion force between non-adjacent nodes, compute the resultant on each node and then update the position pv = pv + µ · f(pv). We have not found papers where authors compute the total energy ... |

353 |
Methods for visual understanding of hierarchical systems
- SUGIYAMA, TAGAWA, et al.
- 1981
(Show Context)
Citation Context .... . . . . . . . . . . . . . 63 9.10 Packaging the contribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 10 Implemented algorithms 65 10.1 The Layered algorithm or Sugiyama algorithm =-=[21, 24]-=- . . . . . . . . . . . . . 65 10.1.1 Phase 1: Layer assignment . . . . . . . . . . . . . . . . . . . . . . . . 65 10.1.2 Phase 2: Crossing minimization . . . . . . . . . . . . . . . . . . . . . . 66 1... |

212 |
Crossing number is NP-complete
- Garey, Johnson
- 1983
(Show Context)
Citation Context ...3, 5, and 7 are similar to those used for compound graphs. The other phases are original. Phase 1: Cycle Management Unlike traditional methods using by layered algorithms such as backward edge search =-=[7]-=-, we do not need to obtain an acyclic graph. Instead, we enumerate the nodes composing each cycle in order to draw them according to graphical constraints. For example the graph given in Figure 10.5 (... |

90 |
How to draw a directed graph
- Sugiyama
- 1991
(Show Context)
Citation Context .... . . . . . . . . . . . . . 63 9.10 Packaging the contribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 10 Implemented algorithms 65 10.1 The Layered algorithm or Sugiyama algorithm =-=[21, 24]-=- . . . . . . . . . . . . . 65 10.1.1 Phase 1: Layer assignment . . . . . . . . . . . . . . . . . . . . . . . . 65 10.1.2 Phase 2: Crossing minimization . . . . . . . . . . . . . . . . . . . . . . 66 1... |

86 |
Edge crossings in drawings of bipartite graphs
- Eades, Wormald
- 1994
(Show Context)
Citation Context ...: Edge-Crossing Minimization The edge-crossing minimization follows the same process in general layers as in compound layers. The edge-crossing minimization is based on the barycentre [24] and median =-=[5]-=- heuristics. Thus we use a 2-layer edge-crossing minimization. Phase 6: Expansion of Compound Nodes In this phase the compound nodes are expanded into the general graph. 85sL-nodes are moved down one ... |

70 |
MISUE K.: Visualization of Structural Information: Automatic Drawing of Compound Digraphs
- SUGIYAMA
- 1991
(Show Context)
Citation Context ...leaf ; it is called a root if indeg(u) = 0. Algorithm Description Usual algorithms for drawing compound graphs are composed of four steps, similar to those for general directed graphs (e.g., [20] and =-=[22]-=-). The CSCGL algorithm is composed of 7 phases: • Phase 1: Cycle management • Phase 2: Compound graph construction • Phase 3: Global layer assignment • Phase 4: Compound layer assignment • Phase 5: Ed... |

68 |
The Pathway Tools software
- Karp, Paley, et al.
- 2002
(Show Context)
Citation Context ...e data. Although researchers in bioinformatics do not agree about which representation model to use, two schools emerge: one represents metabolic pathways as usual in biochemistry books, as in BioCyc =-=[11]-=-, while the second one proposes more expressive models for such pathways, like the Khon model [13], the Cook model [2] or the Maimon and Broming model [15]. The problem with simple models is that they... |

52 |
A forced directed component placement procedure for printed circuit boards
- Quinn, Breuer
- 1979
(Show Context)
Citation Context ...t by moving nodes in an optimal position. But the global optimization of the energy is an NP-complete problem. The most popular heuristic is the spring embedder algorithm. First introduced by [3] and =-=[16]-=-, this algorithm simulates a mechanical system in which graph’s edges are replaced by springs and nodes are replaced by rings connecting edges incident on a node. From the initial configuration (initi... |

35 |
The Java Developer's Guide to Eclipse
- Shavor, D'Anjou, et al.
- 2003
(Show Context)
Citation Context ...ical networks in the same drawing. Such a result is not available yet in other biochemical tools. 2sChapter 2 Installing the Visual BioMaze Framework Visual BioMaze has been implemented as an Eclipse =-=[17]-=- feature. Eclipse is a rich client platform for the development of highly integrated tools. This means that you must first install Eclipse and then update the platefrom with our tool. Visual BioMaze n... |

27 | The aMAZE LightBench: a web interface to a relational database of cellular processes
- Lemer, Antezana, et al.
- 2004
(Show Context)
Citation Context ...traction, analysis, navigation, and visualization; and 3. a Web interface given access to the services providing by those specialized components. The underlying information system of BioMaze is aMAZE =-=[14]-=-. 1.1.2 Visual BioMaze Visual BioMaze (VBM) [28] is the visualization framework of the BioMaze project. Although it was developed under BioMaze, the visualization framework can be used separately. The... |

26 | A fast effective heuristic for the feedback arc set problem
- Eades, Lin, et al.
- 1993
(Show Context)
Citation Context ...Alignment policies Ver. Horiz. Ver. Ver. Ver. Ver. Horiz. Ver. Circular constraints define whether a cycle must be drawn along a circle or must be drawn by inversing the minimal set of backward edges =-=[4]-=-. They are constituted by a set CT of arc types specifying the allowed types for a circle. For cycles having at least one arc which is not contained in CT we inverse the backward edges, otherwise, we ... |

20 |
A Simple and Unified Method for Drawing Graphs: Magnetic-Spring Algorithm
- Sugiyama, Misue
- 1995
(Show Context)
Citation Context ... vertically and its regulation horizontally. From a graph layout point of view this raises the issue of representing a graph with two (or more) different directions according to the subgraph type. In =-=[23]-=- is proposed a force-directed method that applies different magnetic fields in the desired direction of the graphs. Arcs are magnetic-proof or not depending on its type. Although this method provides ... |

19 |
From molecular activities and processes to biological function
- Helden, Naim, et al.
- 2001
(Show Context)
Citation Context ...tool. Visual BioMaze needs an Eclipse the version 3.0 or higher. Although you can use the Visual BioMaze Framework as any graph viewer, this version 1.X.X needs the installation of the aMaze[14] [27] =-=[26]-=- project. You can see how to install it on http://www.northbears.org/thesnowbook and the aMaze web site on http://www. amaze.ulb.ac.be for more information. 2.1 Eclipse Installation 1. Go to the Eclip... |

14 |
A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems
- Cook, Farley, et al.
- 2001
(Show Context)
Citation Context ...: one represents metabolic pathways as usual in biochemistry books, as in BioCyc [11], while the second one proposes more expressive models for such pathways, like the Khon model [13], the Cook model =-=[2]-=- or the Maimon and Broming model [15]. The problem with simple models is that they are sometimes ambiguous: e.g., an arrow in the Kegg model is used both for representing the input/output of a reactio... |

13 |
Diagrammatic notation and computational structure of gene networks
- Maimon, Browning
- 2001
(Show Context)
Citation Context ...as usual in biochemistry books, as in BioCyc [11], while the second one proposes more expressive models for such pathways, like the Khon model [13], the Cook model [2] or the Maimon and Broming model =-=[15]-=-. The problem with simple models is that they are sometimes ambiguous: e.g., an arrow in the Kegg model is used both for representing the input/output of a reaction but also in phosphorylation (i.e., ... |

12 |
Graph Drawing Software
- Jünger, Mutzel
- 2004
(Show Context)
Citation Context ...termine the permutation to apply to each free layer for reducing the number of edge crossing with its previous layer. Thus such methods reduce the problem to the 2-layer crossing minimization problem =-=[9]-=-. We need for each node vi ∈ Li: • indeg(vi) and pos(vi) in Li The 2-layer crossing minimization We consider a subgraph GNS of two consecutive layers, the northern and the southern. We can write GNS =... |

11 | Online animated graph drawing using a modified spring algorithm
- Huang, Eades, et al.
- 1998
(Show Context)
Citation Context ... the algorithm stops, we know all shortest paths from v to all other nodes. We have to run this algorithm for all nodes of V . 10.3 Force-directed algorithm: Spring with repulsion forces Some authors =-=[6, 8]-=- add a repulsion force between non-adjacent nodes, compute the resultant on each node and then update the position pv = pv + µ · f(pv). We have not found papers where authors compute the total energy ... |

7 |
Representing and analyzing molecular and cellular function using the computer
- Helden, Naim, et al.
- 2000
(Show Context)
Citation Context ... our tool. Visual BioMaze needs an Eclipse the version 3.0 or higher. Although you can use the Visual BioMaze Framework as any graph viewer, this version 1.X.X needs the installation of the aMaze[14] =-=[27]-=- [26] project. You can see how to install it on http://www.northbears.org/thesnowbook and the aMaze web site on http://www. amaze.ulb.ac.be for more information. 2.1 Eclipse Installation 1. Go to the ... |

4 |
3d-spring embedder for complete graphs
- Simon, Steinbruckner, et al.
- 2000
(Show Context)
Citation Context ...tions of the problem . . . . . . . . . . . . . . . . . . . . . . . . . 69 10.2.2 Solving the equations . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 iis10.2.3 The Simon et al. contribution =-=[18]-=- . . . . . . . . . . . . . . . . . . . . 71 10.2.4 Our contribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 10.2.5 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . ... |

2 |
dit Gabouje. Semantic visualization of biochemical databases
- Zimányi, Skhiri
- 2004
(Show Context)
Citation Context ...n; and 3. a Web interface given access to the services providing by those specialized components. The underlying information system of BioMaze is aMAZE [14]. 1.1.2 Visual BioMaze Visual BioMaze (VBM) =-=[28]-=- is the visualization framework of the BioMaze project. Although it was developed under BioMaze, the visualization framework can be used separately. The aim of the Visual BioMaze project is to provide... |

1 |
Molecular interaction map of the mamalian cell cycle control and DNA systems repair. Molecular Biology of the Cell
- Kohn
(Show Context)
Citation Context ...e, two schools emerge: one represents metabolic pathways as usual in biochemistry books, as in BioCyc [11], while the second one proposes more expressive models for such pathways, like the Khon model =-=[13]-=-, the Cook model [2] or the Maimon and Broming model [15]. The problem with simple models is that they are sometimes ambiguous: e.g., an arrow in the Kegg model is used both for representing the input... |

1 |
Element de théorie des graphes
- Sopena
- 2004
(Show Context)
Citation Context ...ready said, we need to find the for each pair (u, v) inE the shortest way du,v. This research take a lot of time and no really efficient algorithm exists. We have implemented the Dijkstra’s algorithm =-=[19]-=-. The problem can be enounced as follows: We research the shortest way between: • a given start node and a given target node • one node and all others • n start nodes and m target nodes The Dijkstra’s... |

1 |
Graph drawing and applications: For sofware and knowledge engineers. World Scientific
- Sugiyama
- 2002
(Show Context)
Citation Context ...called a leaf ; it is called a root if indeg(u) = 0. Algorithm Description Usual algorithms for drawing compound graphs are composed of four steps, similar to those for general directed graphs (e.g., =-=[20]-=- and [22]). The CSCGL algorithm is composed of 7 phases: • Phase 1: Cycle management • Phase 2: Compound graph construction • Phase 3: Global layer assignment • Phase 4: Compound layer assignment • Ph... |