cytoscape.github.com/documentation_users.html at develop · khanspers/cytoscape.github.com · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="utf-8">

    <title>User Documentation</title>

    <meta name="description" content="Documents for Cytoscape users">
    <meta name="author" content="Keiichiro Ono">

    <meta name="viewport" content="width=device-width, initial-scale=1.0">

    <script src="http://code.jquery.com/jquery-2.1.0.min.js"></script>

    <link rel="stylesheet" href="http://netdna.bootstrapcdn.com/bootstrap/3.1.0/css/bootstrap.min.css">
    <script src="http://netdna.bootstrapcdn.com/bootstrap/3.1.0/js/bootstrap.min.js"></script>
    <link href="css/main.bootstrap.css" rel="stylesheet">
</head>

<body>

<div class="belt white">
    <div class="container">
        <div class="row">
            <div class="col-md-6 panel">
                <h2>Quick Start Guides</h2>
                <ul>
                    <li>
                        <a href="http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3">
                            Introduction to Cytoscape (3.x)
                        </a>
                    </li>
                    <li>
                        <a href="http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape">
                            Introduction to Cytoscape (2.x)
                        </a>
                    </li>
                </ul>
                <h3>Tutorials</h3>
                <ul>
                    <li>
                        <a href="http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3">
                            Open Tutorials: for 3.x
                        </a>
                    </li>
                    <li>
                        <a href="http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape">
                            Open Tutorials: for 2.x
                        </a>
                    </li>
                </ul>

                <h2>Papers about Cytoscape</h2>

                <p class="lead">
                    <a href="http://www.nature.com/nprot/journal/v2/n10/abs/nprot.2007.324.html">
                        Nature Protocols sample workflow paper
                    </a>
                    by Cytoscape Consortium - a quick overview of Cytoscape functions.
                </p>
                <p class="lead">
                    <a href="http://www.ncbi.nlm.nih.gov/pubmed/23132118">Nature Methods paper</a>
                    by Cytoscape Consortium - a quick overview of Cytoscape App (Plugin) universe.
                </p>
            </div>
            <div class="col-md-6 panel">
                <h2>User Documents</h2>

                <h3>User Manual for the latest version of Cytoscape</h3>
                <ul>
                    <li>
                        <a href="http://wiki.cytoscape.org/Cytoscape_3/UserManual">3.x HTML Version</a>
                    </li>
                    <li>
                        <a href="manual/Cytoscape3_1_0Manual.pdf">3.x PDF Version</a>
                    </li>
                    <li>
                        <a href="http://cytoscape.org/manual/Cytoscape2_8Manual.html">2.x HTML Version</a>
                    </li>
                    <li>
                        <a href="http://cytoscape.org/manual/Cytoscape2_8Manual.pdf">2.x PDF Version</a>
                    </li>
                </ul>

                <h3><a href="manual">Manuals for older versions</a></h3>

                <h3>Presentations</h3>
                <ul>
                    <li>
                        <a href="http://wiki.cytoscape.org/InternationalConferenceOnSystemsBiologyDemos">
                            International Conference on Systems Biology Demos
                        </a>
                    </li>
                    <li>
                        Cytoscape presentation slides at <a href="https://speakerdeck.com/cytoscape">Speaker Deck</a>
                    </li>
                </ul>

                <h3><a href="http://www.biostars.org/show/tag/cytoscape/" target="_blank">User FAQ at Biostar</a></h3>
            </div>
        </div>
        <div class="row">
            <div class="col-md-6 panel">
                <h2>Data Sources</h2>

                <h3>Biological Networks</h3>
                <ul>
                    <li><a href="http://www.pathguide.org/">Pathguide</a> - Comprehensive list of pathway/interaction
                        databases
                    </li>
                    <li><a href="http://code.google.com/p/psicquic/">PSICQUIC</a> - Standardized web service supported by
                        most of the major data providers
                    </li>
                </ul>

                <h3>Social Science</h3>

                <p>
                    Social networking services are good data sources. You can write simple web crawler using scripting
                    languages and save it as standard data format such as GML, GraphML, or simple tab-delimited text.
                    Cytoscape supports many standard graph file formats.
                </p>
            </div>
            <div class="col-md-6 panel">
                <h2>Getting Help</h2>
                <img src="images/icon/Gnome-Dialog-Question-64.png"/>

                <p><strong>Still cannot find answer for your question? Ask your question in the <a href="community.html">mailing
                    list</a>.</strong></p>
                <br/>

                <div class="important">
                    <h3>Tips for Asking Questions</h3>
                    <ul>
                        <li>Be specific: write down steps to reproduce your issues or details about new feature you want.
                        </li>
                        <li>Write information about your platform: OS/Java version, memory size, etc.</li>
                        <li>Add example files: network/attribute files</li>
                    </ul>
                </div>
            </div>
        </div>
    </div>
</div>

<footer></footer>

<script src="js/setup_page.js"></script>
</body>
</html>