-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.html.orig
203 lines (192 loc) · 12.5 KB
/
index.html.orig
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
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>
BioHackathon 2009
</title>
<link rel="search" href="/search" />
<link rel="help" href="/wiki/TracGuide" />
<link rel="alternate" href="/wiki/WikiStart?format=txt" type="text/x-trac-wiki" title="Plain Text" />
<link rel="start" href="/wiki" />
<link rel="stylesheet" href="/chrome/common/css/trac.css" type="text/css" /><link rel="stylesheet" href="/chrome/common/css/wiki.css" type="text/css" />
<link rel="shortcut icon" href="/chrome/common/trac.ico" type="image/x-icon" />
<link rel="icon" href="/chrome/common/trac.ico" type="image/x-icon" />
<link type="application/opensearchdescription+xml" rel="search" href="/search/opensearch" title="Search BioHackathon 2009" />
<script type="text/javascript" src="/chrome/common/js/jquery.js"></script><script type="text/javascript" src="/chrome/common/js/trac.js"></script><script type="text/javascript" src="/chrome/common/js/search.js"></script>
<!--[if lt IE 7]>
<script type="text/javascript" src="/chrome/common/js/ie_pre7_hacks.js"></script>
<![endif]-->
<script type="text/javascript">
jQuery(document).ready(function($) {
$("#content").find("h1,h2,h3,h4,h5,h6").addAnchor("Link to this section");
});
</script>
</head>
<body>
<div id="banner">
<div id="header">
<a id="logo" href="http://hackathon2.dbcls.jp/"><img src="/chrome/site/bh2009-logo.jpg" alt="" /></a>
</div>
<form id="search" action="/search" method="get">
<div>
<label for="proj-search">Search:</label>
<input type="text" id="proj-search" name="q" size="18" value="" />
<input type="submit" value="Search" />
</div>
</form>
<div id="metanav" class="nav">
<ul>
<li class="first"><a href="/login">Login</a></li><li><a href="/wiki/TracGuide">Help/Guide</a></li><li><a href="/about">About Trac</a></li><li class="last"><a href="/prefs">Preferences</a></li>
</ul>
</div>
</div>
<div id="mainnav" class="nav">
<ul>
<li class="first active"><a href="/wiki">Wiki</a></li><li><a href="/timeline">Timeline</a></li><li><a href="/roadmap">Roadmap</a></li><li><a href="/browser">Browse Source</a></li><li><a href="/report">View Tickets</a></li><li class="last"><a href="/search">Search</a></li>
</ul>
</div>
<div id="main">
<div id="ctxtnav" class="nav">
<h2>Context Navigation</h2>
<ul>
<li class="first"><a href="/wiki/WikiStart">Start Page</a></li><li><a href="/wiki/TitleIndex">Index</a></li><li><a href="/wiki/WikiStart?action=history">History</a></li><li class="last"><a href="/wiki/WikiStart?action=diff&version=189">Last Change</a></li>
</ul>
<hr />
</div>
<div id="content" class="wiki">
<div class="wikipage searchable">
<h1 id="BioHackathon2009">BioHackathon 2009</h1>
<p>
</p><div class="wiki-toc"><ol><li><a href="#BioHackathon2009">BioHackathon 2009</a><ol><li><a href="#AbouttheHackathon">About the Hackathon</a></li><li>
<a href="#Objectives">Objectives</a></li><li>
<a href="#Expectedoutcomes">Expected outcomes</a></li><li>
<a href="#Mailinglist">Mailing list</a></li><li>
<a href="#Venue">Venue</a><ol><li><a href="#Access">Access</a></li><li>
<a href="#Housing">Housing</a></li></ol></li><li>
<a href="#Misc">Misc</a><ol><li><a href="#SVNrepository">SVN repository</a></li><li>
<a href="#Streamingandsocialnetworking">Streaming and social networking</a></li><li>
<a href="#Photoalbum">Photo album</a></li></ol></li></ol></li></ol></div><p>
</p>
<p>
This is our 2nd BioHackathon for the integrated and interoperable bioinformatics infrastructure.
</p>
<ul><li><a class="wiki" href="/wiki/Participants">Participants</a>
</li><li><a class="wiki" href="/wiki/Schedule">Schedule</a>
</li><li><a class="wiki" href="/wiki/Symposium">Symposium</a> (<a class="wiki" href="/wiki/Poster">Poster</a>)
</li><li><a class="wiki" href="/wiki/Hackathon">Hackathon</a> (Satellite meetings & Final Objectives)
</li><li><a class="wiki" href="/wiki/Report">Report</a>
</li></ul><h2 id="AbouttheHackathon">About the Hackathon</h2>
<p>
The hackathon (hacking + marathon) basically is a camp where invited participants discuss about current issues and implement software to solve the problems on site collaboratively. This kind of meeting is very effective for the intensive development of projects, because face-to-face meeting of developers, who are usually spread around the world, accelerates communication and collaboration to exchange their ideas.
</p>
<p>
BioHackathon 2009 is sponsored by the Database Center for Life Science (<a class="ext-link" href="http://dbcls.rois.ac.jp/en/"><span class="icon"> </span>DBCLS</a>) and the Okinawa Institute of Science and Technology (<a class="ext-link" href="http://www.irp.oist.jp/"><span class="icon"> </span>OIST</a>), and will be held in Tokyo and Okinawa, Japan.
</p>
<ul><li>BioHackathon 2009 <a href="http://hackathon2.dbcls.jp/">http://hackathon2.dbcls.jp/</a>
</li><li>BioHackathon 2008 <a class="ext-link" href="http://hackathon.dbcls.jp/"><span class="icon"> </span>http://hackathon.dbcls.jp/</a>
</li><li>DBCLS <a class="ext-link" href="http://dbcls.rois.ac.jp/en/"><span class="icon"> </span>http://dbcls.rois.ac.jp/en/</a>
</li><li>OIST <a class="ext-link" href="http://www.oist.jp/"><span class="icon"> </span>http://www.oist.jp/</a>
</li></ul><p>
The DBCLS is being accepted as a national center for the sustainable life science databases in Japan. The OIST is the graduate university of science and technology and aiming to create a leading intellectual hub in the Asian-Pacific region.
</p>
<h2 id="Objectives">Objectives</h2>
<p>
In the <a class="ext-link" href="http://hackathon.dbcls.jp/"><span class="icon"> </span>BioHackathon 2008</a>, we focused on the standardization of bioinformatics web services and the exchange data formats to create bioinformatics workflows. To make these global efforts to be fully utilized by the biologists, we need to integrate these services into the various end-user applications.
</p>
<p>
For this purpose, we will organize the second BioHackathon gathering software developers of mash-up services and web service providers. Additionally, we will also involve semi-wet biologists to apply their data for testing these services and applications in combination to address the real world use cases.
</p>
<p>
Our goal is to develop stable and usable platforms for emerging demands, such as
</p>
<ul><li>Workflow for the massive sequence annotation (Galaxy, BioMart, Taverna, MOWserve etc.)
</li><li>Automatic genome sequence assembly and mapping (GMOD/GBrowse, UTGB etc.)
</li><li>Visualization of the large scale data sets (Cytoscape, Processing etc.)
</li><li>Interoperable web services and database resources (BioMOBY, TogoWS, TogoDB etc.)
</li></ul><p>
and test these infrastructures with several biological use cases.
</p>
<p>
For example, the Marine Genomics Unit in OIST is equipped with Roche 454 sequencers and they are hoping to start environmental genomics of the coral reef in Okinawa. We have been working
on the integration of our database resources into the Galaxy, and would like to offer them to use the services provided by the DBCLS. Additionally, we will start to select some suitable use cases to deal with, based on the discussion in the mailing list.
</p>
<h2 id="Expectedoutcomes">Expected outcomes</h2>
<ul><li>Improve end-user applications like Galaxy or Taverna by testing with the use cases.
</li><li>Document how to solve the biological problems using these software and resources based on the hands-on seminar.
</li><li>Issue a manifesto and guidelines for creating interoperable web services with SOAP and/or REST.
</li><li>Publication of the meeting report.
</li></ul><h2 id="Mailinglist">Mailing list</h2>
<ul><li><a class="ext-link" href="http://kml.dbcls.jp/pipermail/biohack2/"><span class="icon"> </span>http://kml.dbcls.jp/pipermail/biohack2/</a>
</li><li>biohack2_at_kml.dbcls.jp
</li></ul><h2 id="Venue">Venue</h2>
<p>
Our preliminary plan is to gather on Sunday in Tokyo for the reception.
On Monday morning, we will have a public symposium, then fly together to Okinawa on Monday afternoon.
We'll be back to Tokyo on Saturday after we are tired of the hacking activities.
</p>
<ul><li>Tokyo (DBCLS) - for the 1st day (reception and symposium)
</li><li>Okinawa (OIST) - rest of the days (hack, hack, hack)
</li></ul><h3 id="Access">Access</h3>
<ul><li><a class="ext-link" href="http://dbcls.rois.ac.jp/en/access/index.html"><span class="icon"> </span>DBCLS</a> (Tokyo venue)
</li><li><a class="ext-link" href="http://www.oist.jp/access_1.html"><span class="icon"> </span>OIST</a> (Okinawa venue)
</li></ul><p>
Annotated Google Maps and KML file for Google Earth are available:
</p>
<ul><li><a class="ext-link" href="http://tinyurl.com/ch7ytg"><span class="icon"> </span>Google Maps for the BioHackathon 2009</a>
</li><li><a href="http://hackathon2.dbcls.jp/attachment/wiki/WikiStart/biohackathon2009-locations.kmz">KML file for Google Earth</a>
</li></ul><h3 id="Housing">Housing</h3>
<ul><li><a class="ext-link" href="http://www.oist.jp/seasidehouse.html"><span class="icon"> </span>OIST Seaside House</a>
</li><li><a class="ext-link" href="http://www.rizzan.co.jp/english/index.html"><span class="icon"> </span>Rizzan Sea-Park Hotel Tancha Bay</a>
</li></ul><h2 id="Misc">Misc</h2>
<p>
What should you bring with you?
</p>
<ul><li>Laptop computer
</li><li>Conversion plug for your AC adaptor (identical to the US type; 100 volt)
</li><li>Local liquor as always (for the Liquorthon at night or for the reception :-)
</li><li><a class="ext-link" href="http://www.linkedin.com/"><span class="icon"> </span>LinkedIn</a> account to share your contact address
</li></ul><h3 id="SVNrepository">SVN repository</h3>
<ul><li><a href="http://hackathon2.dbcls.jp/svn/">http://hackathon2.dbcls.jp/svn/</a>
</li></ul><h3 id="Streamingandsocialnetworking">Streaming and social networking</h3>
<ul><li><a class="ext-link" href="http://www.ustream.tv/channel/biohackathon2009"><span class="icon"> </span>http://www.ustream.tv/channel/biohackathon2009</a>
</li><li>IRC: #biohackathon2009 on chat1.ustream.tv:6667
</li></ul><ul><li><a class="ext-link" href="http://friendfeed.com/rooms/biohackathon-2009"><span class="icon"> </span>http://friendfeed.com/rooms/biohackathon-2009</a> -- FriendFeed room for BioHackathon 2009
</li><li>#biohackathon2009 -- official hash tag for <a class="ext-link" href="http://search.twitter.com/search?q=%23biohackathon2009&lang=all"><span class="icon"> </span>twitter</a>, citeulike and so on.
</li><li><a class="ext-link" href="http://www.linkedin.com/groups?gid=1864599"><span class="icon"> </span>LinkedIn Group</a>
</li></ul><h3 id="Photoalbum">Photo album</h3>
<blockquote>
<p>
<a class="ext-link" href="http://kml.dbcls.jp/BioHack2/photo/"><span class="icon"> </span>BioHackathon 2009 Photo Album (in preparation)</a>
</p>
</blockquote>
</div>
<h3>Attachments</h3>
<ul>
<li>
<a href="/attachment/wiki/WikiStart/biohackathon2009-locations.kmz" title="View attachment">biohackathon2009-locations.kmz</a>
<a href="/raw-attachment/wiki/WikiStart/biohackathon2009-locations.kmz" title="Download" class="trac-rawlink"><img src="/chrome/common/download.png" alt="Download" /></a>
(<span title="2798 bytes">2.7 KB</span>) - added by <em>ktym</em>
<a class="timeline" href="/timeline?from=2009-03-05T03%3A19%3A59%2B0900&precision=second" title="2009-03-05T03:19:59+0900 in Timeline">16 years</a> ago.
<q>BioHackathon 2009 locations for Google Earth</q>
</li>
</ul>
</div>
<div id="altlinks">
<h3>Download in other formats:</h3>
<ul>
<li class="last first">
<a rel="nofollow" href="/wiki/WikiStart?format=txt">Plain Text</a>
</li>
</ul>
</div>
</div>
<div id="footer" lang="en" xml:lang="en"><hr />
<a id="tracpowered" href="http://trac.edgewall.org/"><img src="/chrome/common/trac_logo_mini.png" height="30" width="107" alt="Trac Powered" /></a>
<p class="left">
Powered by <a href="/about"><strong>Trac 0.11.6</strong></a><br />
By <a href="http://www.edgewall.org/">Edgewall Software</a>.
</p>
<p class="right">Visit the Trac open source project at<br /><a href="http://trac.edgewall.org/">http://trac.edgewall.org/</a></p>
</div>
</body>
</html>