View source for BioCC: An Openfree Hypertext Bio Community Cluster for Biology

<font size="2" color="#c0c0c0">Genomics &amp; Informatics Vol. 4(3) 125-128, September 2006<br />
<br />
</font><strong><font size="5">BioCC: An Openfree Hypertext Bio Community Cluster for Biology</font></strong><br />
<br />
<font size="4">Sungsam Gong, TaeHyung Kim, Jungsu Oh, Jekeun Kwon, SuAn Cho, Dan Bolser and Jong Bhak</font><br />
<br />
<font color="#999999">Korean Bioinformation Center (<a rel="nofollow" title="http://www.kobic.re.kr" class="external text" href="http://www.kobic.re.kr/">KOBIC</a>), KRIBB, Daejeon 305-806, Korea,&nbsp;<br />
MRC-DUNN, Cambridge CB2-2XY, England, United Kindom</font><br />
<br />
<strong><font size="4">Abstract</font></strong><br />
We present an openfree hypertext (also known as wiki) web cluster called BioCC. BioCC is a novel wiki farm that<br />
lets researchers create hundreds of biological web sites.<br />
The web sites form an organic information network. The contents of all the sites on the BioCC wiki farm are<br />
modifiable by anonymous as well as registered users. This enables biologists with diverse backgrounds to form their<br />
own Internet bio-communities. Each community can have custom-made layouts for information, discussion,and<br />
knowledge exchange. BioCC aims to form an everexpanding network of openfree biological knowledge<br />
databases used and maintained by biological experts, students, and general users. The philosophy behind<br />
BioCC is that the formation of biological knowledge is best achieved by open-minded individuals freely exchanging<br />
information. In the near future, the amount of genomic information will have flooded society. BioCC can be an<br />
effective and quickly updated knowledge database system. BioCC uses an opensource wiki system called<br />
Mediawiki. However, for easier editing, a modified version of Mediawiki, called Biowiki, has been applied. Unlike<br />
Mediawiki, Biowiki uses a WYSIWYG (What You See Is What You Get) text editor. BioCC is under a share-alike<br />
license called BioLicense (<a rel="nofollow" title="http://biolicense.org" class="external free" href="http://biolicense.org/">http://biolicense.org</a>). The BioCC top level site is found at <a rel="nofollow" title="http://bio.cc/" class="external free" href="http://bio.cc/">http://bio.cc/</a><br />
<br />
<strong><font size="4">Introduction</font><br />
</strong>The internet as we know it was formed in the early 1990's when Tim Berners-Lee distributed a daemon program<br />
called HTTPD (<a href="http://www.w3.org/People/Berners-Lee/Longer.html">http://www.w3.org/People/Berners-Lee/Longer.html</a>). HTTPD is a hypertext text processing<br />
daemon or server that runs on a hardware computer network (Berners-Lee et al., 1994). In the mid 1990s, many<br />
web sites using the HTTPD and HTML (Hypertext Markup Language) format sprang up (<a rel="nofollow" title="http://en.wikipedia.org/wiki/" class="external free" href="http://en.wikipedia.org/wiki/">http://en.wikipedia.org/wiki/</a><br />
History_of_the_World_Wide_Web). These sites were mostly static in that only the web masters can edit and add<br />
to the contents of the information provided by the web servers. However, as technology developed and the<br />
general public started to access the Internet, there was a higher demand for more up-to-date information and more<br />
knowledge exchange (Cunningham et al., 2001; Stephen et al., 2006). This resulted in a new system that can be called<br />
an &quot;openfree hypertext web&quot; (<a href="http://en.wikipedia.org/wiki/">http://en.wikipedia.org/wiki/</a> Web_2) (Kevin et al., 2006).<br />
The major difference between the open free hypertext and the existing web service is that the open free hypertext<br />
allows clients to add, delete, and edit web contents with minimum restriction. Often the web contents were also free<br />
(i.e., CopyLeft). This seems radically progressive and risky in information management. However, that is in fact closer<br />
to the early practice of using the Internet in the early 1990s. While openfree technology such as wiki was not widely<br />
available, the Internet became more restricted in the mid 1990s. One of the major fields of science that benefited<br />
most by the advance of the Internet has been biology (Guest et al., 2003). Biological data are complex, diverse,<br />
and messy to handle. Also, human annotation is often a critical component of the biological data and its updates.<br />
Therefore, many large biological institutes have been running web sites with a remarkably open and free license<br />
scheme such as GNL (<a rel="nofollow" title="http://www.gnu.org" class="external free" href="http://www.gnu.org/">http://www.gnu.org</a>). The majority of such data and databases has been free (Holger et al.,<br />
2005; Kai et al., 2006). In that open culture, there have been various community projects such as Bioperl, Biojava,<br />
Biopython, and Biolinux (<a rel="nofollow" title="http://bioperl.net" class="external free" href="http://bioperl.net/">http://bioperl.net</a>, <font color="#810081"><a rel="nofollow" title="http://bioperl.org" class="external free" href="http://bioperl.org/">http://bioperl.org</a></font>, <a href="http://biojava.net/">http://biojava.net</a>, <a rel="nofollow" title="http://biojava.org" class="external free" href="http://biojava.org/">http://biojava.org</a>, <a rel="nofollow" title="http://biolinux.net" class="external free" href="http://biolinux.net/">http://biolinux.net</a>,<br />
and <a rel="nofollow" title="http://bioinformatics" class="external free" href="http://bioinformatics/">http://bioinformatics</a>. org). These individual projects have been linked by groups of researchers who advocate an<br />
open, free, and fast exchange of biological information. As one such openfree project, we present BioCC. BioCC is<br />
a top level portal site for open hypertext web sites that use Wiki (<a rel="nofollow" title="http://wiki.org" class="external free" href="http://wiki.org/">http://wiki.org</a>). The concept behind BioCC is the<br />
ongoing construction of a large scale network of wiki-based 126 Genomics &amp; Informatics Vol. 4(3) 125-128, September 2006<br />
web sites. BioCC can be found at the following URL; <font color="#810081"><a rel="nofollow" title="http://bio.cc/" class="external free" href="http://bio.cc/">http://bio.cc/</a></font>. The history of BioCC and its diverse activities<br />
date as far back as 1996 with the first community project proposals for bioperl and biojava. BioCC's scope of activity<br />
is similar to those of <a rel="nofollow" title="http://bioinformatics.org" class="external free" href="http://bioinformatics.org/">http://bioinformatics.org</a>, that has been successfully implemented some years later. BioCC,<br />
however, is different in its philosophy in that it is intended to form a networked cluster of very specialized wiki sites<br />
that have a common license, templates, and a philosophy for sharing, instead of becoming one single top level portal<br />
site such as <a rel="nofollow" title="http://bioinformatics.org" class="external free" href="http://bioinformatics.org/">http://bioinformatics.org</a>, <a rel="nofollow" title="http://google.com" class="external free" href="http://google.com/">http://google.com</a> and <a href="http://yahoo/">http://yahoo</a>. com. BioCC maintains over 1000 biologically<br />
relevant internet domains that function as dynamically changing nodes for the whole cluster.<br />
Overall, it forms a gigantic knowledge network database with many volunteers from diverse backgrounds. BioCC's<br />
development or evolution roadmap includes 1) a network of special knowledge domains, 2) a deep search engine that<br />
finds database entries as well as web pages, 3) an automatic word linking for an infinite number of word<br />
connections, 4) anautomatic renewal and weighting system for web site interconnection, and 5) an artificial<br />
intelligence knowledge query system for easier and contextual knowledge retrieval. below the BioCC level,<br />
there are high level portal sites that are more abstract than specialized domains such as <a rel="nofollow" title="http://zincfinger" class="external free" href="http://zincfinger/">http://zincfinger</a>. org.<br />
<br />
<strong><font size="4">Methods</font><br />
</strong>BioCC uses Mediawiki as the basis for developing its own WYSIWYG (What You See Is What You Get) wiki program<br />
called Biowiki. Mediawiki is based on the PHP (<a href="http://php/">http://php</a>. net) programming language which is flexible, manageable,<br />
and scaleable. Mediawiki has its own simple wiki grammar called wiki markup. The wiki markup is a set of syntax used<br />
to format and edit Mediawiki pages. Many users who do not know the wiki markup find it difficult to write a wiki web<br />
page. Although Mediawiki has its own editing tool, it provides a limited set of functions to format a variety of<br />
HTML codes. To solve this problem, the Biowiki wiki program integrates a graphical editor called FCKeditor<br />
(<a rel="nofollow" title="http://www.fckeditor.net" class="external free" href="http://www.fckeditor.net/">http://www.fckeditor.net</a>) as its major editing tool. FCKeditor enables an easy and intuitive editing in a visual<br />
and straight forward WYSIWYG environment. BioCC farm has thousands of domain names that<br />
point to a single or multiple server machines. It takes advantage of Apache (<a rel="nofollow" title="http://www.apache.org" class="external free" href="http://www.apache.org/">http://www.apache.org</a>), one of<br />
the most common HTTP daemons, as a main server engine. To successfully handle hundreds of active<br />
Biowiki sites within a small number of machines, the &quot;NameVirtualServer&quot; Apache module has been adopted.<br />
BioCC has 2 dual core AMD Opteron 275 processors and 10GB RAM based on theFedoreaCore version 5<br />
operating system with a 2.6.17 Linux kernel. The virtual web sites (called bio-domains),such as<br />
bioperl.net, biocourse.org, biocorea.org, and biopeople. org, are diverted to the Apache web server's virtual server,<br />
and users outside access the bio-domains as distinct individual and international internet domains.<br />
<br />
<strong><font size="4">Results</font><br />
</strong>BioCC, which is the mother of all the Biowiki operated sites, hosts hundreds of openfree hypertext sites for biology.<br />
Among them, we introduce the five most active Biowiki sites (Fig. 1). They are 1) BioCourse.org, 2) BioPedia.org,<br />
3) BioSpecies.org, 4) BioPeople.org, and 5) BioCorea.org. Each of these sites is discussed in moredetail below.<br />
However, there are many other useful sites, for example, omics.org and Variome.org. Omics is the top level directory<br />
site for all the new-omicsdisciplines in biology such as genomics, proteomics, and interactomics. Variome.net is<br />
for SNP (Single Nucleotide Polymorphism) related research portals.<br />
<br />
BioCourse is an open information archive designed for novice or intermediate level students and researchers in<br />
the field of bioinformatics, including general biology. There have not been many useful educational portal&nbsp;<br />
sites for bioinformatics which deal with a wide variety of subjects such as statistics, computer systems,&nbsp;<br />
genomics, microbiology, and programming languages. Internet users usually visit web sites of interest&nbsp;<br />
and manage them by using Bookmark utilities. However, this is tedious to maintain and update. <br />
Also, clients (internet users) cannot actively add, edit or remove the contents of such web pages. In order to overcome<br />
these limitations, we have developed BioCourse.org, an openfree web system for the exchange of learning and<br />
teaching materials. The purpose of BioCourse is to help students quickly grasp large amounts of information about<br />
research methods in various fields. The contents of BioCourse can be classified into six main categories:1)<br />
BioLanguage, 2) BioTool, 3) BioSystem, 4) BioDatabase, 5) BioLecture, and 6) BioJournal. BioLanguage deals with<br />
programming languages such as Perl, Java and Python. BioTool introduces biological and bioinformatics utilities,<br />
such as BLAST, and users can post their home-made utilities. BioSystem and BioDatabase deal with computer<br />
operating systems and Database Management Systems (DBMS). BioLecture contains introductory course materials<br />
BioCC: An Openfree Hypertext Bio Community Cluster for Biology and BioJournal cites scientific journals in the fields of biology<br />
and bioinformatics.<br />
<br />
BioPedia is an openfree encyclopedia dedicated to all biological glossaries and vocabulary. An enormous<br />
amount of terms and jargons in the filed of life science has been accumulated due to the rapid development of life<br />
sciences in the last couple of decades. Many novel terms, such as interactome and interactomics, have been coined<br />
in this -omics era. Even bioinformatics, genomics, and proteomics are fairly recent terms. However, such -omics<br />
jargon can create problems in communication among biologists due to ever-changing definitions. Hence, we<br />
developed an openfree web-based encyclopedia with the aim of keeping technical terms accurate, and can be<br />
modifiable in order to keep up with the rapid development in the life science. Biopedia will be utilized as a resource<br />
database for semantic web and ontology networks in biology.<br />
<br />
BioSpeices is an openfree directory service for listing all the species in the world. Its top level category has three<br />
major super kingdoms; prokaryote, eukaryote, and virus. It has amodel organisms section such as human, mouse,<br />
rat, C.elegance, and E.coli. BioSpecies is designed to satisfy the professional needs of biologists rather than<br />
general users. Most of BioSpecies&rsquo;s pages contain classification information from kingdoms down to subspecies, and a basic<br />
description of the organismsuch as scientific or common name, habitat, diet, genome size, and industrial productivity.<br />
Any newly identified organism which acquires an official authentication can be freely posted.<br />
128 Genomics &amp; Informatics Vol. 4(3) 125-128, September 2006<br />
<br />
BioPeople is a web based who&rsquo;s who service in a biology domain. It aims to maintain information about scientists in<br />
the biology fields, providing a person&rsquo;s profile such as affiliation (s), research interests, collaborations, and<br />
publication information. It aims to be a voluntary community site. We have classified groups of scientists by region,<br />
research field, and affiliation, so that users are able to search for researchers' names by country, research field, or<br />
affiliation. We selected the top level directory for people who are in life sciences related jobs. Biopeople is a publicly open<br />
utility providing cyber-communication which gathers information worldwide for life scientists to help connect them to each other.<br />
<br />
Biology is an extensive branch of science, consisting of many research centers, companies, and laboratories. BioCorea.<br />
org is an openfree portal site for scientists in Korean life science fields. BioCorea.org has been developed to facilitate<br />
communications among local researchers.<br />
<strong><br />
<font size="3">Discussion</font></strong><br />
We have introduced a Bio Community Cluster farm, BioCC, and its five major Biowiki web based services:<br />
BioCourse, BioPedia, BioSpecies, BioPeople, and BioCorea. Biowiki sites in BioCC form an organic<br />
information network whose contents are modifiable by anonymous users. While this enables a very fast and<br />
up-to-date knowledge exchange amongst internet communities, there can also be copyright problems that<br />
could cause originality disputes. To settle this possible issue, BioCC advocates a license scheme called<br />
Biolicense. Biolicense (<a rel="nofollow" title="http://biolicense.org" class="external free" href="http://biolicense.org/">http://biolicense.org</a>) enables any human being and machine to openfreely share information<br />
and knowledge for a limitless number of purposes. It is a share- alike license that aims to protect biological information<br />
and knowledge from being legally monopolized by a small number of companies, classes, races, and economic<br />
groups in the world. The most important aspect of BioCC is that it is based on voluntary contribution. Users manage<br />
and maintain the information in BioCC. If users accept the underlying philosophy of BioCC, that research information<br />
should be freely exchangeable through an open-minded community, BioCC can become a valuable human<br />
heritage that should be transferred to future generations who will live in the era of 'personal omics' such as personal<br />
genomics.<br />
<br />
<strong><font size="4">Acknowledgements</font><br />
</strong>This work was supported by M10407010001-06N0701-00110, and M10508040002-06N0804-00210 grant of<br />
MOST. JKK was supported by R01-2004-000-10172-0 (2005) grant of KOSEF. SSG would like to acknowledge all<br />
the supports of KOBIC in his previous period of stay and thanks his colleagues at KOBIC and OITEK, Inc.<br />
<br />
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