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Companion Website

Sansom & Horton: Internet for Molecular Biologists

Chapter 07

Overview and basic tools
Overview
Resources for internet collaboration
A companion web page to internet collaboration, Chapter 10, In: The Internet for molecular biolotists, Oxford University Press, Oxford, 2002 http://www.internetbiologists.org/collaboration/
Challenges of Internet Collaboration
Schrage, M. Concepts of collaboration
Shared Spaces as Collaborative Tools. Information TEchnology 'summIT'. (Internet Archive March 10, 2000) http://web.archive.org/web/20000310033144/www.dtic.mil/summit/ma01.html
Schrage M. Leading lights: Technology Designer Michael Schrage Interview http://www.webcom.com/quantera/schrage.html
Asynchronous communications and E-mail
Multipurpose internet mail extensions (MIME)
MIME extends the format of internet mail to allow non-US-ASCII textual messages, non-textual messages, multipart messaging bodies, and non-US-ASCII information in message headers http://www.oac.uci.edu/indiv/ehood/MIME/MIME.html
Eudora version 5.2 E-mail client from Qualcomm http://www.eudora.com/
Wincode Encoder/Decoder Freeware utility supporting UUencode, BASE64, BinHex and other formats for Windows 3.x and 95 http://www.winsite.com
Enter search for wincode
In a Nutshell. Using wincode Unofficial tips (and alternate download for wincode) http://www.telecommunications.com/nutshell/wincode.htm
Pretty Good Privacy (PGP) Freeware MIT Distribution Center for PGP cryptographic software http://web.mit.edu/network/pgp.html
Mail Lists
LISTSERV
Commercial maling list management software (list server) http://listserv.acsu.buffalo.edu
Majordomo Another widely used list server favoured by internet biologists (IB) http://www.greatcircle.com/majordomo
CataList reference site Official catalogue of LISTSERV lists (75,353 lists available) http://www.lsoft.com/catalist.html
Lyris.net E-mail marketing resource guide. Link to LIstManager list server http://www.lyris.net/
QuickTopic.com Create a hosted single topic discussion list (bulletin board) http://www.quicktopic.com
QuickTopic document review A private space for consolidating comments from collaborators on an HTML or Word document under review http://www.quicktopic.com/cgi-bin/docreviewintro.cgi
Topica Manage and participate in e-mail discussion lists (free membership registration). There are currently 49 biology discussion groups. Topica acquired Liszt Newsgroups but does not support newsgroups. http://www.topica.com
Newsgroups and Bionet
GoogleGroups
Search and brose Usenet discussion forums (formerly DejaNews) http://groups.google.com
BioSci Set of electronic communications forums (bionet newsgroups and parallel e-mail lists) used by biological scientists worldwide http://www.bio.net
BioSci bionet Newsgroup archives Advertising on this site supports newsgroup maintenance http://www.bio.net
Marcato, D. Host a Discussion Forum with the Windows 2000 NNTP Service News server software built into Windowns 2000. May be installed at time of operating system installation or at a later time. http://www.microsoft.com/mind/0100/NNTP.NNTP.asp


Specialized tools
Synchronous communications and shared tools and Internet chatrooms and whiteboards
ZDNet
A convenient source of software reviews and downloads for Internet tools http://www.zdnet.com/
Groupboard.com Install a collaborative whiteboard, chat or message board on your web page. Demo available. http://www.groupboard.com
ICQ homepage Acronym intended to sound like 'I Seek You'. Prototypic instant messenger software with many features. Allows private messaging, but like most IM systems the Interest Groups are not professionally oriented. http://web.icq.com
Yahoo! Messenger Instant messenger from the Yahoo family of Internet services. http://messenger.yahoo.com
AIM A widely used instant messenger for AOL customers http://www.aim.com
MSN Messenger for Windows Another instant messenger from Microsoft http://messenger.microsoft.com
Cerulean Studios Trillian Pro An instant messenger client intended to provide interoperability with other systems http://www.ceruleanstudios.com/trillian/index.html
Jabber Software Foundation An instant messenger protocol designed to provide interoperability http://www.jabber.org
Integrated websites
Yahoo! Groups
Everything in one site for mail lists, file sharing, chat, etc., was called eGroups before becoming part of the Yahoo family of services. A favorite of IB. http://www.groups.yahoo.com
Intranets.com A commercial all-in-one collaboration site with many features http://www.intranets.com
Blackboard.com Develop a free online course with many features. Commercial versions of this courseware are widely used by universities and colleges. (There are many other courseware products and hosted services.) http://company.blackboard.com/courses/index.htm
Multi-user virtual environments
LambdaMOO
The prototypic Multi-user Object Oriented (MOO) collaborative environment http://trace.ntu.ac.uk/community/Lambda.htm
MOO home page Links to MOO resources http://www.moo.mud.org
LambdaMOO's Programmer Manual (April 1996) Resources for building in a LambdaMOO-based environment http://www.bvu.edu/ctown/Progman/ProgrammersManual_Toc.html
WebDeveloper.com. VRML Virtual Reality Modeling Language (VRML) resource http://www.webdeveloper.com/vrml/
BioMOO home page (now defunct--see web archive) Past example of a premier biology community online (Internet Archive February 24, 1999). BioMOO was the collaborative home of IB and many other biology collaborations until 2002. http://web.archive.org/web/19990224020349/
http://bioinformatics.weizmann.ac.il/biomoo/
BioMOO: Teaching Biology in Virtual Reality by Clare Sansom An article on teaching in a MOO environment, based on the now defunct BioMOO http://science.uniserve.edu.au/mirror/vCUBE97/html/clare_sansom.html
Diversity University (DU) at DU Educational Technology Services, Inc. (non-profit educational organization) A collaborative MOO currently used by IB. DU hosted IB online lectures and discussions for its 'Perl for Biologists' course in 2002-2003. http://www.du.org
IB MOO Guide for DU by Zev Leifer Describes the options for connecting to DU and accessing the IB classroom http://www.ib-perl.org/class/MOO/MOOguide.html
Collaborative Virtual Workspace (CVW) Find information on the open source CVW prototype collaborative environment. This 'pre-built' MOO environment based on LambdaMOO was developed by Mitre Corporation and released to the public domain. http://cvw.souceforge.net/cvw/info/CVWOverview.php3
SourceForge Official site for open source software http://sourceforge.net
SjSWorld Community Forum Instant Messaging simply explained http://publ69.ezboard.com/fsjsworldforumsfrm7.showMessage?topicID=1.topic
Other real-time tools
Conferencing on the Web by David R. Wooley
Categorized listing of software for Internet discussion and collaboration http://thinkofit.com/webconf/index.htm
ConferZone Resource Center, Newsletter, and Vendor Information http://www.conferzone.com/
CollabTools Listing of tools for Internet collaboration http://www.voght.com/cgi-bin/pywiki?CollabTools
Microsoft Windows Technologies Windows NetMeeting Windows software for online collaborative meetings. Supports A/V conferencing, whiteboard, chat, and file sharing. Comes with Windows 2000. http://www.microsoft.com/windows/NetMeeting/Features/default.ASP
pcAnywhere Symantec's remote control software. May be useful in controlling collaborative applications on another computer and for file transfers. http://enterprisesecurity.symantec.com/products/products.cfm?productID=2
Community of Science (COS) Various tools to assist professional scientists and soceities. Access to databases of funding information, experts, and online reference databases through the COS Workbench http://www.cos.com
COS Abstract Management System COS Abstract Management System is suitable for managing review of abstracts for scientific societies. A demonstration is available. http://ams.cos.com/demo/overview/shtml
EPanel from Humanitas. The On-Line Panel Evaluation Website. Software for collaborative panel evaluations. In use by government agencies. Supports Windows and Macintosh http://www.epanel.cc/
NIH VideoCasting at the NIH Center for Information Technology (CIT) What is NIH VideoCasting http://videocast.nih.gov/videocastinfo.asp
NIH VideoCasting Direct access to NIH current events and archived scientific lectures on video http://videocast.nih.gov/
Usability First. Your online guide to usability resources Link to groupware resources http://www.usabilityfirst.com/
Udell, John. Internet Groupware for scientific collaboration In depth guide to groupware for scientific collaboration (ca 2000) http://udell.roninhouse.com/GroupwareReport.html


Courses, conferences and virtual laboratories
Courses
IB Homepage
A small international online comunity of biologists that pursues educational and research collaborations using Internet tools and resources http://www.internetbiologists.org/
BRI course homepage (now defunct--see web archive) BRI is Internet Biologists first course and has had several international editions introducing the use of the Internet to biologists (Web archive 23 January, 2001) http://web.archive.org/web/20010123085400
http://www.internetbiologists.org/bri99.index.html
BRI course content (now defunct--see web archive)
DBRI course homepage (now defunct--see web archive)
Description of BRI course content (Web archive 21 April, 2001)
DBRI is Internet Biologists advanced course covering topics for Internet-based research (e.g. collaborative systems, sequence-based analyses, molecular visualization, virtual laboratories). There have been several international editions. (Web archive 7 October, 2001.)
http://web.archive.org/web/20010421090738/www.netbio.org/bri99/content.html
DBRI course homepage (now defunct--see web archive)">http://web.archive.org/web/20011007083707/http://www.internetbiologists.org/dbri99/
Perl for biologists homepage IB most recent online course introducing the PERL scripting language from the basics to bioinformatics applications. The first edition in 2002-2003 consisted of lectures/discussions, web resources, and exercises http://www.ib-perl.org
Lau, C.H., Leifer, Z., Kossida, S., and I.R. Schaffner, Jr. (1997). BRI: a model solution for remaining current on Internet resources and technology. Presented at the Virtual Conference on Computers in University Biology Education An early article about the BRI course that was the beginning of IB http://science.uniserve.edu.au/mirror/vCUBE97/html/chin_hoon_lau.htm
Order out of chaos: organizing your Internet searches by Zev Leifer A lecture from the IB BRI course http://emile-21.com/BRI/BRI97_transcript_19970619.html
Course: Principles of protein structure A course presented by the Department of Crystallography, Birkbeck College, University of London http://www.cryst.bbk.ac.uk/PPS2/top.html
Biocomputing hypertext coursebook (1996) Workbook from online course given by the Virtual School of Natural Sciences (VSNS)--BioComputing Division, University of Bielefeld http://www.techfak.uni-bielefeld.de/bcd/Curric/welcome.html
Course: Structure-Based Drug Design (defunct site--see web archive) Certificate/diploma course given by the Virtual School of Molecular Sciences, University of Nottingham (ca 1997) (Web archive 6 December, 2000) http://web.archive.org/20001206143600/
http://www.vsms.nottingham.ac.uk/vsms/s bdd/index.html
The Genome Web. Bioinformatics Course Information UK Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk/GenomeWeb/docs-bioinf-course-info.html
Conferences
Glycoscience Conference
Sponsored by Eurotron, presented by Netconferences. A meeting of glycoscience researchers http://www.netconferences.net/eurotron
Virtual Conference on Computers in University Biology Education (Virtual CUBE97) An online conference sponsored by CTI Biology, University of Liverpool http://science.uniserve.edu.au/mirror/vCUBE97/home.html
Laboratories
Leifer, Z. (1997). A microbiology office-laboratory in cyberspace
A paper presented at the vCUBE conference about a virtual microbiology laboratory writeen in MOO language, previously hosted on BioMOO, now reporduced in DU http://science.uniserve.edu.au/mirror/vCUBE97/html/zev_leifer.html
The Cybertory® Virtual Molecular Biology Laboratory. A web-based virtual laboratory written in JavaScript http://www.attotron.com/cybertory/


Research and project collaborations
Leifer, Z. Research Collaboration via MOO An article in HMS Beagle on the use of the MOO format for online research collaboration (Prior rapid, free registration with BioMedNet is required) http://news.bmn.com/hmsbeagle/24/webres.insitu.htm
Virtual Institute of Experimental (Wet) Biology (VIWB) A venue to publicize member's projects and a call for collaboration. An IB project. http://www.md.huji.ac.il/biology
VIWB Projects A listing of the members and their projects http://bioinfo.weizmann.ac.il:3680/porjects.html
Globewide Network Academy Distance learning catalogue and related GNA projects. 31645 courses and 4348 programs listed http://www.gnacademy.org/
Overcoming distance and language barriers
Language Choice Online: Globalization and Identity in Egypt by M. Warschauer and G.R. El Said
Cultural factors affecting online language use and translation http://www.ascusc.org/jcmc/vol7/issue4/warschauer.html
Multilingual Internet: language, culture and communication in instant messaging, e-mail and chat. A call for papers Annoucement in the Journal of Computer-Mediated Communications (at the University of Southern California) http://www.ascusc.org/jcmc/cfpmultilingual.html
Babel Fish, World: translation One of the first and best online free language translators by AltaVista http://babelfish.altavista.com/translate.dyn
Systran information and translation technologies Systran software is used by several language translators http://www.systransoft.com
Internet interpreters. CNET Reviews The CNET site may be searched for reviews of AltaVista Babel Fish, Transparent Language FreeTranslation, and Translation Experts InterTran http://www.cnet.com/
Open Translation Engine 0.7.9 Open source project for language translation http://www.ibiblio.org/dbarberi/ote/stable/
Google language tools Translate text or web pages http://www.google.com/language_tools?hl=en
Langenberg.com Language Translation Another online translator for English, French, German, Danish, Spanish, Finnish, Czech and Italian http://translation.langenberg.com/
WorldLingo.com Add an online language translator to your browser (subscription)
Conduct multilingual chat in 10 languages (demo available)
http://www.worldlingo.com/products_services/browser_tool.html
http://www.worldlingo.com/products_servic es/chat.html
IBM Research. Translation Description of the IBM web intermediary (WBI) as a language translation plugin, using the FreeTranslation engine as an example http://www.almaden.ibm.com/cs/wbi/doc/examples/translation/
Language Partners International Reference Center for foreign language translation http://languagepartners.com/reference-center/start-here/index.htm
Overcoming cultural barriers
Lau, C.H. (1998). In Search of Permanency: A Founder's Perspective on Sustainability of Purely Virtual Team
Article from the founder of IB on virtual teaming http://emile-21.com/NetBio/permanency.html
Collaboration with grid computing
A Grid Computing Primer
Describes the background to grid computing and gives links to other useful resources http://www.grids-center.org/grids_primer.asp
Scientists giddy about the grid by Randy Dotinga. Wired News. 20 January, 2003 Short article touting the possibilities for grid computing http://www.wired.com/news/print/0,1294,57265,00.html
BIRN. Biomedical Informatics Research Network Introduces the BIRN initiative and describes the motivation and role of grid infrastructure http://www.nbirn.net/About/Overview/Objectives.htm
Scientific Objectives of the Biomedical Informatics Research Network (BIRN) Describes exemplary uses of BIRN resources in the field of neuroimaging http://birn.ncrr.nih.gov/birn/birn_getpage.php?fname=about_birn_bg.html
About BioGRID at the National University of Singapore (NUS) Brief introduction to BioGRID http://www.bid.nus.edu.sg/biogrid/
Biology Workbench portal at the San Diego Supercomputer Center A portal that simplifies access to sophisticated biological research tools (registration required) http://workbench.sdsc.edu/