- 2.1 What is the Internet and how does it work ?
- 2.2 Internet Services
- 2.3 Access to the Network
- 2.4 Retrieval of Information from the Network
- 2.5 Display of Information on Network Servers
- 2.6 Check of Network Performance
- 2.7 Enhancement of Internet Performance:
- 2.8 Network Search Tools
- 2.9 Computer Virus Detection
1. Introduction
Cytometry is a fast developing multidisciplinary science. The high interest in improved diagnostic, prognostic and therapy control procedures in medicine as well as cellular aspects in immunology, cancer research, molecular biology, biotechnology and microbiology is concurrent with the development of cytometric assays for a variety of biochemically specific cell functions and markers, of instrumentation for flow and image cytometry and of software for cytometric multiparameter data processing.Due to the multidisciplinary nature of the cytometric field it is increasingly difficult for scientists to overlook the individually relevant progress due to cytometric contributions in many different journals and meetings.
At this point, the Internet is attractive for several reasons. A major interest concerns the potential for fast international information exchange e.g. by bulletin boards (3.1) of scientific societies and user groups for the announcement of meeting, workshop and courses ( 3.1.1), by displaying extracts of the scientific literature (abstracts, table of contents of journals (3.1.2) or by providing collections of laboratory procedures ( 3.1.4).
Another even more important aspect concerns the interactive potential of the Internet for the conceptual development ( 3.2) of science e.g. by the installation of concept fora ( 3.2.1) by the preparation of consensus processes ( 3.2.2), by participating in the discussion of E-mail groups (e.g. Purdue E-mail box) ( 3.2.3), by advancing scientific software development ( 3.2.7) for the standardized establishment of individual patient disease diagnosis and especially disease prognosis from multiparameter cytometric and other data and by promoting international quality assurance ( 3.2.2) programs and educational offers (STEP program, telelearning ( 3.2.6) in this area.
The Internet provides a significant lead time for the early recognition of new interest areas in this fast expanding multidisciplinary research field especially when compared to the traditional time lapse between scientific concept, experimental phase and result publication.
Due to the rapidly increasing importance of the Internet for the cytometric field during the last year, it is the goal of the Rimini 1996 tutorial to provide the essential basic information on Internet access, operation, diagnostics and performance enhancement for the interested scientist.
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2. Network Operation
2.1 What is the Internet and how does it work ?
The Internet is a world wide electronic network. It consists
physically of wire and glassfiber cables supplemented by terrestrial or
satellite radio communication and terrestrial infrared laser links.
Data in this network are exchanged between computers by the standardized
TCP/IP protocol.
The network is mostly accessed from PC, MacIntosh or Unix computers via fast ethernet lines (250Kbytes/sec), by digital ISDN telephone lines (8 or 24Kbytes/sec) or by modem connections via slower analogue telephone lines (3.6Kbyte/sec = 28800baud) using the SLIP or PPP data exchange protocol.
The hardware connection between computer and network is established by computer bus access via a plug-in network card, via external interfaces attached to the parallel printer port or via telephone modem attached to a serial (RS232) port of the computer.
Appropriate driver software establishes the data communication between computer and network. Telephone modem access to the Internet is assured by access provider companies. Such companies operate gateway computers to the Internet. Universities or other larger organisation uses typically the faster ethernet access to the network.
Each network computer is identified and accessed by its unique URL (Universal Relocater) address consisting of a mnemonic name e.g. pcv4.biochem.mpg.de which is transformed into a unique computer address number e.g. 141.61.1.64 by a name server computer of the network. Network computers are set up either as clients or as server computers. Most computers are client computers. Client computers can demand, display and download information from server computers and send messages to server and client computers.
Name server computers contain address lists and access information comparable to e.g. telephone books. This information is required to identify and access each computer in the network.
Gateway computers provide network access from multiclient and server environments of large institutions like universities, hospitals, administrations, access providers or companies.
Routing computers distribute the network traffic within the network in an optimized way.
Network analysis programs permit the analysis of network performance to the individual user.
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2.2 Internet Services
The Internet offers different services. The most wellknown is the display of www-pages with text, graphic, audio and video information. In addition E- mail messages can be exchanged between www-clients, file download by FTP (file transfer protocol) and off-line display of downloaded www-pages are available. The Gopher information system and a multitude of Newsgroups and Companies display continuously updated information.A variety of commercial TCP/IP intranets are installed in the Internet like the Compuserve, America On-Line, Europe On-Line, T-OnLine etc. nets. The individual user has access from any of these nets to the general Internet.
2.3 Access to the Network
Ethernet access to the network is typical for universities and other public research institutions. The local computer center will usually provide the necessary help for new users. Telephone modem access from home occurs either through large Internet access providers like Compuserve, America On-line, T-OnLine or smaller local companies, identified through the Yellow Pages or the Internet search services.
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2.4 Retrieval of Information from the Network
2.4.1 Client Access:
The client's software access to the network is assured by either freely
downloadable network browser programs like or Netscape, Mosaic,
Microsoft (2.4.2) or by commercial programs like e.g. Chameleon. These
programs operate form a user surface like WINDOWS in PC's or the MacIntosh
MAC-OS operating system. For proper operation they additionally require a
TCP/IP network communication or telephone modem software
2.4.2 Network Browser Programs:
The actual features and download possibilities for a variety of web browsers can be obtained e.g. by a Lycos search for: Mosaic Download Site using the: Match All Words option to find software download sites or by the direct download of Netscape, Mosaic or Microsoft Explorer browser software. It is advisable to download Netscape Gold versions for multimedia applications because the most essential plug-in drivers (2.5.3.2) for these applications are already enclosed in the browser download.
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2.5 Display of Information on Network Servers
2.5.1 Network Servers:
The potential for the display of information in the Internet requires the
presence of a www-server computer. Server computers are installed
in the majority of universities or large public research centers and mostly
set up under a Unix operation system. Departments, laboratories or
individual researchers can localize their www-pages either on the central
www-server computer or they can install separate www-servers e.g. in PCs by
appropriate programs.
A comparatively cheap possibility for the installation of personalized www-pages outside public institutions is provided on the www-server computers of access providers or in commercial nets like Compuserve, America On-line etc. The installation of www-servers on PCs accessible by telephone modem is also possible but the data link is slow and the telephone costs are high for continuous server operation. Access is faster by ISDN telephone lines (64Kbit/sec i.e. 8 Kbyte/sec) but telephone costs are still significant i.e. the operation of www-servers outside public institutioons is mostly restricted to commercial access providers.
2.5.2 Preparation of www-Pages:
The display of www-pages requires the establishment of electronic pages in HTML (hypertext markup language, NCSA, WWW-Consortium). The textual, graphic, video and audio information of HTML files is displayed by network browser programs like Netscape of Mosaic. The files are editable by normal editors and contain ASCII text intermixed with display and link commands to outside computers, contained within: < > brackets. Examples of cytometric web pages are provided in fig.1-3
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2.5.3 Use of Images, Graphics, Video and Audio Information:
In addition to text formatting that can make information on the computer monitor appear like the familiar pages in books or journals, the Web is a unique computer-based communication medium in that it affords the use of still images, animation, and sound. All can be used on the same page, but may require the use of special programs that work with the browser. There are two types: helper applications that work with files accessed by the browser, and plug-ins that work with the browser and extend the capabilities of the browser. Many are available at no charge from the sites that supply browsers.Graphics may consist of two types: in-line graphics (fig.4) and full-sized graphics (fig.5) In-line graphics are small to large images that are embedded in the web page. Small scale images (so-called thumbnail images) may be used to show the user a sample a larger scale image that is typically accessed by clicking on the thumbnail. Virtually all browsers will display the image directly, although some image types require a plug-in.
Image maps (fig.6) are graphics that contain embedded reference points that can be selected with the mouse. Such reference points contain hypertext links to other files or images. This is useful for organizing menus or for the examination of features of complex images.
An excellent introduction to images can be seen on the Internet at: Cornell University or at the www-Consortium
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2.5.3.1 Images:
2.5.3.1.1 Charts, Graphics, Photomicrographs:
Images may contain anything graphical from drawings, plots, charts,
photomicrographs, etc. (fig.7)
For the Web, all images are displayed as bitmapped images. This means, the image is made up as a mosaic of PIcture ELementS (pixels) on the computer monitor. Several familiar formats include TIFF (tagged interchange file format), GIF (graphical interchange format), JPEG (joint photographic experts group). All three formats use file size compression. This is important because it reduces transfer time via the Internet. (As an example, an image file that contains large numbers of the same pixel (areas of black or white) can save information about the numbers and location of the same pixel and reduce the size of the file substantially; a ten-fold reduction in size is not unusual.)
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2.5.3.1.2 Page Images: PostScript and Adobe Acrobat:
Instead of graphical objects on a Web page, one can also display entire pages as graphics. Adobe developed Acrobat to provide page images in PostScript. This format has the advantage that it is scaleable (that is, you can enlarge the image and see more detail unlike bit mapped formats where you see only bigger pixels). Thus you can display any type of information (text or pictures) at any resolution. The disadvantage is that you need a special viewer to see Acrobat (pdf : portable document format) files although the viewer is available at no cost. (You can get a plug-in (see below), the Acrobat Amber reader, for Netscape web browsers that allow you to view pdf documents within Netscape). A further disadvantage is that the contents are not accessible. That is, you cannot capture part of the image and keep the same resolution; you can only capture the image that is on the computer monitor.
2.5.3.2 Video and Audio: Approaches to Multimedia:
This kind of information has time structure; some can have non-linear sequences. All time-based media costs more to create and to use, but if used well, has greater value than traditional "mono"-media. Streaming video or audio provides sound/video as continuous delivery. That is, there is no need to download and play back the entire file. Streaming video requires very large transfer rates to be useful. That is, individual images must have sufficient spatial resolution and must be transferred at a sufficient speed to give an adequate illusion of motion. Such speed is only possible with a direct (i.e., T1) Internet connection.
Animation, on the other hand, can work with few images, but can give the illusion of speed. There are several instance in cytometry where animation can provide more information. Displays of kinetics data are obvious, but complex multi-parameter data sets that require multiple views may be more understandable if time is used as a feature.
Most video/animation cannot be viewed directly in a browser, but must be viewed with another helper application or plug-in. Depending on the file source, you will need the appropriate viewer. There are several file formats in use. MPEG (motion pictures joint experts group) is one standard that is widely implemented.
QuickTime is to store, edit and play synchronized graphics, sound, video, text and music. QuickTime is available for both Macintosh and PCs. A good source for viewers is: Lentz or: Quicktime or at Apple.
Typical video/audio formats for PCs are the .AVI or .WAV format. Practical applications in cytometry concern the visualization of intracellular processes or the display and commenting of critical steps in cell preparation or staining procedures as well as the demonstration of instrument setup features like laser focusing or particular flow conditions in cytometric analysis or sorting chambers as well as in microscopic imaging.
Streaming video is available from VDO
In the future, we may expect Java scripts (applets), JavaScript or Java programs to deal with animation directly. This can include various virtual reality displays as well.
QuickTimeVR provides interactive objects for manipulations in space. Another standard, VRML (the virtual reality modeling language), provides for a variety of ways to use graphical display and interaction in time. 3D animation is of interest for the intuitive display of multidimensional measurements in flow and image cytometry.
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2.5.3.3 Acquiring and using Helper Applications and Plug-ins:
Helper applications are available from a variety of sources like Netscape , NCSA (Macintosh) or WindowsPlug-ins are designed to work within the net browser. These are mostly proprietary formats and there is no standard at this time. Some are quite useful. An overview and various plug-ins can be obtained at Netscape
2.5.4 Input in Search Forms:
Internet www-pages offer in many instances interactive services e.g. for sending E-mails, or for filling in search (fig.8) or abstract forms (ISAC electronic abstract service for the Rimini meeting).
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2.6 Check of Network Performance
The functionality of the network can be checked by the individual user.Look-up programs search either the mnemonic name or the numeric computer addresses. Ping programs send a sequence of byte packages to a distant network computer. The round trip time until the return of the echo of the Ping byte sequence and the number of lost data packages are provided by these programs. Trace programs provide the exact routing of calls to distant computers by displaying the numeric and mnemonic addresses of server, gateway and routing computers (fig.9). Watch programs permit fast checks of entire sets of www-server, gateway and routing computers e.g. for the availability of intra- and extramural (fig.10 right and left)
Systematic network analysis shows that large distance traffic e.g. over the atlantic is organized "freeway" like i.e. it mostly proceeds via the same sequence of commercial network stations in e.g. the t3answer.net, mci.net, dante.net, dfn.net etc. Final access e.g. within universities or larger cities, in contrast, may be by "country road" traffic via variable roads.
"Hotspots" occur presently in some network areas like e.g. San Francisco but also in certain parts of Europe where network calls may circle in waiting loops a substantial number of times (e.g. 5-10 times) between the same routing stations. The call reaches finally either the wanted station or is terminated by a time out mechanism e.g. of the network browser.
2.7 Enhancement of Internet Performance:
2.7.1 Limitations of Network Speed
The response time between call and build-up of a wanted www-page on
the computer screen is frequently very significant especially for graphic
information. While in theory network waiting times should
decrease by the installation of faster data lines, the influx of more and more
network users so far outweighs in practice most speed gains. Network
waitings times can be decreased or avoided in various ways:
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2.7.2 Installation of Mirror Sites
The installation of mirror sites ( Cardiff, ISAC, Martinsried, Oviedo), speeds up information access by reducing transatlantic long distance network traffic.
2.7.3 Off-Line Internet on CD-ROM
The recording of www-pages, file repositories, E-mail box contents and software on periodically updated CD-ROMs eliminates network waiting time. The information on the CD remains fully accessible with current network browsers. The off-line available information is read from the CD while on-line calls are serviced on-line as long as the computer is actively connected to the network. In case no network access is given the off-line files are correctly displayed while on-line calls cause a bypassable error message.
2.7.4 Off-Line Internet by FTP-download
Because CD-ROM updating is limited for practical reasons to six month or one year periods, a substantial interest for delay free updates in between remains in certain areas (e.g. meeting and course announcements, consensus processes). Such updates can be achieved automatically if cytometric www-page providers store their pages in compressed form on FTP-server computers from where they can be collected by suitable programs (e.g. all Martinsried www-pages) daily, weekly or monthly according to the interest of the individual user. Following decompression, the received files can be inspected with the network browser off-line from harddisk in the same way as CD-ROM files.
2.8 Network Search Tools
Network searches for cytometry and cytometry related topics are of fundamental importance to find specific subjects in the fastly growing number of Internet server sites.
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2.8.1 Database Searches:
Searches can be initially started from the Directory menu e.g. of the Netscape browser. Consulting various databases for the term: cytometry provides quite different results. While some databases like Alta Vista, Lycos or Infoseek provide a high number of entries, other databases cover cytometry at present only comparatively scarcely like: Yahoo or WWWW. Lycos has a good tendency to find realistic answers to complex queries and Alta Vista performs frequent updates on screened www-sites.Due to the fast development of the cytometric field and the high activities on the Purdue E-mail box, searches have usually to be narrowed down e.g. cytometry AND calcium AND intracellular like in Alta Vista Advanced Query searches.
2.8.2 Robot Search Programs:
The search databases are updated by robot search programs which continuously explore thousands of www-homepages and subdirectories per day for their actual information content. The results of these searches are indexed and introduced into the above searchable databases. The characteristics of some robot programs for various purposes are described. Besides identified robot program, the network is also searched by an unknown number of unidentified robot programs
2.9 Computer Virus Detection
Computer viruses may be imported from the download of infected programs but also from text documents containing program bound but operating system independent Macro Viruses. It is useful to periodically check computers with Internet access by anti-virus programs and to follow the documention on the appearence of new viruses.
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3. Display of Cytometric Information in the Internet
The variety of media that are supported on the Internet provide good opportunities for the exchange of information and for the interaction among individuals and groups involved in cytometry throughout the world. Announcements via the Internet are instantaneously accessible and www-pages can be frequently updated if required.Websites may entertain an E-mail forum to ask questions or exchange comments with colleagues, and to view or discuss results. The future will see the formation of "electronic" meetings or workshops taking place.
3.1 Bulletin Board Information
Currently there are several cytometric societies international and national on-line. These are listed at ISAC, Martinsried, Purdue University [Purdue CD-ROM], and at the Wiley WebsiteAccess to several websites has been made more rapid by regional mirror sites. Such mirrors duplicate the contents of other websites on remote web sites. Examples include mirrors for the ISAC WWW site in Germany, Spain and the UK. For Europe the Cytorelay Node at the Max Plank Institute, Martinsried web site has mirrors of ISAC, Purdue University, Scripps Research Institute, and JCSMR in Australia. For North America, the ISAC Web site will soon have a mirror for the Sociedad Iberica de Citometria (Iberian Society for Cytometry) in Oviedo.
3.1.1 Meetings, Meeting Abstracts, Workshops, Courses:
Notification of upcoming meetings, some meeting abstracts ( ISAC, Deutsche Gesellschaft für Zytometrie (DGZ), Europ.Soc.Anal.Cell.Pathology (ESACP), Abstract Text 1995, workshops, and courses are available at regional web sites (ISAC, Purdue and Martinsried).
3.1.2 Table of Contents of Scientific Journals:
Journal table of contents for Cytometry (since 1995) are available from the Wiley Cytometry Website . It is expected that tables of contents for Clinical Communications in Cytometry will follow. Tables of contents for Analytical Cellular Pathology (ACP) are available at Martinsried, and recent volumes at the publisher, Elsevier Scientific. In addition, tables of contents for other journals are available at the Elsevier Science Tables of Contents service.
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3.1.3 Book Reviews:
Some are available at Purdue [Purdue CD-ROM], and more are to be expected at the Wiley Cytometry Website.
3.1.4 Laboratory Procedures:
A source of information on cytometric methods and procedure is available from several laboratories on the Internet. Coverage is still uneven, but more are expected. An informative example is the listing of Functional Cell Biochemistry by Flow Cytometry.
3.2 Potential for the Scientific Development of Cytometry
3.2.1 Electronic Meetings, Concept Fora:
The Internet provides the opportunity for on-line organized meetings
on specific topics in cytometry. As in traditional meetings, participants may
present results using any variety of graphics, and respond to questions from
the audience. Several are planned for the near future.
Concepts in Clinical Cytometry
at Martinsried has the goal to advance the scientific discussion on the
clinical use of cytometry. This should favor consensus processes and
standardized data classification on an international and interdisciplinary scale.
The ISAC Web Site is planning an on-line forum on cytometric assays of apoptosis.
The format of these platforms will be to present one or two page communications on current issues. They will be grouped by themes. The communications can be backed up by links in greater depth. E-mail discussion remarks are welcome and will be appended to the communications.
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3.2.2 Consensus Documents Ring trials:
The Internet can speed access to working groups and proposals for consensus protocols in cytometry. The inclusion of graphics makes these on-line discussion fora valuable sources of current thinking and practice in cytometry as well as proposals for new methodologies. Consensus documents that contain information on several protocols are available at Martinsried [ Purdue CD-ROM]. These include immunephenotyping in leukemia as well as DNA flow cytometry and DNA morphometry (fig.12).Ring trial results on standards and quality control are useful references and several are on-line at the Martinsried site. They include: leukocyte and thrombocyte immunophenotyping or DNA flow cytometry. [ Purdue CD-ROM].
3.2.3 E-Mail Boxes:
Mailboxes have been very useful as a methodological and instrumental discussion forum. The Purdue mailbox was started in 1989 as an E-mail service at Purdue University. The display of the messages on the Internet since early 1995 has greatly enhanced the popularity of this mailbox (fig.11).
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3.2.4 Cytometry CD-ROM:
The goal of the Purdue CD-ROM project is to periodically compile the Internet information in cytometry. This facilitates the access to larger documents like E- mail archives, video, image and audio sequences, software, data file repositories which is for their size are slow to transport through the network. CD sequences will be of interest to easily visualize the scientific progress in this research area.3.2.5 Electronic Publications:
The potential for publication on the Internet is large, and just beginning. The advantages of electronic publication include: rapid publication, the inclusion of multimedia illustrations, and the potential for swift commentary and response from readers. Valuable Internet publications will be those publications that produce quality papers that are peer-reviewed. Currently the ISAC Web Site has an issue in preparation. Examples of other biomedical electronic publications include: Journal of Image Guided Surgery and the Global Emergency Medicine Archives.
3.2.6 Education and Telelearning (STEP and TATIANA Programs):
The STEP and TATIANA Programs are examples for learning and telelearning programs in cytometry.
3.2.7 Software Development and Download:
There are several sources for cytometry software on the Internet. A catalog of free flow cytometry software is at Amherst [Purdue CD-ROM].A popular download site is at Scripps
The image analysis program for the Macintosh, NIH Image, is available by FTP along with a number of image files and associated programs.
In addition, useful Internet software is at Martinsried [Purdue CD-ROM].
Furthermore databases and cytometric list mode data can be on-line classified (fig.13) and practical application of the Standardized Multiparameter Data Classification (SMDC) in research and medicine are shown.
3.2.8 Data File Repositories:
It is the intention of data file repositories to provide list mode files from various cytometers as well as data sets on typical measurement, evaluation and classification schemes. Such repositories are presently being built up.back to: Table of contents
Off-line Internet, a timesaver !
Download all Martinsried cytometry pages, check the concept, follow the installation instructions (PC) and display text and graphics from your harddisk without network delay
For problems or comments, please contact: G.Valet E-mail: valet@vms.biochem.mpg.de , Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, Germany, Tel: +49/89/8578-2518, -2525, Fax: +49/89/8578-2563, INTERNET address: http://www.biochem.mpg.de/valet/cytorel.html
Last Update: Oct.30, 1996
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