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It is quite brief in many areas, but the notes should be of some help as to
specific sources and their electronic addresses. The addresses are given from
the point of view of the US.
Please note item #3 below, and post your remarks to the Cytometry mailing list.
Dave Coder
email: dcoder@u.washington.edu
*******************************************************************
ISAC XVII Internet Workshop, Tues. 18 October 1994
Chaired by Dave Coder and Paul Robinson
Speakers:
Dave Coder , Univ. of Washington, dcoder@u.washington.edu
Robb Habbersett, Los Alamos Nat. Lab., robb@beatrice.lanl.gov
Steve Kelley, Purdue Univ., skelley@flowcyt.cyto.purdue.edu
Paul Robinson, Purdue Univ., robinson@flowcyt.cyto.purdue.edu
Guenter Valet, Max Plank Inst. Biochem., valet@vms.biochem.mpg.de
Purpose:
1. Provide an introduction to the Network Information Systems
Internet and the World Wide Web (Dave Coder)
How to get access to the world network (Steve Kelley)
2. Illustrate example services of interest to ISAC members
The Purdue Univ. Cytometry Mailing List (Paul Robinson)
The National Flow Cytometry Resource Data Repository (Robb Habbersett)
Cytometry networks in Europe; ISAC and network opportunities (Guenter Valet)
3. Solicit comments, suggestions, and assess needs of ISAC members
==================================================
I. Introduction to Electronic Information Systems
Why should you be interested?
1. time saved
2. efficiency increase
3. new ways/places to work
4. increased internationalization of the cytometry community
5. cost reduction
6. it's waaaay cool
The Internet: what is it?; where is it?; how big is it?
Connections and means
1. remote connections to other computers (telnet)
2. file access/transfer (ftp, eg. Fetch)
3. information access/exchange:
(email, bulletin boards, listserves, usenet, Gopher, World Wide Web)
4. searching the network:
(Archie, Veronica, WAIS, Web crawler)
Types of information available over the Internet
1. joural literature
2. software
3. electronic mail
4. bulletin boards
5. data
6. publications
7. telemedicine
II. World Wide Web
A graphical face on the world's electronic information
1. compatible with ftp, Gopher, and other information servers
2. provides hypertext links to related information anywhere on the Internet
3. the coolest thing on the Info Superhighway
Acronymorrhea
WWW: world wide web
URL : universal resource locator
http: hypertext transfer protocol
html: hypertext markup language
How does it work?
a web server computer stores the data and provides world-wide access
a web browser runs on your computer and
* connects you to a server
* transfers html and associated files
* interprets and displays transferred files
* allows you to send information back to the server
other software displays images or plays animation or sound files sent by the web server
for an example of the varieties of information the WWW can employ, connect
using Mosaic or another full-featured browser to:
http://www.ncsa.uiuc.edu/demoweb/demo.html
Server, browser and graphics display software are available for free
Graphical Browser or client software;
Mosaic (MS-Windows, Mac, X-Windows)
source: NCSA [see below]
Cello (MS-Windows)
source: ftp.law.cornell.edu in directory /pub/LII/Cello
Omniweb (NeXTStep)
source: http://www.omnigroup.com/Software/OmniWeb/
Text-mode browsers
DosLynx (MS-DOS) ftp.cc2.ukans.ledu in /pub/WWW/DosLynx
[note this may already be on shared-access computers that
you reach via ethernet or modem. At the prompt on your screen
enter the command lynx (remember lower case) and enter/return]
a complete list of software and sources is available via WWW at:
http://info.cern.ch/hypertext/WWW/Clients.html
----------------------------------------------------------
How to Access the Internet and Retrieve Software
I. Computer connections to the network
What you need:
1. computer terminal
2. network connection
ethernet (fast; expensive)
telephone modem (slower; cheaper)
3. software:
connection to the network
ethernet: Internet connection
(e.g., Telnet)
communications software for dial-up computer or
Internet over telephone lines using
SLIP (serial line internet protocol)
PPP (point to point protocol)
using network services
remote computer connections (e.g. Telnet)
file transfers (e.g. ftp)
network browsers (e.g., Gopher, Mosaic)
network searches (e.g., Archie, WAIS)
Getting connected:
1. institutions: find the network person and ask them
2. commercial providers
II. Sources of software over the Internet:
(that is, you have to be connected to the Internet to get it)
addresses listed are anonymous ftp servers
note: your institution may have all of these available locally
ask someone who is already using the network
Some sources of network software:
National Center for Supercomputing Applications (NCSA)
telnet, Mosaic for Windows, Macintosh and X-Windows
[see end of article]
Univ. of South Carolina: DOS Internet Kit
a complete start-up kit for DOS or Windows
for ethernet or serial connections
via ftp at tbone.biol.scarolina.edu
in directory /pub/kit/
read the file 00README.DOC for instructions
Commercial services:
Delphi
text-based interface over the telephone
email to: askdelphi@delphi.com
Pipeline for Windows
graphical interface over the telephone
email to: info@pipeline.com
Flow cytometry software available for free:
DOS-based list mode analysis
MFI 3.4E by Eric Martz
ftp at flowcyt.bio.umass.edu
Windows-based list mode analysis
WinMDI by Joe Trotter
via ftp or WWW at flosun.salk.edu
DOS-based utilities
Purdue Cytometry [see below]
DOS-based software for Skatron
Aberystwyth, Wales
via WWW at http://144.124.112.37/home.html
Image Analysis software available for free:
NIH Image for the Macintosh
via ftp at zippy.nimh.nih.gov
in /pub/nih-image
III. Recent Books and Guides to the Internet
Adam C. Engst et al. Internet Starter Kit,
Hayden Books, 1994; 608 pgs. and software
ISBN 1-56830-094-8
[provides software and concise instructions how
get connected via the telephone]
H. Hahn and R. Stout The Internet Complete Reference
Osborne/McGraw-Hill; 818 pgs.
ISBN 0-07-882023-5
[a complete and clear guide with lots of examples]
PC Magazine vol. 13 No. 17 (Oct. 11, 1994)
[a complete series of articles on the Internet and
a review of services and software]
------------------------------------------------------------------
The Purdue Cytometry Mailing List
Source of Information Cytometry:
The only on-line discussion group dealing cytometry in general
(there is an image analysis discussion group (see below) setup by Bruce Milthorpe
email: brucem@cbme.unsw.edu.au)
Although not set up as a listerserve (you can't review old messages)
there is a large set of potentially valuable information that may be
setup as a frequently-asked-questions file.
Available via email over the internet
email address: cytometry@flowcyt.cyto.purdue.edu
Acts like a bulletin board: via email, anyone can post a question or comment
to those on the list.
Purdue also has data files and utility programs for data analysis
ftp server: flowcyt.cyto.purdue.edu
This is the anonymous ftp archive of the
Purdue University Cytometry Laboratories.
If you upload any files, please send a note to
Steve Kelley: kelley@flowcyt.cyto.purdue.edu
---------------------
The Cytometry Data Repository
ABSTRACT:
Historically, the commercially available computer software for the display
and analysis of flow cytometry data has left a great deal to be desired.
This has prompted numerous individuals to write their own software to meet
their own needs. Since there are many different data file formats for flow
data there has always been a need to test this software on at least a subset
of data file types the individual software developer intends to support.
Although there has been a standard file format for flow data since 1984, it
has only achieved wide spread acceptance in the last 5 years or so. Also,
even though most of the manufacturers of flow cytometers have adopted the
"standard", there is actually considerable variation in its implementation.
Therefore, the need for a broadbased collection of data file formats, against
which software can be tested for compatibility, is still a pressing issue.
- From this perspective, it was proposed by Dave Coder and Eric Martz that an
internet based data file repository be established. Furthermore, it seemed
appropriate that the NFCR host this data base. Accordingly a repository was
established at the NFCR utilizing the "gopher server" available through the
Los Alamos National Lab's computer network. Flow cytometrists at large are
free to contribute data files for the repository (although they will be
screened for suitability prior to inclusion). Criteria for inclusion will be
based on uniqueness: the files need to be representative of files from a
particular type of flow cytometer, or they must contain a useful data set
which others would find to be of interest (such as a good example of staining
for BrdU {bromodeoxyuridine} incorporation or multi-color
immunofluorescence). At present only about 20 files have been deposited but
this is expected to grow considerably.
In the future the collection to be an archive of cytometry data (flow
cytometry initially) that provides examples of the diversity of flow
cytometric applications from both biological and technical perspectives. From
the biological perspective, data for different cells types, disease states,
cell surface markers, DNA contents, etc. would be available. From a technical
perspective, data from different acquisition systems and instruments would be
present, along with calibration data sets, and data sets that can serve as
references for new analytical and statistical procedures.
Future issues include:
* construction of the repository as a WWW server
* forms-based searches of repository contents
* posting of criteria for adding files to the repository
* acquisitions from users
---------------------
Cytometry networks in Europe; ISAC and network opportunities
Several societies and groups have setup on-line information servers in Europe.
CytometryNet is a Gopher server:
address: cytogerm.biochem.mpg.de
This Node provides data on the: Gesellschaft fuer Zytometrie (GZ)
in Germany.
==Information in the CYTOGERM directory covers:
- Secretariat
- Bylaws
- Executive Committee
- Council
- Membership
- Meetings
- Abstract Titles
- Newsletter
- History
==Connections to other CytometryNet nodes in the: LINKS directory
- CYTOESACP
- CYTOFRANC
- CYTOIBER
- CYTOITALY
- CYTORUSS
- CYTOUK
===== please address suggestions and comments to:
===== Guenter Valet valet@vms.biochem.mpg.de
It is clear that members of ISAC will benefit from a similar information server
*********************************************************************
Internet addresses of interest in Cytometry
[I believe this to be a complete list as of now, Thu Oct 27 11:21:15 PDT 1994.
Note that you may be unable to reach some of the servers listed below. If you
can't connect, try again later.]
format of URL (universal resource locator):
service_type://computer.internet.address/directory/file.name
Cytometry:
==========
Purdue Cytometry Mailing List
email: cytometry@flowcyt.cyto.purdue.edu
ftp://flowcyt.cyto.purdue.edu
Gopher
------
CytometryNet
gopher://cytogerm.biochem.mpg.de
Cytometry Data Repository
gopher://telomere.lanl.lan/pub/NFCR
WWW Servers
-----------
Salk Institute for Biological Studies
http://flosun.salk.edu
Dana Farber Cancer Institute Flow Cytometry Facility
http://sorter.dfci.harvard.edu:8000/www/facslab.html
Univ. of Washington Immunology WWW Server
http://nucleus.immunol.washington.edu/Research_facilities/cell_analysis.html
Division of Cellular and Gene Therapy, CBER FDA
http://www.cber.nih.gov/welcome.html
Center for Disease Control and Prevention
http://158.111.115.15/mosaic/home/home.html
Flow Cytometry at Aberystwyth
http://144.124.112.37/home.html
Flow Cytometry at Dartmouth
http://mmm.dartmouth.edu/Pages/marcl/flowcyt.html
Nick's Home Page at MD Anderson, Texas Medial Center
http://drad52.mda.uth.tmc.edu/index.htm
Image
======
Image analysis discussion group
email: imagecyt@cbme.unsw.edu.au
NIH Image discussion
email: nih-image@soils.umn.edu
+++++++++++++++++++++++++++++++++++++
How to Obtain NCSA-developed Software
NCSA software may be obtained via
* CD-ROM
* anonymous FTP [note this service was unavailable when tried 26Oct95]
* an e-mail archive server
* or U.S. mail
NCSA software and manuals are also available for purchase-- either
individually or as part of the anonymous FTP reel or cartridge tapes through
the NCSA Technical Resources Catalog. Orders can be processed only if
accompanied by a check in U.S. dollars made out to the University of
Illinois. To obtain a catalog, contact:
NCSA Documentation Orders
152 Computing Applications Building
605 East Springfield Avenue
Champaign IL 61820-5518
tel. (217) 244-4130
email orders@ncsa.uiuc.edu
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CD-ROM Vol 3 was produced by Monica M. Shively and other staff at the
Purdue University Cytometry Laboratories and distributed free of charge
as an educational service to the cytometry community.
If you have any comments please direct them to
Dr. J. Paul Robinson, Professor & Director,
PUCL, Purdue University, West Lafayette, IN 47907.
Phone: (765)-494-0757;
FAX(765) 494-0517;
Web