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Organisation: European Molecular Biology Laboratory
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No 2
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-= INDEPENDENT NEWSLETTER PRODUCED BY HELSINKI UNIVERSITY =-
<< EDITED BY ROBERT HARPER >>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
If you are reading this edition of BIOBIT did you ever stop and
wonder how it came to you... magic isn't it? Well back in the dim
past of biological networking (say half a year ago) there were
three separate sources of information BIONET, BIOTECH and SEQNET.
These have now been amalgamated into a "super" net called BIOSCI
which takes care of the distribution of all the postings that you
receive in your mail box.
But BIOSCI is only the PUBLIC face of what is happening on the
networks... the tip of the iceberg. There is alot of activity that
remains un-noticed because it is hidden from the
Internet/EARN/BITNET/NETNORTH user. There is more going on in the
world that what you happen to read in your mailbox.
This version of BIOBIT has a look under the surface, and reports
on what happens behind the scenes at BIONET.
There is an article by Dave Kristofferson from BIONET and then an
interview which looks at some aspects of how BIONET functions. The
main point to arise from the interview is why is there not a
European equivalent of BIONET?
There is a proverb which says that a fool can ask more questions
than seven wise men can answer... so here are my questions for the
European community to answer.
1) Is there a need for a central molecular biology computing
resource in Europe?
2) How would it be financed?
3) Where would it be situated?
4) Who would be responsible for its running and upkeep?
5) Who would be able to use it, and at what cost?
If you have answers to ANY of these questions then you can post
them e-MAIL to HARPER@FINFUN or BIOBIT@COM.KPO.FI if you want
to keep it private, and if you want to discuss the issue upfront
then reply to this forum at your nearest BIOSCI node.
Or for LIFESCI aficionados you can now send e-MAIL to
RPRLSCI@TECHNION with SUBMIT BIOBIT as the first line of your
text.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
<< The Dave Kristofferson Article >>
The BIONET National Computer Resource for Molecular Biology
David Kristofferson, Ph.D.
BIONET Resource Manager (kristoff@net.bio.net)
BIONET is the national computer network for molecular biology.
It is run as a non-profit service for the scientific community by
IntelliGenetics, Inc. with funding provided by the Division of
Research Resources at the National Institutes of Health (Grant
Number RR01685-06) and also by the individual resource users.
BIONET is used by over 800 laboratories in the U.S., Canada,
Europe, and Japan comprising a total of over 2800 researchers.
These investigators have access to some of the most powerful
software available for nucleic acid and protein sequence analysis.
BIONET also provides scientists with recent releases of the major
molecular biology databanks including those for nucleic acid and
protein sequences. Finally, the BIONET community has access to an
extensive electronic mail and bulletin board system which puts
them in contact with other users of the Resource as well as
scientists on other electronic networks around the world.
The cost of the service to academic or non-profit researchers in
the United States is $400 per year per laboratory. This sum
covers ALL costs including telecommunications with the BIONET DEC
2065 computer via the Telenet or Compuserve public data networks
and unlimited processing time on the computer. (Users outside the
U.S. are not assessed the $400 fee but must pay their own
telecommunication costs.) Because most U.S. colleges and
universities have access to a local Telenet or Compuserve number,
no additional phone charges are incurred when contacting the
BIONET computer. BIONET also distributes free copies of the
public-domain Kermit communications software. Thus, beyond paying
the subscription fee, all a scientist needs is a personal
computer, workstation, or terminal, and a modem to access an
impressive amount of software, information, and communications
facilities. NIH regulations require that each principal
investigator have his/her own account, but subaccounts can be set
up at no extra charge for subinvestigators in the same lab.
Recently, BIONET has received a generous donation of equipment
from Sun Microsystems. This will enable the resource to retire
the aging DEC 2065 and provide increased compute power to its user
community. The new BIONET central resource will consist of a Sun
3/280 file server together with a network of diskless Sun 3/60's.
This configuration will allow for future expansion as BIONET usage
grows. In addition scientists with Sun or VAX computers can
establish "BIONET satellite" computers. These scientists will do
most of their computing locally but will still have network access
to BIONET for the purpose of exchanging electronic mail and
bulletin board notices.
The majority of the software on BIONET consists of the commercial
IntelliGenetics sequence analysis programs. The programs are used
for analyzing nucleic acid and protein sequences. There are
programs for managing large-scale DNA sequencing projects and
several programs that search the major sequence databases to find
sequence similarities and draw the resulting alignments. Two new
programs have recently been added to BIONET: GENALIGN for aligning
several protein or nucleic acid sequences simultaneously and
DDMATRIX for graphical comparison of sequence similarities. The
software also can be used to analyze restriction enzyme data. The
MAP program determines the order of fragments in restriction maps.
The CLONER program uses map data graphically to plan cloning
experiments. Assistance in using the software is available by
calling BIONET's technical support number (415)324-GENE.
Besides the IntelliGenetics programs on BIONET, there is
additional software donated by the academic community. Among the
programs are Roufa's sequence analysis package for the PC, Zuker's
RNA-folding program, Pearson's FASTP, FASTN, and FASTA database
searching programs, and Kanehisa's "Ideas" package. A library of
free PC software is available to users. Besides molecular biology
software the lending library includes communications software,
utilities, and even a free editor program (MicroEMACS).
BIONET has prepared a version of Pearson's FASTA program to run as
a mail server on Sun fileservers. This allows users to conduct
sequence database searches by submitting a query sequence in an
electronic mail message.
BIONET provides access to the latest releases of the GenBank and
EMBL nucleic acid sequence databases in addition to the PIR and
SWISS-PROT protein sequence databanks. Dr. Richard Roberts of the
Cold Spring Harbor Laboratory provides BIONET with his
comprehensive restriction enzyme database. IntelliGenetics
maintains databanks of cloning vectors and consensus sequence
patterns for use with its programs. Finally, several smaller
databases are available on the system.
One of BIONET's main purposes is to foster communication among the
scientists. Researchers can exchange information, manuscripts,
data, etc., with anyone else on an electronic network by using the
electronic mail facility. Electronic mail can be sent to
non-BIONET users via the ARPANET and BITNET computer networks.
Besides individual exchanges through the mail, investigators can
contact a large number of scientists by sending messages to one of
the numerous electronic bulletin boards. Bulletin boards are
available for requesting experimental reagents, for discussing
scientific topics such as oncogenes, gene expression, plant
molecular biology, or molecular evolution, etc., and also for
obtaining information about computer hardware and software.
Recently BIONET joined together with other computer centers to
form an international bulletin board network called BIOSCI. The
network of bulletin boards has been expanded to include
contributions submitted via the University of Uppsala in Sweden,
the SERC Daresbury Laboratory in the U.K., and the Univeristy
College in Dublin, Ireland. Bulletins can be posted to either
BIONET or any of the other three sites. Each site automatically
redistributes its postings to the others as well as to many
readers in their respective regions. This makes it even easier
for scientists on the EARN and JANET networks to post and receive
bulletin board messages. The bulletins are also available from
BIONET on the USENET network for computer systems running the UNIX
operating system.
The usefulness of the BIONET resource has been reflected in its
steady growth. Between 20 to 40 new labs join per month. Sixteen
Telenet ports, six Compuserve ports and six direct dial ports are
available to access the system. Unfortunately, the demand for
time on the system has reached the point where it is causing a
slowdown in response time during peak hours. Sun's equipment
donation is helping to alleviate this problem. The new Sun
configuration will allow the Resource to add new computing
hardware as demand increases. This will allow the resource to
continue to expand and enhance its role as a facilitator of
important discoveries in molecular biology.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Well that was the article and since I am a person who only
gets mail droping into my mailbox, and who has had no hands-on
experiance of running anything on the BIONET. I decided
to ask a few more questions.
I extracted some passages from the above article and asked Dave
Kristofferson to comment on them. Here is the first "electronic
hot pistol" interview
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
<<The Harper intervew>>
>> BIONET also provides scientists with recent releases of the
>> major molecular biology databanks including those for nucleic
acid and protein sequences.
> 1) What are the databases and how are they used?
> Who is the contact person?
The GenBank and EMBL nucleic acid sequence databases are available
on BIONET as well as the SWISS-PROT and PIR (NBRF) protein
sequence databases. A database of restriction enzymes is supplied
by Richard Roberts of Cold Spring Harbor. IntelliGenetics (IG)
supplies its Vectorbank (tm) database of cloning vector sequences
and restriction maps as well as KeyBank (tm), a database of
consensus and other sequence information for use with the IG QUEST
database pattern searching program. In addition to the above, the
"Genetic Variations of Drosophila" database from John Lindsley,
the LiMB database of molecular biology databases (Los Alamos), an
SV40 mutant database (Jim Pipas), and a list of laboratory
protocols (Dr. Bajwa, a BIONET user) are on-line. Access to the
databases is limited to direct logins to the system and requests
for accounts can be directed to the electronic address
bionet@bionet-20.bio.net.
> > Finally, the BIONET community has access to an
> > extensive electronic mail and bulletin board system which puts
> > them in contact with other users of the Resource as well as
> > scientists on other electronic networks around the world.
>
> 2) What does the BBoard look like from the inside... example
> perhaps. (BITNET users only get the messages dropping into there
> mailboxes every now and then)
BIONET users can read bboards by calling the appropriate bboard
file while in the MM mail program. Alternately, they can
"subscribe" to a bulletin board, i.e., arrange to see any new
messages at login. In this later format message headers are
presented as follows at login:
Reading file: METHODS-AND-REAGENTS
Tue, 11 Oct 88 09:23 +1200 CHCHMEDS%otago.ac.nz@RELAY.CS.NET
Lambda Cloning vector
(419 chars; more?)
If the user decides to read the message he/she pushes Y or the
spacebar and the text of the message scrolls across the screen a page
at a time. Pressing N skips to the next message without displaying
the text.
> > The majority of the software on BIONET consists of the commercial
> > IntelliGenetics sequence analysis programs.
>
> 3) Short summary of the programmes that can be used would be useful
> and who to contact for support if you can not get the thing
> to work.
A SUMMARY OF THE INTELLIGENETICS PROGRAMS
(last update 8-23-88 - D.K.)
PROGRAM NAME FUNCTION
------------ -------- [B
GENED Entry (from keyboard, files, or digitizer) and
editing of nucleic acid and protein sequences.
FINDSEQ Searches for and retrieves sequences based on
accession numbers, author names, species names,
organism names, locus names, and keywords.
MAP Generates and displays all possible restriction
maps consistent with restriction enzyme cleavage
data.
SIZER Calculates restriction fragment lengths using
data from digest gels.
GEL Merges overlapping regions from sequencing gels
into a consensus sequence. Maintains a history
of a sequencing project and produces sequence
data files for use in other programs.
SEQ Analyzes nucleic acid sequences. Finds
restriction sites, internal repeats, palindromes,
open reading frames, translates DNA, analyzes base
composition and codon usage, finds homology between
and aligns two similar sequences.
PEP Analyzes polypeptide sequences. Reverse
translates proteins and searches for possible
restriction sites, does Chou & Fasman secondary
structure prediction, determines hydropathicity,
amino acid composition, and molecular weight,
searches for homology between and aligns two
similar sequences.
CLONER Models complex recombinant DNA experiments and
provides detailed recordkeeping of plasmid
constructions. Predicts the results of
restriction enzyme digestions. Tests the results
of insertion direction and insertional
inactivation. Adds biological sites and regions
to recombinant DNA maps. Creates and edits
restriction maps of vectors. If used with a
Tektronix 4014 terminal emulator (see DDMATRIX
below) CLONER will produce graphical output
of plasmid restriction maps, etc.
IFIND Rapidly searches databases for sequences
which are homologous to a given sequence.
Saves the results of a search, displays
histograms of similarity scores, and
aligns two chosen sequences.
QUEST Rapidly searches databases for specified
patterns of characters, keywords, sequences,
nucleotide patterns, etc. Handles Boolean
(AND OR) search patterns. Has a "language"
for handling ambiguous patterns, i.e.,
allows multiple possibilities at specified
positions in the search pattern.
GENALIGN A powerful multiple sequence alignment program
which can align up to 49 protein or nucleic acid
sequences and generate a consensus sequence.
DDMATRIX A dot-matrix homology program for aligning two
sequences. Can work on an alphanumeric terminal,
but a Tektronix 4014 emulator such as found in
the communications software packages Smarterm 240
or PC-Plot IV (IBM PC) or Versaterm (Mac)
will allow better graphical output.
Technical support is available Monday through Friday either by phone
or e-mail to bionet@bionet-20.bio.net.
> > BIONET has prepared a version of Pearson's FASTA program to run as
> > a mail server on Sun fileservers. This allows users to conduct
> > sequence database searches by submitting a query sequence in an
> > electronic mail message.
>
> 4) Short sample session of some BIONET programme
(Most sessions are longer than one would want to read in a mail
message. The following just starts up a program and shows the
HELP facility.)
@seq
> O <
O| |O IntelliGenetics
> O <
SEQ - Sequence Analysis System
For information enter one of these commands after "SEQ:":
Introduction - Gives an overview of this program
? - Lists commands
Help - Lists commands with short explanations
Help topics - Shows a list of informative topics
Help help - Explains how to use on-line assistance
SEQ: help
Here is a menu of all valid "SEQ: " commands:
ALIgn - The rigorous SEQ similarity search
Base-comp - Counts the numbers of each base in a sequence
CODon-tables - Counts codon frequencies in each reading frame
COMment - Displays comments from a specified sequence file
DEFault-parameters - Sets all SEQ parameters to default values
DELete - Delete sequences from SEQ
DIRectory - List files in your or any other directory
DINucleotides - Counts dinucleotides in both frames combined
DOuble-strand-print - Displays DNA sequences and their complementary strands
GEned - Enters the GENED program to edit or enter a sequence
GRipe - Send suggestions or complaints to IntelliGenetics staff
HElp - Print information about a specified command or topic
Introduction - An overview of SEQ and how to use it
LExicon - Finds unique oligonucleotides
LIst - Lists the sequence names with short descriptions
LOad - Enters sequences from files
Match - Sets bases equivalent to each other in SEARCH and ALIGN
Quit - Leaves the SEQ program
RECord - Copies the output of SEQ commands to a file
REStore-parameters - Replaces current parameter settings with those from a file
RETrieve - Loads a single sequence from a specified file
RIch - Find regions containing high levels of sets of two bases
SAve-parameters - Writes current parameter settings in a file
SEarch - Finds regions of DNA that are similar or complementary
SHow-parameters - Lists all the current SEQ parameter settings
SINgle-strand-print - Displays the specified sequences
SITe - Searches for restriction sites, shows maps and fragment lists
SPlice - Combines or fragments specified sequences
TRAnslate - Translates DNA sequences into peptide sequences
TRInucleotides - Counts trinucleotides in all frames combined
Write - Writes sequences or portions of sequences in a file
Help TOPIcs - Typing "Help TOPIcs" will list some help topics which are
not commands.
SEQ: quit
No changes made since last save, file(s) not written.
It's 10 October 1988 17:55:18
Do svedanya!
@
> > One of BIONET's main purposes is to foster communication among the
> > scientists. Researchers can exchange information, manuscripts,
> > data, etc., with anyone else on an electronic network by using the
> > electronic mail facility.
>
> 5) Again I suspect that the MM system is used for PRIVATE
> messaging which never hits the PUBLIC sector (BIOSCI for
> example). It would be nice to know that network activity in
> PRIVATE is as equally active as PUBLIC activity... and are there
> any European users?
MM is used a lot for private messages, far more than for public
postings. I can't give you accurate statistics other than to say
that the MM program is used about 4000 times per month on the
system.
I have mixed emotions about encouraging European users to get on
to our system. Our computer facilities were getting saturated just
trying to handle our load in the Western Hemisphere. Our usual
experience with European accounts is that people request accounts
and then don't use them because of the high telecommunications
costs.
The response on the system varies dramatically from country to
country in Europe. Some people have told me that it is just like
using a computer in the next room while others found it
intolerable.
It would make far more sense to set up counterparts to BIONET in
Europe, Japan, etc., and I would be happy to let people examine
our system for that purpose. Economically it doesn't make sense
for people on your side of the pond to connect all the way over
here to compute.
>> I have mixed emotions about encouraging European users to get on
to our system.
> 6) So what would it need for a European system to be set up?
The EMBL is supposed to be setting up some kind of BIONET-like
facility and the SERC lab at Daresbury is doing likewise although
I really don't know what stage either of these facilities are in.
When we consider the costs to the USA user the $400 is only
charged U.S. users and goes to cover their telecommunications
costs. They have unlimited access to the system for this one
annual fee (no additional phone bills or anything else), but we
found that an average figure of $400 per year per lab covered the
entire U.S. telecommunications bills since we were able to
negotiate volume rates with the Telenet and Compuserve public data
networks. In this respect BIONET is the best offer available in
the U.S. and is why we have always been overburdened and
overworked here. I can not say what the European situation would
be.
Users outside of the U.S. don't pay us anything for their
accounts, but have to cover their own telecommunications costs.
The operating expenses of BIONET are paid for by the NIH (BIONET
is non-profit) and our grant was for about $3.7 million US over
the last five years.
Anyone who does this in Europe will have to come up with some
source of funding. I can forewarn you though that anyone
opening their machine to the outside has to do it with care or
else their current users will have all their CPU cycles robbed
from them. In addition you will be inundated with requests to
sign up for the system and constant questions and demands from
users when you are up and going.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
END OF BIOBIT No 2