BROE@AARDVARK.UCS.UOKNOR.EDU (Bruce Roe) (07/07/89)
We all live and die by the peer review system and the rules established by the NIH for the review process. Be that as it may, what do we now do to maintain a National Network for BioComputing? I suggest that for the present, The NIH could modify its contract with GenBank to provide the funding necessary for continuing the following, much needed services at a National Resource Level, maybe through the Human Genome Project (to suggest one source of funds). 1. National access to and the programs needed to search the latest GenBank, EMBL, and NBRF data bases for sequence similarities, etc. 2. A national mail network devoted to similar topics as BIONET was. 3. An ftp facility to distribute timely (eg. weekly) updates to the three major data bases and serve as a distribution center for public domain programs useful for those interested in molecular biology, evolution, etc. The former is more important to me than the latter. What is needed is for those of us who have been silent up to now to find out who to contact to voice our displeasure, outrage and inability to do our research if a BIONET-like facility is not available for a low-cost and at one location with national access. I suggest that one person to contact is Dr. Jim Cassett, the Program Project Officer at the NIH responsible for GenBank. Maybe he can do something if enough of us contact him. Dr. Cassett's e-mail address is CZJ@NIHCU.BITNET Let's get moving and see what can be done. Bruce A. Roe, Professor of Chemistry and Biochemistry University of Oklahoma, Norman, OK 73019
gilbertd@silver.bacs.indiana.edu (Don Gilbert) (07/08/89)
BioNet goals (from "The BIONET(tm) Resource" manual, page 1): (1) To provide computational assistance in data analysis and problem solving to molecular biologists and researchers in related fields. (2) To serve as a focus for development and sharing of new software. (3) To promote rapid sharing of information and collaboration among the community of scientists. I read Dr. Kristofferson's notice about the failure of NIH to renew funding for BioNet. It is distressing news, because BioNet is the _only_ resource providing the above services (2) and (3), and the only one providing a complete molecular biology computational service (1) on national basis, that I am aware of. Many other people I have talked with are similarly at a loss to know where to turn for these needs. It may have been suggested by the NIH reviewers that computational assistance can be met by computers and software purchased by each local researcher or group of researchers. That may be a nice dream but is not achievable by many of those who need molecular biology computing services. The stumbling blocks are hardware and software costs, and lack of personnel trained in biocomputing software to assist researchers. Indiana U molecular biologists recently spent $55K for VAX computer, and are currently spending $40K/year on personnel to manage it (me), software and maintenance. I now have people calling from off- campus to get accounts on our VAX because BioNet is shutting down. I don't have time or resources to do the job that BioNet is doing! Is it cost-effective for NIH to fund such local setups at all universities? David Kristofferson stated: "Unfortunately the BIONET Resource was not recommended for further "funding primarily due to the opinion of the site committee that the "requirement for a strong research program had not been met." I don't know what the committee's criteria for strong research program were, but goals (2) and (3) of BioNet are as strong a stimulus to my research as they could provide. My "research" involves developing software for molecular biology, for use on Macintoshes, VAXes, and any UNIX box, including Crays. I have made two of these programs available at Bionet and plan (or planned) to make several more available in the next few years. I also have been encouraging other developers to drop their programs there. There is no other good national repository of molecular biology software. Some individuals, schools, or clubs collect software and make it available at meetings, but it is very hard to find and get hold of. While there are other molecular databanks, Bionet has the nice feature of allowing _user_ involvement, meaning I can contribute my software or database directly, in the form I believe is most useful to others. Without BioNet, I have no good way to contribute my software to the world. No, I don't need their computer to do research on. Any developer now a days has a good Mac or PC that is 1000x faster to develop on than a multi-user computer. Yes, I do need BioNet to archive and distribute my research. I need people to use it, to test it and find bugs. My other distribution options are limited: a long delayed paper report in some journal such as CABios which doesn't actually distribute the software, it just tells people to bother me with requests (then we go through a dance of what format the sender and receiver can both handle). We all need a national (or world) archive and news center for molecular biology data and software. Without such a resource as Bionet, which handles all three areas specified above as the BioNet goals, molecular biology computing will flounder and be set back several months (a month in computing is a year in other areas) or years. Developers won't have anywhere to contribute software. People who need to find this or that software won't know where to look. The community of researchers, developers, users, and others that BioNet is fostering, and it is a _growing_ resource, will disappear. Don Gilbert BioComputing Office <BitNet> GilbertD@IUBACS <InterNet>GilbertD@Gold.Bacs.Indiana.Edu <other > Biology Dept., Indiana Univ., Bloomington, IN 47405 USA
kramer@bionette.ucs.orst.edu (Jack Kramer -- Biochem) (07/08/89)
Is there any way to get a list of all financial affiliations, with potentially benefitting competitors of BIONET, of all those at NIH who helped make the decision to shutdown the resource. Since there is no rational basis for a decision such as this maybe we should look for other reasons. Perhaps "60 Minutes" may be interested.
steeg@ai.toronto.edu ("Evan W. Steeg") (07/08/89)
Dr. Davison,
I would like to add my voice to the chorus of disappointment
over the proposed loss of the BioNet. I appreciate the concerns
of the several scientists from small biological sciences labs who
need the BioNet software and databases in order to tackle
computationally tough tasks. I am actually in a sort of opposite
situation. I am a computer science grad student, with access to the
biggest and best in computer software and hardware, but without the normal
access to information and contacts in the biological sciences community.
I am very interested in, and have worked on, applying advanced computer
techniques to problems in biochemistry, and I rely on the communications
services of the BioNet -- the e-mail and the newsgroups -- to keep
me informed and connected. Not being in a biochemistry department,
I don't see biological abstracts and conference announcements posted
around me every day, but I do have access to the newsgroups, and
I would hate to lose this service.
In a time when there is so much talk about interdisciplinary
science and the need for cooperation and communication in solving
huge problems (mapping the human genome, molecular structure
prediction, finding an AIDS vaccine, etc.), it is ironic and
sad that shortsighted policymaking will take away the BioNet,
a major resource for interdisciplinary and international
communication and research.
-- Evan
--
Evan W. Steeg (416) 978-7321 steeg@ai.toronto.edu (CSnet,UUCP,Bitnet)
Dept of Computer Science steeg@ai.utoronto (other Bitnet)
University of Toronto, steeg@ai.toronto.cdn (EAN X.400)
Toronto, Canada M5S 1A4 {seismo,watmath}!ai.toronto.edu!steeg
--
Evan W. Steeg (416) 978-7321 steeg@ai.toronto.edu (CSnet,UUCP,Bitnet)
Dept of Computer Science steeg@ai.utoronto (other Bitnet)
University of Toronto, steeg@ai.toronto.cdn (EAN X.400)
Toronto, Canada M5S 1A4 {seismo,watmath}!ai.toronto.edu!steegKristofferson@BIONET-20.BIO.NET (David Kristofferson) (07/09/89)
Due to my direct connection with the BIONET Resource, it is inappropriate for me to be expressing my personal feelings on the outcome of our review in this public forum. However, I do want to state publicly that I feel no rancor towards members of the site team, and I *strongly* deplore in no uncertain terms any attempts to suggest that our site visit was improper. To prevent such uninformed speculations, I will present a few matters of fact as objectively as possible. Members of the site team and I are not at liberty to discuss details of the review, but the decision made appears to follow the letter of the law of DRR regulations, although opinions on the interpretation of these regulations are not unanimous. After seeing how the rules were finally applied in practice during our review we decided that our odds for approval would increase if we withdrew the first application and submitted a new application, since a substantial portion of our in-house research was omitted from the first application and submitted to another agency for reasons that I cannot detail here. However, it is still a requirement under DRR regulations to have an in-house research program. Unfortunately due to budgetary restraints and the demands placed on our staff in running a Resource which has continually increased its available services and grown by 200 labs a year on average for the last five years, it is virtually impossible to do both. Unless one actually tries to run a service the size of BIONET, it is hard to understand the amount of effort involved. As there are few, if any, other molecular biology computing resources the size of BIONET, there are no true "peers" to appreciate this fact. (This response for that matter is being composed on a portable computer via Telenet in Tehachapi, California at the edge of the Mojave Desert while I am supposedly on vacation!) For these reasons trying to continue to force fit a primarily service-oriented organization such as BIONET into the Research Resource mold does not seem appropriate. We are appreciative of the support provided to us during our first five years by the DRR, but the almost dialectical logic has run its course. The bottom line is that the decision was made according to the regulations as explained to the reviewers. In this sense it was "rational" and no other motives should be read into it. If this message still doesn't answer all of your questions, take solace in the fact that it wasn't intended to. Sincerely, Dave Kristofferson BIONET Resource Manager kristoff@net.bio.net -------
c_rawlings%UK.AC.ICRF@CUNYVM.CUNY.EDU (Chris Rawlings) (07/11/89)
Dear Jim and Dan,
I would like to express my support for the continuation of the BIONET
service or an equivalent US national computing resource for molecular
biologists.
It seems somewhat paradoxical that NIH should intend to remove all support
from BIONET at this time when they are increasing their support for
molecular biology computing on many other fronts (e.g. MBCRR, NLM etc).
Everyone seems to agree that developing better computational tools
for experimental molecular biologists is essential for the future success
of molecular genetics, in particular in view of the US committment to the
human (and other) genome projects. Developing new software is one thing;
making sure that it is used by the people who need it is another.
The BIONET resource has provided a very valuable service to the
international molecular biology and bioinformatics community at a
critical time in its development. That critical period is not yet over
and I believe there will be a continuing need for centralised services
such as BIONET until such time (if it ever comes) when we all have
high quality software and research biologists put a proportionate amount
of effort into understanding and using their computational tools as they
currently do into learning laboratory techniques.
The strengths of BIONET, and areas that I think should be considered for
continued support on a national level are:
Support for Occasional Users:
It is to be expected (at the moment) that scientists whose major
research interests come from their experimental science will be
relatively infrequent users of computational analysis tools.
Those of us who spend most, or all, of our working time
at a computer terminal easily forget how difficult it is for
occasional users to keep their (often patchy) knowledge of computing
and software up to date. I suspect that the stereotypical BIONET
user falls into this category and needs and appreciates the level
of user-support and documentation that has been provided.
A centralised service with a committment to the occasional or
novice user seems the most cost effective way of supporting large
sections of todays molecular biology community.
Software Archive:
A central software archive and the opportunity to try recently
developed methods is a valuable service to both biocomputing
specialists and the molecular biology research community in
general.
Up-todate databases:
There are still relatively few sites that have the resources to
maintain fully up to date molecular sequence and structure databases.
A centralised service provides a cost effective way to give easy access
to the rapidly growing databases.
Specialist services:
There will inevitably be services, software, databases or using
specialist computer hardware that can only reasonably be offered
by central resources.
Bulletin board and Electronic Community:
Perhaps the hardest benefits to quantify, and the most difficult for
outsiders to see are those that accrue through the sharing of
experience and informal exchanges that occur in a community served
by an electronic conferencing/bulletin board service. The
central role played by BIONET in the development of the BIOSCI
bulletin boards has been essential in bringing these benefits to
the biology community.
International Links:
Many of us outside the US have found BIONET and more
recently BIOSCI an essential link to colleagues in the US and
I hope that this is reciprocated. The human genome (and
other genome) projects *have* to be international
and the demise of BIONET means a step backward for the
mechanisms of realising these projects as "Laborartories without
frontiers".
The need for support of all these issues have been recognised in the UK
and we now have a small-scale service (by BIONET standards) called
SEQNET funded centrally by the UK Science and Engineering Council. The
rapid growth in the number of SEQNET users bears out the experience at
BIONET that there is a considerable need for such national resources by
the research community. Plans are also being hatched in the CEC for a
European Bio-Informatics network linking national nodes such as SEQMET
that would provide many of the same types of service as BIONET does.
It seems then ironic that at a time when the rest of the world is at last
recognising the scientific and economic arguments for nationally coordinated
biocomputing resources, the US/NIH seems to undervalue the importance of
its own achievments and to underestimate the needs of its own molecular
biology research community.
The usual disclaimers apply; these are my personal opinions and should not
taken as the official views of the Imperial Cancer Research Fund.
Regards
Chris Rawlings
===========================================================================
C. Rawlings
Biomedical Computing Unit
Imperial Cancer Research Fund
JANET: c_rawlings@uk.ac.icrf
EARN/BITNET: c_rawlings%uk.ac.icrf@ukacrl.bitnet
NSFNET: c_rawlings%uk.ac.icrf@nsfnet-relay.ac.uksteeg@ai.toronto.edu ("Evan W. Steeg") (07/11/89)
A few days ago I posted a note in which I criticized and lamented
the possible loss of the BioNet facilities. In particular, I
discussed the importance of the communications resources currently
made available by the Bionet, and how unfortunate it would be -- for
individual scientists and for the state of biological research -- if
this conduit for international and interdisciplinary communication
were to vanish.
I hope I did not convey the impression that the communications
activities on Bionet -- the e-mail and the newsgroups -- could not or
would not be replaced. In theory, nobody should lose any
communications functions permanently, though, in practice, there could
be severe disruptions, and it was this unnecessary disruption that
concerned me.
In particular, the Bionet users should be aware that**:
1) Usenet is a self-supporting communications net.
2) The European and Australian bboard systems that receive Bionet
messages pay for their own access.
3) Several of the biological science journals post their tables of
contents to Bionet free of charge.
Therefore, several key communications links and functions are paid
for by parties other than Bionet. Moreover, there is no *technical*
reason why these functions couldn't be handled by the Usenet and
bboards directly. My point in my previous letter was simply that
technical feasibility does not always imply simple, efficient, and
timely implementation. With such a large distributed network, serving
many people (of varying computer proficiency) with many functions,
there are likely to be delays and glitches.
My gut feeling on this was: If it ain't broke don't fix it. The
"activation energy" needed to carry the transition through is likely
to be very high. Who needs it?!
But, if this transition must happen, let's make it as smooth as
possible. Perhaps administrators of the various subnets and bulletin
boards will post some hints/instructions. As for the software
resources of Bionet, perhaps the managers can arrange for some space
on the Stanford Sumex machine (Stanford U. is geographically close to
Bionet's home), so that users can have ftp access to contributed
software. This would ease the transition.
Thanks for your attention (sorry for posting such long notes!).
-- Evan
**I am fairly confident, though not 100% certain, of these claims about
the networks. My understanding of the workings was corroborated by
several people well-versed in computer bboards and networks. I do not
work for Bionet, the company that manages it, nor any competitors.
And, of course, I do not speak for the University of Toronto.
--
Evan W. Steeg (416) 978-7321 steeg@ai.toronto.edu (CSnet,UUCP,Bitnet)
Dept of Computer Science steeg@ai.utoronto (other Bitnet)
University of Toronto, steeg@ai.toronto.cdn (EAN X.400)
Toronto, Canada M5S 1A4 {seismo,watmath}!ai.toronto.edu!steeg
--
Evan W. Steeg (416) 978-7321 steeg@ai.toronto.edu (CSnet,UUCP,Bitnet)
Dept of Computer Science steeg@ai.utoronto (other Bitnet)
University of Toronto, steeg@ai.toronto.cdn (EAN X.400)
Toronto, Canada M5S 1A4 {seismo,watmath}!ai.toronto.edu!steegSCHWARTZ@BIONET-20.BIO.NET (IRA S. SCHWARTZ) (07/13/89)
I have just completed sending a message to Jim Cassatt at NIH regarding my dismay at the imminent loss of the resources of BIONET. As others already have, I urge you to make your voices heard on this matter. Maybe we can prevent this disaster. Be that as it may, it is necessary to make plans for life after BIONET. I would appreciate hearing from you as to your plans for replacing BIONET's services. What are the alternatives? Are there other outfits that provide similar sequence analysis and searching capabilities? What are the best microcomputer alternatives to BIONET's programs? If any of you have struggled with these questions and have some ideas please share them with the rest of us. Ira Schwartz Dept. of Biochem. & Mol. Biol. New York Medical College Valhalla, NY 10595 (914)993-4064 schwartz@bionet -------