From owner-gcg@net.bio.net Tue May 04 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: A.J.Bleasby@daresbury.ac.uk ("A.J. Bleasby") Newsgroups: bionet.software.gcg Subject: Test of INFO-GCG@DARESBURY. Ignore Message-ID: <1993May5.194623.28027@gserv1.dl.ac.uk> Date: 5 May 93 19:44:58 GMT Sender: list-admin@daresbury.ac.uk Reply-To: ajb@cxa.daresbury.ac.uk Distribution: bionet Lines: 3 Original-To: info-gcg@uk.ac.daresbury Alan Bleasby SERC Daresbury Laboratory From owner-gcg@net.bio.net Wed May 05 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: kristoff@net.bio.net (Dave Kristofferson) Newsgroups: bionet.software.gcg Subject: test of info-gcg@daresbury.ac.uk Message-ID: <1993May6.204010.25540@gserv1.dl.ac.uk> Date: 6 May 93 20:40:13 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 2 Original-To: info-gcg@uk.ac.daresbury test, please ignore From owner-gcg@net.bio.net Wed May 05 23:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software.gcg Subject: test of bionet.software.gcg Message-ID: Date: 6 May 93 20:41:10 GMT Organization: BIOSCI International Newsgroups for Biology Lines: 2 test of USENET group From owner-gcg@net.bio.net Wed May 05 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (Dave Kristofferson) Newsgroups: bionet.software.gcg Subject: test of info-gcg@net.bio.net Message-ID: Date: 6 May 93 20:39:34 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 4 This group is not yet operational. Please await the opening announcement before posting. From owner-gcg@net.bio.net Wed May 05 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: A.J.Bleasby@daresbury.ac.uk ("A.J. Bleasby") Newsgroups: bionet.software.gcg Subject: TFurther Daresbury Test. Ignore Message-ID: <1993May6.100840.9210@gserv1.dl.ac.uk> Date: 6 May 93 10:06:42 GMT Sender: list-admin@daresbury.ac.uk Reply-To: ajb@cxa.daresbury.ac.uk Distribution: bionet Lines: 5 Original-To: info-gcg@uk.ac.daresbury Test. Please ignore. Alan Bleasby SERC Daresbury Laboratory From owner-gcg@net.bio.net Wed May 05 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!gatech!concert!news-feed-1.peachnet.edu!umn.edu!tsp.med.umn.edu!nrd From: nrd@tsp.med.umn.edu (Neal Dalton) Newsgroups: bionet.software.gcg Subject: GCG and GENBANK Message-ID: Date: 5 May 93 22:32:46 GMT Sender: news@news2.cis.umn.edu (Usenet News Administration) Organization: University of Minnesota Lines: 12 Nntp-Posting-Host: tsp.med.umn.edu X-Newsreader: TIN [version 1.1 PL9] I just built GCG 7.1 or 7.2 (it was patched code) and tried to make the entire GENBANK by hand. I added the new database entries and tried to build it. Everything was fine except for HIV. I get: *** No Accession Number for sequence "0HIVHAN". *** No Accession Number for sequence "0HIVJRFL". Should there be Accession Numbers for these? Neal nrd@lenti.med.umn.edu From owner-gcg@net.bio.net Thu May 06 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: A.J.Bleasby@daresbury.ac.uk ("A.J. Bleasby") Newsgroups: bionet.software.gcg Subject: Further test of info-gcg@daresbury Message-ID: <1993May7.232255.6371@gserv1.dl.ac.uk> Date: 7 May 93 22:50:19 GMT Sender: list-admin@daresbury.ac.uk Reply-To: ajb@cxa.daresbury.ac.uk Distribution: bionet Lines: 11 Original-To: info-gcg@uk.ac.daresbury I apologise for the plethora of test postings to this group. We are ironing out an aliasing bug which has been causing some confusion between `bionet.software' and `bionet.software.gcg'. Please bear with us. This *MAY* be the last test posting Alan Bleasby SERC Daresbury Laboratory Warrington WA4 4AD UK From owner-gcg@net.bio.net Thu May 06 23:00:00 1993 Path: biosci!daresbury!news!ajb From: ajb@s-crim1.dl.ac.uk (Alan Bleasby) Newsgroups: bionet.software.gcg Subject: Test on bionet.software.gcg Message-ID: Date: 8 May 93 00:30:38 GMT Distribution: bionet Organization: SERC Daresbury Laboratory, Warrington, UK Lines: 8 NNTP-Posting-Host: s-crim1.dl.ac.uk Please ignore. Apologies for the plethora of test messages in the creation of this group. More may unfortunately follow until some technical difficulties are sorted out. No other groups are affected. Alan Bleasby SERC Daresbury Laboratory From owner-gcg@net.bio.net Fri May 07 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: A.J.Bleasby@daresbury.ac.uk ("A.J. Bleasby") Newsgroups: bionet.software.gcg Subject: Yet another test of info-gcg@dl. Apologies again Message-ID: <1993May8.012530.8721@gserv1.dl.ac.uk> Date: 7 May 93 23:39:08 GMT Sender: list-admin@daresbury.ac.uk Reply-To: ajb@cxa.daresbury.ac.uk Distribution: bionet Lines: 3 Original-To: info-gcg@uk.ac.daresbury Ignore AJB From owner-gcg@net.bio.net Fri May 07 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: A.J.Bleasby@daresbury.ac.uk ("Alan Bleasby") Newsgroups: bionet.software.gcg Subject: Test: ignore Message-ID: <1993May8.014424.9206@gserv1.dl.ac.uk> Date: 8 May 93 00:54:29 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 3 Original-To: info-gcg@uk.ac.daresbury AJB Daresbury From owner-gcg@net.bio.net Fri May 07 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: A.J.Bleasby@daresbury.ac.uk ("Alan Bleasby") Newsgroups: bionet.software.gcg Subject: Another info-gcg@daresbury test. Delete Message-ID: <1993May8.015143.9505@gserv1.dl.ac.uk> Date: 8 May 93 01:14:03 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 5 Original-To: info-gcg@uk.ac.daresbury Investigations continue. Alan Bleasby SERC Daresbury Laboratory From owner-gcg@net.bio.net Sat May 08 23:00:00 1993 Path: biosci!daresbury!daresbury!not-for-mail From: mbpcr@s-crim1.dl.ac.uk (A. Parsons) Newsgroups: bionet.software.gcg Subject: Re: Further test of info-gcg@daresbury Message-ID: <1sk061INN1k4@s-crim1.dl.ac.uk> Date: 9 May 93 22:21:53 GMT References: <1993May7.232255.6371@gserv1.dl.ac.uk> Distribution: bionet Organization: Daresbury Lab., Warrington, U.K. Lines: 15 NNTP-Posting-Host: s-crim1.dl.ac.uk In article <1993May7.232255.6371@gserv1.dl.ac.uk> ajb@cxa.daresbury.ac.uk writes: > >I apologise for the plethora of test postings to this group. We are >ironing out an aliasing bug which has been causing some confusion >between `bionet.software' and `bionet.software.gcg'. > >Please bear with us. This *MAY* be the last test posting > >Alan Bleasby >SERC Daresbury Laboratory >Warrington WA4 4AD >UK Wrong! ;-) From owner-gcg@net.bio.net Fri May 14 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: A.J.Bleasby@daresbury.ac.uk ("A.J. Bleasby") Newsgroups: bionet.software.gcg Subject: Test of Mail->News at DL Message-ID: <1993May15.185601.22524@gserv1.dl.ac.uk> Date: 15 May 93 18:54:48 GMT Sender: list-admin@daresbury.ac.uk Reply-To: ajb@cxa.daresbury.ac.uk Distribution: bionet Lines: 1 Original-To: info-gcg@uk.ac.daresbury Original-Cc: ajb Test. Please ignore From owner-gcg@net.bio.net Fri May 14 23:00:00 1993 Path: biosci!daresbury!news!ajb From: ajb@s-crim1.dl.ac.uk (Alan Bleasby) Newsgroups: bionet.software.gcg Subject: Test of NEWS->email at DL. Ignore Message-ID: Date: 16 May 93 03:22:07 GMT Distribution: bionet Organization: SERC Daresbury Laboratory, Warrington, UK Lines: 7 NNTP-Posting-Host: s-crim1.dl.ac.uk Apologies again for the software problems. If this works all is well and an official announcement will be posted. Alan Bleasby SERC Daresbury Laboratory UK From owner-gcg@net.bio.net Sat May 15 23:00:00 1993 Path: biosci!daresbury!news!ajb From: ajb@s-crim1.dl.ac.uk (Alan Bleasby) Newsgroups: bionet.software.gcg Subject: INFO-GCG: Daresbury tests over + explanation Message-ID: Date: 16 May 93 09:36:08 GMT Distribution: bionet Organization: SERC Daresbury Laboratory, Warrington, UK Lines: 28 NNTP-Posting-Host: s-crim1.dl.ac.uk Please don't post to this group until the official announcement (already sent to bionet.announce) appears and until the introduction by the group discussion leader is posted. HOWEVER, The reason for all these tests was due to an `alias' feature of the NEWS<->email gateway caused by the NEWS heirarchy i.e. bionet.software bionet.software.gcg This is the first time such a structure has existed on bionet (e.g. the structure is different from bionet.molbio.x and bionet.molbio.y) The gateway software has never (to our knowledge) caused any LISTSERV-type (or other) bounces so we were loathe to apply any hasty patches to solve the heirarchy problem [ergo the tests]. Having said that, some minor tweaking of headers may be necessary at this end over the next few weeks but this will not affect routine operation of the group. Thanks once again for your forebearance. Rgds Alan Bleasby SERC Daresbury Laboratory Warrington WA4 4AD UK From owner-gcg@net.bio.net Sun May 16 23:00:00 1993 Path: biosci!lldmpc.dnet.dupont.com!mitchkf From: mitchkf@lldmpc.dnet.dupont.com Newsgroups: bionet.software.gcg Subject: subscription Message-ID: <9305171551.AA18302@esds01.es.dupont.com> Date: 17 May 93 15:51:32 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 3 Please add my name to the list of subscribers to INFO-GCG -Ken From owner-gcg@net.bio.net Sun May 16 23:00:00 1993 Path: biosci!parc!decwrl!decwrl!concert!gatech!howland.reston.ans.net!zaphod.mps.ohio-state.edu!menudo.uh.edu!tamsun.tamu.edu!bioch.tamu.edu!whitsitt From: whitsitt@bioch.tamu.edu (Mark S. Whitsitt, N5RJF) Newsgroups: bionet.software.gcg Subject: stringsearch batch jobs Message-ID: <17MAY199317433948@bioch.tamu.edu> Date: 17 May 93 23:43:00 GMT Reply-To: mwhitsitt@tamu.edu Organization: Texas A&M University, Biochemistry Department Lines: 13 NNTP-Posting-Host: bioch.tamu.edu News-Software: VAX/VMS VNEWS 1.41 I am wondering if anyone has written or knows of a VMS command file or executable which will automate the submission of stringsearches etc. as batch jobs. The GCG package we use does not have the '/batch' option for stringsearch and the users of the computers in our lab are not necessarily able or interested in learning how to create command files for batch submission. I can write this myself, but figured, why reinvent the wheel? Thanks Mark S. Whitsitt, N5RJF Texas A&M University, Dept of Biochemistry Internet: mwhitsitt@tamu.edu College Station, Tx. 77843-2128 AMPRnet: n5rjf@n5rjf.ampr.org (409) 845-0832 Packet/APLINK: N5RJF @ KE5HE.TX.USA.NA From owner-gcg@net.bio.net Sun May 16 23:00:00 1993 Path: biosci!CUCCFA.CCC.COLUMBIA.EDU!MARK From: MARK@CUCCFA.CCC.COLUMBIA.EDU (T. Mark Reboul) Newsgroups: bionet.software.gcg Subject: Credit where credit is due Message-ID: <930517122630.58c7@CUCCFA.CCC.COLUMBIA.EDU> Date: 17 May 93 16:26:30 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 7 Thanks to John Cargill for his support of INFO-GCG@UTORONTO over the years! Mark Reboul Columbia University Columbia-Presbyterian Cancer Center Computing Facility mark@cuccfa.ccc.columbia.edu From owner-gcg@net.bio.net Mon May 17 23:00:00 1993 Path: biosci!AARDVARK.UCS.UOKNOR.EDU!BROE From: BROE@AARDVARK.UCS.UOKNOR.EDU (Bruce Roe) Newsgroups: bionet.software.gcg Subject: Thanks John Message-ID: <9305181349.AA19431@net.bio.net> Date: 18 May 93 13:13:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 6 Hi, Just another voice giving praise to John Cargill for his work to establish and maintain INFO-GCG@UTORONTO Thanks John and good luck with your future work. Bruce broe@aardvark.ucs.uoknor.edu From owner-gcg@net.bio.net Mon May 17 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: ROUCHDA@VAX1.COMPUTER-CENTRE.BIRMINGHAM.AC.UK (Duncan Rouch) Newsgroups: bionet.software.gcg Subject: VADMS and Other Horses Message-ID: <1993May18.193315.21327@gserv1.dl.ac.uk> Date: 18 May 93 20:34:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 221 Original-To: INFO-GCG@UK.AC.DARESBURY VADMS and Other Horses >Message-ID: >Date: Wed, 12 May 1993 10:27:00 PST >From: "Steve Thompson: VADMS genetics" >Subject: Not to beat a dead horse, but, more VADMS ... The proposed change to the VADMS biocomputing service is a complex local problem but involves clear general issues about how a biocomputing service should be run, as Steve pointed out previously. VADMS seems to fit the view that "if it ain't broken then don't fix it", but the budget blues and some institutional logic demand otherwise. I present selected sections of the administration response included in Steve's posting, and comment on the proposed action. I look here at three major issues that are relevant to many computing services: (1) whether the service or an education/research department should teach the science involved in the computing methods; (2) whether an important front-line user support position should be eliminated to help with reducing the institution's budget, and the role of institutional politics in this; (3) charging for services. >In response to the onslaught of support letters Central Administration sent the >following political no-speak announcement out to all whom sent letters in: > > From: WSUCSC PROFS Administrator > SUBJECT: VADMS Reconfiguration All PROFS News Announcement 1. WHO TEACHES? > Thus, it became apparent that the original mission > developed for the VADMS Center, one of research and service, had now > shifted to service and teaching. That is a typical piece of institutional logic, which argues for at least a change in funding source, and in addition apparently justifies hiving off the education function of VADMS. > And since ORU's do not have the > academic oversight appropriate for teaching functions, it was our > judgment that the Center's teaching function be shifted to an academic > unit such as the Department of Biochemistry and Biophysics. Who should perform the teaching? This is a central efficiency/budget issue. First we must define the two types of teaching involved: (1) Training molecular biologists in how to use the complex array of programs and services offered by the computing facility; (2) Educating molecular biologists in the science relating to the programs, to help them set appropriate input parameters and interpret the results; in other words, to integrate biocomputing methods into the scientific research these people are carrying out. The computing service must be responsible for training molecular biologists to use the facilities, since this is where the relevant expertise is centred and where feedback must return for maintaining the service as responsive to user needs [1]. For the second type of teaching, educating in the science involved, there are related efficiency and budgetary reasons why this is usually best performed by the research/education departments of an institution, and not the computing service: (1) Departments have facilities and support for educating. An education need requires proper recognition and support for it to be properly dealt with. Further, the collective educating skills of a department can be called on and centralized education brings economies of scale. Department-based biocomputing education may also be better integrated into the general education of molecular biologists than that from an interdepartmental computing service. (2) Departments may get funds directly for educating, perhaps in proportion to the number of students. In contrast an interdepartmental computing service normally does NOT bring in education funds. So, for an institution that has both research and education functions, training for how to run programs is usually most efficiently performed by the computing service and educating in the science of the computing methods by the departments. 'Most efficiently' can be defined as doing the best job given the available resources. Thus when there is a squeeze on budgets it may be even more desirable than normal that the two types of teaching are divided as suggested. For a site where the two teaching types are not yet in place they would likely be best divided. In contrast, the decision is not all that clear cut if the computing service, such as VADMS, has a successful past history of teaching in both areas, due to favourable local factors: "if it ain't broke then don't fix it". It is unclear from the administrative response about VADMS whether they understand the difference between the two types of teaching. Assuming they only plan to transfer the science education type of teaching from VADMS to an academic department then this appears to be not an unreasonable decision. An underlying consequence of transferring some functions from VADMS to an academic department is that it renders less drastic the affect on computing facilities of eliminating one of the staff positions at VADMS. Thus we can conclude there are two reasons for shifting the science education function from VADMS to an academic department: (1) the notional higher efficiency of education by an academic department; and (2) reduced effect on performance of the computing service by a potential staff cut. Both reasons provide enhanced justification when the aim is to reduce the budget. Such reasoning may apply to other computer centres in a similar position. In counterpoint, a non-teaching, research-only, institution would need a highly integrated service and education/training facility, as occurs for example with the biocomputing service of the Agricultural and Food Research Council (AFRC) in the UK. 1.1 INTEGRATING TRAINING AND EDUCATION Having argued that service/training and education functions may best be split where an institution has education facilities, however, VADMS shows the advantages of highly integrating these functions. This supports the argument that when the education and service/training functions are split there must be a close liaison between the two. This is not all that easy to do, and requires some imagination and commitment. One type of solution revolves around the education personnel spending time in both their home department and at the computing service. Also, appropriate course units can be jointly run by training and education personnel. (For a larger service than VADMS the converse can be useful, to place user support personnel from the service for part of their time in the academic education/research departments.) 2. KEEPING FRONT-LINE USER SUPPORT, WITH POLITICAL HELP > In the meantime, we value your > ideas and counsel on a future course of action--one that will assist > the University with its budget shortfall without extraordinarily > depriving WSU faculty and students of needed services. Unfortunately, but not surprisingly, the 11th commandment holds, the budget is always the bottom line. To negotiate with an institutional administration you have to speak their language. Since computer services in general receive no funds for education or research it is difficult to negotiate directly. Without self-funding such services are dependant on institutional political support to gain funds from the institution. So, maintaining an interdepartmental computer service requires interdepartmental political support. Mobilizing molecular biologist users on-site as well as their departmental heads to support the facility is important [1]. The dangers of underfunding a computer service, and in particular eliminating front-line user support, have been pointed out previously [2]. However, for VADMS the Systems and Computing unit fund Susan Johns' molecular modelling support job, and they have suggested one of the two jobs should go. It seems therefore that the modelling support might not survive without some good on-site political support. 2.1 A POLITICAL GAME > ... VADMS has not been successful in attracting research funds or > in instituting a system for recovering partial costs through user fees, > despite encouragement from administration. They have you here Steve :-( , even if it was impractical for VADMS to introduce user fees. Apparent recalcitrance on the part of the organization being reviewed is a standard political tactic to justify making the changes the reviewers want. 3. CHARGING > To make up the difference between the $51,944 and $40,000, we > suggested a $100/year user fee for the >100 users on campus and > elsewhere. This fee might be assessed once yearly like a subscription > service fee .... This is a reasonably mild charging strategy, given the five general ways to obtain funds for a facility (with no direct research or teaching derived income). These are listed in order of increasing effect on individual molecular biologist users: (1) Central subscription; (2) Departmental subscription; (3) User subscription; (4) User charged per service, but with free time (to promote learning) (5) User charged for all services. $100/year for a molecular biologist is not a lot, more like an introductory offer to smooth the way. Expect a significant increase next year. Several comments in the discussion about VADMS have been made to the effect that general charging for computer services is inevitable. This may be so, however, it is important to keep in mind there are different ways to charge user molecular biologists, and these alternatives have differing affects on the efficiency of the scientific research being supported by the services. Some strategies have more deleterious consequences for research efficiency than others [2]. We must be prepared to argue whether charging is necessary, and if so, for the best choice of charging strategy. Well, Steve, this may be not all to your liking but I hope it helps. Duncan Rouch Molecular Biology Computing Group, Birmingham UK. References 1. Duncan Rouch & Tim Littlejohn (Bio-Soft, March 1993; BINARY, 1993 5:50-53). What Makes a Successful Biocomputing Service. 2. Duncan Rouch & Tim Littlejohn (Bio-Soft, May 1993; BINARY, 1993 in press). Future of Academic Biocomputing Services. From owner-gcg@net.bio.net Mon May 17 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!howland.reston.ans.net!noc.near.net!uunet!destroyer!cs.ubc.ca!unixg.ubc.ca!kakwa.ucs.ualberta.ca!news From: cup@bones.biochem.ualberta.ca Newsgroups: bionet.software.gcg Subject: database retrieval Message-ID: <1993May18.180310.22644@kakwa.ucs.ualberta.ca> Date: 18 May 93 18:03:10 GMT Sender: news@kakwa.ucs.ualberta.ca Reply-To: cup@bones.biochem.ualberta.ca Organization: University of Alberta Lines: 29 Nntp-Posting-Host: mac02.biochem.ualberta.ca Hi, I hope this newsgroup is open for teh public!! Just seen tests so far. I've just installed GCG for our dept and have to support it for a bunch of people who previously used the IG-Suite (it's on UNIX). Before I reinvent the wheel, does anyone have a set of examples/tutorials they'd be willing to share? Also, does everyone make do with stringsearch and names for retrieval from the databases or is there a better way? One of the redeeming features of the IG-Suite was "findseq" a great program for getting into the databases. I guess one could just use ENTREZ!! (I'm a new convert after trying the network version). But it would be nice to get things straight into GCG format. I'd like to make this as smooth a transition as possible :-) Oh, another question..... is there a color tektronix emulator for IBM-like machines (I use Versatermpro for teh mac -- it's great) Thanks in advance, Chris Upton Biochemistry Unversity of Alberta Edmonton Alberta cup@bones.biochem.ualberta.ca From owner-gcg@net.bio.net Tue May 18 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.software.gcg Subject: IMPORTANT BIOSCI INFORMATION Message-ID: <9305190900.AA25925@net.bio.net> Date: 19 May 93 09:00:03 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 143 Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ ... **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add you name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database will serve as a directory that will enable biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database will be indexed for WAIS and waismail access (waismail is our WAIS e-mail server, more below) and will also be available for access via other gopher sites if they wish to permit it. The raw unindexed data will be available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. (Note as of 5 May 93 - the address database will be updated nightly and will go on-line soon after we have collected and processed the initial rush of data). IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-gcg@net.bio.net Tue May 18 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!wupost!uunet!mcsun!sun4nl!sci.kun.nl!caos.kun.nl!jackl From: jackl@caos.kun.nl (Jack Leunissen) Newsgroups: bionet.software.gcg Subject: Re: stringsearch batch jobs Message-ID: <1993May18.093114.29672@caos.kun.nl> Date: 18 May 93 09:31:14 GMT References: <17MAY199317433948@bioch.tamu.edu> Organization: CAOS/CAMM Lines: 29 whitsitt@bioch.tamu.edu (Mark S. Whitsitt, N5RJF) writes: >I am wondering if anyone has written or knows of a VMS command file or >executable which will automate the submission of stringsearches etc. as batch >jobs. Sure, Steve Clark did this job already several years ago. The so-called GCGSHELLS are available from numerous anonymous ftp-sites or fileservers, a.o. ftp.embl-heidelberg.de (or mail to "netserv@embl-heidelberg.de", putting "HELP" or "DIR SOFTWARE" in the body of the message). Good luck Jack +----------------------------+-----------------------------------+ Jack A.M. Leunissen, Ph.D. | CAOS/CAMM Center Email: jackl@caos.kun.nl | University of Nijmegen Tel. : +31 80 65 22 48 | Toernooiveld 1 Fax : +31 80 65 29 77 | 6525 ED Nijmegen, The Netherlands +-------- CAOS/CAMM is the Dutch National Node in EMBnet --------+ -- +----------------------------+-----------------------------------+ Jack A.M. Leunissen, Ph.D. | CAOS/CAMM Center Email: jackl@caos.kun.nl | University of Nijmegen Tel. : +31 80 65 22 48 | Toernooiveld 1 Fax : +31 80 65 29 77 | 6525 ED Nijmegen, The Netherlands +-------- CAOS/CAMM is the Dutch National Node in EMBnet --------+ From owner-gcg@net.bio.net Wed May 19 23:00:00 1993 Path: biosci!HAL.HAHNEMANN.EDU!keenan From: keenan@HAL.HAHNEMANN.EDU ("Paul Keenan, Library Database Administrator") Newsgroups: bionet.software.gcg Subject: Help setting up an HP plotter on a VAX Message-ID: <0096CC88.7A91EA40.8778@hal.hahnemann.edu> Date: 20 May 93 15:15:05 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 48 We're trying to set up a queue that our GCG users can use to output their graphics to an HP7550+. There seems to be a flow control or communications problem. When we run PLOTTEST the three characters of "Page" are plotted and then it just stops. The queue is idle, having sent everything off to the plotter. At this point we're not sure whether it is a problem with the serial connector or if we're not configuring something properly. We'd appreciate any advice from anyone who has already figured this out. Our configuration follows: MicroVAX 3100/80 DECServer 90/TL (connected to a DEChub) VMS 5.5-2 DECconnect office cable (twisted pair) DEC H8571-A serial connector The LAT port setup is /APPLICATION/QUEUE/NODE DSV306/PORT=PORT_4 The Queue setup is: /AUTOSTART/BASE_PRIORITY=3/CHAR=(127)/DEFAULT=(FORM=NORMAL)/OWNER=[SYSTEM] /PROCESSOR=LATSYM/PROTECTION=(S:E,O:D,G:R,W:W) The Terminal Server Port setup is: character size=8 Flow control=XON Stop Bits+Dynamic Access=Remote Input/Output Speed=9600 Signal Control Disabled Autobaud,autoconnect,autoprompt are all disabled The Plotter setup is: baud=9600 hardwire=off XON/XOFF=ON PARITY=8 BITS OFF Thanks in advance for any advice Paul ================================================================================ H H U U |Paul Keenan, Database Administrator |Voice: 215-762-3270 HHHH U U |Hahnemann University Library M.S.449 |FAX: 215-762-8180 H H UUUU |Broad & Vine Phila., PA 19102 |Keenan@Hal.hahnemann.edu ================================================================================ From owner-gcg@net.bio.net Wed May 19 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: kristoff@net.bio.net (Dave Kristofferson) Newsgroups: bionet.software.gcg Subject: test of info-gcg@daresbury.ac.uk Message-ID: <1993May20.005048.17936@gserv1.dl.ac.uk> Date: 20 May 93 00:49:32 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 1 Original-To: info-gcg@uk.ac.daresbury test of info-gcg@daresbury.ac.uk From owner-gcg@net.bio.net Wed May 19 23:00:00 1993 Path: biosci!HAL.HAHNEMANN.EDU!keenan From: keenan@HAL.HAHNEMANN.EDU ("Paul Keenan, Library Database Administrator") Newsgroups: bionet.software.gcg Subject: RE: Help setting up an HP plotter on a VAX Message-ID: <0096CCAE.E4E6B8A0.9410@hal.hahnemann.edu> Date: 20 May 93 19:50:04 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 54 >We're trying to set up a queue that our GCG users can use to output their >graphics to an HP7550+. There seems to be a flow control or communications >problem. When we run PLOTTEST the three characters of "Page" are plotted and >then it just stops. The queue is idle, having sent everything off to the >plotter. At this point we're not sure whether it is a problem with the serial >connector or if we're not configuring something properly. We'd appreciate any >advice from anyone who has already figured this out. Thanks to all those who responded. My problem with setting up the queue for a plotter concerned how the form was defined. I was embarassed to learn that there are instructions in the GCG manual for setting up plotting queues. If I had followed these from the start, I would have been fine. Michael Hogan from GCG gave me the following instructions which as he notes also appear in the Installation section of the System Support Manual. You don't say how your form is defined. It sounds like this may be a "wrap" problem. The form for a queued device should be /nowrap/ttsync/notruncate to prevent interruption of the stream of graphics commands. If this queue is sys$print you might try the following; $ define/form/nowrap/notruncate default 0 $ stop/queue/next sys$print $ set device/nospooled $printer $ set terminal/perm/nowrap/ttsync $printer $ set device/spooled=(sys$print, sys$sysdevice:) $printer $ start/queue sys$print /on=$printer/form=default $ assign "|print/queue=sys$print" plotport Instructions for setting up a queue frm scratch are in the System Support Manual (page 46 of the installation section). Regards, Michael ------------------------------------------------------ Michael Hogan, PhD phone: (608) 231-5200 Genetics Computer Group, Inc. fax: (608) 231-5202 575 Science Dr., Suite B e-mail: help@gcg.com Madison, WI 53711 e-mail: hogan@gcg.com ------------------------------------------------------ Thanks again to Michael and everyone else who replied. Paul ================================================================================ H H U U |Paul Keenan, Database Administrator |Voice: 215-762-3270 HHHH U U |Hahnemann University Library M.S.449 |FAX: 215-762-8180 H H UUUU |Broad & Vine Phila., PA 19102 |Keenan@Hal.hahnemann.edu ================================================================================ From owner-gcg@net.bio.net Sun May 23 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!wupost!decwrl!decwrl!concert!rutgers!mcclb0.med.nyu.edu!sci.wfeb.edu!macrides From: macrides@sci.wfeb.edu Newsgroups: bionet.software.gcg Subject: Re: stringsearch batch jobs Message-ID: <1993May23.192336.116@wfeb2> Date: 23 May 93 23:23:36 GMT References: <17MAY199317433948@bioch.tamu.edu> Organization: Worcester Fndn. for Exptl. Biol. Lines: 396 In article <17MAY199317433948@bioch.tamu.edu>, whitsitt@bioch.tamu.edu (Mark S. Whitsitt, N5RJF) writes: > I am wondering if anyone has written or knows of a VMS command file or > executable which will automate the submission of stringsearches etc. as batch > jobs. The GCG package we use does not have the '/batch' option for > stringsearch and the users of the computers in our lab are not necessarily able > or interested in learning how to create command files for batch submission. I > can write this myself, but figured, why reinvent the wheel? > > Thanks > > Mark S. Whitsitt, N5RJF Texas A&M University, Dept of Biochemistry > Internet: mwhitsitt@tamu.edu College Station, Tx. 77843-2128 > AMPRnet: n5rjf@n5rjf.ampr.org (409) 845-0832 > Packet/APLINK: N5RJF @ KE5HE.TX.USA.NA Here's an update I did (two years ago, though) of Steve Clark's shell. Since you're on the internet, you'd be better off doing such searches via gopher. Fote ========================================================================= Foteos Macrides Worcester Foundation for Experimental Biology MACRIDES@SCI.WFEB.EDU 222 Maple Avenue, Shrewsbury, MA 01545 ========================================================================= $!------------------------ CUT HERE ------------------------------------- $ orig_veri = f$environment("VERIFY_PROCEDURE") $ v = f$verify(0) ! (StringSearch turns off verification) $ $ ! STRINGSEARCH.COM $ $ ! June 7, 1991 -- Foteos Macrides MACRIDES@WFEB2.BITNET $ MACRIDES@SCI.WFEB.EDU $ $ ! This procedure helps the user execute the GCG program STRINGSEARCH. $ ! The program is run interactively, and the actual search is done in $ ! batch mode. $ $ ! Based on STRINGS.COM for GCG V6: $ ! Written by Steve Clark $ ! Samuel Lunenfeld Research Institute $ ! Mt. Sinai Hospital, Toronto, Canada $ ! Modifications by F.M. for GCG V7: $ ! Properly handles strings with quotes, e.g., " globin" to get hits $ ! for words beginning with globin (and exclude hemoglobin). $ ! Accepts list files. $ ! Gets /MATCH qualifier if relevant. $ ! Submits both "definitions" and "complete sequence record" searches $ ! to batch. $ $ ! Installation: $ ! $ ! Define command in GENETICS.COM: $! $ If f$mode() .eqs. "INTERACTIVE" then - $! String*Search :== @device:[directory]StringSearch $ ! $ ! Create queue in SYSTARTUP_V5.COM: $! $ INITIALIZE/QUEUE/START/BATCH/JOB_LIMIT=1/BASE_PRIORITY=3 STRIN$BATCH $ ! $ ! Define queue-query command in SYLOGIN.COM: $! $ STQ :== "SHOW QUEUE/ALL STRIN$BATCH " $ $ on control_y then goto terminate $ bell[0,7] = 7 $ ws := "write sys$output" $ iq := inquire/nopunctuation $ $ ws "" $ ws "STRINGSEARCH finds sequences by searching sequence library" $ ws "documentation for character patterns such as 'globin' or 'Human'." $ ws "" $ ws "STRINGSEARCH can search either definitions or complete sequence" $ ws "records. The records take 100 times as long to search as the" $ ws "catalogue. If you specify more than one word to search for," $ ws "(separated by commas) you will have the option to seek entries" $ ws "that contain all the specified words, any one of them, or a $ ws "minimum number of them." $ ws "" $ ws "STRINGSEARCH through which database?" $ ws "" $ ws "1) GenEMBL (GE)" $ ws "2) GenBank (GB)" $ ws "3) EMBL (EM)" $ ws "4) Swiss-Prot (SW) $ ws "5) PIR-Protein (PIR)" $ ws "6) PIR-Nucleic (NUCL)" $ ws "7) VecBase (VEC)" $ ws "8) Let me use my own list file (e.g., @MYFILE.LIST) $ ws "" $ database := "" $ myfile := "" $ mode := "" $ outfile := "" $ $get_database: $ $ iq choice "Please choose one (* 1 *): " $ if(choice.EQS."") then choice := 1 $ if(choice.EQS."1") then database := GE $ if(choice.EQS."2") then database := GB $ if(choice.EQS."3") then database := EM $ if(choice.EQS."4") then database := SW $ if(choice.EQS."5") then database := PIR $ if(choice.EQS."6") then database := NUCL $ if(choice.EQS."7") then database := VEC $ if(choice.EQS."8") then goto get_list $ if(database.EQS."GE") then goto get_genemblset $ if(database.NES."") then goto ask_subset $ ws "''bell'" $ ws "Valid choices are 1,2,3,4,5,6,7 or 8." $ goto get_database $ $get_list: $ $ iq choice "Please specify the list file (e.g., MYFILE.LIST): " $ if(choice.EQS."") then goto get_list $ if(f$locate("@",choice).NE.0) then myfile := 'choice' $ if f$search(myfile) .eqs. "" then goto myfile_not_found $ if(myfile.NES."") then database := "@''myfile'" $ if(database.NES."") then goto get_searcharea $ ws "''bell'" $ ws "Re-enter the file name without an @." $ goto get_list $ $myfile_not_found: $ $ ws "''bell'" $ ws "''myfile' does not exist." $ ws "" $ goto get_list $ $get_genemblset: $ $ ! Find out which of the GenEMBL databases should be searched, or $ ! if all of them should be. $ $ ws "" $ ws "GenEMBL sequence set to search:" $ ws " 1) All of the sequences (GE)" $ ws " 2) Primate sequences (PR)" $ ws " 3) Rodent sequences (RO)" $ ws " 4) Other Mammalian sequences (OM)" $ ws " 5) Other Vertebrate sequences (OV)" $ ws " 6) Invertebrate sequences (IN)" $ ws " 7) Plant sequences (PL)" $ ws " 8) Bacterial sequences (BA)" $ ws " 9) Organelle sequences (OR)" $ ws "10) Phage sequences (PH)" $ ws "11) Viral sequences (VI)" $ ws "12) Structural RNA sequences (ST)" $ ws "13) Synthetic sequences (SY)" $ ws "14) Unannotated sequences (UN)" $ ws "" $ $ask_genemblset: $ $ iq choice "Please enter choice (* 1 *): " $ if(choice.EQS."") then choice := 1 $ database := "" $ if(choice.EQS."1") then database := GE $ if(choice.EQS."2") then database := PR $ if(choice.EQS."3") then database := RO $ if(choice.EQS."4") then database := OM $ if(choice.EQS."5") then database := OV $ if(choice.EQS."6") then database := IN $ if(choice.EQS."7") then database := PL $ if(choice.EQS."8") then database := BA $ if(choice.EQS."9") then database := OR $ if(choice.EQS."10") then database := PH $ if(choice.EQS."11") then database := VI $ if(choice.EQS."12") then database := ST $ if(choice.EQS."13") then database := SY $ if(choice.EQS."14") then database := UN $ if(database.NES."") then goto ask_subset $ ws "''bell'" $ ws "Valid responses are 1 - 14, inclusive." $ goto ask_genemblset $ $ask_subset: $ $ ! Find out if a subset of the database should be searched $ $ subset := "*" $ ws "" $ ws "How much of ''database' do you want to search?" $ ws "" $ ws "1) All of it (i.e., ''database':*)." $ ws "2) Only a subset (e.g., ''database':HUM*)." $ ws "" $ $ask_subset_choice: $ $ iq choice "Please enter your choice (* 1 *): " $ if(choice.EQS."") then goto get_searcharea $ if(choice.EQS."1") then goto get_searcharea $ if(choice.EQS."2") then goto get_subset $ choice := "" $ ws "''bell'Valid choices are 1 or 2." $ goto ask_subset_choice $ $get_subset: $ $ ! Find out what subset of the database to search $ $ ws "" $ iq subset "Specify the ''database' subset to search (e.g., HUM*): " $ if(subset.NES."") then goto get_searcharea $ ws "''bell'Invalid answer." $ ws "If you want to search the whole database, type *" $ goto get_subset $ $get_searcharea: $ $ ! See which part of the sequence headers to peruse. $ $ ws "" $ ws "Do you want to search through:" $ ws "" $ ws "1) Definitions" $ ws "2) Complete sequence records" $ ws "" $ $ask_searcharea: $ $ iq choice "Please choose one (* 1 *): " $ if(choice.EQS."") then choice := 1 $ if(choice.EQS."1") then mode := "DEFINITIONS_ONLY" $ if(choice.EQS."2") then mode := "COMPLETE_RECORDS" $ if(mode.NES."") then goto get_text $ ws "''bell'" $ ws "Valid choices are 1 or 2." $ goto ask_searcharea $ $get_text: $ $ ! From owner-gcg@net.bio.net Thu May 27 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!biox!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.software.gcg Subject: Concatenation of FASTA output files Keywords: Need Software which will concatenate (fuse) FASTA output Message-ID: Date: 28 May 93 05:47:08 GMT Organization: EMBnet Switzerland [Basel] Lines: 13 I need a software which will parse GCG 's output of FASTA (i.e., the scoring histogram, the listing, and the alignments) and will concatenate this into one single file. Has anyone attempted to write such a program (VMS or UNIX), please mail (doelz@urz.unibas.ch) . Thanks Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | From owner-gcg@net.bio.net Fri May 28 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.software.gcg Subject: Concatenation of FASTA output files (more precise) Keywords: Need Software which will concatenate (fuse) FASTA output Message-ID: <1993May29.152603.11524@comp.bioz.unibas.ch> Date: 29 May 93 15:26:03 GMT References: Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 20 Nntp-Posting-Host: biox.embnet.unibas.ch In article , doelz@comp.bioz.unibas.ch (Reinhard Doelz) writes: |> I need a software which will parse GCG 's output of FASTA (i.e., the |> scoring histogram, the listing, and the alignments) and will concatenate |> this into one single file. Has anyone attempted to write such a |> program (VMS or UNIX), please mail (doelz@urz.unibas.ch) . More specifically, I think of a utility which reads two output files (e.g., vs. SWISSPROT:* and PIR:*) and concatenates these to one. I am aware of the fact that this could be done with a FOSN but this cannot be applied to this problem because the FASTAs shall not run on the same CPU. -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- From owner-gcg@net.bio.net Sun May 30 23:00:00 1993 Path: biosci!agate!spool.mu.edu!torn!nott!uotcsi2!news From: sbaird@mgcheo.med.uottawa.ca (Stephen Baird) Newsgroups: bionet.software.gcg Subject: tcsh and SUN Message-ID: <1993May31.194515.22404@csi.uottawa.ca> Date: 31 May 93 19:45:15 GMT Sender: news@csi.uottawa.ca Organization: Dept. of Computer Science, University of Ottawa Lines: 22 Nntp-Posting-Host: mgcheo.med.uottawa.ca X-Newsreader: TIN [version 1.1 PL8] I remember first reading about tcsh in this group when people converting from the VAX to UNIX versions were looking for the command line replacement and command line editing on the vax instead of the history command line editing of csh on UNIX. I now use it all the time, but on the SUN itself in the "cmdtool" window, the curser keys don't work and give me the previous commands. Is this a termcap problem or does tcsh only capture the key commands on simpler terminals? Thanks |--------------------------------------------------------------------| | Stephen Baird sbaird@mgcheo.med.uottawa.ca | | Molecular Genetics tel: 613-738-3925 | | Children's Hospital of Eastern Ontario fax: 613-738-4833 | | 415 Smyth Rd. | | Ottawa, Ontario | | Canada | | K1H 8M8 | |--------------------------------------------------------------------| From owner-gcg@net.bio.net Mon May 31 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!wupost!spool.mu.edu!enterpoop.mit.edu!news.mcrcim.mcgill.edu!sifon!ego!francis From: francis@ego.psych.mcgill.ca (Francis Ouellette) Newsgroups: bionet.software.gcg Subject: Re: tcsh and SUN Message-ID: Date: 1 Jun 93 07:42:20 GMT References: <1993May31.194515.22404@csi.uottawa.ca> Sender: news@sifon.cc.mcgill.ca Organization: McGill University Lines: 24 sbaird@mgcheo.med.uottawa.ca (Stephen Baird) writes: >vax instead of the history command line editing of csh on UNIX. >I now use it all the time, but on the SUN itself in the "cmdtool" >window, the curser keys don't work and give me the previous commands. >Is this a termcap problem or does tcsh only capture the key commands >on simpler terminals? a couple of suggestions: 1) try a shelltool window instead of cmdtool window. 2) remove the scrolling function from the window (right button when the arrow is over the window) best of luck, francis -- | B.F. Francis Ouellette (old address: francis@monod.biol.mcgill.ca) | | new temporary address: francis@ego.psych.mcgill.ca |