From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!rc1!ub4b!mcsun!Germany.EU.net!sunmbx.netmbx.de!mailgzrz.TU-Berlin.DE!news.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Newsgroups: bionet.software Subject: Re: PIR/GCG Message-ID: <1993Nov1.165737.54@immunbio.mpg.de> Date: 1 Nov 93 17:57:37 GMT References: <1993Oct30.184049.4664@gserv1.dl.ac.uk> Organization: Max-Planck-Institut fuer Immunbiologie Lines: 40 Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24In-Reply-To: risler%FRCGM51.earn@uk.ac.earn-relay's message of Sat, 30 Oct 1993 23:40:27 GMTLines: 40 In <1993Oct30.184049.4664@gserv1.dl.ac.uk> risler%FRCGM51.earn@uk.ac.earn-relay writes: > ... > Well, finally it worked. The .REF and .SEQ files seem to be OK. Thanks for the hint! > Now, if I run PIRTOGCG or DBINDEX, I get the following message for *ALL* the > sequences: > > * no accession number for sequence XXXX * > > Anyway the programs go on, I get the usual .NAMES, .OFFSET, etc...files > whose size seem reasonable. > > *BUT* I can't FETCH any sequence. If I try to fetch CCHU from PIR1, for > example, I get * no files in PIR1:CCHU * ..... > > NOTE 1: I am lazy and I always wait for a certain time before installing the > minor releases, waiting for other people to find the new bugs ... :-) > Hence I'm still under GCG #7.0 Is this the reason? > > NOTE 2: The files are NOT in CODATA format. They just look like the good > old PIR files. However, the accession number is hidden in a line such as: > c;Accession: xxxxxx > Our .REF-files look like yours and we have no trouble reindexing them. Perhaps why we have GCG V7.3? Regards Christoph +----------------------------------------------------------------------------+ | Christoph Gartmann Phone : +49-761-5108-465 Fax: -221 | | Max-Planck-Institut fuer PSI : PSI%(0262)45050160374::GARTMANN | | Immunbiologie Internet: gartmann@immunbio.mpg.de | | Postach 1169 | | D-79011 Freiburg, FRG | +------------- Do you know MENUE, the user environment for VMS? -------------+ From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!rice From: rice@embl-heidelberg.de (Peter Rice) Newsgroups: bionet.software Subject: Re: PIR/GCG Message-ID: <1993Nov1.201235.125613@embl-heidelberg.de> Date: 1 Nov 93 19:12:35 GMT References: <1993Oct30.184049.4664@gserv1.dl.ac.uk> Distribution: bionet Organization: EMBL, European Molecular Biology Laboratory Lines: 44 In article <1993Oct30.184049.4664@gserv1.dl.ac.uk>, risler%FRCGM51.earn@uk.ac.earn-relay writes: > Up to now I received the PIR database from MIPS on a magtape. Like many many > others, I had troubles with the GCG files provided on the tape, which were > fixed by re-running DBINDEX. > > Now I receive PIR on their CD-ROM. Since I want to use GCG, I have to copy > the files onto my VAX/VMS. *NOTE* this was a pain in the neck, a CD_MOUNT > followed by a COPY doesn't work because the resulting file are "undefined". > The CD_ACCESS program from P. Stockwell, available from the EMBL server, > doesn't work either on these CD-ROMs (it's the only case I know of). > > You MUST mount the CD-ROM with the following command: > > CD_MOUNT/media=cdrom/UNDEFINED=(STREAM_LF:512) > > It was rather hard to be aware of the UNDEFINED switch ... this may be > useful to other people... > > Well, finally it worked. The .REF and .SEQ files seem to be OK. Now, if I > run PIRTOGCG or DBINDEX, I get the following message for *ALL* the > sequences: > > * no accession number for sequence XXXX * A wild guess, but perhaps you still have stray characters in the files, probably carriage returns or line feeds, from not having exactly the right /undefined definition (which should define the record type to VMS as the CD-ROM is lacking the necessary information). Try looking at the REF files with DUMP /BLOCK=END=5 and see what characters appear. You then have to change the /undefined qualifier on the mount until they look OK. I have seen similar problems with other CD-ROM copies, but don't have the PIR one around to check the exact command you need. It's not their fault - most CD-ROMS suffer from the problem. PIR should be able to tell you the correct syntax. ----------------------------------------------------------------------------- Peter Rice, EMBL | Post: Computer Group | European Molecular Internet: Peter.Rice@EMBL-Heidelberg.DE | Biology Laboratory | Postfach 10-2209 Phone: +49-6221-387247 | 69012 Heidelberg Fax: +49-6221-387306 | Germany From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!moe.ksu.ksu.edu!osuunx.ucc.okstate.edu!constellation!aardvark.ucs.uoknor.edu!aardvark.ucs.uoknor.edu!broe From: broe@aardvark.ucs.uoknor.edu (Bruce Roe) Newsgroups: bionet.software Subject: Re: Trace Editors for Macs Message-ID: <1NOV199308565526@aardvark.ucs.uoknor.edu> Date: 1 Nov 93 13:56:00 GMT References: <9310292144.AA27674@farber.harvard.edu> Distribution: bionet Organization: University of Oklahoma - University Computing Services Lines: 107 Nntp-Posting-Host: loopback.uoknor.edu News-Software: VAX/VMS VNEWS 1.41 In article <9310292144.AA27674@farber.harvard.edu>, morrison@FARBER.HARVARD.EDU (Paul Morrison) writes... >Harry Mangalam, VCO/Micro+Mol Genetics, Irvine Hall, Coll of Med, UC >replied to kinneya@esvax.dnet.dupont.com: > >>In article <9310251805.AA10757@esds01.es.dupont.com>, >>kinneya@esvax.dnet.dupont.com wrote: >>> >>> >I'm looking for Macintosh-based software to help us edit ABI-format >>> >sequence files. I would like something like the unix-based TED, which >>> >prints the ABI-called sequence beneath the DNA migration absorption >>> >curves and allows you to make adjustments. >>> >>> The "EDITSEQ" sequence editor software for the Mac from DNAStar (which is >>> also part of their Lasergene package) will do this. >>> >>> Their phone number is (608)258-7420 >> >> So will Sequencher, from Gene Codes (and is very expensive if all you're >>looking for is an editor), but is a complete, powerful, and very easy to >>use fragment assembly program. Their phone number is: 313 769 7249; ~$1200 >>w/ hardware lock, site/multiple copy discounts. >> IMHO, Sequencher is the much better of the two for editing and fragment >>assembly, but it is not a 'full-featured' Sequence analysis pkg ie no >>protein analysis, not a lot of DNA analysis, which Lasergene does offer. >> >> >>Std Disclaimers.. >>Harry >> > >Yes indeed there is more than one contig builder out there and I agree >completely with Harry that Sequencher is the most powerful. One thing that >caught my attention in the original post was the wording "allows you to >make adjustments". Now if that is meant to mean make adjustments to the >called sequence by comparing to other sequences then yes, the programs >mentioned do this. If it means make adjustments to the raw data data signal >that comes out of a 373A so that one might be able to tweak paramaters so >that more sequence is called, I don't think that program exists. It becomes >evident after using the 373 for awhile that a program that would either >circumvent or enhance the algorithm in ABI's analysis program might be a >useful tool. What do I want this tool to do? 1) Allow me to get inside and >change the base space number if I want. 2) Figure a way to get around the >"all DNA is 25%A25%G25%C25%T" problem. These are _easy_ fixes. Others are >hard. I hear rumours and papers of neural net analysis of this data. >Anybody out there working on something that looks good? > >Paul Morrison Dana1030 >Molecular Biology Core Facility >Dana Farber Cancer Institute >44 Binney Street >Boston, MA 02115 Hi, Sorry to include all of the above with this reply but thought the thread was worth including. The problem of improving base calling from the ABI is non-trivial. We and others have been trying to do just that for what seems like years now. ABI also has been working on the problem for quite a while also and I'd look for something to surface soon. The bottom line is THERE ARE NO "_easy_ fixes" to this problem. Clark Tibbets at Vanderbilt has done lots of work with neural nets for DNA sequence analysis and demonstrated a working version of his program at the Hilton Head Genome Sequencing meeting just last week. He's published extensively on the subject and his papers make interesting reading. He's trained a neural net to develop the algorithms that allow for (according to what I saw) more accurate (when compared to ABI's) base calls within the range from the priming site out to about 400 bases. It's pretty cool stuff and he may have something there. Several other groups have looked at the ABI-lane files, and allow one to proof read the data once ABI has manipulated it. Sequencher, DNAStar, and SeqEd are three programs on the Mac that allow the user to re-interpret the data (as discussed by others). On the SunSparcStation, the Staden, et al TED (trace editor) and XBAP also allow such manipulations. These 4 programs all provide the user with access to already manipulated data and make changes they feel are appropriate. As for dealing with the raw-raw data (the approx. 20 meg gel file), the new ABI Analysis program, Clark's program, our program (which is not yet ready for prime time), and others which are at even earlier stages, may produce something that is better than the existing ABI Analysis program. I could go on almost forever with the list of issues that need to be addressed before a new and improved base calling algorithm becomes available. The major bottleneck is that the sample spacing eventually reaches a point where more than one band is in the window at the same time. This causes problems in assigning base calls at longer read lengths, especially when the signal is usually lower the further out you get. Longer gel plates and a more focussed lens can help resolve this data and several years ago I presented data at the Cold Spring Harbor Human Genome meeting showing data that was manually read-able out to around 750 bases using 60 cm plates and a 2x more focussed lens. ABI now has come out with a lowered optical stage, is testing longer gel plates, and attempting to improve their base calling algorithm. Data presented at the Hilton Head meeting was very exciting. So things along this line are moving, slowly but still moving forward. Hang in there and in the future (hope sooner than later), some better base calling options will become available. In the mean time, you could contact ABI and obtain their "tool-kit" that is an object library that will allow you to manipulate the data yourself. It's free but you have to sign an agreement with them not to distribute your code. You also could contact Clark and get a copy of his neural net program. Cheers to one and all.........bruce - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ Bruce A. Roe Professor of Chemistry and Biochemistry / / Dept. of Chem. and Biochem. INTERNET: BROE@aardvark.ucs.uoknor.edu \ \ University of Oklahoma BITNET: BROE@uokucsvx / / 620 Parrington Oval, Rm 208 AT&TNET: 405-325-4912 or 405-325-7610 \ \ Norman, Oklahoma 73019 FAXnet: 405-325-6111 / - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!mnemosyne.cs.du.edu!nyx!cagrant From: cagrant@nyx.cs.du.edu (Clinton Grant) Newsgroups: bionet.software Subject: Software manipulation of ABI 373a traces Keywords: 373a ABI sequenceing Message-ID: <1993Nov1.215442.25113@mnemosyne.cs.du.edu> Date: 1 Nov 93 21:54:42 GMT Sender: usenet@mnemosyne.cs.du.edu (netnews admin account) Organization: Nyx, Public Access Unix at U. of Denver Math/CS dept. Lines: 10 X-Disclaimer: Nyx is a public access Unix system run by the University of Denver for the Denver community. The University has neither control over nor responsibility for the opinions of users. Greetings, I'm interested in hearing how people are using ABI traces in presentations. Specifically, what is the best software to use when making annotations to gel traces. What software are you using to capture and work on the traces? Are you working on a Mac or an IBM etc? We have access to PC's, Mac's and colour printers. Any comments would be appreciated. Clint. From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: W.Chen@de.dkfz-heidelberg (Weiyun Chen) Newsgroups: bionet.software Subject: POSITIONS IN SOFTWARE DEVELOPMENT Message-ID: <1993Nov2.120739.1728@gserv1.dl.ac.uk> Date: 2 Nov 93 12:04:41 GMT Sender: dok419@cvx12.inet.dkfz-heidelberg.de Distribution: bionet Lines: 32 Content-Type: text/plain; charset=US-ASCII Precedence: first-class Original-To: emb-gen@uk.ac.daresbury Content-Transfer-Encoding: 7bit Mime-Version: 1.0 Original-Cc: bio-software@uk.ac.daresbury X-Mailer: ELM [version 2.4 PL21] Content-Length: 1141 POSITIONS FOR SOFTWARE DEVELOPERS AT THE GERMAN CANCER RESEARCH CENTER (DKFZ), HEIDELBERG Positions for programmers are available at the Department of Molecular Biohysics (0810) of DKFZ starting from January 1993 for two years (continuation will depend on external grants). DKFZ is participating in several national and international bioinformatics projects and hosts the European Data Resource for Human Genome Research and the German node of EMBnet. You would work in a team on the development of an integrated information management system for the Human Genome Project. Good working knowledge of UNIX, X11, C or C++ is required, as well as experience in at least one of the following areas: relational or object-oriented database programming, GUI development, Smalltalk, logic programming. Interest in molecular biology or genetics will be an advantage. Salaries will fall within the German BAT IIa group. Applicants should send their cv, history of experience, and two references to the Personnel Department, Reference No. 100/93, DKFZ, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: daj@uk.ac.ic.nhm ((David Johnston) daj) Newsgroups: bionet.software Subject: Trace editors for the Mac and other stuff Message-ID: <1993Nov2.100117.2722@gserv1.dl.ac.uk> Date: 2 Nov 93 10:37:44 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 62 Precedence: first-class Original-To: bio-software@uk.ac.daresbury X-Popmail-Charset: British Sorry this is a bit long but here goes: Bruce Roe's comments on the above yesterday, and especially the problems of getting longer sequences from the ABI sequencer got me thinking. Much of our sequencing is "into the unknown"" rather than routine and so the rate limiting factor is not the speed of gel reading but the speed with which we can get the next oligo made. Hence it is vital that we maximise read length from any reaction set. We have extensively played with mannual sequencing to optimise this. Sequenase sequencing using both manganease and extension mix in the reaction labels well and evenly from approx 10 to 2000 plus bases from the primer and Hydrolink Long Ranger gels maintain good tight bands (albeit closely spaced) up to at least 750 bases from primer (best read to date). When I was looking to select an automated sequencer, read length was a significant factor. Because I knew what was possible from manual sequencing, I asked the ABI guys about the flexibility of electrophoresis on the 373A and was basically told that, since the bands must pass the detection zone at a fixed rate (12+-2 laser scans per band), you did electrophoresis how they told you to do it or it wouldn't work and that was it. Ie. They were not interested in getting longer reads. Since, if current adverts are to be believed, both LKB and LiCor are way ahead of ABI on this score, this seemed an extreemly short sighted attitude. All power, therefore, to Bruce and his collegues who are trying to improve matters but I do wonder if there might be an "easier" way. Point 1: I know that reactions can be made good for a couple of thousand bases Point 2: the standard ABI base calling algorithm works (or you wouldn't get any sequence at all) Point 3: surely then, we should be looking not to make the algorithms even more complicated (and thus vunerable) than they are at the moment but to improve the electrophoresis conditions so as to be able to better space the bands that are far from the primer. LKB make extensive use of Hydolink Long Ranger gels in the ALF which presumably must help acheive their long reads. The problem with these gels is that you usually run them more slowly than standard gels (hence the scans/band problem). Has anyone out there in 373A land tried any of the following to increase read length: Long Ranger gels run slow or fast (by altering electrical supply and/or buffer concentration or gradient) Composite gels with standard acrylamide in the detection zone (so bands pass through it at the correct rate) and Long Ranger above (to keep the bands tight), or gradients of the 2 forms of acrylamide. or anything else on the electrophoresis front My 2 cents worth, Cheers, DAJ David A. Johnston Dept of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5DB. (tel 071 9389297, fax 071 9388754, email daj@nhm.ic.ac.uk) From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!rainer-mac.embl-heidelberg.de!user From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs) Newsgroups: bionet.software Subject: Mail server utility available Message-ID: Date: 1 Nov 93 16:09:00 GMT Followup-To: bionet.software Organization: EMBL Data Library Lines: 29 Nntp-Posting-Host: rainer-mac.embl-heidelberg.de A new utility program called MSU (mail server utility) is available that assists scientists in using electronic mail servers for sequence analysis, such as BLITZ, BLAST, GRAIL, etc. It is written in standard C and runs on various OpenVMS and UNIX platforms. In contrast to existing similar tools, MSU takes its knowledge about the request format a server expects from an external service description file. There's no in-built, hard-wired knowledge. This approach makes MSU extremely flexible and allows easy modification, extension and customisation. MSU is distributed with a default specification file that defines about twenty email services. New services can be added easily as they come up. When MSU starts up, it reads this file and creates a menu system which guides the user through the process of producing a well-formed service request. Additional options include the downloading of help files and the registration with services that require it prior to use. Most popular sequence formats are supported. Copies can be obtained from ftp.embl-heidelberg.de (/pub/software/unix/msu.tar.Z and /pub/software/vax/msu.uue) or by email from netserv@embl-heidelberg.de ("get unix_software:msu.uue" or "get vax_software:msu.uue"). -- Rainer Fuchs EMBL Data Library Fuchs@EMBL-Heidelberg.DE From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!mcsun!sun4nl!news.sara.nl!HASARA11.SARA.NL!A428ENDE From: A428ENDE@HASARA11.SARA.NL Newsgroups: bionet.software Subject: Re: Calculating codon usage Message-ID: <16C7A78A1.A428ENDE@HASARA11.SARA.NL> Date: 2 Nov 93 16:55:10 GMT References: <16C76CBAES85.MYGALP01@ulkyvm.louisville.edu> Organization: S.A.R.A. Academic Computing Services Amsterdam Lines: 21 Nntp-Posting-Host: vm1.sara.nl X-Newsreader: NNR/VM S_1.3.2 In article <16C76CBAES85.MYGALP01@ulkyvm.louisville.edu> MYGALP01@ulkyvm.louisville.edu writes: > Hi, > I haven't found the codon usage table for Streptococcus on IUBio or EMBL > servers and probably will need to construct one myself. However, I don't know > of any program to do, other than one in the GCG package. Does anybody have > any shareware that will calculate the codon usage at least for a given gene? A while ago somebody else asked the same. I have a TurboPascal unit and some pr ograms which can do the job quickly, but dirty (it is not very user friendly). I offered to translate the code and sample programs to englisch and I am almost finished. The program is capable of extracting exon information from the featur e table of EMBL sequences. You must have TurboPascal 5.0 or higher (lower isn't tested but would probaly work, because there isn't anything fancy in it). If y ou want I can mail the source to you or to this group if somebody can explain t o me how to do it. It probaly takes another two weeks because I'll write an small docfile to expla in what it is doing and my english isn't that good. Henk van de Kamer CHLAMY@SARA.NL From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!UVVM.UVIC.CA!JCOWARD From: JCOWARD@UVVM.UVIC.CA Newsgroups: bionet.software Subject: ITCH'94 - STUDENT POSTER CONTEST Message-ID: <9311012356.AA06625@net.bio.net> Date: 1 Nov 93 22:23:41 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 57 ITCH'94 - INFORMATION TECHNOLOGY IN COMMUNITY HEALTH Victoria, B.C. Canada: October 30 - November 3, 1994. STUDENT PAPER (POSTER) COMPETITION Open to students in disciplines with a Community Health Informatics component. Prize = $500 & Registration Fee. The Conference on Information Technology in Community Health (ITCH'94) invites you to submit a paper for its 2nd. student poster session and competition, sponsored by Metro-McNair Clinical Laboratories Limited. It is an ideal opportunity to meet and show your work to an international group of specialists working in areas of community health and information systems. ELIGIBILITY: The author must be a full time student registered in a program of a recognized post-secondary academic institution during 1994. SUBJECT: Any recently completed project (major course project, directed study, work-term research, etc.) related to informatics applications in community health care. Topics/issues range from available/appropriate technologies, specific/specialized software and policy applications. (n.b. "community health" is meant to have the broadest of interpretations - from acute care, to home care, to health promotion, to research and education) DEADLINE FOR PAPERS: MAY 15, 1994 SUBMISSION: A maximum of six pages that includes; the title, the author's name and school affiliation, an abstract of less than 200 words, and introduction (background of the work), the body of the paper, a discussion and conclusion (your own thoughts/ideas on your subject) and numbered references (no footnotes). The winning paper will be selected by a panel of judges on the basis of originality, academic and scientific merit, and presentation. The author of the winning poster will receive a $500 cash prize and full conference registration. SEND ALL SUBMISSIONS TO: Gail Peterson, ITCH'94 School of Health Information Science University of Victoria, PO Box 3050 Victoria, B.C., Canada - V8W 3P5 FOR INFORMATION VIA E-MAIL: JAMES H. COWARD, CHE ITCH'94 - INFORMATION TECHNOLOGY IN COMMUNITY HEALTH ORGANIZING COMMITTEE, SPONSORS AND EXHIBITORS, 220, 1641 Hillside Avenue, Victoria BC V8T 5G1 PHONE: (604) 598-3681 FAX: (604) 592-6341 From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!SANGER.OTAGO.AC.NZ!peter From: peter@SANGER.OTAGO.AC.NZ (Peter Stockwell) Newsgroups: bionet.software Subject: Re: unarchiving pc files Message-ID: <9310312219.AA20855@net.bio.net> Date: 31 Oct 93 20:42:07 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 28 Sarah Tilley (sjt@newt.phys.unsw.edu.au) wrote: > Keywords: > -- > Hi, > I have just obtained some public domain files for my pc by ftp. They are of th e format *.exe, and they are meant to automatically unarchive themselves to give me the programs I have downloaded. However whenever I type the filename all I g et is a screen and keyboard freeze-up. Should I be unarchiving them on my unix m achine? How do I get at these files? I am even having problems unarchiving pkunz ip! Help! I have a directory full of software I want to use but can't get at. > Thanks in advance, > ** > Sarah Tilley > sjt@newt.phys.unsw.edu.au Also make sure you obtained those files from a directory of files for PC. Another hint: try decompression on another PC (although very unlikely, but it CAN be a problem with your configuration). Wagner Fotnes Brazilian Center of Protein Sequencing University of Brasilia - Brazil From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!uni-heidelberg!rz.uni-karlsruhe.de!xlink.net!howland.reston.ans.net!pipex!uunet!spcuna!spcvxb!thomas_l From: thomas_l@spcvxb.spc.edu (Larry Thomas, Mathematics Faculty) Newsgroups: bionet.software Subject: Malaria program Message-ID: <1993Nov2.155611.1@spcvxb.spc.edu> Date: 2 Nov 93 20:56:11 GMT Sender: news@spcuna.spc.edu (Network News) Organization: St. Peter's College, US Lines: 5 Nntp-Posting-Host: spcvxa.spc.edu A colleague had (but somehow messed up) a public domain program that simulated the effects of various methods of controlling the spread of malaria. Apparantly the program was widely disseminated a few years ago. The program is intended for classroom use. Does anyone know where it can be found? We need a DOS version. Thanks. From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.software Subject: Re: PIR/GCG Message-ID: <01H4U7I30D529EEGRO@NBRF.Georgetown.Edu> Date: 2 Nov 93 17:01:40 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 111 In message <9310301907.AA04875@net.bio.net> posted to Bio-Soft Jean-Loup Risler wrote: > Up to now I received the PIR database from MIPS on a magtape. Like many many > others, I had troubles with the GCG files provided on the tape, which were > fixed by re-running DBINDEX. > > Now I receive PIR on their CD-ROM. Since I want to use GCG, I have to copy > the files onto my VAX/VMS. *NOTE* this was a pain in the neck, a CD_MOUNT > followed by a COPY doesn't work because the resulting file are "undefined". > The CD_ACCESS program from P. Stockwell, available from the EMBL server, > doesn't work either on these CD-ROMs (it's the only case I know of). > > You MUST mount the CD-ROM with the following command: > > CD_MOUNT/media=cdrom/UNDEFINED=(STREAM_LF:512) > > It was rather hard to be aware of the UNDEFINED switch ... this may be > useful to other people... > > Well, finally it worked. The .REF and .SEQ files seem to be OK. Now, if I > run PIRTOGCG or DBINDEX, I get the following message for *ALL* the > sequences: > > * no accession number for sequence XXXX * > > Anyway the programs go on, I get the usual .NAMES, .OFFSET, etc...files > whose size seem reasonable. > > *BUT* I can't FETCH any sequence. If I try to fetch CCHU from PIR1, for > example, I get * no files in PIR1:CCHU * ..... > > NOTE 1: I am lazy and I always wait for a certain time before installing the > minor releases, waiting for other people to find the new bugs ... :-) > Hence I'm still under GCG #7.0 Is this the reason? > > NOTE 2: The files are NOT in CODATA format. They just look like the good > old PIR files. However, the accession number is hidden in a line such as: > c;Accession: xxxxxx As we understand it you would like to use the GCG sequence analysis package with the CD-ROM. Although the ATLAS package is designed to be a standalone database query/retreival system, the data may be used in conjunction with other applications. This summarizes the procedure we believe you are looking for. Since the GCG index files do not exist on the CD you must off-load all data files to disk and create the necessary auxiliary files. The CD_ACCESS program should work, but after in-house testing we have determined that it does not. Apparently the CD format is incompatible with our specifications; we are discussing this issue with the CD publisher. In order to copy files from the CD to disk one must use the CD_MOUNT command with the UNDEFINED_FAT (for non-VMS users that is "undefined file access type" :-) qualifier as you have discovered. Two types of files can be retrieved: 1) binary files (PIR1.INX, TERM.TDX) If you want the BINARY files such as PIR1.INX, use the following CD_MOUNT command with no further file modifications but substituting the correct device name for your CD-ROM: $ CD_MOUNT/MEDIA=CDROM/UNDEFINED_FAT=(FIXED:NONE:512) $1$dka100: 2) ASCII files (PIR1.SEQ, PIR1.REF) The process of downloading ASCII files is a little more complicated. The files MUST end up in their native format with the following file attributes: Record format: Variable length, maximum XXX bytes Record attributes: Carriage return carriage control where XXX is "490" for a .SEQ file and "500" for a .REF file depending on the PIR release. After copying the files from CD, the DCL CONVERT command must be used to create files with the proper attributes. The following is an FDL file describing the resulting file after using the CONVERT utility. Extract this file between the "----cut here----" marks (exclusive) and call it PIRCD.FDL. ----------------------------------cut here----------------------------------- IDENT "27-JAN-1993 13:30:42 VAX-11 FDL Editor" RECORD CARRIAGE_CONTROL carriage_return FORMAT variable ----------------------------------cut here----------------------------------- Protocol: a) $ CD_MOUNT/MEDIA=CDROM/UNDEFINED_FAT=(STREAM:500) $1$dka100: !! DO _NOT_ USE "STREAM_LF" !! b) $ COPY $1$dka100:[DATA.NBR]PIR1.SEQ PIR1.SEQTMP $ COPY $1$dka100:[DATA.NBR]PIR1.REF PIR1.REFTMP ... c) $ CONVERT/FDL=PIRCD.FDL PIR1.SEQTMP PIR1.SEQ $ CONVERT/FDL=PIRCD.FDL PIR1.REFTMP PIR1.REF ... d) $ CD_DISMOUNT $1$dka100: After this procedure use the DCL command DIRECTORY/FULL to make certain the ASCII files have the proper file attributes. Please use the above protocols and report any problems to us. We appreciate notification of a problem with the ATLAS product. If you like, we will supply you with a detailed DCL COMMAND procedure to facilitate file manipulation for future releases. ------------------------------------------------------------------------ Christopher Marzec MARZEC@NBRF.Georgetown.Edu Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!d.love From: d.love@dl.ac.uk (Dave Love) Newsgroups: bionet.software Subject: Re: ccp4 mailing list Message-ID: Date: 2 Nov 93 19:34:39 GMT References: <12150E3280201597@dccc.med.umn.edu> Reply-To: ccp4@uk.ac.daresbury Distribution: bionet Organization: SERC Daresbury Laboratory, Warrington, UK Lines: 29 NNTP-Posting-Host: dlpx1.dl.ac.uk In-reply-to: HOEFFNER@DCCC.MED.UMN.EDU's message of 26 Oct 93 03:52:00 GMT >>>>> On 26 Oct 93 03:52:00 GMT, HOEFFNER@DCCC.MED.UMN.EDU said: Ed> Would someone please tell me how to get on the ccp4 mailing Ed> list. Many thanks. Since I gather others enquired: The approved way for the e-mail (not paper) list is to send sub ccp4bb to ccp4bb-requests@dl.ac.uk ^ which will be serviced by a daemon. Problems to the address below if all else fails. >>>>> On 26 Oct 93 10:31:26 GMT, vinz@PCLSP2.KUICR.KYOTO-U.AC.JP (Vinz-san) said: Vinz-san> could you please somebody explain to me what is ccp4 mailing list??? It's related to the CCP4 protein crystallography software recently mentioned here. (ftp to ccp4.dl.ac.uk) --Dave (not the secretary) -- Thank you for your interest in the CCP4 protein crystallography programs. Secretary to CCP4 | Telephone: (+44) 925 603530 (direct line) SERC Daresbury Laboratory | (+44) 925 603000 (switchboard) Warrington WA4 4AD | Facsimile: (+44) 925 603174 UK | e-mail: ccp4@daresbury.ac.uk From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!rc1!ub4b!mcsun!uunet!noc.near.net!saturn.caps.maine.edu!maine.maine.edu!rroxby From: RROXBY@MAINE.MAINE.EDU (Robert Roxby) Newsgroups: bionet.software Subject: How do you subscribe to this group? Message-ID: <93306.113830RROXBY@MAINE.MAINE.EDU> Date: 2 Nov 93 16:38:30 GMT Organization: University of Maine System Lines: 2 Thanks. Bob Roxby From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!news From: sfm@manduca.neurobio.arizona.edu (Stephen Matheson) Newsgroups: bionet.software Subject: Re: Calculating codon usage Message-ID: <2b67k9$p2p@organpipe.uug.arizona.edu> Date: 2 Nov 93 18:07:05 GMT References: <16C76CBAES85.MYGALP01@ulkyvm.louisville.edu> Organization: University of Arizona UNIX Users Group Lines: 47 NNTP-Posting-Host: manduca.neurobio.arizona.edu From article <16C76CBAES85.MYGALP01@ulkyvm.louisville.edu>, by MYGALP01@ulkyvm.louisville.edu: > I haven't found the codon usage table for Streptococcus on IUBio or EMBL > servers and probably will need to construct one myself. However, I don't > know of any program to do, other than one in the GCG package. Does > anybody have any shareware that will calculate the codon usage at least > for a given gene? I have a simple program written in QBasic (comes with DOS 5 & 6). It extracts the amino acid and nucleic acid sequences from GenBank records obtained via the RETRIEVE E-Mail Server (retrieve@ncbi.nlm.nih.gov); I assume that this format would exist in any GenBank report. The input consists of a text file containing GenBank records. No editing of a RETRIEVE report containing GenBank records is necessary, unless the format has been altered or if the report contains untranslated sequences (i.e., records with nucleic acid sequence but no amino acid sequence). The input must be in the original GenBank format. The output of the program is to a text file that can be printed via any word processor (the output is designed to be printed in landscape orientation; minor editing of the text file would enable one to print in portrait orientation). The program translates the nucleic acid sequence as it reads in and tabulates the codons, then compares the translation with the reported amino acid sequence. This serves as a sort of error checker. At this time, unfortunately, the program is unable to assemble complete messages from exons. This, however, should be easy to accomplish with fairly minor additions to the code. For now, the program skips any gene whose CDS entry begins with the word "join". This limitation can be circumvented by editing the input file to exclude exons from the nucleic acid sequence (using the "join" information as a guide, then editing the CDS entry to reflect the new position of the coding sequence. I'm working on a more sophisticated version of this program, using Visual Basic, and intend to have a stand-alone DOS program ready in a few months. If there is any interest in this program, I'll be happy to uuencode it and post it and/or distribute it via Email. If it isn't already obvious, I'll make it clear that I'm an amateur programmer, so... buyer beware. -- Steve Matheson Program in Neuroscience University of Arizona sfm@neurobio.arizona.edu From owner-software@net.bio.net Mon Nov 01 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!pipex!uknet!pavo.csi.cam.ac.uk!webmac9.vrl.path.cam.ac.uk!user From: ps10000@mbuc.bio.cam.ac.uk (Peter Speck) Newsgroups: bionet.software Subject: histone association Message-ID: Date: 2 Nov 93 10:27:45 GMT Sender: news@infodev.cam.ac.uk (USENET news) Followup-To: bionet.software Organization: Div. Virology, Cambridge, UK Lines: 3 Nntp-Posting-Host: webmac9.vrl.path.cam.ac.uk I've heard that there is software available that will predict whether a given DNA sequence will or will not associate with histone proteins. Does anyone know what this software is called and where I can get it? Thanks. From owner-software@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!CHPC.UTEXAS.EDU!mwitten From: mwitten@CHPC.UTEXAS.EDU Newsgroups: bionet.software Subject: URGENT: DEADLINE CHANGE FOR WORLD CONGRESS Message-ID: <9311031736.AA08868@morpheus.chpc.utexas.edu> Date: 3 Nov 93 17:36:47 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 68 UPDATE ON DEADLINES FIRST WORLD CONGRESS ON COMPUTATIONAL MEDICINE, PUBLIC HEALTH, AND BIOTECHNOLOGY 24-28 April 1994 Hyatt Regency Hotel Austin, Texas ----- (Feel Free To Cross Post This Announcement) ---- Due to a confusion in the electronic distribution of the congress announcement and deadlines, as well as incorrect deadlines appearing in a number of society newsletters and journals, we are extending the abstract submission deadline for this congress to 31 December 1993. We apologize to those who were confused over the differing deadline announcements and hope that this change will allow everyone to participate. For congress details: To contact the congress organizers for any reason use any of the following pathways: ELECTRONIC MAIL - compmed94@chpc.utexas.edu FAX (USA) - (512) 471-2445 PHONE (USA) - (512) 471-2472 GOPHER: log into the University of Texas System-CHPC select the Computational Medicine and Allied Health menu choice ANONYMOUS FTP: ftp.chpc.utexas.edu cd /pub/compmed94 (all documents and forms are stored here) POSTAL: Compmed 1994 University of Texas System CHPC Balcones Research Center 10100 Burnet Road, 1.154CMS Austin, Texas 78758-4497 SUBMISSION PROCEDURES: Authors must submit 5 copies of a single-page 50-100 word abstract clearly discussing the topic of their presentation. In addition, authors must clearly state their choice of poster, contributed paper, tutorial, exhibit, focused workshop or birds of a feather group along with a discussion of their presentation. Abstracts will be published as part of the preliminary conference material. To notify the congress organizing committee that you would like to participate and to be put on the congress mailing list, please fill out and return the form that follows this announcement. You may use any of the contact methods above. If you wish to organize a contributed paper session, tutorial session, focused workshop, or birds of a feather group, please contact the conference director at mwitten@chpc.utexas.edu . The abstract may be submitted electronically to compmed94@chpc.utexas.edu or by mail or fax. There is no official format. If you need further details, please contact me. Matthew Witten Congress Chair mwitten@chpc.utexas.edu From owner-software@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!daresbury!daresbury!ajt From: ajt@uk.ac.sari.rri (Tony Travis) Newsgroups: bionet.software Subject: Re: Mac-to-PC Integration Message-ID: <1993Nov3.105155.18954@gserv1.dl.ac.uk> Date: 3 Nov 93 10:46:01 GMT References: <931130040.~INN-PCAa29501.bionet-news@uk.ac.daresbury> Sender: list-admin@daresbury.ac.uk Reply-To: ajt@uk.ac.sari.rri Distribution: bionet Organization: Rowett Research Institute Lines: 32 Apparently-To: Precedence: first-class X-Newsreader: TIN [version 1.2 PL0] Allen Delaney (allen@ca.ubc.brc.sparc) wrote: : If what Bill Gates is saying about Windows/NT is true, then replacing : DOS with NT might be the way to go. Microsoft claims transparent : networking to Macs, UNIX, OS/2, DOS, Netware ...... Iff all the DOS machines are 386DX or better with at least 12Mb RAM and 100Mb disk space! : I'd be interested if anyone has had any experience doing this. In my opinion the widely held view that NT stands for 'NOT TRUE' tells you all you need to know. Yes, we have tried NT ... : We use UNIX servers here, which works quite well, but if you don't have : any unix machines, you might want to look into this. We network everything from the feeblest XT to the latest top end Macs via PCNFS and Netatalk using the Unix filesystem to share files on both Mac and PC platforms. I've seen people posting on comp.os.linux to say that they are running Linux as an NFS server to DOS PCNFS clients. A 'minimum' configuration PC for NT would perform well as a Linux NFS server, and run X11 easily. Linux can be installed from CDROM too ;-) Tony. -- Dr. A.J.Travis, | JANET: Rowett Research Institute, | other: Greenburn Road, Bucksburn, | phone: +44 (0)224 712751 Aberdeen, AB2 9SB. UK. | fax: +44 (0)224 715349 From owner-software@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!CHPC.UTEXAS.EDU!mwitten From: mwitten@CHPC.UTEXAS.EDU Newsgroups: bionet.software Subject: URGENT: DEADLINE CHANGE FOR WORLD CONGRESS Message-ID: <9311031731.AA07946@morpheus.chpc.utexas.edu> Date: 3 Nov 93 17:31:14 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 68 UPDATE ON DEADLINES FIRST WORLD CONGRESS ON COMPUTATIONAL MEDICINE, PUBLIC HEALTH, AND BIOTECHNOLOGY 24-28 April 1994 Hyatt Regency Hotel Austin, Texas ----- (Feel Free To Cross Post This Announcement) ---- Due to a confusion in the electronic distribution of the congress announcement and deadlines, as well as incorrect deadlines appearing in a number of society newsletters and journals, we are extending the abstract submission deadline for this congress to 31 December 1993. We apologize to those who were confused over the differing deadline announcements and hope that this change will allow everyone to participate. For congress details: To contact the congress organizers for any reason use any of the following pathways: ELECTRONIC MAIL - compmed94@chpc.utexas.edu FAX (USA) - (512) 471-2445 PHONE (USA) - (512) 471-2472 GOPHER: log into the University of Texas System-CHPC select the Computational Medicine and Allied Health menu choice ANONYMOUS FTP: ftp.chpc.utexas.edu cd /pub/compmed94 (all documents and forms are stored here) POSTAL: Compmed 1994 University of Texas System CHPC Balcones Research Center 10100 Burnet Road, 1.154CMS Austin, Texas 78758-4497 SUBMISSION PROCEDURES: Authors must submit 5 copies of a single-page 50-100 word abstract clearly discussing the topic of their presentation. In addition, authors must clearly state their choice of poster, contributed paper, tutorial, exhibit, focused workshop or birds of a feather group along with a discussion of their presentation. Abstracts will be published as part of the preliminary conference material. To notify the congress organizing committee that you would like to participate and to be put on the congress mailing list, please fill out and return the form that follows this announcement. You may use any of the contact methods above. If you wish to organize a contributed paper session, tutorial session, focused workshop, or birds of a feather group, please contact the conference director at mwitten@chpc.utexas.edu . The abstract may be submitted electronically to compmed94@chpc.utexas.edu or by mail or fax. There is no official format. If you need further details, please contact me. Matthew Witten Congress Chair mwitten@chpc.utexas.edu From owner-software@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!psinntp!execnet!peter.foiles From: peter.foiles@execnet.com (Peter Foiles) Newsgroups: bionet.software Subject: Genbank Search software Message-ID: <1.4467.570.0NB42ACB@execnet.com> Date: 2 Nov 93 20:06:00 GMT Organization: The Executive Network Information System Lines: 12 Hello ALL! I would like some information on PC based software that is available for searching the Genbank database on CD-ROM. We have been using the IBI Pustel program but it apparently is not compatible with the Genbank data on CD-ROM. The commercial software we have found so far has been prohibitively expensive. Any suggestions would be greately appreciated. ==Peter Foiles, PhD== --- ~ CmpQwk #UNREG~ UNREGISTERED EVALUATION COPY From owner-software@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!uni-heidelberg!xlink.net!howland.reston.ans.net!agate!spool.mu.edu!umn.edu!lynx.unm.edu!triton.unm.edu!news-user From: dkim@unm.edu Newsgroups: bionet.software Subject: Re: unarchiving pc files Message-ID: <2b6k44$ebm@triton.unm.edu> Date: 2 Nov 93 21:40:20 GMT References: <9310312219.AA20855@net.bio.net> Organization: University of New Mexico, Albuquerque Lines: 15 NNTP-Posting-Host: triton.unm.edu Sender: kim@flovax.lanl.gov (Daniel Kim) Followup-To: Distribution: bionet Organization: University of New Mexico, Albuquerque Keywords: Cc: You may also have inadvertantly transferred the files in ASCII mode instead of Binary. Try getting them again, but specify binary transfer. Daniel KiM From owner-software@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!usenet.ins.cwru.edu!agate!spool.mu.edu!olivea!decwrl!decwrl!morrow.stanford.edu!morrow.stanford.edu!not-for-mail From: HF.JSL@forsythe.stanford.edu (Joseph Lipsick) Newsgroups: bionet.software Subject: Re: Genbank Search software Message-ID: <2b7n7h$amh@morrow.stanford.edu> Date: 3 Nov 93 07:39:29 GMT Sender: news@morrow.stanford.edu Distribution: usa Organization: Stanford University Lines: 31 NNTP-Posting-Host: morrow.stanford.edu In article <1.4467.570.0NB42ACB@execnet.com>, peter.foiles@execnet.com (Peter Foiles) writes: >Hello ALL! > >I would like some information on PC based software that is available for > searching the Genbank database on CD-ROM. We have been using the IBI >Pustel program but it apparently is not compatible with the Genbank data >on CD-ROM. The commercial software we have found so far has been >prohibitively expensive. Any suggestions would be greately appreciated. > >==Peter Foiles, PhD== I would recommend that you use the NCBI resources. There is a great CD-ROM Genbank/Medline suite called ENTREZ that is available for the price of the plastic alone. Updates are available quarterly I think. For that up-to-the-minute search, the Genbank resource can be searched by e-mail using BLAST and interesting sequences can be retrieved using RETRIEVE. Both of these are free. For information on BLAST and RETRIEVE, send a "help" message to: BLAST@ncbi.nlm.nih.gov or RETRIEVE@ncbi.nlm.nih.gov There is also a great local homology program for protein sequences called MACAW that is also available from NCBI by FTP. I strongly urge people to use these valuable resources and acknowledge them properly. A number of years ago there was a useful BIONET resource that was discontinued by the NIH and not enough people complained. Use it or lose it... Joe Lipsick From owner-software@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!rc1!ub4b!mcsun!uknet!pipex!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!csulb.edu!csus.edu!netcom.com!biodata.slip.netcom.com!vern From: vern@BioData.COM (Vernon Keenan) Newsgroups: bionet.software Subject: Re: Mac-to-PC Integration Message-ID: Date: 3 Nov 93 18:26:14 GMT References: Sender: netnews@netcom.com (USENET Administration) Organization: BioData, Inc. Lines: 16 X-Xxmessage-Id: X-Xxdate: Wed, 3 Nov 93 18:25:09 GMT X-Useragent: Version 1.1.3 In article Vernon Keenan, vern@BioData.COM writes: >However, the memory requirements of PhoneNET Talk are great...over 100Kb >of the precious 640Kb DOS low memory. Depending on your hardware's memory >configuration and BIOS, you can reduce the memory overhead, but you can't >count on more than 500Kb for DOS applications. This causes problems with >many data acquisition programs. I've been informed by a colleague that PhoneNET Talk PC will run in as little as 40Kb RAM when using DOS 6.0 and MemMaker. That should give you about 580Kb RAM for applications, which should be OK for a lot of people. If you have a Mac-centric network, and you need to get PCs transfering data, then I would take a look at Farallon's PhoneNET PC product. Vern From owner-software@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!rc1!ub4b!mcsun!uknet!pipex!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!csulb.edu!csus.edu!netcom.com!biodata.slip.netcom.com!vern From: vern@BioData.COM (Vernon Keenan) Newsgroups: bionet.software Subject: Re: Mac-to-PC Integration Message-ID: Date: 3 Nov 93 18:23:29 GMT References: Sender: netnews@netcom.com (USENET Administration) Organization: BioData, Inc. Lines: 22 X-Xxmessage-Id: X-Xxdate: Wed, 3 Nov 93 18:22:23 GMT X-Useragent: Version 1.1.3 In article <1993Nov2.192140.13539@brc.ubc.ca> Allen Delaney, allen@sparc.brc.ubc.ca writes: >If what Bill Gates is saying about Windows/NT is true, then replacing >DOS with NT might be the way to go. Microsoft claims transparent >networking to Macs, UNIX, OS/2, DOS, Netware ...... > >I'd be interested if anyone has had any experience doing this. > The way I understand NT, you need an NT Advanced Server to get all this integration. Based on what I've heard about the performance pentalty of running DOS and Windows apps on NT Client (as poor as 50% compared to Win3.1), I'm not terribly excited about NT for now. Vern *************************************************************** | Vernon Keenan | Voice: 415-513-8940 | | President | Fax: 415-312-8086 | | BioData, Inc. | Internet: vern@BioData.COM | | 1826 S. Grant St. Suite 620 | | | San Mateo, California 94402 | | *************************************************************** From owner-software@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!uni-heidelberg!rz.uni-karlsruhe.de!xlink.net!howland.reston.ans.net! sol.ctr.columbia.edu!hamblin.math.byu.edu!news.byu.edu!cwis.isu.edu!u.cc.utah.edu!mac64_09.med.utah.edu!stillman From: stillman@bioscience.utah.edu (David Stillman) Newsgroups: bionet.software Subject: MacTetrad6 available - Excel spreadsheet for yeast genetics Message-ID: <2b8ri5$l6k@u.cc.utah.edu> Date: 3 Nov 93 17:59:33 GMT Organization: University of Utah Lines: 69 NNTP-Posting-Host: mac64_09.med.utah.edu X-UserAgent: X-XXMessage-ID: X-XXDate: Wed, 3 Nov 93 11:00:32 GMT Hi Netters! We have updated our MacTetrad Excel spreadsheet designed for tetrad data for yeast genetics. One enters the genotypes of haploid spores into the spreadsheet and a Macro automatically classifies each tetrad as PD, NPD, or T for each pair of markers. The data is presented in a table, along with recombination distances. When one is performing a cross with multiple markers segregating, it is often difficult to identify the spores with a particular genotype. The spreadsheet macro makes this procedure simple. The macro also allows one to identify tetrads with a particular characteristic (i.e. tetrads that are NPD for two specific markers). Two new features in MacTetrad6: 1. The macro automatically creates your spreadsheet after you enter how many tetrads and what markers. 2. When searching for spores with a particular genotype, one can use the "Pull Strains" command to put the desired strains into a new spreadsheet. This spreadsheet requires Excel (version 3.0 or 4.0) for the Macintosh. The spreadsheet also works with Excel for Windows running on an IBM PC, but we have not extensively tested it. For Mac Users: The MacTetrad Package was compressed with Stuffit Deluxe into a self-extracting archive, and this was then binhexed. The package is called MacTetrad6.hqx. For PC Users: The MacTetrad Package was compressed with PCZIP. The package is called MCTETRD6.ZIP. The MacTetrad macro, examples, and an instruction manual are available over the Internet network via Gopher or FTP: For Gopher, point Gopher to merlot.welch.jhu.edu Use the "Search the Titles of All Items in this Gopher Hole" command to search for "MacTetrad" For anonymous FTP, log onto the IUBio Archive (Intenet address = FTP.Bio.Indiana.Edu). Open up the folder Molbio, and then open up the folder Mac. (The PC version is in the folder molbio/IBMPC). The MacTetrad package is also accessible from the Gopher side of the IUBio Archive, where it is in the IUBio-Software+Data/Molecular Biology/Mac folder. (The PC version is in the IBMPC folder, instead of the Mac folder.) For those without access to the Internet, MacTetrad is available from either Jonathan Greene or David Stillman. Please send a formatted Macintosh disk to one of the addresses listed below. Happy Dissecting! David Stillman Department of Cellular, Viral and Molecular Biology University of Utah Medical Center Salt Lake City, UT 84132 e-mail: stillman@bioscience.utah.edu Dr. Jon Greene Schering-Plough Research Institute Mail Stop K15-4,4700 2015 Galloping Hill Road Kenilworth, NJ 07033-0539 e-mail: jgreene@phantom.com From owner-software@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!daresbury!mrccrc!news.dcs.warwick.ac.uk!warwick!uknet!pipex!uunet!math.fu-berlin.de!xlink.net!fauern!lrz-muenchen.de!ipp-garching.mpg.de!lmubmac26.biochem.mpg.de!user From: ibelgaufts@vms.biochem.mpg.de (horst ibelgaufts) Newsgroups: bionet.software Subject: EM heteroduplex tracing/drawing programme wanted Message-ID: Date: 3 Nov 93 14:30:02 GMT Followup-To: bionet.software Organization: MPI Biochemistry, Munich Lines: 14 NNTP-Posting-Host: lmubmac26.biochem.mpg.de Dear netters, Does anyone know of a Macintosh graphic programme that would allow one to simulate EM pictures of DNA heteroduplices? For this purpose the programme should be able to tell you the lengths of curved lines/loops. I know that programmes are available that allow you to trace EM pictures and give you lengths of loops and curved lines. What I need is somethings that tells you the lengths of curved lines/loops while you are drawing them. Thanks Horst Ibelgaufts Institute of Biochemistry, MPI of Biochemistry Munich Martinsried, FRG ULTRA POSSE NEMO OBLIGATUR From owner-software@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!max.physics.sunysb.edu!psinntp!psinntp!cmcl2!news.ans.net!europa.eng.gtefsd.com!library.ucla.edu!news.mic.ucla.edu!unixg.ubc.ca!brc.ubc.ca!sparc.brc.ubc.ca!allen From: allen@sparc.brc.ubc.ca (Allen Delaney) Newsgroups: bionet.software Subject: Re: Mac-to-PC Integration Message-ID: <1993Nov2.192140.13539@brc.ubc.ca> Date: 2 Nov 93 19:21:40 GMT References: Sender: news@brc.ubc.ca Distribution: brc Organization: B. R. Centre Ltd. Lines: 12 Nntp-Posting-Host: sparc If what Bill Gates is saying about Windows/NT is true, then replacing DOS with NT might be the way to go. Microsoft claims transparent networking to Macs, UNIX, OS/2, DOS, Netware ...... I'd be interested if anyone has had any experience doing this. We use UNIX servers here, which works quite well, but if you don't have any unix machines, you might want to look into this. -- Allen Delaney (allen@brc.ubc.ca) Biomedical Research Centre, U.B.C., Vancouver, B.C. Canada, V6T 1Z3 From owner-software@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!CHPC.UTEXAS.EDU!mwitten From: mwitten@CHPC.UTEXAS.EDU Newsgroups: bionet.software Subject: URGENT: DEADLINE CHANGE FOR WORLD CONGRESS Message-ID: <9311031731.AA08086@morpheus.chpc.utexas.edu> Date: 3 Nov 93 17:31:47 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 68 UPDATE ON DEADLINES FIRST WORLD CONGRESS ON COMPUTATIONAL MEDICINE, PUBLIC HEALTH, AND BIOTECHNOLOGY 24-28 April 1994 Hyatt Regency Hotel Austin, Texas ----- (Feel Free To Cross Post This Announcement) ---- Due to a confusion in the electronic distribution of the congress announcement and deadlines, as well as incorrect deadlines appearing in a number of society newsletters and journals, we are extending the abstract submission deadline for this congress to 31 December 1993. We apologize to those who were confused over the differing deadline announcements and hope that this change will allow everyone to participate. For congress details: To contact the congress organizers for any reason use any of the following pathways: ELECTRONIC MAIL - compmed94@chpc.utexas.edu FAX (USA) - (512) 471-2445 PHONE (USA) - (512) 471-2472 GOPHER: log into the University of Texas System-CHPC select the Computational Medicine and Allied Health menu choice ANONYMOUS FTP: ftp.chpc.utexas.edu cd /pub/compmed94 (all documents and forms are stored here) POSTAL: Compmed 1994 University of Texas System CHPC Balcones Research Center 10100 Burnet Road, 1.154CMS Austin, Texas 78758-4497 SUBMISSION PROCEDURES: Authors must submit 5 copies of a single-page 50-100 word abstract clearly discussing the topic of their presentation. In addition, authors must clearly state their choice of poster, contributed paper, tutorial, exhibit, focused workshop or birds of a feather group along with a discussion of their presentation. Abstracts will be published as part of the preliminary conference material. To notify the congress organizing committee that you would like to participate and to be put on the congress mailing list, please fill out and return the form that follows this announcement. You may use any of the contact methods above. If you wish to organize a contributed paper session, tutorial session, focused workshop, or birds of a feather group, please contact the conference director at mwitten@chpc.utexas.edu . The abstract may be submitted electronically to compmed94@chpc.utexas.edu or by mail or fax. There is no official format. If you need further details, please contact me. Matthew Witten Congress Chair mwitten@chpc.utexas.edu From owner-software@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!kimbark!jm68 From: jm68@midway.uchicago.edu (James R. Mensch Jr.) Newsgroups: bionet.software Subject: Re: MACAW Message-ID: <1993Nov3.203946.24411@midway.uchicago.edu> Date: 3 Nov 93 20:39:46 GMT References: <1993Oct20.205320.23537@nlm.nih.gov> Sender: kristoff@net.bio.net Reply-To: jm68@midway.uchicago.edu Distribution: na Organization: University of Chicago Lines: 11 Apparently-To: bionet-announce@ncar.ucar.edu I would like very much to be able to use MACAW, especially as now available with the Gibb's sampler. I find, however, that the MACAW available at ncbi. pub/macaw is executables for IBM PCs with Windows. How may we who use Macs or unix machines orVAXen obtain this program touse? -- ========================================================================== James R.Mensch Jr. "My opinions are usually my own" Snail mail: 5841 S. Maryland Ave., MC5058; Chicago IL 60637 POTFB! ========================================================================== From owner-software@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!europa.eng.gtefsd.com!howland.reston.ans.net!ee.und.ac.za!hippo.ru.ac.za!caesar.wits.ac.za!Witsvma.wits.ac.za!030NEILV From: 030NEILV@Witsvma.wits.ac.za (Neil van der Merwe) Newsgroups: bionet.software Subject: Trumpet and winsoc Message-ID: <16C7CDC3A.030NEILV@Witsvma.wits.ac.za> Date: 4 Nov 93 14:23:10 GMT Organization: Wits University Lines: 5 NNTP-Posting-Host: witsvma.wits.ac.za Hi, Can anyone tell me where I can get hold of Trumpet and Winsoc? I also need some info on winsoc, as I am totally unfamiliar with it. Thanks in advance, Neil From owner-software@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!nih-csl!jeffs From: jeffs@elsie.nci.nih.gov (Jeffrey Alan Silverman) Newsgroups: bionet.software Subject: cloning software Summary: cloning software Message-ID: <1993Nov4.140837.17153@alw.nih.gov> Date: 4 Nov 93 14:08:37 GMT References: <1993Oct20.205320.23537@nlm.nih.gov> <1993Nov3.203946.24411@midway.uchicago.edu> Sender: postman@alw.nih.gov (AMDS Postmaster) Distribution: na Organization: National Institutes of Health Lines: 15 Does anyone know of any software that will figure out a cloning scheme automatically if you give it an insert sequence and designate a vector (or multiple cloning region)?? What I have in mind is to be able to give the program a sequence, range of interest , choice or orientation and other "constraints" and then let the computer figure out the best cloning scheme for selecting compatible enzymes and vectors. Obviously for many cloning schemes this is simple but for others it is not but since there is a finite set of possibilities is should be easy to do by computer. So is there a program that does this or something similar? If not is there any interest? we are thinking of developing something along these lines. Thanks Jeff Silverman NCI, NIH From owner-software@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!cornell.edu!mal5 From: mal5@cornell.edu (Muhammad A. Lodhi) Newsgroups: bionet.software Subject: dominant RAPD markers Message-ID: <199311041432.AA19040@postoffice.mail.cornell.edu> Date: 4 Nov 93 10:37:02 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 17 Dear Friends What is the way of differentiating between heterozygous and homozygous dominant RAPD markers, if any. I think that may be very helpful in linkage analysis with pseudotest crosses in woody plants. This is a part of the problem that I am facing for linkage analysis that I posted earlier on this group. Thanks in advance ============================ Muhammad A. Lodhi Cornell University, NYSAES Geneva, NY 14456 Ph: 315 787 2239 Fax: 315 787 2216 e-mail:mal5@cornell.edu From owner-software@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!nigel.msen.com!yale.edu!cmcl2!netnews!hill From: hill@mcclb0.med.nyu.edu (John Edward Hill) Newsgroups: bionet.software.gcg,bionet.software Subject: Saving list of hits with Gopher Message-ID: Date: 4 Nov 93 16:07:59 GMT Followup-To: bionet.software.gcg Organization: Research Computing Resource, Cell Biology, NYUMC Lines: 12 Xref: biosci bionet.software.gcg:195 bionet.software:6386 NNTP-Posting-Host: mcrcr1.med.nyu.edu X-Newsreader: VersaTerm Link v1.1 After doing a TurboGopher (Macintosh) search on GenBank (or other databases), is there a way to save the list of hits as a text file? I can see how to print the list and to save it as a Bookmark file, but the only way I could see to save a text file is to open an individual sequence. Thanks! ------------------------------------------------------------------------------ John Edward Hill, Ph.D. Email (Internet): hill@mcclb0.med.nyu.edu 212-263-7689 (phone) 212-263-7135 (alt. phone) 212-263-8139 (FAX) Research Computing Resource & Dept. of Cell Biology NYU Medical Center, 550 First Ave., NY, NY 10016 From owner-software@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!spool.mu.edu!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Digitizer software (measurement not dna gels) for mac Message-ID: Date: 4 Nov 93 17:09:47 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 24 Nntp-Posting-Host: sunflower.bio.indiana.edu Does anyone have suggestions for digitizing software for Macintoshes (using a CalComp? digitizer board) that would record measurements of plant parts (projected from slides onto the digitizer pad)? The person looking knows that Jandel Scientific makes the right kind of software (expensive) for their (expensive) digitizer. This is called Sigma-Scan (or possibly Sigma-Scan Calibrating File Converter version 3.9) Any suggested less expensive equivalents for recording measurements will be appreciated. I am aware that NIH Image (and such general graphics programs like Canvas) can meaure images. But I don't know details like (a) will Image or others allow meaurements to be automatically saved into spreadsheet type data files, (b) do digitizers act like mouse input on Macs so that you don't need special software for them. P.S., I did use gopher to iubio archive to search the bionet news first for previous tips on digitizers. Only found info on dna gel digitizing. -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!europa.eng.gtefsd.com!library.ucla.edu!agate!news.ucdavis.edu!pbmac-1.ucdavis.edu!user From: jmbraverman@ucdavis.edu (John M. Braverman) Newsgroups: bionet.software Subject: SeqApp+Phylip Message-ID: Date: 4 Nov 93 17:40:20 GMT Sender: usenet@ucdavis.edu (News Administrator) Followup-To: bionet.software Organization: U.C. Davis Lines: 7 Is anyone else having a problem running Phylip with SeqApp? I have followed the instructions exactly but can't get the Phylip objects to appear under the Tasks. -- John M. Braverman U.C. Davis From owner-software@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!daresbury!not-for-mail From: jenkins@aidsun.nibsc.ac.uk Newsgroups: bionet.software Subject: G/C rich regions Message-ID: <2bbbmn$c71@mserv1.dl.ac.uk> Date: 4 Nov 93 16:47:19 GMT Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Lines: 10 To: bio-software@dl.ac.uk Hello fellow netters The PC package DNASIS has a utility to graphically display the G/C content of a sequence. Does anybody know of a unix program/utility which will do the same?? If the program/utility is part of a PCR/sequencing primer designing package, all the better. yours ever wonderingly.... Adrian Jenkins Jenkins@uk.ac.nibsc.comp From owner-software@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!ee.und.ac.za!hippo.ru.ac.za!caesar.wits.ac.za!Witsvma.wits.ac.za!030NEILV From: 030NEILV@Witsvma.wits.ac.za (Neil van der Merwe) Newsgroups: bionet.software Subject: Suggestions Message-ID: <16C7C920F.030NEILV@Witsvma.wits.ac.za> Date: 4 Nov 93 12:14:56 GMT Organization: Wits University Lines: 8 NNTP-Posting-Host: witsvma.wits.ac.za Hi, We are very soon to have our LAN linked up to the rest of the world and are looking for suggestions of good news-reader and telnet (?) (eg Clarksons telnet??) software for Microsoft Windows 3.1. Any useful tips will be much appreciated, as well as where this software can be obtained. Thanks in advance Neil From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!spool.mu.edu!howland.reston.ans.net!pipex!uknet!mcsun!julienas!genethon!pat From: pat@genethon.fr (Patricia Rodriguez-Tome) Newsgroups: bionet.software Subject: catalog of Moleuclar Biology Programs Message-ID: <1993Nov5.165853@genethon.fr> Date: 5 Nov 93 15:58:53 GMT Sender: news@genethon.fr Organization: Genethon -- Human Genome Research Centre Lines: 297 Originator: pat@fourmi.genethon.fr Nntp-Posting-Host: fourmi.genethon.fr (the english version is at line : 43) Le CEPH-Fondation Jean Dausset et Genethon, avec le soutien du projet ReSIG (Reseaux de Serveurs Informatiques pour les Genomes) mettent en place un catalogue des logiciels d'interet general dans le champ de la biologie et de la genetique moleculaire. Ce catalogue devrait contenir, a terme, la majorite des programmes existants (academiques, serveurs de traitement, commerciaux). L'accent est mis plus particulierement sur les environnments multi-utilisateurs orientes reseaux (eg. UNIX, VAX/VMS, IBM370/VM). Ce catalogue ne peut etre maintenu a jour qu'avec l'aide de la communaute : auteurs des programmes, administrateurs des archives et utilisateurs. Nous serions heureux de recevoir vos corrections, commentaires et annonces de nouveaux logiciels aux adresses suivantes : - Patricia.Rodriguez-Tome@genethon.fr - Dominique.Caterina@genethon.fr Dans un premier temps les domaines retenus sont les suivants : - l'analyse de sequence (version 1.0) - la phylogenie (version 1.0) - l'analyse de liaisons genetiques (version 2.0) - l'acquisition des donnees experimentales, en particulier traitements d'images. (version 3.0) D'autres domaines seront pris en compte ulterieurement, mais ou s'arrete la biologie moleculaire? Le catalogue des bases de donnees disponibles est maintenu par Amos Bairoch (bairoch@cmu.unige.ch) sur expasy.unige.ch . Merci a tous pour votre cooperation et Enjoy it! Patricia Rodriguez-Tome CEPH - GENETHON Patricia.Rodriguez-Tome@genethon.fr ========================================================================= (english) With the support of the RESIG project (Networks of computer servers for Genomes), the CEPH-Fondation-Jean-Dausset and Genethon have been collecting a software directory of general interest in molecular biology and genetics. In the long run, such a directory ought to contain most of the existing programmes (from academic, processing servers to commercial programmes), with some emphasis on network-oriented multi-user environments (eg UNIX, VAX/VMS). This directory cannot be up-to-date without the help of the computer community, that is to say the programme authors, archive adminsitrators and end-users. Thus, any corrections, comments and announcements of new software would be mostly welcome at the following addresses : - Patricia.Rodriguez-Tome@genethon.fr - Dominique.Caterina@genethon.fr At first, the areas taken into account are as follows : - sequence analysis (release 1.0) - phylogeny (release 1.0) - linkage analysis (release 2.0) - experimental data acquisition, specially image processing (release 3.0) Subsequently, other areas will be taken into account, but where does molecular biology stop ? The directory of available databases is maintained by Amos Bairoch (bairoch@cmu.unige.ch) on expasy.unige.ch Thank you very much for your cooperation and Enjoy it ! Patricia Rodriguez-Tome CEPH - GENETHON Patricia.Rodriguez-Tome@genethon.fr ----------------------------------------------------------------------------- USAGE : Cette premiere version, encore experimentale et incomplete est disponible sur le serveur de genethon avec les procedures suivantes : The first release, which is still experimental and uncomplete, is available on genethon's server with the following procedures : ftp anonyme sur ftp.genethon.fr pub/resig/catalogue/bio-catal.1.0 pub/resig/catalogue/bio-catal.1.0.resume ========= gopher a (at) gopher.genethon.fr : 1. About Genethon's Gopher 2. Biblio/ --> 3. Bio Catalog/ 1. Bio Catalog (Thanks) 2. Bio Catalog release 1.0 (resume) 3. Bio Catalog release 1.0 4. Bio Catalog release 1.0 =========== WAIS : le texte a ete indexe, et la source est : the text is indexed, and the source is : (:source :version 3 :ip-name "wais-server.genethon.fr" :tcp-port 210 :database-name "bio-catal" :cost 0.00 :cost-unit :free :maintainer "Patricia.Rodriguez-Tome@genethon.fr" :description "Server created with Wais release 8 b5 (BIO) on Nov 2 1993 The files of type para used in the index were: /gopher-data/bio_catal/bio-catal.1.0 This is the indexed version of CEPH-GENETHON catalogue for Molecular Biology programs. " ) ============= World Wide Web : (tres bientot - very soon) URL: http://www.genethon.fr:80/genethon_fr.html (en francais) URL: http://www.genethon.fr:80/genethon_en.html (in english) ============= REMERCIEMENTS: La premiere edition de ce catalogue a ete realisee par compilation des multiples documents disponibles sur l'Internet, completes par des communications personnelles d'experts du domaine. Nous tenons a remercier tous ceux qui, meme involontairement, nous ont prete leur concours. Toute erreur dans ce catalogue est notre faute, non la leur. ACKNOWLEDGEMENTS : The first edition of this directory comes from the compilation of various documents available on Internet and has been completed by personal communications from experts of each field. We would like to thank all the people who have cooperated, even unintentionally. Lists : ------ NAME List of molecular biology email servers AUTHOR Amos Bairoch / Dept. Medical Biochemistry / University of Geneva ADDRESS Dept. Medical Biochemistry / University of Geneva, Switzerland ADDRESS bairoch@cmu.unige.ch NAME List of molecular biology FTP servers for databases and software AUTHOR Amos Bairoch ADDRESS Dept. Medical Biochemistry / University of Geneva, Switzerland ADDRESS bairoch@cmu.unige.ch NAME Catalogue des programmes AUTHOR Philippe Dessen ADDRESS Service de BioInformatique/ CNRS INSERM, France ADDRESS dessen@gnome.inserm-vjf.fr NAME BIRCH AUTHOR ADDRESS University of Manitoba, Canada NAME UNIX Molecular Biology Software on EMBL File Server AUTHOR ADDRESS EMBL, Germany ADDRESS nethelp@embl-heidelberg.de NAME VMS Molecular Biology Software on EMBL File Server AUTHOR ADDRESS EMBL, Germany ADDRESS nethelp@embl-heidelberg.de NAME GENBANK SOFTWARE CLEARINGHOUSE AUTHOR Dave Kristofferson ADDRESS Intelligenetics, Inc. USA ADDRESS kristoff@net.bio.net NAME References for DNA seq..... NAME (article in the News) AUTHOR Sanjay Nayar ADDRESS USA NAME Reviews of Seq Analysis Progs NAME (article in bionet.software) AUTHOR Harry Mangalam ADDRESS Dept of Biocomputing / The Salk Institute , USA ADDRESS mangalam@salk-sgi.sdsc.edu NAME List of phylogenie programs AUTHOR Joe Felsenstein ADDRESS Dept. of Genetics, Univ. of Washington, USA ADDRESS joe@genetics.washington.edu FTP sites : ---------- ORGANISM : European biology Molecular Laboratory NAME : EMBL Anonymous Ftp Server ADDRESS : ftp.embl-heidelberg.de (192.54.41.33) ADDRESS : Germany ORGANISM : Indiana University / Biology Department NAME : IuBio archive for biology ADDRESS : ftp.bio.indiana.edu (129.79.224.25) ADDRESS : USA ORGANISM : University of Houston NAME : University of Houston Gene-Server ADDRESS : ftp.bchs.uh.edu (129.7.2.43) ADDRESS : USA ORGANISM : National Institute of Genetics (NIG) (Japan) NAME : National Institute of Genetics ftp server ADDRESS : ftp.nig.ac.jp (133.39.16.66) ADDRESS : Japan ORGANISM : National Center for Biotechnology Information (NCBI) ADDRESS : ncbi.nlm.nih.gov (130.14.20.1) ADDRESS : USA ORGANISM : Dept. of Genetics, Univ. of Washington ADDRESS : evolution.genetics.washington.edu (128.95.12.41) ADDRESS : USA ORGANISM : ADDRESS : anthro.utah.edu (128.110.192.93) ADDRESS : USA ORGANISM : ADDRESS : ftp.cs.utoronto.ca (128.100.3.6 or 128.100.1.105) ADDRESS : Canada ORGANISM : University of Manitoba ADDRESS : ccu.umanitoba.ca (130.179.16.8) ADDRESS : Canada ORGANISM : University of Geneva Switzerland ADDRESS : expasy.hcuge.ch (129.195.254.61) ADDRESS : Switzerland ORGANISM : New Mexico State University ADDRESS : haywire.nmsu.edu (128.123.001.032) ADDRESS : USA ORGANISM : NCI/FCRDC ADDRESS : ncifcrf.gov (129.43.2.10) ADDRESS : USA ORGANISM : University of Virginia ADDRESS : uvaarpa.virginia.edu (128.143.2.7) ADDRESS : USA ORGANISM : Department of Molecular biology / Massachussetts General Hospital ADDRESS : frodo.mgh.harvard.edu (132.183.190.10) ADDRESS : USA ORGANISM : Department of Mathematics / Stanford University ADDRESS : gnomic.stanford.edu (36.120.0.19) ADDRESS : USA ORGANISM : Molecular Biology Computer Research Resource (MBCRR) ADDRESS : mbcrr.harvard.edu (134.174.51.4) ADDRESS : USA ORGANISM : New England BioLabs (NEB) ADDRESS : vent.neb.com (192.138.220.2) ADDRESS : USA ORGANISM : Intelligenetics Inc. ADDRESS : net.bio.net (134.172.2.69) ADDRESS : USA ORGANISM : ADDRESS : groucho.cs.psu.edu (130.203.2.12) ADDRESS : USA -- ------------------------------------------------------------- Patricia RODRIGUEZ-TOME Genethon Internet : pat@genethon.fr ------------------------------------------------------------- From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!yeshua.marcam.com!zip.eecs.umich.edu!destroyer!news.itd.umich.edu!geneva.csmil.umich.edu!cash From: cash@geneva.csmil.umich.edu (Howard Cash) Newsgroups: bionet.software Subject: Re: Software manipulation of ABI 373a traces Keywords: 373a ABI sequenceingn Message-ID: <2be15b$oqe@terminator.rs.itd.umich.edu> Date: 5 Nov 93 17:05:47 GMT References: <1993Nov1.215442.25113@mnemosyne.cs.du.edu> Organization: Cognitive Science and Machine Intelligence Lab, U. of MIichigan Lines: 25 NNTP-Posting-Host: geneva.csmil.umich.edu Clint, I tried to email you directly, but could not reach your host. Several programs allow you to work with ABI trace files. The ones that come to mind are SeqEd (Macintosh, Applied Biosystems, Foster City, CA) Inherit (Sun SPARC with Macintosh front end [Mac stand-alone version is in the works], also Applied Biosystems) SeqMan/LaserGene (Macintosh and, I think, PC versions, DNAStar, Madison, WI) Sequencher (Macintosh, Gene Codes Corp., Ann Arbor, MI) Generation (Sun SPARC, IntelliGenetics/Betagen, Inc., Mountain View, CA) XDAP and its revisions (SUN workstations, by Roger Staden, MRC, England) I am biased, so my opinion must be suspect, but there has been discussion of these programs in this newsgroup and in the recent literature. I have phone numbers for most, if not all of the companies, so drop me a note if you want more information. Good luck, Hobie Cash cash@csmil.umich.edu 313-769-7249 From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!rc1!is1e!rlippens From: rlippens@vub.ac.be (Lippens Renee) Newsgroups: bionet.software Subject: Reference Manager Message-ID: <3391@rc1.vub.ac.be> Date: 5 Nov 93 13:27:35 GMT Sender: news@rc1.vub.ac.be Organization: Brussels Free Universities (VUB/ULB), Belgium Lines: 17 X-Newsreader: TIN [version 1.1 PL9] Our laboratory wants to purchase the bibliografic manager program named REFERENCE MANAGER (Windows version including the Capture module) at the best price. Anybody who has good addresses ... Thanks in advance -- +_______________________________________________________________+ + + + Lippens Renee | Internet : rlippens@ulb.ac.be + + Computer Support Assistant + + + + Universite Libre de Bruxelles | Fax : 32 67 287777 + + Departement de Biologie Moleculaire | Phone : 32 67 287762 + + 1400 Nivelles Belgium | CP 800 + +_______________________________________________________________+ From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!spool.mu.edu!uwm.edu!rpi!utcsri!utnut!torn!nott!cunews!freenet.carleton.ca!Freenet.carleton.ca!aj429 From: aj429@Freenet.carleton.ca (Andrew St. Jean) Newsgroups: bionet.software Subject: MOTIF alignment program Message-ID: Date: 5 Nov 93 14:35:14 GMT Sender: news@freenet.carleton.ca Organization: National Capital Freenet, Ottawa, Canada Lines: 11 I have in my possession a paper by Hamilton Smith et al. (PNAS, vol. 87:826, 1990) describing a program called MOTIF. This program searches for conserved patterns of amino acid residues in widely divergent proteins. I would very much like to know where I might get this program. I have already found a program called MOTIF on the EMBL ftp server. The output from this pragram is completely different from that described in the paper, though, so I don't think it is the program I am looking for. Any help would be greatly appeciated. An Andrew St. Jean University of Ottawa From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: seqapp -- Mac sequence analysis Message-ID: Date: 5 Nov 93 11:48:53 GMT References: <2bdb6n$rbe@mserv1.dl.ac.uk> Sender: news@usenet.ucs.indiana.edu (USENET News System) Distribution: bionet Organization: Biology, Indiana University - Bloomington Lines: 84 Nntp-Posting-Host: sunflower.bio.indiana.edu Regarding recent questions about how to get seqapp to work with child tasks: I don't have any answers at this time. There are bugs in the program. I'm sorry that I don't have time a present to make it completely bug-free, or to get it to work properly on all Mac systems. There will be a new release eventually, but not in the next few months. In the mean time, send any bug reports to the address below. They will help in curing problems for the next release. -- don Here is a previous description for the curious: SeqApp is a Macintosh biosequence editor, analyzer, and network handyman. It includes links to network services and external analysis programs. Features include multiple sequence alignment editor single sequence editor window read and write several sequence file formats * easy hand alignment features including colored bases and sliding * automatic multiple sequence alignment thru Clustal external app automatic gel fragment alignment to contigs thru CAP exernal app * consensus,reverse,complement,degap operations restriction maps dot plots translate dna to/from protein using various codon tables automatic preference saving * internet send mail, read mail internet gopher, information retreival including genbank. internet sequence analysis services user-definable links to external analysis programs and more * These features were updated in release 1.9a. See below for details. NOTICE: This program is not finished, and may fail in various ways. Please send notice of any problems you have using it to the address below. This release will expire on a date indicated in the About dialog. SeqApp is being written by Don Gilbert, using the MacApp extensible Macintosh programming framework from Apple Computer. You can obtain updates of this release thru anonymous ftp to ftp.bio.indiana.edu, in folder /molbio/seqapp, as seqapp.hqx. You may also obtain updates directly thru an internet-connected Mac with SeqApp, using Gopher to the IUBio archive. Look for a folder called "IUBio Software+Data/ SeqApp, Mac sequence editor". There may be additional distribution software, data or information in this /molbio/seqapp folder. See the Readme files in it for details. As of release 1.9a157, SeqApp fails once again to work on a Mac SE, or on any Mac running system software earlier than 7.0. Comments, bug reports and suggestions for new features may be sent by e-mail to SeqApp@Bio.Indiana.Edu History SeqApp was started Sept. 1990 as MacApp sequence editor/analysis platform on which analysis programs from other authors, typically command line w/ weak user interfaces, could be easily incorporated into a useable Mac interface. 12 June 93, version 1.9a159 -- a semi-major update, and time extension with various enhancements and corrections. These include -- lock/unlock indels (alignment gaps). Useful when sliding bases around during hand alignment, to keep alignment fixed in some sections. -- color amino (and nucleic) acids of your choice. -- added support for more sequence file formats: MSF, PAUP, PIR. SeqApp now relies on the current Readseq code for sequence reading & writing. -- save selection option to save subset of bases to file. -- addition the useful contig assembly program CAP, written by Xiaoqiu Huang. -- major revision of preference saving method (less buggy, I hope) -- major revision of the underlying application framework, due to moving from MacApp 2 to MacApp 3. -- fixed a bug that caused loss of data when alignment with a selection was saved to disk. -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!pipex!sunic!trane.uninett.no!news.eunet.no!nuug!news.eunet.fi!funic!nic.funet.fi!csc.fi!harper From: Rob.Harper@csc.fi (Rob Harper) Newsgroups: bionet.software Subject: Yet another gopher for Windows and Winsock Message-ID: <199311050659.AA26091@csc.fi> Date: 5 Nov 93 06:59:52 GMT Sender: root@nic.funet.fi (The FUnny NET guru) Organization: Finnish Academic and Research Network Project - FUNET Lines: 165 >Path: funic!news.funet.fi!sunic!pipex!howland.reston.ans.net!spool.mu.edu!umn.edu!news2.cis.umn.edu!gopher-news-daemon@boombox.micro.umn.edu >Date: Thu, 4 Nov 1993 16:57:19 -0700 >From: dob@tis.inel.gov (Dave Brooks) >Message-ID: <9311042357.AA18523@dewey.inel.gov> >Original-To: Brewster@wais.com, gopher-news@boombox.micro.umn.edu, > winsock@sunsite.unc.edu, Lois.Schoen@Forsythe.Stanford.EDU, > aaron@datatools.com, saint@wais.com, bjs@inel.gov, tis@inel.gov, > jason.levine@columbia.edu, jim@netmanage.com, rcq@ftp.com, > bruce@frontiertech.com, davidtr@microsoft.com, vikas@distinct.com, > PETER@psychnet.psychol.utas.edu.au, chrisl@ncms.org, martinh@jsbus.com, > amonson@amonson.ag.uidaho.edu, trier@odin.INS.CWRU.Edu, > howardd@ricks.edu, daniel@mudhoney >Subject: Announcing (Yet Another) WinSock Gopher Client >Newsgroups: comp.infosystems.gopher >Distribution: comp >Sender: news@news2.cis.umn.edu >Approved: comp.infosystems.gopher@news.cis.umn.edu >Lines: 145 [Note: I just uploaded this software to boombox.micro.umn.edu:pub/gopher/incoming and microdyne.com:pub/incoming ... sunsite does not seem to be responding, but I'll keep trying] Announcing A Windows Sockets Gopher WinSock Gopher Version 0.9f November 4, 1993 ** Introduction WSGopher is a Gopher client for Microsoft Windows 3.1 and Windows Sockets (or WinSock) version 1.1. It was designed from the ground up to take advantage of, and build up, Windows and WinSock. In particular WSGopher uses the parallel capabilities of WinSock to allow the user to fetch as many items at once as they care to. It also takes advantage of Windows "associations", the Clipboard, printer, etc. WSGopher has many features which support ease of use, speed and flexibility, including: - Data appears in a window AS IT ARRIVES on your computer; you don't have to wait for something to be completely transferred. There is no hourglass cursor in WSGopher. - As soon as data appears on your screen, you can start using it. This means you can select items from a directory window while the directory is still downloading. I do this all the time with the "All the Gopher Servers in the World" directory. You can also scroll through your text window, and even mark text and copy it to the clipboard, print it or save it to disk while the text file is downloading. - You can easily do more than one thing at a time; in fact, you can do as many things as you want, until you run out of resources (like using up all your network sockets). I often have four to six file downloads going on at once, or a similar number of directories and text documents. The only limitation is my attention span. - WSGopher uses the Windows MDI feature, giving you multiple document windows within a single containing window. WSGopher windows are highly customized to the document type. - WSGopher has built in viewers for text and CSO types. The text viewer can display up to 32K lines (unlimited in future versions). You can also configure the font for the text viewer. The CSO viewer supports the "fields" feature by downloading the fields from the CSO server into a "drop list", which can then be used while forming queries. You can perform multiple queries on a CSO server. - WSGopher uses File Manager associations for external document viewing, so if your PC can view PostScript, so can WSGopher. However you can still customize or override viewers within WSGopher. - There are many, many other features. Please consult the file "features.txt" which is included in the distribution. ** Important legal info Copyright (C) 1993 EG&G Idaho, Inc. "All Rights Reserved" Idaho National Engineering Laboratory, Idaho Falls, Idaho, USA DISCLAIMER This program was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees or contractors, makes any warranty, express or implied, or assumes any legal liability of responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product or process disclosed, or represents that its use would not infringe privately owned rights. PERMISSION TO USE, COPY, AND DISTRIBUTE THIS SOFTWARE AND ITS DOCUMENTATION FOR ANY NON-COMMERCIAL PURPOSE, WITHOUT FEE, IS HEREBY GRANTED, PROVIDED THAT THE ABOVE COPYRIGHT NOTICE AND THIS PERMISSION NOTICE APPEAR IN ALL COPIES OF THE SOFTWARE AND SUPPORTING DOCUMENTATION, AND THAT ALL EG&G IDAHO, INC. IDENTIFICATION IN THE USER INTERFACE REMAIN UNCHANGED. NO INTEREST IN OR TITLE TO THIS SOFTWARE IS GRANTED HEREIN. ** What this distribution includes The file "wsg-09f.exe" is a self extracting archive. I've found that not everyone has the latest and greatest version of popular archiving tools, so I've chosen this method as the one that provides the least hassle to the greatest number of users. The files in the archive include: wsgopher.exe the executable wsgopher.ini the "resource" file Important note: this file does NOT have to be copied to the WINDOWS directory. It can safely reside in the same directory as the executable; but you can move it to the WINDOWS directory if you wish. wsgopher.hlp Incomplete, not very useful (yet) announce.txt this file install.txt installation instructions features.txt A quick list of WSGopher features powerusr.txt A guide for power users ** Availability WSGopher is (or will be) available via anonymous FTP on the following hosts: boombox.micro.umn.edu pub/gopher/Windows sunsite.unc.edu pub/micro/pc-stuff/windows/winsock/apps I've placed it to the appropriate upload directories, so hopefully it will show up soon in the directories indicated. Look for the file "wsg-09f.exe" and be sure to transfer it with binary mode. ** Installation The file 'install.txt' contains installation instructions. However, since the file is included in the archive, I've included few paragraphs here to help you get started: Decide where on your disk you plan to install WSGopher. Let's say, for the sake of discussion, that you make a directory c:\wsgopher and decide to put the software there. The file 'wsg-09f.exe' is a self extracting archive that contains the WSGopher executable, INI file and several documentation files. Change directory to c:\wsgopher, and execute the wsg-09f program. After this, you will not need the wsg-09f program any longer. [ end of excerpt ] You are invited to read the entire file. It is short, because there's not much you need to know to make WSGopher work for you. ** Known bugs Known bugs are listed at the end of 'features.txt'. Dave Brooks From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!munnari.oz.au!metro!usage!news From: Shaharin Yussof Newsgroups: bionet.software Subject: Re: Trumpet and winsoc Message-ID: <1993Nov5.005248.28440@usage.csd.unsw.OZ.AU> Date: 5 Nov 93 00:52:48 GMT Sender: news@usage.csd.unsw.OZ.AU Organization: Department of Safety Science, USNW Lines: 13 Nntp-Posting-Host: 149.171.28.200 X-Newsreader: In article <16C7CDC3A.030NEILV@Witsvma.wits.ac.za> 030NEILV@Witsvma.wits.ac.za (Neil van der Merwe) writes: >Hi, >Can anyone tell me where I can get hold of Trumpet and Winsoc? I also >need some info on winsoc, as I am totally unfamiliar with it. >Thanks in advance, >Neil Try anonymous ftp to biochemistry.cwru.edu You might also try the shareware QVTNET as a TCP/IP, mail, newsreader, and FTP program. It is available in the same place. Shaharin From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!PCLSP2.KUICR.KYOTO-U.AC.JP!vinz From: vinz@PCLSP2.KUICR.KYOTO-U.AC.JP (Vinz-san) Newsgroups: bionet.software Subject: SeqApp problem Message-ID: <9311050809.AA12234@pclsp2> Date: 5 Nov 93 08:09:27 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 23 I have just read the letter of John M. Braverman that states the following: >Is anyone else having a problem running Phylip with SeqApp? I >have >followed the instructions exactly but can't get the Phylip objects to >appear under the Tasks. Also in my case I can not launch Phylip. Moreover I can not launch any child task as ClustalV, and if I try the computer shows a Disk Reading Error. I have tried to retrieve several times the program from the gopher, but it does not seem to be a retrivial error. Can anyone suggest me how to implement SeqApp in order to run it properly? Thank you very much indeed Vincenzo nardi-Dei Kyoto University vinz@pclsp2.kuicr.kyoto-u.ac.jp From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!howland.reston.ans.net!usc!yeshua.marcam.com!zip.eecs.umich.edu!destroyer!news.itd.umich.edu!spencer From: spencer@med.umich.edu (Spencer W. Thomas) Newsgroups: bionet.software Subject: Re: Saving list of hits with Gopher Message-ID: Date: 5 Nov 93 18:57:34 GMT References: Organization: University of Michigan HSITN Lines: 14 NNTP-Posting-Host: guraldi.itn.med.umich.edu In-reply-to: hill@mcclb0.med.nyu.edu's message of Thu, 4 Nov 93 16:07:59 GMT In article hill@mcclb0.med.nyu.edu (John Edward Hill) writes: > After doing a TurboGopher (Macintosh) search on GenBank (or other > databases), is there a way to save the list of hits as a text file? Try MacMosaic. The current version is ftp.ncsa.uiuc.edu:/Mac/Mosaic/NCSAMosaicMac.B6.sit.Hqx You can save any "page" as a text file. You also get access to the whole WWW (World Wide Web), which includes gopher as a subset. -- =Spencer W. Thomas | Info Tech and Networking, B1911 CFOB, 0704 "Genome Informatician" | Univ of Michigan, Ann Arbor, MI 48109 Spencer.W.Thomas@med.umich.edu | 313-764-8065, FAX 313-764-4133 From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!pipex!uknet!nessie!nessie.mcc.ac.uk!sr From: sr@zen.mp.co.umist.ac.uk (Simon Read) Newsgroups: bionet.software Subject: Quanta and SGIs Message-ID: Date: 5 Nov 93 14:53:14 GMT Sender: news@nessie.mcc.ac.uk (Usenet News System) Organization: Umist/Manchester Computing Centre Sun 630MP Lines: 14 A friend of mine over in Pharmacy is having problems getting picture files of molecules modelled in this package. The function in the package itself seems to be broken. Does any one have any suggestions about fixing the function? Does anyone know how we could get just a screen dump from and SGI (or for that matter an Indigo)? Thanks in advance Simon Read ---------- Simon.Read@umist.ac.uk From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!nih-csl!helix.nih.gov!chuck From: chuck@helix.nih.gov (Chuck Buckler) Newsgroups: bionet.software Subject: Re: Trumpet and winsoc Message-ID: <1993Nov5.095110@helix.nih.gov> Date: 5 Nov 93 14:51:10 GMT References: <16C7CDC3A.030NEILV@Witsvma.wits.ac.za> Sender: postman@alw.nih.gov (AMDS Postmaster) Reply-To: chuck@helix.nih.gov (Chuck Buckler) Organization: National Institutes of Health Lines: 22 In article <16C7CDC3A.030NEILV@Witsvma.wits.ac.za>, 030NEILV@Witsvma.wits.ac.za (Neil van der Merwe) writes: |> Hi, |> Can anyone tell me where I can get hold of Trumpet and Winsoc? I also |> need some info on winsoc, as I am totally unfamiliar with it. |> Thanks in advance, |> Neil -- follow what's happening in alt.winsock and comp.protocols.tcp-ip.ibmpc +-=-=-=-=-=-=-=-=-=-=-=-=-=-=-+-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- -=-+ | Chuck Buckler | internet - chuck@mizzen.niaid.nih.gov | | Build. 4, Rm. 301, NIH | NIAID-LAN MBUG | | Bethesda, MD 20892, USA | 301-496-1498 FAX - 301-402-0226 | +-=-=-=-=-=-=-=-=-=-=-=-=-=-=-+-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- -=-+ From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!utcsri!utnut!torn!nott!cunews!freenet.carleton.ca!Freenet.carleton.ca!aj429 From: aj429@Freenet.carleton.ca (Andrew St. Jean) Newsgroups: bionet.software Subject: Looking for a protein analysis program Message-ID: Date: 5 Nov 93 14:44:08 GMT Sender: news@freenet.carleton.ca Organization: National Capital Freenet, Ottawa, Canada Lines: 9 I looking for a program that will predict a protein`s secondary structure from its sequence and then allow me to compare the secondary structures of a number of proteins. The program must be able to run either under UNIX or DOS/Windows. Any help in this matter would be greatly appreciated. Andrew St. Jean University of Ottawa From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!VAX86.LIUNET.EDU!SHODELL From: SHODELL@VAX86.LIUNET.EDU Newsgroups: bionet.software Subject: molecular graphics query Message-ID: <9311051824.AA27305@net.bio.net> Date: 5 Nov 93 17:20:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 4 I am seeking any programs -- commercial or public -- which can be recommended for early college use in bio courses for demonstrating molecular bonding, macromolecular structure and molecular interactions. Please respond to: IN%"shodell@vax86.liunet.edu" Many thanks. From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!AUDREY.LMF.ORG!jim From: jim@AUDREY.LMF.ORG (Jim Gale) Newsgroups: bionet.software Subject: Windows telnet and ftp software Message-ID: <9311051920.AA19760@audrey.lmf.org> Date: 5 Nov 93 19:20:39 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 8 I am a Windows PC user. However I cuurently use a dos Kermit to do Telnet and a dos FTP. Are there any good WINDOWS software to do telnet and FTP?? What are you using??? I had heard that early windows software for this purpose used a large amount of needed conventional memory (as a TSR), is this true now?? Thanks in advance Jim From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!nih-csl!postman From: dspete@helix.nih.gov Newsgroups: bionet.software Subject: Re: Windows telnet and ftp software Message-ID: <1993Nov5.225654.17587@alw.nih.gov> Date: 6 Nov 93 01:54:34 GMT References: <9311051920.AA19760@audrey.lmf.org> Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: National Institutes of Health Lines: 22 Content-Type: TEXT/PLAIN; charset=US-ASCII Mime-Version: 1.0 In article <9311051920.AA19760@audrey.lmf.org>, writes: > I am a Windows PC user. However I cuurently use a dos Kermit to do Telnet > and a dos FTP. Are there any good WINDOWS software to do telnet and FTP?? > What are you using??? I had heard that early windows software for this > purpose used a large amount of needed conventional memory (as a TSR), is this > true now?? > Thanks in advance > Jim Jim, I've been using Chameleon TCP/IP from NetManage for several months now and find it to be a very slick package. The memory requirements are small (approx 20K) since it is a true Windows implementation, not a kludge built upon dos TSRs. The package does telnet, FTP, has a news reader, and a POP3 mail client. Overall very nice. The one drawback is price, about $400 for the package. It also includes a WinSock interface that works great with the Gopher+ client I've got running. David From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!spool.mu.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!news.cso.uiuc.edu!fenton From: fenton@nemo.life.uiuc.edu (Jim Fenton) Newsgroups: bionet.software Subject: Re: Trumpet and winsoc Message-ID: Date: 5 Nov 93 20:21:42 GMT References: <1993Nov5.005248.28440@usage.csd.unsw.OZ.AU> Organization: University of Illinois at Urbana Lines: 25 NNTP-Posting-Host: nemo.life.uiuc.edu Shaharin Yussof writes: >In article <16C7CDC3A.030NEILV@Witsvma.wits.ac.za> 030NEILV@Witsvma.wits.ac.za (Neil van der Merwe) writes: >>Hi, >>Can anyone tell me where I can get hold of Trumpet and Winsoc? I also >>need some info on winsoc, as I am totally unfamiliar with it. >>Thanks in advance, >>Neil >Try anonymous ftp to biochemistry.cwru.edu >You might also try the shareware QVTNET as a TCP/IP, mail, newsreader, and FTP >program. It is available in the same place. >Shaharin Is it just me or did QVTNET work for others. I never got the lpr print stuff to work properly, the windows version was amazingly slow and wouldn't work with our NFS network (yes, we have a weird mix of unix and pc's that adds some difficulties). I'm much more happy since I turned our PC's running windows into X terminals with eXceed/W for windows. Of course, this isn't shareware, but it wouldn't surprise me to find that there are public domain versions of X emulators available. -- Jim Fenton fenton@nemo.life.uiuc.edu From owner-software@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!xlink.net!scsing.switch.ch!swidir.switch.ch!news.unige.ch!cmu.unige.ch!dlowry From: dlowry@cmu.unige.ch (Dorothy Lowry) Newsgroups: bionet.software Subject: Re: Trumpet and winsoc Message-ID: Date: 5 Nov 93 12:28:17 GMT References: <1993Nov5.005248.28440@usage.csd.unsw.OZ.AU> Sender: usenet@news.unige.ch Organization: University of Geneva Lines: 136 X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] In article <1993Nov5.005248.28440@usage.csd.unsw.OZ.AU> Shaharin Yussof writes: >In article <16C7CDC3A.030NEILV@Witsvma.wits.ac.za> 030NEILV@Witsvma.wits.ac.za >(Neil van der Merwe) writes: >>Hi, >>Can anyone tell me where I can get hold of Trumpet and Winsoc? I also >>need some info on winsoc, as I am totally unfamiliar with it. >>Thanks in advance, >>Neil >Try anonymous ftp to biochemistry.cwru.edu >You might also try the shareware QVTNET as a TCP/IP, mail, newsreader, and FTP >program. It is available in the same place. >Shaharin I have just installed Trumpet and Winsock and all the other super software that needs Winsock (including Winmosaic). I cannot tell you how much I like Trumpet, in fact, I am writing this using Trumpet at this very minute. Anyway, here is a brief tutorial on Winsock, etc, hopefully it will save somebody a little time: Winsock is a set of routines that link dynamically to various programs that can use Winsock. Trumpet Winsock is one of a number of Winsocks, however, I believe it is the only one that is a shareware version, and it is certainly the one that is most widely used among the people I know... NOTE 1: If you are using FTP Software Inc, PC/TCP, you need FTP Software's version of Winsock...this is downloadable from many anonymous FTP sites. The good news: Your program will detect your Winsock, and auto-magically run ... IF YOU SET UP THE WINSOCK PROPERLY ... although, of course various programs such as Trumpet and WinQVT need to know various parameters about your network, so you will need to READ THE DOCUMENTATION that comes with each of these programs before you install them. You should know that the following "layers" are required: [ Program that uses Winsock: [ runs under Win 3.1 - example Trumpet News Reader "on top of" [ Winsock " on top of " [ a program that creates "virtual" packet drivers for Winsock [ that lets you multitask your Winsock applications [ example: winpkt.com or pktmux "on top of" [ a Crynwyr packet driver (used to be called Clarkson drivers). The purpose of the packet driver is to talk to your ethernet card and direct any packets that arrive at your computer addressed to it, to the program that they should go to. Note 2: Each packet driver is written SPECIFICALLY for each Ethernet card. You must have the packet driver that is written for that card that is in your computer. In fact, if you are connected to the network, you probably already have the one that you need! Look in your network.bat or autoexec.bat file (hopefully you will have such a thing) for more information. With luck, you will be able to match up the name of your packet driver with one of the Crynwyr drivers...if not follow the documentation that comes with the Crynwyr drivers in order to install it. Run the packet driver, THEN run the virtual packet driver addressing program. I THINK that the only card that is known not to work with winpkt.com, is the BICC 16 bit card (4110 - 2/3) Guess which card is in MY computer ??? :-) if you have this card then you need to run pktmux then pktdrv. See the pktmux documentation for more details... winpkt.com is called like this: winpkt 0x[vv] 0x[nn] where [vv] is the address that you choose to put the virtual packet driver at. [nn] is the actual address that the packet driver is located at. The 0x part says that it is in HEX - I think that most packet driver addresses are already in hex - but check the Crynwyr documentation for your packet driver. Now you are ready to start your trumpet winsock. I assume you have unzipped it and put it in whatever directory, plus made an icon for it in Windows. Before you start Windows make sure that you have the following information: the ip address of your computer the ip address of your default gateway the ip address of your nameserver, timeserver your domain name I got all this information out of my existing setup...you may need some help with this from the network administration- type people. Click on the Trumpet Winsock icon and fill in the network setup information. THE ADDRESS THAT YOU GIVE, WILL BE THE VIRTUAL ADDRESS THAT YOU TOLD WINPKT.COM to use. Now, restart Trumpet winsock and use some of the programs that come with it to see if it is working...try using PING and ping at the ip address of a computer near you, your nameserver, etc. Then try to ping on a name...if all goes well, you are ready to start installing the rest of your software that uses Winsock. If you see an ARP Timeout error in the debug screen, it may mean you have the same kind of ethernet card that I have and you will have to use pktmux and pktdrv instead of winpkt.com Make sure that the winpkt.com that you get is up to date! Get the latest version that you can find. Happy winsocking !!!! -- Dorothy Lowry PS: you WILL need to read the documentation... ============================================================ Dorothy Lowry E-mail: dlowry@cmu.unige.ch Graduate Student & phone: +41-22-702-5490 PC/GENE Programmer Fax: +41-22-346-8758 Dept. Medical Biochemistry, University of Geneva CMU, 1 rue Michel Servet, CH-1211 Geneva 4, Switzerland ============================================================ From owner-software@net.bio.net Fri Nov 05 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!spool.mu.edu!sgiblab!barrnet.net!noc.usfca.edu!Dr.Chihara From: Chihara@alm.admin.usfca.edu (Dr. Chihara) Newsgroups: bionet.software Subject: Looking for restriction mapping program Message-ID: <2beoes$3fi@noc.usfca.edu> Date: 5 Nov 93 23:43:24 GMT Sender: -Not-Authenticated-[5160] Organization: USF Lines: 8 NNTP-Posting-Host: 138.202.6.144 X-Posted-From: InterNews 1.0@noc.usfca.edu. Xdisclaimer: No attempt was made to authenticate the sender's name. Does anyone know of a simple restriction mapping program I could use in upper division courses in genetics to give students help in making linear and circular maps? Dr. Chihara Chihara@usfca.edu USF __________________________________ From owner-software@net.bio.net Fri Nov 05 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!mcsun!sun4nl!star.cs.vu.nl!balaena!mac_dw2_2.bio.vu.nl!user From: deboer@bio.vu.nl (Thon de Boer) Newsgroups: bionet.software Subject: Re: Software manipulation of ABI 373a traces Message-ID: Date: 6 Nov 93 14:46:50 GMT References: <1993Nov1.215442.25113@mnemosyne.cs.du.edu> <2be15b$oqe@terminator.rs.itd.umich.edu> Sender: news@bio.vu.nl Followup-To: bionet.software Organization: Vrije Universiteit, Amsterdam Lines: 31 In article <2be15b$oqe@terminator.rs.itd.umich.edu>, cash@geneva.csmil.umich.edu (Howard Cash) wrote: > Clint, > > I tried to email you directly, but could not reach your host. > > Several programs allow you to work with ABI trace files. The ones that come > to mind are > > SeqEd (Macintosh, Applied Biosystems, Foster City, CA) > Inherit (Sun SPARC with Macintosh front end [Mac stand-alone version is in > the works], also Applied Biosystems) > SeqMan/LaserGene (Macintosh and, I think, PC versions, DNAStar, Madison, WI) > Sequencher (Macintosh, Gene Codes Corp., Ann Arbor, MI) > Generation (Sun SPARC, IntelliGenetics/Betagen, Inc., Mountain View, CA) > XDAP and its revisions (SUN workstations, by Roger Staden, MRC, England) > > I am biased, so my opinion must be suspect, but there has been discussion > of these programs in this newsgroup and in the recent literature. I have > phone numbers for most, if not all of the companies, so drop me a note if > you want more information. > The new version of GeneJockey II (BioSoft) can also handle the ABI files in a sequencing project or so I am told by their catalog. I have not tried it yet for I am waiting on my demo disk (oohoo BioSoft, are you listening :-) Maybe there is someone out there who could send me the Demo version of GeneJockey or put it in a ftp site ? Sincerely, Thon de Boer From owner-software@net.bio.net Fri Nov 05 22:00:00 1993 Path: biosci!THEORY.BCHS.UH.EDU!dbd From: dbd@THEORY.BCHS.UH.EDU (Dan Davison) Newsgroups: bionet.software Subject: PIR Release 38 available for FTP Message-ID: <9311062211.AA17162@theory.BCHS.UH.EDU> Date: 6 Nov 93 22:11:26 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 26 Courtesy of the National Biomedical Research Foundation staff, PIR Release 38 is available for anonymous FTP from ftp.bchs.uh.edu 129.7.2.43, in the directory ~ftp/pub/gene-server/pir/pir_rel38/{ascii,vms}/... I have checked the ASCII version and it appears to be OK; I no longer have the disk space to check the VMS version. Remember that to use the VMS version with GCG 7.X you must run dbindex first! The files are stored as compressed format, so you must transfer them in FTP's "binary" mode, the use the Unix "uncompress" command. There are decompress utilities for VMS: for example, see ~ftp/pub/gene-server/pir/decompress-vms.exe and the readme file. The UH Gene-Server PIR Gopher (gopher to gopher.bchs.uh.edu) and PIR e-mail service (send the command SEND PIR HELP to gene-server@bchs.uh.edu) are serving the new release. If you have any question, please contact Dan Davison at davison@uh.edu. dan davison gene-server manager From owner-software@net.bio.net Fri Nov 05 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!sol.ctr.columbia.edu!howland.reston.ans.net!ee.und.ac.za!csir.co.za!op1.up.ac.za!alang From: alang@op1.up.ac.za (Alan Guthrie) Newsgroups: bionet.software Subject: Asyst Users Message-ID: Date: 6 Nov 93 17:25:02 GMT Organization: Faculty of Veterinary Science, Onderstepoort Lines: 15 NNTP-Posting-Host: 137.215.115.89 X-Disclaimer: None of the opions expressed herein are the official X-Disclaimer: opinions of the CSIR or any of its subsidiaries. X-Disclaimer: ** So don't freak out at _us_ about anything ** We use Asyst 4.01 from Asyst Software Technologies (now Keithley Instruments) for data capture and analysis in our laboratory. A number of other people are using Asyst locally and we are in the process of setting up an Asyst Users Group. I have been asked to try to make contact with other Asyst users and/or Asyst Users Groups. Please could anyone with information that could help me in this regard reply to this message. Alan Guthrie Director: Equine Research Centre Faculty of Veterinary Science University of Pretoria Republic of South Africa Internet: ALANG@OP1.UP.AC.ZA From owner-software@net.bio.net Fri Nov 05 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!umn.edu!msus1.msus.edu!TIGGER.STCLOUD.MSUS.EDU!Q00001 From: q00001@TIGGER.STCLOUD.MSUS.EDU Newsgroups: bionet.software Subject: remote data acquisition from greenhouse modules Message-ID: <1993Nov6.161226.6452@msus1.msus.edu> Date: 6 Nov 93 22:12:26 GMT Reply-To: q00001@TIGGER.STCLOUD.MSUS.EDU Organization: ST. CLOUD STATE UNIVERSITY, ST. CLOUD, MN Lines: 15 Nntp-Posting-Host: tigger.stcloud.msus.edu I am the faculty supervisor of a small university greenhouse. I have investigated data acquisition and logging of temperature/humidity from the six growing modules. Those which are available from Johnson Control et. al. are acquisition and control as well as quite expensive. I can get a IBM/DOS computer (286 or 386) from the computer center as they upgrade and dedicate it to data logging. Does anyone have any suggestions on what types of software and remote sensors might be available for this purpose. David DeGroote q00001@tigger.stcloud.msus.edu snail mail: Department of Biology St. Cloud State University St. Cloud, MN 56301-4498 USA Thanks in advance for your time and experience. From owner-software@net.bio.net Sat Nov 06 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!uknet!pipex!uunet!ulowell!woods.ulowell.edu!leylandr From: leylandr@woods.ulowell.edu Newsgroups: bionet.molbio.methds-reagnts,bionet.software,bionet.software.pc Subject: DATABASE for Restriction Enzyme Buffers! Message-ID: <1993Nov7.094217.1@woods.ulowell.edu> Date: 7 Nov 93 14:42:17 GMT Organization: University of Massachusetts Lowell Lines: 13 Xref: biosci bionet.molbio.methds-reagnts:8880 bionet.software:6413 NNTP-Posting-Host: aspen.uml.edu Our Massachusetts-based software development group is in need of feedback regarding our development of a database which facilitates buffer selection for use with commercially-available restriction enzymes. Has anyone experience with similar databases, and if so, which improvements would you suggest? We're always interested in researchers' suggestions for new and innovative laboratory software products, so drop us a line and outline your ideas! If we develop your suggestion, your lab will receive a complimentary copy! From owner-software@net.bio.net Sat Nov 06 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!europa.eng.gtefsd.com!library.ucla.edu!csulb.edu!csus.edu!netcom.com!vdvk From: vdvk@netcom.com (Didier Vanderveken) Newsgroups: sci.chem,comp.sys.mac.scitech,fj.sci.chem,bionet.software,sci.comp-aided,sci.techniques.xtallography Subject: List of Molecular Graphic Packages Message-ID: Date: 7 Nov 93 02:27:08 GMT Organization: Catalytica Lines: 73 Xref: biosci sci.chem:8435 comp.sys.mac.scitech:639 bionet.software:6412 sci.comp-aided:279 sci.techniques.xtallography:20 X-Newsreader: TIN [version 1.2 PL1] Hi, I'm creating a list of molecular graphic packages for the "Frequently Asked Questions" of the Computational Chemistry List. The programs must be able to display a molecular structure from Cartesian, internal, or fractional coordinates. A first version of the database is available in the pub/vdvk directory at netcom5.netcom.com and at the osc server. The actual list of programs described in the database is : Subject: PC MOBY Subject: Unix/VMS AMPAC with Graphical User Interface Subject: UNIX MOIL-View Subject: SGI INTERCHEM Subject: Unix, VMS, POSIX, DOS, LINUX, SUN-OS : WHAT IF Subject: Macintosh CSC_Chem3D_Plus Subject: Mac Ball & Stick Subject: Mac PC ALCHEMY III Subject: PC STR3DI.EXE, Ver. 6.30 Subject: CRAY/SGI/X-Window UniChem If you are an author or distributor of such program, could you please send me the appended form. If you are aware of other programs, could you please forward this message to the author or distributor of the missing software. Thanks in advance for your cooperation, Didier Vanderveken Catalytica Inc. email: vdvk@netcom.com 430 Ferguson Drive phone: +1-415-940-6241 Mountain View CA 94043-5272 fax: +1-415-960-0127 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The format of the database is like a mailbox. You are able to read it with your mail reader. I would like to limit my job to the merging of all emails. Anonymous posting will not be accepted and your email address will appear in the database. The subject line MUST be the type of computer (UNIX, PC, Mac) and the name of the program, like: UNIX MyProgram Feel free to remove a line or to duplicate a line. Each line must start with one of the defined keyword. If you would like to see more keywords, send me a separate email. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Program_Name: Program_Version: latest version available Program_Date: date of the latest version Topic: simple_molecule, drug, crystal, polymer, protein, inorganic, ... Bibliographic_Ref: If you published an article about your program Input_Format: PDB, CSD, ORTEP, XYZ, MOPAC, ... Output_Format: PDB, CSD, ORTEP, XYZ, ... Molecular_Model: wire, stick, stick_and_ball, CPK, ribbon, alpha_trace, ... Output_Type: display, PostScript, HPGL, PICT, GIF, ... Operating_System: Unix, Mac, MSDOS, Windows, ... Computer_Type: IBM RS/6000, SGI Indigo, ... Hardware_Requested: dials, coprocessor, ... Hardware_Supported: stereo_display, ... Graphic_Library: GL, PHIGS, X11, ... Distribution_Method: public_domain, freeware, shareware, commercial, ... Ftp_Site: Ftp_Directory: Price_Academic: Price_Private: Contact_Affiliation: Contact_Name: Contact_Phone: +1-234-567-8901 (international number of the headquarters) Contact_Fax: Contact_Email: From owner-software@net.bio.net Sun Nov 07 22:00:00 1993 Path: biosci!micro.uct.ac.za!ED From: ED@micro.uct.ac.za ("RYBICKI, ED") Newsgroups: bionet.software Subject: Re: Windows telnet and ftp software Message-ID: Date: 8 Nov 93 07:36:53 GMT Sender: news@net.bio.net Reply-To: ed@micro.uct.ac.za Distribution: bionet Lines: 34 > In article <9311051920.AA19760@audrey.lmf.org>, writes: > > > I am a Windows PC user. However I cuurently use a dos Kermit to do Telnet > > and a dos FTP. Are there any good WINDOWS software to do telnet and FTP?? ... > > I've been using Chameleon TCP/IP ... The one drawback is price, about $400 for the package. It > also includes a WinSock interface that works great with the Gopher+ client I've > got running. Try QVTNET from your favourite FTP site: shareware, excellent telnet capabilities, good newsreader, good ftp, mailer...I regularly have up to 3 VAX windows open simultaneously and an ftp session grinding away, then read mail! Also newest version(s? up to 3.8 now) support Winsock 1.1, otherwise packet-driven. ____________________________________________________________________ | Ed Rybicki, PhD | | | (ed@micro.uct.ac.za) | "Lord, won't you buy me | | Dept Microbiology | A Mer-ce-des Benz | | University of Cape Town | My friends all have Porsches | | | I must make amends..." | | | Private Bag, Rondebosch | | | 7700, South Africa | - Janis Joplin | | fax: 27-21-650 4023 | (Pearl, 1971) | -------------------------------------------------------------------- From owner-software@net.bio.net Sun Nov 07 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!sunic!news.funet.fi!news.csc.fi!funic!nic.funet.fi!csc.fi!harper From: Rob.Harper@csc.fi (Rob Harper) Newsgroups: bionet.software Subject: Lynx 2.0.12 now available! Message-ID: <199311080851.AA18928@csc.fi> Date: 8 Nov 93 08:51:30 GMT Sender: root@nic.funet.fi (The FUnny NET guru) Organization: Finnish University & Research Network Lines: 115 I suppose many people are becoming interested in WWW/Xmosaic For those of you who do not have Xwindows capabilities and would like to experiment with the World Wide Web then Lynx will highlight options within a hypertext document and allow you to select them by moving through the text with the tab key. Get it if you wont give up your VT100 terminal;-) %%%%%%%%%%%%%%%%%%%%%%%%%% CLIP %%%%%%%%%%%%%%%%%%%%%%%%%%% Lynx Ver. 2.0.12 is now available for anonymous ftp from FTP2.cc.ukans.edu as /pub/lynx/lynx2-0-12.tar.Z ( ftp://ftp2.cc.ukans.edu/pub/lynx/lynx2-0-12.tar.Z ) Lynx is a distributed hypertext browser with full World Wide Web and Gopher capibilities. For an explanation of features and a demo, telnet to "kufacts.cc.ukans.edu" and login as "www". This release of Lynx has been compiled by me on the following platforms: o IBM (AIX 3.2) o DEC Ultrix o DEC Alpha OSF/1 o Sun 4 o NeXT (Mine is an older version of NeXTStep, but it should work with newer ones too.) o VMS (Multinet) This release is rumored to compile on the following platforms: o HP-UX (snake) o Solaris 2 o SVR4 o VMS (UCX) o LINUX o SGI o SUN 3 o AIX 3.1 o NeXTStep 3.x Binaries for the following platforms are available: o IBM (AIX 3.2, will work with 3.1 as well) o Ultrix o Alpha OSF/1 o Sun 4 o VMS (Multinet) A listserv list has been created for the distribution of Lynx related information and updates. o Lynx-Dev@ukanaix.cc.ukans.edu Send a subscribe request to listserv@ukanaix.cc.ukans.edu to be added to the list. All new releases will be anounced on this list. Please do not send subscribe requests to the the Lynx-Dev list directly. The following new features have been added: * added preliminary level 1 forms support. (Parsing and user display works, but nothing else) I'm looking for input on the forms interface! * interuptable I/O added. Hit the 'a' key for "abort" during transfers. Its a little flakey right now during connections, but it works most of the time :) * local HTML documents ending in .html can now be referenced with just a filename and/or path from the command line. * Added preloaded searches to gopher URL's. They previously didn't work. This is readily apparent as preloaded CSO searches, which alot of people wanted. (bug?) * added descriptive subject lines to files mailed from lynx * added "X-within-URL" mail header line to specify which URL from which files, comments, and mailto links are sent from. * The user's specified editor is now spawned for mail messages. If no editor is defined or if the user is anonymous, the built-in lynx mail sender is used. * added progress messages to all transfers. * added -cache=# command line option to specify the number of WWW documents cached in memory. * added VMS port fixes from Foteos Macrides. Lynx now compiles and works on VMS! (bug?) * Moved many configuration options including printer setup to lynx.cfg file. The default placement of the lynx.cfg file will be /usr/local/lib & sys$public. Printers can now be configured without recompiling! * Removed STARTDIR variable from userdefs.h STARTDIR is now inferred from the STARTFILE. (doesn't effect HTML files) * Ported to SVR4 courtesy of Nickolay Saukh (from Russia, Wow this is really getting around!) * Uneditable documents don't get refetched. (Nickolay Saukh) * National language support through LOCALE (instead of ISOLATIN1), protected by #ifdef LOCALE (Nickolay Saukh) A partial list of bugs that have been fixed * disabled FTP connection caching to help fix multiple FTP problems * fixed a bunch of gopher holes * gopher lists are turned into URL's now instead of lynx internal format document links * removed old hytelnet compatibility code which looked in multiple directories to find the correct file. If you still need this capibility talk to me. * changed all static data structures to be dynamic This was a pretty major change of code which may add several bugs. :) * rewrote parse_links routine to make it more efficient and to work with dynamic structures. * added VMS port fixes from Foteos Macrides. Lynx now compiles and works on VMS! * fixed ftp bug in WWWlib that didn't de-escape URL's before sending request to FTP server. * fixed coredump bug for some files with no links. * Fixed bug with only one link selectable out of many on the last line of the display. From owner-software@net.bio.net Sun Nov 07 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!munnari.oz.au!metro!usage!news From: Shaharin Yussof Newsgroups: bionet.software Subject: Re: Trumpet and winsoc Message-ID: <1993Nov8.005857.8220@usage.csd.unsw.OZ.AU> Date: 8 Nov 93 00:58:57 GMT Sender: news@usage.csd.unsw.OZ.AU Organization: Department of Safety Science Lines: 34 Nntp-Posting-Host: 149.171.28.200 X-Newsreader: In article fenton@nemo.life.uiuc.edu (Jim Fenton) writes: >Shaharin Yussof writes: > >>In article <16C7CDC3A.030NEILV@Witsvma.wits.ac.za> 030NEILV@Witsvma.wits.ac.za (Neil van der Merwe) writes: >>>Hi, >>>Can anyone tell me where I can get hold of Trumpet and Winsoc? I also >>>need some info on winsoc, as I am totally unfamiliar with it. >>>Thanks in advance, >>>Neil > >>Try anonymous ftp to biochemistry.cwru.edu > >>You might also try the shareware QVTNET as a TCP/IP, mail, newsreader, and FTP >>program. It is available in the same place. > >>Shaharin > >Is it just me or did QVTNET work for others. I never got the lpr print stuff >to work properly, the windows version was amazingly slow and wouldn't >work with our NFS network (yes, we have a weird mix of unix and pc's that >adds some difficulties). I'm much more happy since I turned our PC's running >windows into X terminals with eXceed/W for windows. Of course, this isn't >shareware, but it wouldn't surprise me to find that there are public domain >versions of X emulators available. >-- > Jim Fenton fenton@nemo.life.uiuc.edu Frankly, I haven't the foggiest idea whether or not the lpr stuff works. We don't run a UNIX machine in our department, and our remote printing is done using Windows for Workgroups. All the other bits work wonderfully though. Shaharin From owner-software@net.bio.net Sun Nov 07 22:00:00 1993 Path: biosci!news.cs.umb.edu!hsdndev!howland.reston.a