From owner-software@net.bio.net Fri Jul 01 23:00:00 1994 Newsgroups: bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Subject: Re: Power PC Stats Message-ID: Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: sunflower.bio.indiana.edu Organization: Biology, Indiana University - Bloomington References: <199407012100.OAA02046@net.bio.net> Date: Fri, 1 Jul 1994 23:49:32 GMT Lines: 19 I'm using a quadra 700 with a PowerPC card (that was the first quadra). With the PowerPC turned on, running at the speed of a PowerMac 6100, general non-powerpc software "feels" about the same as with the old quadra 700. When I run software compiled for the PowerPC, zoom-zoom... (meaning from 3 to 10 times faster than the Quadra). You don't have to worry about this choice -- your PowerPC Mac will only get faster (as the software companies update their programs with PowerPC versions). Get WordPerfect version 3.1, due out very soon, which is a "fat binary" that runs native PowerPC code on such macs. It'll outperform MS Word (and speed can be important in a wordprocessor when doing complex formats or graphics). I don't know if Systat has a powerpc version yet, but be certain they will soon. -- Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Fri Jul 01 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!newsserver.jvnc.net!yale.edu!yale!hsdndev!nmr-z.mgh.harvard.edu!Frodo.MGH.Harvard.EDU!BURGLIN From: burglin@Frodo.MGH.Harvard.EDU (Thomas Burglin) Newsgroups: bionet.software Subject: Re: Power PC Stats Date: 2 Jul 1994 15:34:33 GMT Organization: Molecular Biology, Massachusetts General Hospital Lines: 27 Distribution: world Message-ID: <2v41e9$92f@nmr-z.mgh.harvard.edu> References: <199407012100.OAA02046@net.bio.net> Reply-To: burglin@Frodo.MGH.Harvard.EDU NNTP-Posting-Host: frodo.mgh.harvard.edu >Hello, I am in the process of deciding whether or not to get a Power PC and co >uld use some advice from anyone who has and is using one. The machine I am con >sidering is a 7100 with 8MB and CD and 250HD. What I want to run are word proc >essing like word or Wordperf, spreadsheet like Excel, and stats package such as > systat. Additionally I may add on something to edit photo images for slide pr Hello, It all depends on the software, if you can get it in PowerPC native code. Wordperferct is out in PPC code. The emulation of the PPCs is about equivalent to a IIci or a Quadra 605, depending on what operation it is. However, the emulation does not emulate a FPU (math coprocessor)! If systat is not available in PPC code, it won't run! CAll them up and ask about a PPC version Excel will run, since it automatically determines the presence of a FPU, but in emulation mode any math operations will be slow. Excel and Word should come out later in the year in PPC code. You might want to consider a Quadra 650, plus a PPC upgrade card from Apple, it's a combination that is slightly cheaper than a 7100, but has a similar CPU power (except you won't get a couple of PowerPC goodies such a geoport and 2 meg vram expansion) and you can run software screaming fast in 68040 or PPC (you need to restart to switch though). Thomas Burglin From owner-software@net.bio.net Fri Jul 01 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!doc.ic.ac.uk!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!uunet!newsgate.watson.ibm.com!hawnews.watson.ibm.com!puffin!dflash From: dflash@watson.ibm.com (The dFLASH Project) Subject: Announcing GENBANK and PIR search engine (The dFLASH server) Sender: news@hawnews.watson.ibm.com (NNTP News Poster) Message-ID: Date: Tue, 28 Jun 1994 04:07:19 GMT Disclaimer: This posting represents the poster's views, not necessarily those of IBM. Nntp-Posting-Host: puffin.watson.ibm.com Organization: IBM T.J. Watson Research Lines: 417 The dFLASH Group announces the release of a new electronic mail server that allows GENBANK and PIR similarity searches with the FLASH algorithm. The server is accessible through the internet and is now operating 24 hours a day, 7 days a week. Appended, you will find the new server's help file. Sincerely, The dFLASH Group ------------------------------> CUT HERE <----------------------------------- !! ==================== MESSAGE OF THE DAY ========================== !! !! !! !! June 14, 1994: We are now supporting both GENBANK & PIR searches !! !! Releases: PIR 40 (no incremental updates) !! !! & GENBANK 82 (no incremental updates) !! !! June 12, 1994: The VERBOSE directive now works correctly. !! !! November 16, 1993: Beginning today, *NO* registration is required !! !! in order to use the dflash server. !! !! !! !! ==================== MESSAGE OF THE DAY ========================== !! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !! !! !! N O T A B E N E !! !! The dFLASH server is still under development. If some of the answers do !! !! not make sense it is very likely that this is due to a bug in our code. !! !! Please, help us improve this service by reporting such bugs: you can !! !! email bug reports and comments to dflash@watson.ibm.com with subject line !! !! "bug" or "comments". !! !! !! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Dear User, welcome to the dFLASH server! The dFLASH server is a "homologous sequence retrieval" program for PROTEIN and DNA sequences. We currently support the following databases: PIR -- Release 40 with *no* incremental updates. For more information, contact: Protein Information Resource (PIR), National Biomedical Research Foundation 3900 Reservoir Road, N.W., Washington, DC 20007, USA GenBank -- Release 82 with *no* incremental updates For more information, contact: National Center for Biotechnology Information National Library of Medicine, 38A -- 8N805, 8600 Rockville Pike Bethesda, MD 20894, USA dFLASH is a parallel system running on a prototype 16-node IBM SP/1. Intra-node communication, evidence integration and alignment are performed in parallel and use a prototype interconnection network. The currently observed performance is estimated to be between 2 and 5 times slower than that of a production line SP/1. The system has been implemented using IBM's Concert/C language for distributed programming. The server is now available 24 hours a day, 7 days a week. Backups are perfomed daily between 01:00 and 01:30 Eastern Standard Time, so performance is likely to be affected during this period. At the moment we automatically alternate service between the GenBank and PIR servers and thus certain lag may be observed: this will be alleviated in future releases of the server code. Incremental changes and improvements made to the server will be reflected in the "Message of the day" at the beginning of this help file: we recommend that users periodically issue a `send help' request for up to date information on the server. For the moment, we can process requests originating from email addresses of the form user@[machine.][subdomain.]institution.type or user%machine@[machine.][subdomain.]institution.type or "string::user"@[machine.][subdomain.]institution.type We plan to further expand the accepted formats, depending on demand. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ HOW TO USE THE SERVER: You can use the dFLASH facilities by sending an email ---------------------- message with the appropriate syntax to the address "dflash@watson.ibm.com" (without the quotes). SUBJECT LINE: It is important that the "Subject" line of your message contain ------------- one of: { dflash, dFlash, dFLASH, DFLASH }. Messages whose subject line does NOT conform to this rule, **WILL BE LEFT UNPROCESSED**. The reason for that restriction is that we want to be able to automatically distinguish between messages that are addressed to the server and those that are meant for one of the group members. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ MESSAGE FORMAT: The typical message-body of an email request looks as follows --------------- BLOSUM 250 (optional | DIRECTIVE) VERBOSE 10 20 (optional | DIRECTIVE) SEQUENCES 100 (optional | DIRECTIVE) ALIGNMENTS 50 (optional | DIRECTIVE) THRESHOLD 30 (optional | DIRECTIVE) TARGET PROTEIN (optional | DIRECTIVE) BEGIN (mandatory | DIRECTIVE) >A_ONE_LINE_TEST_SEQ_LABEL (mandatory -- notice the '>' ) a_sequence_of_{amino_acids,spaces,tabs} 1 (mandatory terminator) The PAM/BLOSUM, VERBOSE, SEQUENCES, ALIGNMENTS, THRESHOLD, and TARGET directives can appear in any order but they *must* precede the BEGIN directive. The BEGIN line must be followed by the LABEL line which in turn should be followed by the test sequence. The test sequence should contain at least 30 and not more than 3,000 amino acid or nucleotide characters. But it may contain ANY NUMBER of CARRIAGE RETURN TAB and SPACE characters; the latter are not of course counted while computing the length of the test sequence. There is NO case sensitivity in the label and the test sequence itself. The words appearing on the lines marked DIRECTIVE above can be in lower case or upper case; in other words, you can have pam or PAM, threshold or THRESHOLD, alignments or ALIGNMENTS, etc. However, something like ThReShOlD will not work. The directive pertaining to the scoring matrix allows the user to specify the matrix to be used for computing the alignment scores. You can use either the word PAM followed by a space and the desired distance, or the word BLOSUM followed by space and the desired distance. Examples: PAM 250, BLOSUM 62 etc. If no matrix directive is included in the message, PAM 250 is used as the default. Depending on the values of the directive TARGET (see below) the matrix directive if present may be ignored. The VERBOSE line allows the sender to also retrieve the data about authors, dates, entries, superfamilies etc. that are contained in the original PIR and GenBank databases. This directive accepts one OR two arguments; for example: verbose 15 25 means "send me the text data for the sequences occupying positions 15 through 25 in the final ranking." On the other hand, verbose 15 means "send me the text data for the sequences occupying the first 15 positions in the final ranking." If no verbose line appears, no citation data is sent. The SEQUENCES line allows one to restrict the reported sequences to the given number. This directive controls the number of entries in the ``short list'' of recovered database sequences only. If no SEQUENCES line is given, the server code will set it to an appropriate default value. The ALIGNMENTS line allows one to restrict the reported alignments to the given number. If no ALIGNMENTS line is given, the server code will set it to an appropriate default value. The ALIGNMENTS value cannot exceed 1000. Values larger than 1000 are reduced to 1000. The THRESHOLD line allows one to restrict the number of reported sequences (and thus alignments) to only those whose Score exceeds the given THRESHOLD value. If no THRESHOLD line is given the server code will set it to an appropriate default value. The default values are 50 for DNA sequences, and 80 for PROTEIN sequences. There is also a *hard* threshold value of 20 for DNA, and 30 for PROTEIN sequences; if the user-requested values are smaller than these hard-thresholds, the requested threshold will be increased accordingly. NOTA BENE: (1) if the THRESHOLD value is too small, you are running the danger --------- of upsetting your mailer program since chances are that you will receive a very big file as a reply from the server. (2) if the THRESHOLD is too high the list of recovered entries will be empty, or very short; you should decrease the threshold's value and resubmit your query. The TARGET line allows the user to specify the type of the target database, as being one of { PROTEIN , DNA }. This way the user controls the database in which the search will be carried out. If TARGET is set to PROTEIN, the search will take place in the PIR database. If TARGET is set to DNA, the search will take place in the GenBank database. We will soon allow users to 'mix and match.' I.e. the users will be able to request that amino acid sequences be searched againt GenBank, nucleotide sequences against PIR etc. by making use of the appropriate directives. If no TARGET line is given, the server will assume the default value PROTEIN and thus will search against the PIR database. The LABEL line allows the user to enter mnemonic information pertaining the the test sequence, the time of the day etc. The information of this line will be reproduced in the Subject line of the reply message. Notice that the LABEL line *must* begin with the character '>'. All the submitted messages must be terminated by the number '1' This number can follow the last character of the test sequence or be in a line by itself. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ EXAMPLES: Two example inputs follow --------- Example 1: pam 250 sequences 50 alignments 30 threshold 100 target protein begin > HBA_HUMAN STANDARD; PRT; 141 AA. P01922; HEMOGLOBIN ALPHA VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFP TTKTYFPHFDLSHGSAQVKGHG KKVADALTNA V A H V D D M PNALSALSDLHAHKLRVDPVNFK llshcllvtlaahlpaeftpavhasldkflasvstvltskyr 1 Note: all amino acids from "VLSP" through "ltskyr will be used in the search. Not more than the 50 top scoring sequences will be reported in the short list. Also, the alignments for the top 30 scoring sequences will be returned. No reported sequence will have score that is less than 100. The test sequence is declared to be a sequence of amino acids and should be searched against the PIR database. Example 2: BLOSUM 62 BEGIN > Sequence sent to dflash on Fri May 20 13:40:17 EDT 1994 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFP TTKTYFPHFDLSHGSAQVKGHG KKVADALTNA V A H V D D M PNALSALSDLHAHKLRVDPVNFK llshcllvtlaahlpaeftpavhasldkflasvstvltskyr 1 Note: all amino acids from "VLSP" through "ltskyr" will be used in the search. The server code will set the various parameters to appropriate default values. The server will treat the test sequence as a sequence of amino acids (default) and will search against the PIR database (default) with a score threshold set at 80 (default). $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ SCORING MATRICES: ----------------- You can use both PAM and BLOSUM scoring matrices for protein searches. These can be requested via the optional { pam, PAM, blosum, BLOSUM } directive. The currently supported distances are for BLOSUM: 30, 35, 40, 45, 50, 55, 60, 62, 65, 70, 75, 80, 85, 90, 100 for PAM: 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, and 500. For DNA searches, the PAM/BLOSUM declarations are ignored $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ NOTE ON ALIGNMENT: ------------------ The server's alignment code implements the Smith-Waterman algorithm (dynamic programming) to align each of the retrieved sequences with the test input. This is *NOT* to be confused with the indexing method that we use to determine the candidates to be aligned. The meaning of the variables in the listing that is returned by the dFLASH server ..... .... Score Matrix: PAM250 Max Reported Sequences: 1000 Max Reported Alignments: 10 Score Threshold At: 65 Id Label: Score NRes Ex% Tot% Sig Pk ---------------------------------------------------------------------------- 1. HAHU hemoglobin alpha chain - human 655 141 100% 100% 100 89 2. HACZ hemoglobin alpha chain - chimpanzee 655 141 100% 100% 100 89 3. HACZP hemoglobin alpha chain - pygmy chi 655 141 100% 100% 100 89 4. HAGO hemoglobin alpha chain - lowland go 654 141 99% 100% 99 89 5. HAMQP hemoglobin alpha chain - hanuman l 653 141 97% 100% 99 89 6. B27792 hemoglobin alpha-1 chain - orangu 649 141 97% 100% 99 89 7. A25126 hemoglobin alpha-1 chain - Sumatr 649 141 97% 100% 99 89 ... ..... .. is the following: NRes: the number of residues (amino acids) in the recovered match Score: sequence similarity score of the recovered sequence based on the selected mutation matrix Ex%: percentage of *exact* matching residues Tot%: percentage of *total* (=exact+conservative) matching residues Sig: 100 times the ratio between the actual computed score and the score obtained by matching the retrieved sub-segment with itself; the denominator is the maximum obtainable score for the sub-segment in question (all gaps removed). Peak: the maximum score value over *any* 20 residue-window of the recovered match $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ TO OBTAIN HELP: --------------- You can obtain this message at any moment by sending a message with one of: { dflash, dFlash, dFLASH, DFLASH } in the "Subject" line and a body containing one of { help, HELP, send help, SEND HELP }. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ TO OBTAIN ON-LINE REPRINTS OF PAPERS ------------------------------------ You can obtain reprints (in PostScript) of relevant papers by sending a message with one of: { dflash, dFlash, dFLASH, DFLASH } in the "Subject" line and a body containing one of {flashpaper, FLASHPAPER, send flashpaper, SEND FLASHPAPER } ---> returns to the originator of the request a copy of the FLASH paper one of {dflashpaper, DFLASHPAPER, send dflashpaper, SEND DFLASHPAPER } ---> returns to the originator of the request a copy of a paper that contains a description of dFLASH (long) one of {concertpaper, CONCERTPAPER, send concertpaper, SEND CONCERTPAPER } ---> returns to the originator of the request a copy of a high-level paper describing the CONCERT/C language one of {bayespaper, BAYESPAPER, send bayespaper, SEND BAYESPAPER } --> returns to the originator of the request a copy of a paper describing a computer-vision application based on similar to dFLASH indexing principles (long) Notice there can only be *one* such request per message! Also, make sure you do not issue a new paper request until after the previous request has returned to you all of the postscript files and you have removed the latter from your mailbox: the returned messages are rather big (between 1 and 4 Megabytes) and are guaranteed to overflow the disk set aside for mail messages on most systems. $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ OTHER NOTES: ------------- (1) for the time being we do not incorporate incremental updates of PIR (2) for the time being we do not incorporate incremental updates of GenBank (3) dFLASH searches are currently available through GRAIL of the Oak Ridge National Laboratory. Thank you for your interest in the dFLASH server. Sincerely, The dFLASH Group $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ COMMENTS?? We will appreciate receiving your feedback, suggestions, comments, ---------- or bug reports; all of these can be sent to "dflash@watson.ibm.com" Please, make sure your "Subject" line contains the word "comments" or "bug". $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ REFERENCES If you make use of the dFLASH server, please reference ---------- A. Califano and I. Rigoutsos, "FLASH: A Fast Look-up Algorithm for String Homology." In Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, July 1993, Bethesda, MD. I. Rigoutsos and A. Califano, "Searching In Parallel for Similar Protein Strings." In IEEE Computational Science and Engineering, June 1994. If you wish to find out more, you can contact Isidore Rigoutsos and Andrea Califano at {rigoutso,acal}@watson.ibm.com $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ For more information on the Concert/C language, please refer to J. Auerbach, D. Bacon, A. Goldberg, G. Goldszmidt, A. Gopal, M. Kennedy, A. Lowry, J. Russell, W. Silverman, R. Strom, D. Yellin, and S. Yemini, "High-level language support for programming reliable distributed systems." In Proceedings of the International Conference on Computer Languages, April 1992, Oakland, California. or contact Jim Russell (jrussell@watson.ibm.com) $%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$%$ ------------------------------> CUT HERE <----------------------------------- From owner-software@net.bio.net Fri Jul 01 23:00:00 1994 Newsgroups: bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!msuinfo!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!menzies.su.edu.au!garry From: garry@menzies.su.edu.au (Garry Myers) Subject: GCG and X-windows Message-ID: Lines: 15 Sender: news@ucc.su.OZ.AU Nntp-Posting-Host: 192.94.208.54 Organization: Menzies School of Health Research X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] References: Date: Sat, 2 Jul 1994 00:10:52 GMT Hi, Could somebody point me in the direction of a X-front end for GCG called "gcgnav". I found the reference to this via the bionet archives but have so far been unable to get in contact with the original poster. Any comments or suggestions for other (if any) X interfaces for GCG also appreciated. Cheers, Garry. ___________________________________________________________________ Garry Myers Menzies School of Health Research Molecular Genetics Unit garry@menzies.su.edu.au ___________________________________________________________________ From owner-software@net.bio.net Fri Jul 01 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!rat!decwrl!tribune.usask.ca!canopus.cc.umanitoba.ca!hamel From: hamel@cc.umanitoba.ca (Andre Hamel) Newsgroups: bionet.software Subject: Re: primer design(preferences) Date: 2 Jul 1994 15:46:01 GMT Organization: University of Manitoba, Winnipeg, Manitoba, Canada Lines: 9 Message-ID: <2v423p$f4v@canopus.cc.umanitoba.ca> References: <1994Jun29.082947.4752@tower> NNTP-Posting-Host: asimov.cc.umanitoba.ca Primer design? ... try PRIMER by Lander of Whitehead group at MIT. Free ... works best under UNIX. They provide great service (available by email ... though I ddon't have their address handy). cheers, Andre From owner-software@net.bio.net Sat Jul 02 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!uchinews!gsbacd.uchicago.edu!crsp_nq From: crsp_nq@gsbacd.uchicago.edu Subject: >< Ophthalmology articles on CD >< Message-ID: <1994Jul3.124732.1@gsbacd.uchicago.edu> Lines: 11 Sender: news@uchinews.uchicago.edu (News System) Organization: ˙˙˙˙ Date: Sun, 3 Jul 1994 18:47:32 GMT What's Up Doc, I am posting it for my brother overseas. He is an ophthalmologist. he wants to know if there's any source of information available on CD. i.e. Medical journals, articles etc. He is interested in research in Ophthalmology. BTW, is this the correct place to post this entry? Thanks in advance Naushad A Qureishi (708) 213-0451 From owner-software@net.bio.net Sun Jul 03 23:00:00 1994 Path: biosci!agate!doc.ic.ac.uk!uknet!daresbury!not-for-mail From: "Simon Cook, MRC Virology User/Computer Support x6268: +44 41 330 4017 or +44 41 339 8855." Newsgroups: bionet.software Subject: Email addresses for EMBL and MIPS... Date: 4 Jul 1994 09:42:09 +0100 Lines: 11 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2v8i11$jl0@mserv1.dl.ac.uk> Original-To: BIO-SOFTWARE@dl.AC.UK Hello, I'm trying to find two email addresses for EMBL with reference to the EMBL data library, and Martinsried Institute for Protein Sequences (MIPS) with reference to the PIR data library. Thanks in advance for your help. Cheers, Simon. From owner-software@net.bio.net Sun Jul 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!pipex!sunic!EU.net!uunet!zib-berlin.de!news.dfn.de!gwdu03.gwdg.de!plewe From: plewe@dl.mpi-dortmund.mpg.de (J.Plewe) Subject: Wanted: X-routines for simple 3D diplay Message-ID: <89AQB43I@gwdu03.gwdg.de> Sender: news@gwdu03.gwdg.de (USENET News System) Nntp-Posting-Host: dl.mpi-dortmund.mpg.de Organization: GWDG, Goettingen X-Newsreader: TIN [version 1.1 PL8] Date: Mon, 4 Jul 1994 09:42:20 GMT Lines: 27 Hello! I am looking for a set of X-routines in order to be able to draw molecules and perhaps other geometrical objects. I best would like routines of the form draw_ball(x,y,r) or something like that. Can anybody help me? - Joerg ********************************************************************* Dipl. Phys. Joerg Plewe joerg.plewe@mpi-dortmund.mpg.de MPI fuer molekulare Physiologie Rheinlanddamm 201 44139 Dortmund Germany +49 (0)231 1206 384 ********************************************************************* From owner-software@net.bio.net Sun Jul 03 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!xlink.net!fauern!news.th-darmstadt.de!news From: dh7y@.pop.th-darmstadt.de (Inst. f. Biochemie) Newsgroups: bionet.software Subject: Fig. P from Biosoft: Users wanted! Date: 4 Jul 1994 08:27:54 GMT Organization: TH Darmstadt Lines: 7 Message-ID: <2v8h6a$i0i@rs18.hrz.th-darmstadt.de> NNTP-Posting-Host: bc3.bc.chemie.th-darmstadt.de X-Newsreader: WinVN 0.90.6 We are currently using Biosoft's Fig. P for Data presentation. With the new version 2.1a we have a lot of problems! I would be very happy if there is a Fig. P user who can share his and my problems! Please mail: Internet dh7y@pop.th-darmstadt.de Bye, Michael :-) From owner-software@net.bio.net Sun Jul 03 23:00:00 1994 Newsgroups: bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!torn!utnut!erin.utoronto.ca!tuzo.erin!nwinegar From: nwinegar@tuzo.erin (Neil Winegarden) Subject: Bio-rad Image Analysis Message-ID: Sender: news@credit.erin.utoronto.ca (Usenet News) Nntp-Posting-Host: tuzo.erin Organization: Erindale College, University of Toronto, Canada Date: Mon, 4 Jul 1994 18:27:57 GMT Lines: 13 Does anyone know of a program which can convert standard Tiff or Pict files to ones which can be imported into Bio-rad's image analysis software? Their software is good but it can only load up files which it has saved. I know it can export to Tiff and Pict but it cannot import. Any help would be greatly appreciated. -- ________________________________ Neil Winegarden University Of Toronto nwinegar@credit.erin.utoronto.ca From owner-software@net.bio.net Sun Jul 03 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!pipex!uknet!bcc.ac.uk!arco2.afrc.ac.uk!woodwark From: woodwark@arcu.afrc.ac.uk (Mathew Woodwark) Newsgroups: bionet.software Subject: Re: GCG and X-windows Date: 4 Jul 1994 13:02:55 GMT Organization: Biotechnology & Biological Sciences Research Council Lines: 12 Distribution: world Message-ID: <2v919v$il3@arco2.afrc.ac.uk> References: Reply-To: woodwark@arcu.afrc.ac.uk (Mathew Woodwark) NNTP-Posting-Host: arcu.afrc.ac.uk X-Newsreader: mxrn 6.18-4 In response to Gary Myers request for info on GUI interfaces for GG, the recent issue of CABIOS (vol 10, number 3, June 1994) has an article on a n openlook interface OLGCG. (Sammons and Dykes). Scott Sammons is willing to distribute the software. He is at bcresas@bimcore.emory.edu. It might be worth your while getting in touch with him. All the best Mathew (I just read the article, I have no connnection with the authors etc) From owner-software@net.bio.net Mon Jul 04 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!EU.net!sun4nl!uva.nl!amc.uva.nl!les From: les@amc.uva.nl (Les Grivell) Newsgroups: bionet.software Subject: Problems compiling Fasta and Blast under Linux Date: 5 Jul 94 12:12:41 GMT Organization: Central Computer Department - Faculty of Medicine - Univ. of Amsterdam Lines: 117 Message-ID: NNTP-Posting-Host: amcnol.amc.uva.nl Keywords: Blast Fasta Linux Has anyone successfully compiled Fasta and or Blast under Linux? If so, I would be grateful fo any advice: attempts so far have resulted in the following output. Fasta cc -g -DUNIX -DBIGMEM -DHZ=100 -c time.c time.c:19: conflicting types for `stime' /usr/include/time.h:53: previous declaration of `stime' make: *** [time.o] Error 1 cc -g -DUNIX -DBIGMEM -c -DMAXSAV=10 urdf.c urdf.c: In function `main': urdf.c:152: too few arguments to function `exit' urdf.c:157: too few arguments to function `exit' urdf.c:216: too few arguments to function `exit' urdf.c:239: too few arguments to function `exit' urdf.c: In function `allocdiag': urdf.c:962: too few arguments to function `exit' make: *** [urdfn.o] Error 1 cc -g -DUNIX -DBIGMEM -c bestscor.c bestscor.c: In function `main': bestscor.c:55: too few arguments to function `exit' bestscor.c:60: too few arguments to function `exit' make: *** [bestscor.o] Error 1 cc -g -DUNIX -DBIGMEM -c lalign.c lalign.c: In function `initseq': lalign.c:351: too few arguments to function `exit' make: *** [lalign.o] Error 1 cc -g -DUNIX -DBIGMEM -DTPLOT -c lalign.c lalign.c: In function `initseq': lalign.c:351: too few arguments to function `exit' make: *** [plalign.o] Error 1 cc -g -DUNIX -DBIGMEM -c -DMAXSAV=10 urss.c urss.c: In function `main': urss.c:96: too few arguments to function `exit' urss.c:101: too few arguments to function `exit' urss.c:153: too few arguments to function `exit' urss.c:174: too few arguments to function `exit' make: *** [urss.o] Error 1 cc -g -DUNIX -DBIGMEM -c align.c align.c: In function `initseq': align.c:291: too few arguments to function `exit' make: *** [align.o] Error 1 make: Target `all' not remade because of errors. Blast cd lib; make CC="gcc" CCOPT="-g" OPTIONS=" -DREFINED_STATS " make[1]: Entering directory `/home/les/blaststuff/blast/lib' gcc -g -I../include -I../ncbi/include -I../gish/include -I../dfa -DREFINED_STATS -c banner.c -o banner.o In file included from banner.c:4: ../include/blast.h:169: warning: `NCHUNKS' redefined ../gish/include/gish.h:96: warning: this is the location of the previous definit ion In file included from banner.c:2: ../gish/include/gish.h:129: parse error before `key_t' ../gish/include/gish.h:129: warning: no semicolon at end of struct or union ../gish/include/gish.h:133: parse error before `}' ../gish/include/gish.h:133: warning: data definition has no type or storage clas s ../gish/include/gish.h:152: parse error before `shm_dat' ../gish/include/gish.h:152: warning: no semicolon at end of struct or union ../gish/include/gish.h:153: warning: data definition has no type or storage clas s In file included from banner.c:3: ../gish/include/gishlib.h:134: parse error before `*' ../gish/include/gishlib.h:134: warning: data definition has no type or storage c lass ../gish/include/gishlib.h:135: parse error before `shm_mkkey' ../gish/include/gishlib.h:135: warning: data definition has no type or storage c lass ../gish/include/gishlib.h:136: parse error before `*' ../gish/include/gishlib.h:137: parse error before `*' ../gish/include/gishlib.h:137: warning: data definition has no type or storage c lass ../gish/include/gishlib.h:140: parse error before `key' ../gish/include/gishlib.h:143: parse error before `*' ../gish/include/gishlib.h:143: warning: data definition has no type or storage c lass ../gish/include/gishlib.h:144: parse error before `*' ../gish/include/gishlib.h:145: parse error before `*' ../gish/include/gishlib.h:146: parse error before `*' ../gish/include/gishlib.h:147: parse error before `MFILE' ../gish/include/gishlib.h:148: parse error before `MFILE' ../gish/include/gishlib.h:149: parse error before `*' ../gish/include/gishlib.h:150: parse error before `*' ../gish/include/gishlib.h:153: parse error before `*' ../gish/include/gishlib.h:154: parse error before `*' ../gish/include/gishlib.h:155: parse error before `*' ../gish/include/gishlib.h:156: parse error before `*' ../gish/include/gishlib.h:157: parse error before `*' In file included from ../include/blast.h:187, from banner.c:4: ../include/shmutil.h:14: `shm_dat' redeclared as different kind of symbol ../gish/include/gish.h:133: previous declaration of `shm_dat' ../include/shmutil.h:14: warning: `shm_dat' was declared `extern' and later `sta tic' ../include/shmutil.h:19: conflicting types for `shm_attfile' ../gish/include/gishlib.h:134: previous declaration of `shm_attfile' ../include/shmutil.h:21: conflicting types for `shm_loadfile' ../gish/include/gishlib.h:137: previous declaration of `shm_loadfile' ../include/shmutil.h:23: parse error before `key' In file included from banner.c:4: ../include/blast.h:362: `MFILE' redeclared as different kind of symbol ../gish/include/gish.h:153: previous declaration of `MFILE' ../include/blast.h:362: warning: `MFILE' was declared `extern' and later `static ' ../include/blast.h:364: conflicting types for `mfil_open' ../gish/include/gishlib.h:143: previous declaration of `mfil_open' ../include/blast.h:490: conflicting types for `fatal' ../gish/include/gishlib.h:110: previous declaration of `fatal' make[1]: *** [banner.o] Error 1 make[1]: Leaving directory `/home/les/blaststuff/blast/lib' make: *** [always] Error 1 From owner-software@net.bio.net Mon Jul 04 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!EU.net!uknet!lyra.csx.cam.ac.uk!doc.ic.ac.uk!daresbury!bioftp.unibas.ch!embl-heidelberg.de!stoehr From: stoehr@embl-heidelberg.de (Peter Stoehr) Newsgroups: bionet.software Subject: Re: Email addresses for EMBL and MIPS... Message-ID: <1994Jul4.190337.171389@eros.embl-heidelberg.de> Date: 4 Jul 94 19:03:37 +0100 References: <2v8i11$jl0@mserv1.dl.ac.uk> Distribution: bionet Organization: European Molecular Biology Laboratory Lines: 13 In article <2v8i11$jl0@mserv1.dl.ac.uk>, "Simon Cook, MRC Virology User/Computer Support x6268: +44 41 330 4017 writes: > Hello, > I'm trying to find two email addresses for EMBL with reference to the EMBL > data library, and Martinsried Institute for Protein Sequences (MIPS) with > reference to the PIR data library. EMBL Data Library: DataLib@EMBL-Heidelberg.DE MIPS: mewes@ehpmic.mips.biochem.mpg.de Regards, Peter Stoehr EMBL Data Library From owner-software@net.bio.net Mon Jul 04 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!news.cac.psu.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!news.graphics.cornell.edu!ghost.dsi.unimi.it!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!sun.rediris.es!news.uam.es!samba.cnb.uam.es!jenfedaque From: jenfedaque@samba.cnb.uam.es Newsgroups: bionet.software Subject: Prokaryotic Promoter Recognizing Program (or Database) Date: 5 Jul 94 18:31:24 WET Organization: C.N.Biotecnologia, CSIC Lines: 21 Message-ID: <1994Jul5.183124.1@samba.cnb.uam.es> NNTP-Posting-Host: samba.cnb.uam.es I am looking for a program (PC or UNIX-based) or database of prokaryotic promoter sequences. If it exists, it should be able to build promoter consensus sequences of promoter regions sorted by type of gene: i.e. activators, structurals, etc. Alternatively, it may be able to recognize a putative promoter sequence in a DNA, and assign it to a family of promoters... If such a program does not exist, an structured database of promoters would be of help. (Though scanning it manually would be painful :-( If not, any bibliographic reference or review article will be welcome. Thanks a lot. Please answer to josefina@farmacia.ub.es Josefina Enfedaque josefina@farmacia.ub.es Dept. Microbiology Tel: 34-3-402 44 97 Fac. of Pharmacy Fax: 34-3-402 18 86 Univ. of Barcelona (Spain) From owner-software@net.bio.net Mon Jul 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!sdd.hp.com!nigel.msen.com!emory!gatech!howland.reston.ans.net!spool.mu.edu!torn!utnut!utcsri!newsflash.concordia.ca!sifon!VM1.MCGILL.CA From: Lawrence Kleiman Subject: molecular genetics clip art Message-ID: <05JUL94.15727011.0169@VM1.MCGILL.CA> Lines: 5 Sender: usenet@MUSICA.MCGILL.CA Organization: McGill University Date: Tue, 5 Jul 1994 19:33:43 GMT hi, I am looking for clip art of DNA, tRNA,cells, virus,etc. Anyone know of CD rom available, or somewhere on internet to download this material from.I'm Larry Kleiman, MD26@ MusicA.McGill.CA From owner-software@net.bio.net Mon Jul 04 23:00:00 1994 Path: biosci!agate!po.EECS.Berkeley.EDU!mintu From: mintu@po.EECS.Berkeley.EDU (Mintu Turakhia) Newsgroups: bionet.software Subject: LabVIEW 3.0 bugs Date: 5 Jul 1994 19:38:35 GMT Organization: University of California, Berkeley Lines: 13 Message-ID: <2vccrr$mnd@agate.berkeley.edu> NNTP-Posting-Host: po.eecs.berkeley.edu I just got LabVIEW 3.0 (Mac), but I'm a but reluctant to convert my 2.x VIs to the new version, especially since it is the first release of the rewritten program. Is anyone aware of 3.0 bugs that my severely impede operation? Thanks, Mintu ,,, (o o) --------------------------------------------------oOO--(.)--OOo----------- Mintu Turakhia / mintu@cory.EECS.Berkeley.edu / Phone: 510-792-3900 From owner-software@net.bio.net Mon Jul 04 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!agate!howland.reston.ans.net!xlink.net!news.urz.uni-heidelberg.de!rz.uni-karlsruhe.de!rzstud1.rz.uni-karlsruhe.de!ukra From: ukra@rzstud1.rz.uni-karlsruhe.de (Hermann Samso) Newsgroups: bionet.software,sci.bio,bionet.microbiology Subject: Microbiology - Workstations Date: 5 Jul 1994 11:40:00 GMT Organization: University of Karlsruhe, Germany Lines: 22 Message-ID: <2vbgqg$s4c@nz12.rz.uni-karlsruhe.de> NNTP-Posting-Host: rzstud1.rz.uni-karlsruhe.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software:8675 sci.bio:9970 bionet.microbiology:17 Hi! The Institute of Microbiology of the Karlsruhe University (where I have a student job) is considering the possibility of buying a workstation. The problem is we don't know what kind of software there is for each different workstation, so it would be very helpful if people could post what kind of machines and software they use in this field. Thanks a lot! Hermann Samso -- +---------------------------------------------------+ | The SpaceWalker . * _@ . .| |Walkin' thru Cyberspace..... . o . ukra@rzstud1.rz.uni-karlsruhe.de o / . * | +----------------------------------------`----------+ From owner-software@net.bio.net Mon Jul 04 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!umn.edu!insitu.med.umn.edu!nrd From: nrd@insitu.med.umn.edu (Neal Dalton) Subject: Re: GCG and X-windows Message-ID: Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: insitu.med.umn.edu Organization: University of Minnesota, Twin Cities X-Newsreader: TIN [version 1.2 PL2] References: Date: Tue, 5 Jul 1994 22:51:27 GMT Lines: 16 Garry Myers (garry@menzies.su.edu.au) wrote: : Hi, : Could somebody point me in the direction of a X-front end for GCG called : "gcgnav". I found the reference to this via the bionet archives but have : so far been unable to get in contact with the original poster. Any comments : or suggestions for other (if any) X interfaces for GCG also appreciated. It was on our CD, perhaps in the unsupported or contrib. Now it is gcgcore/script/gcgnav. It uses tcl and they supply a wish executable. Wish is pretty old and it doesn't work with the latest version. It is nothing fancy, just groups the command and give you a menu with the on for the group, then runs a xterm with the help and the command. Neal From owner-software@net.bio.net Mon Jul 04 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!sdd.hp.com!saimiri.primate.wisc.edu!news.doit.wisc.edu!ie.engr.wisc.edu!mlaudon From: mlaudon@ie.engr.wisc.edu (Matthew Finley Laudon) Newsgroups: bionet.software Subject: Mathematical and Computer Modelling (cfp) Date: 5 Jul 1994 20:37:48 GMT Organization: University of Wisconsin - Madison, College of Engineering Lines: 64 Message-ID: <2vcgas$hek@news.doit.wisc.edu> NNTP-Posting-Host: ie.engr.wisc.edu Announcement and Call for Papers TENTH INTERNATIONAL CONFERENCE ON MATHEMATICAL AND COMPUTER MODELLING AND SCIENTIFIC COMPUTING 5-8 July 1995 Boston Marriott Hotel Copley Place Boston Massachusetts, U.S.A ------------------------- The Tenth International Conference on Mathematical and Computer Modelling and Scientific Computing is scheduled to take place 5-8 July 1995 at the Boston Marriott Hotel Copley Place in Boston, Massachusetts, U.S.A. Plenary lectures by world-renowned scientists and technical sessions on many recent developments in engineering and sciences comprise a long-standing tradition at the ICMCM's. The objective of the conference is to bring together researchers, educators, planners, and model users from various disciplines including the traditional and emerging areas of engineering and sciences for cross fertilization and exchange of information. Authors are invited to contribute their work for presentation at the conference in the form of one-page abstracts typed single-space before 15 December 1994. Early submissions are encouraged. The abstracts will be processed as they come in, and decisions on selection will be promptly communicated to the authors by FAX not later than 31 January 1995. Abstracts may be submitted by FAX by dialing to U.S.A.: (314)-364-3351. ------------------------- The topics of interest are broadly categorized into: Modelling and Computation in Engineering and Sciences; Computational Sciences and Technologies; Applied Mathematics and Modelling Methodologies; Systems Theory; Computational Control; Self-Organizing Systems, Fuzzy and Neuro-Control, Neural Networks Theory and Applications; Biomedical Sciences; Computational Physics; Computational Chemistry; Computational Biology; Environmental Sciences and Engineering; Econometrics and Decision Sciences; Defense Related Problems; Resources; Model Validations; Educational Issues, etc. Papers presented at the 10th ICMCM will be published as a special issue of the journal MATHEMATICAL MODELLING AND SCIENTIFIC COMPUTING, Volume 6 1995. (ISSN 1067-0688) All abstracts and inquiries must be sent to the address below in St. Louis, Missouri, U.S.A. Address for correspondence: Scientific Program Committee, 10th ICMCM P. O. Box 31670 St. Louis, MO 63131 U.S.A. Telephone: (314)-341-4585 (Prof. X.J.R. Avula) FAX: (314)-364-3351 E-mail: avula@umr.edu From owner-software@net.bio.net Tue Jul 05 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!pipex!sunic!trane.uninett.no!eunet.no!nuug!EU.net!uunet!sangam!vikram!imtech!raghava From: raghava@imtech.ernet.in (G.P.S.RAGHAVA) Newsgroups: bionet.software Subject: Optimization of Gel electrophoresis Message-ID: <12883@imtech.ernet.in> Date: 5 Jul 94 23:11:27 +0530 Distribution: world Organization: Inst. of Microbial Technology, Chandigarh, India Lines: 16 Dear netter, I am looking for software which may help in optimizing the gel conditions (like temprature, gel concentration etc) and allow to i) compare gel electrophoresis data graphically ii) analysis of the data. I would appreciate your help in this direction. Thanks with warm regards Raghava -- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | G.P.S.Raghava, Scientist ! Phone : +91 172 44252 | | Institute of Micro. Technology ! Email: raghava@imtech.ernet.in | | P O Box 1304, Sector 39A ! UUCP: | | Chandigarh 160 014 India. ! ...!uunet!sangam!vikram!imtech!raghava | ============================================================================ From owner-software@net.bio.net Tue Jul 05 23:00:00 1994 Path: biosci!nii.ernet.in!sudhanshu From: sudhanshu@nii.ernet.in Newsgroups: bionet.software Subject: MSE / William Gilbert Date: 5 Jul 1994 21:14:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <9407050641.AA28214@doe.ernet.in> NNTP-Posting-Host: net.bio.net Dear Netters, I have previously used a multiple sequence alignment software called MSE written by William Gilbert. I want to get in touch with Mr Gilbert regarding the procurement of software. Repeatedly I got no reply from his fax no. 603-427-1327 (USA), so I guess he has moved from this number. If you know his whereabouts kindly let me know diretly as I do not subscribe to BIONEWS. Or else, if this software is available in public domain somewhere, please let me know. Thanks a lot for any helpful information. Sudhanshu Vrati, PhD National Instt. of Immunology, New Delhi 110 067 India Fax 91-11-6862125 Ph. 91-11-6863006 From owner-software@net.bio.net Tue Jul 05 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!usenet.ins.cwru.edu!news.ecn.bgu.edu!psuvax1!news.pop.psu.edu!news.cac.psu.edu!newsserver.jvnc.net!raffles.technet.sg!nuscc.nus.sg!mpengtw From: mpengtw@leonis.nus.sg (Ng Tuck Wah) Newsgroups: bionet.software Subject: Software For Reference Management Date: 6 Jul 1994 00:56:33 GMT Organization: National University of Singapore Lines: 7 Message-ID: <2vcvg1$gho@nuscc.nus.sg> NNTP-Posting-Host: leonis.nus.sg X-Newsreader: TIN [version 1.2 PL2] Dear fellow researchers, If any of you has a need for a PC-based software to handle your reference material and do not intend to spend too much on it, please e-mail to mpengtw@leonis.nus.sg From owner-software@net.bio.net Tue Jul 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!csusac.ecs.csus.edu!csus.edu!netcom.com!netcom9!pkmartin From: pkmartin@netcom9.netcom.com (Doc Martin) Subject: Re: GCG and X-windows In-Reply-To: nrd@insitu.med.umn.edu's message of Tue, 5 Jul 1994 22:51:27 GMT Message-ID: Sender: pkmartin@netcom.com (Doc Martin) Organization: NETCOM On-line services References: Date: Wed, 6 Jul 1994 16:32:32 GMT Lines: 21 In article nrd@insitu.med.umn.edu (Neal Dalton) writes: ( text deleted ) >: so far been unable to get in contact with the original poster. Any comments >: or suggestions for other (if any) X interfaces for GCG also appreciated. > >It was on our CD, perhaps in the unsupported or contrib. Now it is >gcgcore/script/gcgnav. It uses tcl and they supply a wish executable. >Wish is pretty old and it doesn't work with the latest version. i just loaded GCG 7.3 on a Sparc running Solaris 2.3 (SunOS 5.3) and everything, including wish, works fine. we have the Sun on a local network and everyone can access the window front-end from their desktop Macintoshes using the MacX package. the gcgnav support is located in "gcg/gcginterim" from the latest CD distribution. the documentation indicates that in the future, gcgnav will be unsupported in preference to a Motif-based interface. .doc From owner-software@net.bio.net Tue Jul 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!udel!news2.sprintlink.net!news.sprintlink.net!news.clark.net!arsoftwa From: arsoftwa@clark.net (Welcome to ARSoftware) Newsgroups: bionet.software Subject: Re: MSE / William Gilbert Date: 6 Jul 1994 13:29:22 GMT Organization: Clark Internet Services, Inc., Ellicott City, MD USA Lines: 16 Distribution: world Message-ID: <2vebji$r44@clarknet.clark.net> References: <9407050641.AA28214@doe.ernet.in> NNTP-Posting-Host: clark.net Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: TIN [version 1.2 PL2] sudhanshu@nii.ernet.in wrote: : Dear Netters, : I have previously used a multiple sequence alignment software called : MSE written by William Gilbert. I want to get in touch with Try writing to a firen of his Dr. Ken Tupper, Director of Computational Chemistry Applied Research Corporation tupper@indy.arclch.com too, there may some programs you like by opening the URL http://arsoftware.arclch.com Good luck George west From owner-software@net.bio.net Tue Jul 05 23:00:00 1994 Path: biosci!LION.RBGKEW.ORG.UK!ac03kg From: ac03kg@LION.RBGKEW.ORG.UK (Tony Cox) Newsgroups: bionet.software Subject: Debugging terminal Date: 6 Jul 1994 04:06:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <9407061101.AA26465@lion.rbgkew.org.uk> NNTP-Posting-Host: net.bio.net Dear Netter, Could anyone explain to me how to go about setting up a separate debugging terminal on my PC? I'm not really sure if you need an extra card. Any help/ advice would be greatly appreciated. Tony Cox From owner-software@net.bio.net Tue Jul 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!newsserver.jvnc.net!phinet!phm771.sb.com!user From: boones1@sb.com (Scott Boone) Subject: Printing tiffs Message-ID: Followup-To: bionet.software Sender: news@netnews.smithkline.com (USENET News System) Organization: SmithKline Beecham Date: Wed, 6 Jul 1994 08:44:12 GMT Lines: 11 Hello. I am in need of a shareware program (or commercial) that will print tiff images out. I am using Molecular Dynamics ImageQuant and want to be able to batch print a folder of tiffs while in Windows-fWGs. Does anyone know of software to do this? It doesn't need to be fancy, but functional. -- Scott Boone Lab Automation Email- boones1@sb.com SmithKline Beecham From owner-software@net.bio.net Tue Jul 05 23:00:00 1994 Newsgroups: bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!usc!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!moe.ksu.ksu.edu!osuunx.ucc.okstate.edu!yoda.biochem.okstate.edu!user From: yoda@okway.okstate.edu (Jerry Merz) Subject: Re: Cleland's Enzyme Programs Message-ID: Followup-To: bionet.software Sender: news@osuunx.ucc.okstate.edu (USENET News System) Nntp-Posting-Host: yoda.biochem.okstate.edu Organization: OSU Biochemistry References: <2864@alsys1.aecom.yu.edu> Date: Wed, 6 Jul 1994 21:42:35 GMT Lines: 10 In article <2864@alsys1.aecom.yu.edu>, mazzella@bebo.bioc.aecom.yu.edu wrote: > Hi, fellow netters I'm looking for a mac version of Cleland's enzyme kinetics programs. Thanks in advance. John. Contact Dick Essenberg at rceberd@okway.okstate.edu. -- Jerry M. Merz yoda@okway.okstate.edu From owner-software@net.bio.net Tue Jul 05 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!sdd.hp.com!news.cs.indiana.edu!babbage.ece.uc.edu!ucunix.san.uc.edu!ucunix.san.uc.edu!not-for-mail From: silbigrn@ucunix.san.uc.edu (Richard Silbiger PhD) Newsgroups: bionet.software Subject: Re: MSE / William Gilbert Date: 6 Jul 1994 14:24:05 -0400 Organization: University of Cincinnati Lines: 1 Distribution: world Message-ID: <2vess5$9bo@ucunix.san.uc.edu> References: <9407050641.AA28214@doe.ernet.in> <2vebji$r44@clarknet.clark.net> NNTP-Posting-Host: ucunix.san.uc.edu From owner-software@net.bio.net Wed Jul 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sun4nl!uva.nl!amc.uva.nl!news From: roozendaal@amc.uva.nl Newsgroups: bionet.software Subject: RE: Printing tiffs Date: Thu, 7 Jul 94 12:53:10 GMT Organization: Central Computer Organization AMC/UvA Lines: 21 Message-ID: <2vgja8$2qq@amcnix.amc.uva.nl> References: , NNTP-Posting-Host: amccca.amc.uva.nl In Article boones1@sb.com (Scott Boone) writes: >Hello. > >I am in need of a shareware program (or commercial) that will print tiff >images out. I am using Molecular Dynamics ImageQuant and want to be able >to batch print a folder of tiffs while in Windows-fWGs. Does anyone know >of software to do this? It doesn't need to be fancy, but functional. > >-- >Scott Boone >Lab Automation Email- boones1@sb.com >SmithKline Beecham There is a window based program called GWS (Graphics Work Shop) and it prints Tiff files from windows but also modify, enhance or modify them. I think it's shareware and can be found at FTP-site nic.funet.fi login: anonymous i hope this helped you J. Roozendaal Roozendaal@amc.uva.nl From owner-software@net.bio.net Wed Jul 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!Eli.Meir From: meir@zoology.washington.edu (Eli Meir) Newsgroups: bionet.software,bionet.neuroscience Subject: New Spike Studio (Neurophys Data Acq) Date: 7 Jul 1994 02:36:26 GMT Organization: Dept. of Zoology, Univ. of Washington Lines: 25 Sender: -Not-Authenticated-[3641] Message-ID: <2vfpna$fbm@news.u.washington.edu> NNTP-Posting-Host: quaternary.zoology.washington.edu X-Posted-From: InterNews 1.0@news.u.washington.edu. Xdisclaimer: No attempt was made to authenticate the sender's name. Xref: biosci bionet.software:8692 bionet.neuroscience:3716 I recently released a slightly new version of my data acquisition and analysis program Spike Studio. I fixed some bugs in the code which collected data from the microphone input of the Mac. If any of you downloaded Spike Studio to digitize through the Mac sound input port and it didn't work, you might try again. Unfortunetly, some macintosh sound input ports seem to have an automatic gain control which can't be turned off, so on some mac's this is not a feasable way to collect scientific data. For those of you who haven't heard of Spike Studio, its a formerly commercial data acquisition and analysis program geared towards neurophysiologists, for Macintosh computers, which I've now released as freeware. In addition to very flexible digitizing on National Instruments, GW Instruments, or the built-in Mac digitizers, it also has lots of analysis, graphing, and printing features useful to neurophysiologists, and possibly to others. Its used around the world in both laboratories and classrooms. The manual and some sample data is included in the package, which you can download from a number of ftp sites, including wuarchive.wustl.edu, sumex-aim.stanford.edu, and mac.archive.umich.edu (at least last time I checked it was on all these places). Email me if you have questions. Eli Meir Dept of Zoology, Univ of Washington meir@zoology.washington.edu From owner-software@net.bio.net Wed Jul 06 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!zip.eecs.umich.edu!umn.edu!news From: Subject: Re: Source of CATLAB software Message-ID: <55225.wadde001@maroon.tc.umn.edu> X-Minuet-Version: Minuet1.0_Beta_15 Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: dialup-3-135.gw.umn.edu X-Popmail-Charset: English Organization: University of Minnesota, Twin Cities Date: Thu, 7 Jul 1994 17:45:44 GMT Lines: 22 Greetings Netters, Can anyone out there in Net Land recommend a simple (and preferably inexpensive) password protection program for a DOS machine. All it has to do is prevent the computer from booting from the hard disk until a password has been entered from the keyboard. Security doesn't have to be really tight, most of the people around the area would be scared off by a good beep! Some machines let you password protect in the BIOS, but the one we need to protect naturally doesn't. If enough people are interested, I'll post a summary of responses. Thanks in advance. /-----------------------------------------------------------------\ | Dr. James Waddell | Phone: (612) 625-3118 | | Clinical and Population Sciences | Fax: (612) 625-1210 | | College of Veterinary Medicine | Office: 385g An Sci/Vet Med | | University of Minnesota | 1988 Fitch Avenue | | | St. Paul, MN 55108 | \-----------------------------------------------------------------/ From owner-software@net.bio.net Thu Jul 07 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!news.cac.psu.edu!news.pop.psu.edu!psuvax1!ukma!ndlc.occ.uky.edu!not-for-mail From: mowersp@ndlc.occ.uky.edu (Patrick Mowers) Newsgroups: bionet.software Subject: RE: Printing Tiffs Date: 7 Jul 1994 21:49:06 -0500 Organization: The NDLC's Internet Gateway Lines: 8 Message-ID: <2vier2$4k7@ndlc.occ.uky.edu> NNTP-Posting-Host: ndlc.occ.uky.edu X-Newsreader: TIN [version 1.2 PL2] A program that I have had very good luck with is called Paint Shop Pro. It will print tiff, pcx, bmp, pcd etc in either color or B/W and also allows for converting between formats, as well as some nice image processing features. PSP is shareware and available through most ms-dos sites. Good luck. Pat Mowers From owner-software@net.bio.net Thu Jul 07 23:00:00 1994 Path: biosci!agate!ames!lll-winken.llnl.gov!fastrac.llnl.gov!osi-east2.es.net!pnl-oracle!netnews.nwnet.net!news.u.washington.edu!Eli.Meir From: meir@zoology.washington.edu (Eli Meir) Newsgroups: bionet.software,bionet.neuroscience Subject: Re: New Spike Studio (Neurophys Data Acq) Date: 8 Jul 1994 03:02:45 GMT Organization: Dept. of Zoology, Univ. of Washington Lines: 10 Sender: -Not-Authenticated-[3641] Message-ID: <2vifkl$eiq@news.u.washington.edu> References: <2vfpna$fbm@news.u.washington.edu> NNTP-Posting-Host: quaternary.zoology.washington.edu X-Posted-From: InterNews 1.0@news.u.washington.edu. Xdisclaimer: No attempt was made to authenticate the sender's name. Xref: biosci bionet.software:8696 bionet.neuroscience:3728 A couple people have asked me where exactly to find the program. As far as I know, you can find it on mac.archive.umich.edu in the folder /mac/util/science, and on wuarchive.wustl.edu in /systems/mac/info_mac/sci. On sumex-aim.stanford.edu it should probably be in /sci. You can also send me $50 (my costs plus my time) and I'll send you a nicely printed manual and a disk. Eli Meir Dept of Zoology, Univ of Washington meir@zoology.washington.edu From owner-software@net.bio.net Thu Jul 07 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!pipex!uknet!dcs.gla.ac.uk!udcf.gla.ac.uk!mac7-43.genetics.gla.ac.uk!user From: gbga13@udcf.gla.ac.uk (B.L.Cohen) Subject: Do I need a Postscript interpreter? Message-ID: Followup-To: bionet.software Sender: news@udcf.glasgow.ac.uk (News) Organization: Genetics, University of Glasgow Date: Fri, 8 Jul 1994 11:30:07 GMT Lines: 25 My printer is an HP 500 DeskWriter, driven by a Macintosh Quadra 610 with version 5.0 (and previously 3.x) HP software and Mac OS 7.1. I need to use certain scientific programs that either produce Postscript output or have a memory-use conflict with the printer such that the software crashes on exiting from a printing job. I would prefer to find standalone solutions to these two problems, rather than communicate with or buy a laserprinter. I understand that a Postscript Interpreter might enable Postscript output to be sent to the DeskWriter. If this is so, I would welcome advice on choice of software, pros and cons., etc. MacConnection has been mentioned in this context, but it does not seem to be on sale in the UK. If anyone recommends it, please supply the maker's contact details. I cannot describe the memory-use conflict problem any further and anticipate that it probably has no solution other than waiting for the software (or the printer's drivers) to be re-written. But any suggestions will be welcomed. -- Dr Bernard L. Cohen Phone (+44) (0)41 339 8855 ext. 5103/5101 Genetics Dept., Fax 330 5994 University of Glasgow Church St., Glasgow G11 5JS Scotland, UK. From owner-software@net.bio.net Thu Jul 07 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!sdd.hp.com!nigel.msen.com!emory!europa.eng.gtefsd.com!howland.reston.ans.net!agate!doc.ic.ac.uk!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!uunet!osiris.wu-wien.ac.at!i102pc1.vu-wien.ac.at!seb From: seb@i102pc1.vu-wien.ac.at (Sebastian W. Bunka) Newsgroups: bionet.software Subject: Re: Problems compiling Fasta and Blast under Linux Date: 8 Jul 1994 07:59:45 GMT Organization: Veterinary University Vienna Lines: 21 Message-ID: <2vj11h$i7o@osiris.wu-wien.ac.at> References: Reply-To: Sebastian.Bunka@vu-wien.ac.at NNTP-Posting-Host: i102pc1.vu-wien.ac.at X-Newsreader: TIN [version 1.2 PL2] Les Grivell (les@amc.uva.nl) wrote: : Has anyone successfully compiled Fasta and or Blast under Linux? : : LOT OF STUFF DELETED Sorry, I've no answer for you! But propably you might check the dna workbench for your blasta and fasta searches (and Genbank searches) over the net ( no local databases required). It works fine on my linux box. However, I had to do some hand-work/fine tuning. If you're interested, I can send you my installation; just email me. You can find this Perl program at: ftp cbil.humgen.upenn.edu @ /pub/dnaworkbench/unix/dnaworkbench (260kb) Cheers, Sebastian [ Sebastian.Bunka@vu-wien.ac.at ] phone: FAX: +43-1-71155260 +43-1-7149110 Location: earth, europe, austria, vienna Inst. of Bacteriology Vet.Univ. From owner-software@net.bio.net Thu Jul 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!emory!nigel.msen.com!zib-berlin.de!ceres.fokus.gmd.de!nntp.gmd.de!dearn!barilvm!vms.huji.ac.il!marder.agri.huji.ac.il!MARDER Newsgroups: bionet.software Subject: Re: Printing tiffs Message-ID: From: MARDER@agri.huji.ac.il (Jonathan B. Marder) Date: Fri, 8 Jul 1994 05:47:02 GMT References: Distribution: world Organization: The Hebrew University of Jerusalem Nntp-Posting-Host: marder.agri.huji.ac.il X-Newsreader: Trumpet for Windows ÝVersion 1.0 Rev B¨ Lines: 22 In article boones1@sb.com (Scott Boone) writes: >Subject: Printing tiffs >From: boones1@sb.com (Scott Boone) >Date: Wed, 6 Jul 1994 08:44:12 GMT >Hello. >I am in need of a shareware program (or commercial) that will print tiff >images out. The program WINJPEG 2.51 by N&K. Lee will handle TIFF, JPEG, GIF etc. including interconversions and printing. Pick up the file WINJP251.ZIP from CICA or one of its mirrors. The package is SHAREWARE - (i.e. you need to register if you decide to keep it) __ Jonathan B. Marder ' Department of Agricultural Botany | Internet: MARDER@agri.huji.ac.il The Hebrew University of Jerusalem | /\/ Bitnet: MARDER@HUJIAGRI Faculty of Agriculture |/ \ Phone: (08 or +9728) 481918 P.O.Box 12, Rehovot 76100, ISRAEL / Fax: (08 or +9728) 467763 From owner-software@net.bio.net Thu Jul 07 23:00:00 1994 Newsgroups: bionet.software Path: biosci!agate!howland.reston.ans.net!spool.mu.edu!torn!nott!cunews!freenet.carleton.ca!FreeNet.Carleton.CA!ap913 From: ap913@FreeNet.Carleton.CA (Jim Gleason) Subject: UUENCODE:FANCYV1.UUE Message-ID: Sender: news@freenet.carleton.ca (Usenet News Admin) Reply-To: ap913@FreeNet.Carleton.CA (Jim Gleason) Organization: The National Capital FreeNet Date: Fri, 8 Jul 1994 03:04:14 GMT Lines: 774 Hi, This is a program I made called FANCY.EXE. It is a menu of prompts. The prompts are graphic prompt that display a color picture for a prompt instead of the normal C:\>. 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M!A6RCV&XQB8"YPQT%+76&)%CK:W6B;8;]?#^:31U62VDO[,$92)JN;2SP*8]7"<3P594/>>R$P[@303 MO[/['Z3SRM`5>H"..^,Z=QX^IK.*".XTCE$0P,O-<%`R/\(-PQHO_BKTX1C"."48$ M6<>+7^KU0X/_#5!+`0(4`!0````(`-6IYAS0UYG!6G```$`,`0`)```````` M````(`````````!&04Y#62Y%6$502P$"%``4````"`#9JN8<%'0&?KT'``"] M$@``"0`````````!`"````"!<```1D%.0UDN1$]#4$L!`A0`%`````@`ZI5& M&V;\#H6^!0``4`P```D``````````0`@````97@``#%-14Y5+D1!5%!+`0(4 M`!0````(`*V61AN?1BKC0@4``,,+```)``````````$`(````$I^```R345. ;52Y$05102P4&``````0`!`#<````LX,````` ` end sum -r/size 31772/46814 section (from "begin" to "end") sum -r/size 40771/33957 entire input file -- From owner-software@net.bio.net Thu Jul 07 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!quark.scs.uiuc.edu!harvey From: harvey@quark.scs.uiuc.edu (John Harvey) Newsgroups: bionet.software Subject: Antheprot Date: 8 Jul 1994 13:37:14 GMT Organization: University of Illinois Lines: 19 Distribution: world Message-ID: <2vjkqa$pli@vixen.cso.uiuc.edu> Reply-To: harvey@quark.scs.uiuc.edu NNTP-Posting-Host: quark.scs.uiuc.edu -- If anyone out there has gotten the ANTHEPROT package to work on their RS/6000 could you please send me some e-mail. I have talked with the authors and they can't figure out why the package won't work on my system. Thank you. JJJJJ OOOOO H H N N J O O H___H NN N J O O H H N N N ATTGCA AATA GGCC TTAGC JJJJ OOOOO H H N NN A T G C C C G C A John Harvey T A C G G G University of Illinois TAACGA TTAT CCGG AATCG Department of Biochemistry "DON'T TRUST YOUR GENES TO JUST ANYONE" harvey@quark.scs.uiuc.edu From owner-software@net.bio.net Thu Jul 07 23:00:00 1994 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!news.tamu.edu!venus.tamu.edu!j0m1742 From: j0m1742@venus.tamu.edu (MANHART, JAMES) Newsgroups: bionet.software Subject: Xwindow emulator for Mac Date: 8 Jul 1994 08:22 CDT Organization: Texas A&M University OpenVMScluster Lines: 13 Distribution: world Message-ID: <8JUL199408223988@venus.tamu.edu> NNTP-Posting-Host: venus.tamu.edu News-Software: OpenVMS/VAX VNEWS 1.41 I am considering getting an X-windows emulator for my Mac but there is apparently not a lot of information available on them. I am interested in this software because I plan to put some programs on Unix machines but would like to retain access to my regular Mac software. An X-windows emulator seems a good choice for this purpose but I have no experience with the Mac software and would appreciate comments from experienced users. ********************************************************************* Jim Manhart, Dept. of Biology, Texas A&M University, College Station, TX 77843-3258, (409) 845-3356, email: J-Manhart@TAMU.EDU (Internet) ********************************************************************* From owner-software@net.bio.net Thu Jul 07 23:00:00 1994 Newsgroups: bionet.software Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!convex!news.duke.edu!news-feed-1.peachnet.edu!umn.edu!news From: Subject: Pasword Protection Software for the PC Message-ID: <50355.wadde001@maroon.tc.umn.edu> X-Minuet-Version: Minuet1.0_Beta_15 Sender: news@news.cis.umn.edu (Usenet News Administration) Nntp-Posting-Host: dialup-3-133.gw.umn.edu X-Popmail-Charset: English Organization: University of Minnesota, Twin Cities Date: Fri, 8 Jul 1994 16:16:45 GMT Lines: 25 Greetings Netters (again), I posted this request yesterday, but under a totally non-related subject. Please accept my appologies and let me try again. Can anyone out there in Net Land recommend a simple (and preferably inexpensive) password protection program for a DOS machine. All it has to do is prevent the computer from booting from the hard disk until a password has been entered from the keyboard. Security doesn't have to be really tight, most of the people around the area would be scared off by a good beep! Some machines let you password protect in the BIOS, but the one we need to protect naturally doesn't. If enough people are interested, I'll post a summary of responses. Thanks in advance. /-----------------------------------------------------------------\ | Dr. James Waddell | Phone: (612) 625-3118 | | Clinical and Population Sciences | Fax: (612) 625-1210 | | College of Veterinary Medicine | Office: 385g An Sci/Vet Med | | University of Minnesota | 1988 Fitch Avenue | | | St. Paul, MN 55108 | \-----------------------------------------------------------------/ From owner-software@net.bio.net Fri Jul 08 23:00:00 1994 Path: biosci!agate!ames!purdue!lerc.nasa.gov!kira.cc.uakron.edu!malgudi.oar.net!news.pipeline.com!jmack.pipeline.com!user From: jmack@pipeline.com (John Mack) Newsgroups: bionet.software Subject: beta testers needed Followup-To: bionet.software Date: Fri, 08 Jul 1994 23:15:09 -0401 Organization: Mack Computer Services Lines: 17 Distribution: world Message-ID: NNTP-Posting-Host: jmack.pipeline.com I am looking for beta test sites for an interactive multimedia Clinical Research Coordinator Handbook training program (CRC Hbk). The CRC Hbk is a study guide that can help train new CRCs and is also a valuable reference for experienced CRCs to use within a clinical trials setting. The graphical user interface allows point and click navigation, hypertext jumps, animation, and digital video/audio. The CRC Hbk currently runs on a PC equipped with Windows 3.1 and a Windows-compatible sound card with speakers. Beta testers will be able to buy the program at a substantial discount. If you are interested, please contact me for further details and for a beta test package. Please email me (jmack@pipeline.com) your snail mail address if you are interested so that i can send a description of the program with screen dumps and an application/beta agreement. Thanks. From owner-software@net.bio.net Fri Jul 08 23:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: kristoff (David Kristofferson) Newsgroups: bionet.software Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 9 Jul 1994 02:00:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 319 Sender: daemon@net.bio.net Distribution: world Message-ID: <199407090900.CAA01477@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. IF YOU ARE LOCATED IN THE AMERICAS OR PACIFIC RIM COUNTRIES, please send a message to biosci@net.bio.net Instructions will be returned automatically, so the contents of your message do not matter. IF YOU ARE LOCATED IN EUROPE, AFRICA OR CENTRAL ASIA, please send a message to MXT@dl.ac.uk containing the word help in the body of the message to retrieve e-mail server instructions. Any text placed on the Subject: line of your message will be ignored, so be sure to put the "help" command in the body of the message. If you need personal assistance, a BIOSCI staff member can be contacted at either of the following addresses. Please contact the address designated for your location. Support Address Location --------------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci-help@net.bio.net Americas and the Pacific Rim **** SEARCHING BIOSCI ARCHIVES **** The easiest way to search the BIOSCI archives is to use gopher software and connect over the Internet to net.bio.net, the U.S. BIOSCI computer. We maintain three indexes which are searchable from the main gopher menu on net.bio.net: (1) an index of all BIOSCI postings; (2) an index of individual journal article references from the Table of Contents postings on the BIO-JOURNALS newsgroup; and (3) an index of BIOSCI users including regular mail and e-mail addresses, phone/FAX numbers, research interests, and newsgroup participation. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). WAIS software can also be used to search the archives as described in the BIOSCI FAQ (see below). **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/doc/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending the command info faq in the body of an e-mail message to the Internet address biosci-server@net.bio.net. Please do not enter the info faq command on the Subject: line of your message since the e-mail server ignores text on the Subject: line. The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS, waismail, and gopher access. If you have access to gopher, connect to net.bio.net to search the database. If you have access to WAIS, please use our WAIS source biologists-addresses.src. If you are not on the Internet, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.). Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check your database entry from time-to-time to see if your address information is still up-to-date. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters). PLEASE DO NOT alter any of the field identifiers such as "first name: ". If you have nothing to enter after a field identifier, PLEASE LEAVE IT - do not delete it even if there is no data on the line in question. Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 15-05-93 for 15 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 15-05-93, not 15-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.ann