From owner-software@net.bio.net Tue Jun 01 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!uunet!mcsun!news.funet.fi!funic!nic.funet.fi!csc.fi!harper From: Rob.Harper@csc.fi (Rob Harper) Newsgroups: bionet.software Subject: MSDOS uploads to SIMTEL20 for May 1993 Message-ID: <199306020856.AA17798@csc.fi> Date: 2 Jun 93 08:56:49 GMT Sender: root@nic.funet.fi (The FUnny NET guru) Organization: Finnish University & Research Network Lines: 622 %%%%%%%%%%%%%%%%%%%%%%%%%%%%% CLIP %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% File PD1:UPLOADS.MAY Created: June 2, 1993 NOTE: This file is also available in comma-delimited format as SIM9305.IDX MS-DOS files uploaded to WSMR-SIMTEL20.Army.Mil and OAK.Oakland.Edu during the month of May 1993 NOTE: Type B is Binary; Type A is ASCII Filename Type Length Date Description ============================================== Directory PD1: 4D24H20B.ZIP B 22806 930529 TSR critical error handler (INT 24) for 4DOS 4DOSNT10.ZIP B 224504 930517 4DOS/NT v1.0 CMD.EXE replacement for WindowsNT 4UTILS73.ZIP B 128752 930505 4DOS description editor & file finder (free) Directory PD1: C01LAB6.ZIP B 20017 930503 Ada/C++ OO/Programming/Design course, 6 of 15 C01PLAB.ZIP B 217400 930503 Ada/C++ OO/Programming/Design course, 9 of 15 C01POOD.ZIP B 597264 930503 Ada/C++ OO/Programming/Design course, 10 of 15 C01POOP.ZIP B 672600 930503 Ada/C++ OO/Programming/Design course, 11 of 15 C01PSE1.ZIP B 990680 930503 Ada/C++ OO/Programming/Design course, 12 of 15 C01PSE2.ZIP B 422295 930503 Ada/C++ OO/Programming/Design course, 13 of 15 C01RDME.ZIP B 26176 930504 Ada/C++ OO/Programming/Design course, 14 of 15 EDITADA.ZIP B 240366 930519 Ada programmer's editor for Windows 3.1 Directory PD1: AV305.ZIP B 93926 930523 Archive view: Free ZIP etc directory viewer PSDARC.ZIP B 9715 930531 Deletes all files extracted from an ARC file SHEZ90A.ZIP B 233550 930517 Shell interface to ZIP/ARJ/LZH/ZOO/ARC/SQZ/PAK Directory PD1: B_STAR.ZIP B 42026 930524 Program to animate motions of a binary star DIFF_DRA.ZIP B 41906 930524 Displays a binary star system in 3-D GALIL.ZIP B 49987 930524 Animates motions of Jupiter and its satellites SKYMAP.TXT A 6041 930531 SkyMap v1.3 Planetarium for Win31, description SKYMP13A.ZIP B 276010 930531 SkyMap v1.3 for Win3.1, pgm and documentation SKYMP13B.ZIP B 325432 930531 SkyMap v1.3 for Win3.1, essential data files SKYMP13C.ZIP B 222035 930531 SkyMap v1.3 for Win3.1, optional data files Directory PD1: SLDM515A.ZIP B 148347 930507 SlideManager shows and converts SLD->DXF/HPGL Directory PD1: ASET10.ZIP B 80283 930519 Ricki's enhanced SET command HOLDIT10.ZIP B 6910 930506 Like DOS' PAUSE w/timeout & errorcode w/srcTP TSBAT43.ZIP B 93963 930509 Collection of useful batch files by Timo Salmi Directory PD1: GNEWS203.ZIP B 73313 930507 Generates news bulletins for RA, QBBS and SBBS MM20B31.ZIP B 139094 930517 MarkMail v2.00B31: QWK mail door for PCBoard PB125_1.ZIP B 133059 930529 Powerboard DV-aware BBS, easy config, 1 of 4 PB125_2.ZIP B 282503 930529 Powerboard DV-aware BBS, easy config, 2 of 4 PB125_3.ZIP B 215421 930529 Powerboard DV-aware BBS, easy config, 3 of 4 PB125_4.ZIP B 98928 930529 Powerboard DV-aware BBS, easy config, 4 of 4 RAMAIL20.ZIP B 79780 930517 QWK mail door for Remote Access BBS RNET107U.ZIP B 177138 930517 RNet 1.07: QWK networking software for PCBoard Directory PD1: USBBS108.ZIP B 91963 930510 Darwin's nationwide IBM BBS listing, May 1993 Directory PD1: KBIBLE.ZIP B 236710 930529 KJV Bible read/search by topics, file 1 of 5 KBIBLE2A.ZIP B 352549 930529 KJV Bible read/search by topics, file 2 of 5 KBIBLE2B.ZIP B 343648 930529 KJV Bible read/search by topics, file 3 of 5 KBIBLE2C.ZIP B 347248 930529 KJV Bible read/search by topics, file 4 of 5 KBIBLE2D.ZIP B 254599 930529 KJV Bible read/search by topics, file 5 of 5 ONBIBAV1.ZIP B 1446394 930517 Online Bible 6.0, AKJV & Darby version. Disk 1 ONBIBAV2.ZIP B 1446394 930517 Online Bible 6.0, AKJV & Darby version. Disk 2 ONBIBAV3.ZIP B 776044 930517 Online Bible 6.0, AKJV & Darby version. Disk 3 ONBIBINS.ZIP B 1026432 930517 Online Bible 6.0 install, cross ref, pgm files ONBIBLEX.ZIP B 1425428 930517 Online Bible 6.0 Revised Greek&Hebrew Lexicon ONBIBRDM.1ST A 1468 930517 Instructions for Online Bible v6.0 ONBIBSCO.ZIP B 402975 930517 Online Bible 6.0 Scofield notes ONBIBTOP.ZIP B 1326122 930517 Online Bible 6.0 Topics disk ONBIBTS1.ZIP B 1444805 930517 Online Bible 6.0 Treas of Script. Knowlg. 1of2 ONBIBTS2.ZIP B 1431030 930517 Online Bible 6.0 Treas of Script. Knowlg. 1of2 Directory PD1: GEP207A.ZIP B 540523 930512 WIN31: Simulation of biochemical pathways GSRC207A.ZIP B 271167 930512 Source code of GEP207A.ZIP simulation package Directory PD1: ACTLIB14.ZIP B 70763 930527 General purpose libs w/source for C/C++ pgmers LINGUA12.ZIP B 35426 930526 Easy multi-language support for C programs SNIP0493.ZIP B 332708 930531 Collection of C-snippets [mostly] by Bob Stout Directory PD1: TANGO130.ZIP B 1048258 930508 Tango Schematic capture evaluation DEMO v1.30 Directory PD1: C-CALC10.ZIP B 34950 930505 Complex number calculator (free) EASTER12.ZIP B 4902 930505 Calculates the date of Easter in any year Directory PD1: DCAT10.ZIP B 47306 930519 Ricki's disk cataloger Directory PD1: LISTCDS.ZIP B 10539 930524 List CDs in SoundWork's SoundPlay database TLGWP20.ZIP B 238597 930528 TLGWorkplace v2.0. View/search the TLG CD-ROM Directory PD1: NFPAT1.ZIP B 2504 930527 Patch#1 to Nantucket Forum Lib 2.1 for Clipper NFPAT2.ZIP B 4693 930527 Patch#2 to Nantucket Forum Lib 2.1 for Clipper NFPAT3.ZIP B 15111 930527 Patch#3 to Nantucket Forum Lib 2.1 for Clipper NFPAT4.ZIP B 14479 930527 Patch#4 to Nantucket Forum Lib 2.1 for Clipper NFPAT5.ZIP B 2593 930527 Patch#5 to Nantucket Forum Lib 2.1 for Clipper NFPAT6.ZIP B 8864 930527 Patch#6 to Nantucket Forum Lib 2.1 for Clipper NFPAT7.ZIP B 8600 930527 Patch#7 to Nantucket Forum Lib 2.1 for Clipper RSHPCX12.ZIP B 5880 930504 Clipper lib to show PCX-files on EGA/VGA/SVGA Directory PD1: MTL100JE.ZIP B 63618 930508 DOS multithreading library for Borland C++ Directory PD1: AS31.ZIP B 49902 930508 Assembler for 8031/8051 CPU, with C source Directory PD1: CJPOS123.ZIP B 224781 930517 Point of sale, tracks inventory/reads barcodes DDATA_44.ZIP B 116756 930527 Baseball/Softball statistics tracking package PXMNU13.ZIP B 25749 930529 Dynamic heirachical menu system for Paradox Directory PD1: APCAL320.ZIP B 148014 930513 ApCal v3.20: Easy to use appointment calendar DRSC104.ZIP B 256520 930524 Combo desk reference & scientific calculator Directory PD1: ACD221.ZIP B 53256 930525 ChDir FAST; more features than LCD/NCD & FREE DIRTO305.ZIP B 160943 930523 Directory listing and totaller FILUP305.ZIP B 52079 930523 Copy updated files based on a control list L11.ZIP B 43516 930519 Ricki's powerful DIR replacement PPPD301.ZIP B 12270 930524 Push-Pop DOS path string & current drive:\dir WHCH20GR.ZIP B 28281 930508 Roelofs' Which: Locate commands & print paths Directory PD1: COMBI113.ZIP B 48184 930509 RAM disk & disk cache sharing XMS memory FILL305.ZIP B 106576 930523 Stuffs as many files as possible on diskette HICPY25B.ZIP B 60797 930531 High density disk copier, using hard disk QIC02_11.ZIP B 27644 930531 Tape device driver for Archive SC402/499 cards QKOPY332.ZIP B 53682 930531 Quikcopy v3.32: Quick file/diskette copier SHOWF250.ZIP B 31001 930521 Intuitive display of disk FAT & dir structure SMARTPMT.ZIP B 3233 930519 Flushes SmartDrive deferred writes on DOS pmt. Directory PD1: CALVIN22.ZIP B 39629 930531 Calvin v2.2: Text editor; partial vi clone E4V160.ZIP B 85797 930506 Protean outline editor. Mouse/Macros/SVGA JWPEDICT.ZIP B 1157818 930506 JWP: Jim Breen's English-Japanese dictionary JWPFONTS.ZIP B 478934 930506 JWP: 16x16, 24x24 fonts for display+printing JWPK4848.ZIP B 818140 930506 JWP: 48x48 font for display+printing JWPKINFO.ZIP B 219453 930506 JWP: Kanji information files JWPPROG.ZIP B 337658 930506 JWP 1.10 Japanese word processor for Windows JWPSRC.ZIP B 202126 930506 JWP 1.10 source code JWPWNN.ZIP B 251083 930506 JWP: Wnn kanji dictionaries VDE165B.ZIP B 152624 930502 Meyer's small, fast, WordStar-like text editor VIM127S.ZIP B 310324 930531 Source for VIM127X: vi clone, DOS, Unix, Amiga Directory PD1: LABIR20.ZIP B 14809 930523 Program robot to improve programming skills MODULSH1.ZIP B 374136 930529 Design and animation of robots, 1 of 2 MODULSH2.ZIP B 246639 930529 Design and animation of robots, 2 of 2 OTD_15.ZIP B 134927 930527 What happened on this date? (MS-DOS version) WOTD_15.ZIP B 181837 930527 What happened on this date? (Windows version) Directory PD1: MYZ80111.ZIP B 93033 930518 Simeon Cran's Z80 CP/M Z-System emulator Z80-201.ZIP B 327765 930505 ZX Spectrum 48/128 emulator 'Z80' v2.01 Directory PD1: SCHAEF01.ZIP B 72892 930506 Schaeffler diagram (for high alloyed steel) Directory PD1: AAAREAD.ME A 5833 930502 Information about the files in this directory CNVSIM10.ZIP B 82801 930527 Convert SIMTEL20 SIMIBM.IDX to Paradox4 format GET11.ZIP B 2716 930531 Unix script to FTP files from any MS-DOS site OAKFTP03.ZIP B 2666 930502 Unix script to auto-ftp MS-DOS files from OAK QUICKREF.LST A 3985 930527 Quick reference list to SIMTEL20's MSDOS dirs SIM9304.IDX A 27647 930501 Comma-delimited list of April 1993 uploads SIMIBM.ZIP B 293232 930601 Comma-delim list of all MSDOS files w/descrip. SIMLIST.ZIP B 285802 930601 Text format list of all MSDOS files w/descrip. SIMLIST1.ZIP B 147181 930503 Quick and easy SIMTEL20 file lookup program UPLOADS.APR A 26418 930501 List of uploads to SIMTEL20 for April 1993 Directory PD1: CONCT305.ZIP B 57196 930523 Concatenate files incl on multiple floppies FILE10.ZIP B 53226 930519 Ricki's file type guesser (similar to Unix) HFM319B.ZIP B 332496 930521 Mouse oriented filemanager and archive shell RFILEU10.ZIP B 115099 930519 Ricki's misc. arbitrary file utils (filters) Directory PD1: RSA2.ZIP B 280704 930528 Stock technical analysis w/automated updates Directory PD1: TIDY630.ZIP B 121977 930506 Clean up Fortran-77 programs w/Fortran source Directory PD1: Date: 2 Jun 93 12:38:10 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 18 Original-To: bio-soft@uk.ac.daresbury, methods@uk.ac.daresbury X-Popmail-Charset: British Dear Bionetters, It's here, it's ACE, (it's free), it's DOTPLOT for Windows! Available from the usual places as windot.zip: 129.79.224.25 Indiana (Uncle Don) 148.79.64.4 Daresbury in Blighty 129.7.2.43 Houston (Uncle Dan) Tell me whether you like it. /--------------------------------------------------------------------------\ < Ramin Charles Nakisa, "She walks in beauty Tel: 071 589-5111 x 6729 > > Biophysics Section, As the night of FAX: 071 589-0191 < < The Blackett Lab, starry skies and EMAIL: > > Imperial College, cloudless climes..." ramin@ic.ac.uk < < London SW7 2BZ. mbrcn@seqnet.dl.ac.uk > \--------------------------------------------------------------------------/ From owner-software@net.bio.net Tue Jun 01 23:00:00 1993 Path: biosci!CRCVMS.UNL.EDU!CSMITH From: CSMITH@CRCVMS.UNL.EDU Newsgroups: bionet.software Subject: SCIENCE COMPUTING CENTER ? HELP !!! Message-ID: <01GYWHJVJ7Z400440N@crcvms.unl.edu> Date: 2 Jun 93 18:02:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 39 Dear Netters, I am in the process of putting together a proposal to create a specialized computing resource center for biochemistry /molecular biology here at the University of Nebraska. It is my intent that the center will serve as a "centralized" source of information and technical help for both science software and telecommunications. With this and some of our current difficiences in mind, my initial objectives are to focus on software and telecommunications support and training; that is provide a good level of expertise in commonly used software packages (e.g. GCG, MacVector, DNAsis), run a "database" of other commercial and shareware software, provide for some form of formalized training in the common software packages and electronic communications systems, oversee the establishment and running of communications server(s) (e.g., GOPHER, which we currently do not have), and PUBLICIZE the RESOURCES available. I am looking for your help in providing me with some insights you may have on this endeavor. I am particulary interested in hearing from other "Center" managers and users of such "Centers". What are some of the drawbacks or things to avoid with the Center ? What attributes should I emphasize or are the greatest assests ? What features are the most utilized ? You can reply to me via this net or directly to my net address. Your help will be greatly appreciated !!! Thanking You in Advance. Chris Christopher Smith Department of Biochemistry University of Nebraska-Lincoln Lincoln, NE 68583-0718 (402) 472-6806 Internet: CSMITH@CRCVMS.UNL.EDU From owner-software@net.bio.net Tue Jun 01 23:00:00 1993 Path: biosci!uwm.edu!spool.mu.edu!darwin.sura.net!fconvx.ncifcrf.gov!ntet.nctr.fda.gov!wmelchior From: wmelchior@ntet.nctr.fda.gov (Bill Melchior) Newsgroups: bionet.software Subject: question: scanner software Message-ID: <1993Jun2.110600.126@ntet.nctr.fda.gov> Date: 2 Jun 93 17:06:00 GMT Organization: NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH Lines: 22 We have a Molecular Dynamics PhosporImager. We like it, but the ImageQuant software will not do one thing we'd like: produce three dimensional pictures of the data, where the image looks like an aerial photograph of a mountain range (NOT a contour map). The data file is a .TIF file. Does anyone know of a software package, probably commercial, but others are acceptable, that will operate on a .TIF file to produce a 3D image? I will summarize responses sent directly to me. Thanks, Bill ________________________________________________________________________________ Views expressed are not necessarily those of NCTR, its sponsoring agencies, or the United States government. Bill Melchior || National Center for Toxicological Research || ALL statements Jefferson, AR 72079 || in this (501) 543-7206 || signature box || are false. WMELCHIOR@FDANT.NCTR.FDA.GOV || From owner-software@net.bio.net Tue Jun 01 23:00:00 1993 Path: biosci!uwm.edu!rpi!ghost.dsi.unimi.it!37.1!eagle!claudio From: claudio@eagle.bio.unipr.it (Claudio Rivetti) Newsgroups: bionet.software Subject: chromatography Message-ID: <1993Jun2.155605.1171@cine88.cineca.it> Date: 2 Jun 93 14:56:05 GMT Lines: 11 Nntp-Posting-Host: eagle.bio.unipr.it X-Newsreader: TIN [version 1.2 PL0]Lines: 11 I would like to know if it exists a public domain software able to elaborate chromatography elution diagrams; like calculate peak areas. And as well if this program can acquire or transfer acquire data to a PC. If anybody knows about something similar , please send me the information necessary to get it. My adress is : claudio@irisbioc.bio.unipr.it Bye bye Claudio From owner-software@net.bio.net Tue Jun 01 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!darwin.sura.net!haven.umd.edu!umd5.umd.edu!williams.smcm.edu!bwilliam From: bwilliam@oyster.smcm.edu (Bill Williams) Newsgroups: sci.med,sci.bio,bionet.software,sci.physics Subject: Re: Bibliographic software comparison? Message-ID: <1uit55$no2@umd5.umd.edu> Date: 2 Jun 93 18:56:37 GMT References: <1ugbb2$2pi@max.physics.sunysb.edu> Organization: St. Mary's College of Maryland Lines: 14 Xref: biosci sci.med:15848 sci.bio:3527 bionet.software:5150 sci.physics:17006 NNTP-Posting-Host: williams.smcm.edu X-UserAgent: X-XXMessage-ID: X-XXDate: Wed, 2 Jun 93 19:56:36 GMT In article <129101@netnews.upenn.edu> Laura Hyatt, lhyatt@mail.sas.upenn.edu writes: > Try Papyrus. It works with windows and costs $100.00. You can get more > information from them thrugh Also be sure to give EndNote Plus a shot. I think they have an FTP-able demo for the IBM compatible marked (I use the Mac version). Try sending mail to nilesinc@well.sf.ca.us. ___________________________________ William E. Williams, bwilliam@oyster.smcm.edu Divison of Natural Sciences and Mathematics St. Mary's College of Maryland St. Mary's City, MD 20686 From owner-software@net.bio.net Tue Jun 01 23:00:00 1993 Path: biosci!hanv01.dnet.sandoz.com!blume_j From: blume_j@hanv01.dnet.sandoz.com (John E. Blume) Newsgroups: bionet.software Subject: UNIX on my Mac? Message-ID: <199306021822.AA26055@tigger.jvnc.net> Date: 2 Jun 93 18:11:26 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 22 I am looking for information regarding UNIX implementations on the Mac. I am about to become the proud owner of a Centris 650 8/80 w/FPU (I know, I need a bigger HD, more RAM!), and I use a fair amount of Mac-based mobio software. But I also wish to take advantage of the wealth of UNIX software available. Is this practically possible? What are the most compatible UNIX-implementations for the Mac? Minimum HD and RAM requirements? Is the Centris 650 too slow? I direct this question the the BIOSCI netters, because somwhere out there is someone who has already discovered if any of the mobio UNIX-stuff crashes under A/UX 3.0. Thanks for any info, John E. Blume Sandoz Research Institute E. Hanover, NJ From owner-software@net.bio.net Tue Jun 01 23:00:00 1993 Path: biosci!UICVM.UIC.EDU!U50311 From: U50311@UICVM.UIC.EDU ("Robert Paul Malchow, Ph.D. ", 312-996-2025) Newsgroups: bionet.software Subject: Re: Bibliographic Software Search Message-ID: <9306022002.AA03581@net.bio.net> Date: 2 Jun 93 20:01:49 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 37 The issue of bibliographic software has come up before on this list; at that time, someone suggested the following article for those interested in the subject: Neal, PR (1993) Personal bibliographic software programs - a comparative review. Bioscience 43, 44-51. I got a copy of the article and found it helpful in my own software selection. The penultimate paragraph of Neal's article sums it up rather well: "Of the programs reviewed here, four stood out above the others: EndNote Plus, Papyrus, Pro-Cite, and Reference Manager. These programs differed principally in their tradeoffs among flexibility, speed, and price. Papyrus is an extremely flexible program at a low price. However, it is not as fast as the other three programs. The other three programs are fast and only slightly less flexible, but they are relatively expensive. Depending on your needs, Pro-Cite and Reference Manager, in particular, can be very expensive." I tried Papyrus and Reference Manager and found these comments to be quite accurate. Papyrus is very flexible (maybe a touch too flexible), very reasonably priced ($99), and relatively slow. Reference Manager was fast, slick, less flexible for importing references, and over $550 when all options of interest to me were included. Note that Neal's review was done before Reference Manager for Windows, however. I opted for Papyrus, which is working well, albeit somewhat slowly. Hope this helps! Paul "what, another Current Contents diskette to wade through??" Malchow Research Assistant Professor of Ophthalmology University of Illinois at Chicago From owner-software@net.bio.net Tue Jun 01 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!wupost!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.general,bionet.molbio.gene-linkage,bionet.molbio.methds-reagnts,bionet.software Subject: Encyclopedia of the Mouse Genome Now available by Gopher Message-ID: <1993Jun2.160929.22760@welchgate.welch.jhu.edu> Date: 2 Jun 93 16:09:29 GMT Organization: Johns Hopkins Univ. Welch Medical Library Lines: 303 Xref: biosci bionet.general:5044 bionet.molbio.gene-linkage:188 bionet.molbio.methds-reagnts:5742 bionet.software:5146 There is now a gopher version of the The Encyclopedia of the Mouse Genome. Here you can view the genetic maps of each mouse chromosome, search for specific loci on these maps as well as search for references and notes associated with each locus on the map. In addition you can search the Mouse Locus Catalog which contains detailed information on mouse loci. Now for a little tour: Point your gopher client at merlot.welch.jhu.edu and select the following: --> 13. Search Databases at Hopkins (Vectors, Promoters, NRL-3D, EST, OMIM../ --> 17. Mouse Databases (TBASE, Encyclopedia of the Mouse Genome)/ --> 1. Encyclopedia of the Mouse Genome/ And you'll see: --> 1. About the Encyclopedia of the Mouse Genome. 2. Browse through the Chromosomes/ 3. Search Maps for Loci 4. Notes 5. References 6. Mouse Locus Catalog (MLC) If you have a specific locus in mind that you would like to see it's map position select: --> 3. Search Maps for Loci If you want to see the map position of abl: +--------------------------Search Maps for Loci--------------------------+ | _____________________________ | | Words to search for | abl | | | ----------------------------- | | [Cancel ^G] [Accept - Enter] | | | +------------------------------------------------------------------------+ And you'll see: --> 1. Abl - Abelson murine leukemia oncogene (2) If you select this entry you will see the map for Chromosome 2 with the Expanded view which contains Abl. Note that above you are shown the Locus symbol, Abl, the locus name, Abelson murine leukemia oncogene, and the Chromosome on which it resides, (2). These are all searchable. For example your could search for: +--------------------------Search Maps for Loci--------------------------+ | _____________________________ | | Words to search for | leukemia and 2 | | | ----------------------------- | | [Cancel ^G] [Accept - Enter] | | | +------------------------------------------------------------------------+ And you'll see: --> 1. Abl - Abelson murine leukemia oncogene (2) 2. Glvr-1 - gibbon ape leukemia virus receptor-1 (2) 3. Mpmv-14 - modified polytropic murine leukemia virus-14 (2) 4. Mpmv-28 - modified polytropic murine leukemia virus-28 (2) 5. Mpmv-3 - modified polytropic murine leukemia virus-3 (2) 6. Mpmv-43 - modified polytropic murine leukemia virus-43 (2) 7. Pmv-33 - polytropic murine leukemia virus-33 (2) 8. Pmv-63 - polytropic murine leukemia virus-63 (2) 9. Pmv-7 - polytropic murine leukemia virus-7 (2) 10. Xmmv-71 - xenotropic-MCF leukemia virus-71 (2) 11. Xmv-10 - xenotropic murine leukemia virus-10 (2) 12. Xmv-48 - xenotropic murine leukemia virus-48 (2) You may use booleans (and, or, not) and wildcards (*) to broaden or narrow your searches. -------------------- If you would like the notes and references associated with each locus select: --> 4. Notes --> 5. References You can search for loci, authors or journals. You may use booleans (and, or, not), phrase searches ("...") and wildcards (*) to broaden or narrow your searches. -------------------- If you would like detailed information on a locus or to search for loci by topic select: --> 6. Mouse Locus Catalog (MLC) and for example search for: +--------------------------Mouse Locus Catalog (MLC)---------------------+ | _____________________________ | | Words to search for | leukemia and 2 | | | ----------------------------- | | [Cancel ^G] [Accept - Enter] | | | +------------------------------------------------------------------------+ And you will see: 1. LOCUS Igf1r locus, insulin-like growth factor 1 receptor. ... --> 2. LOCUS Insr locus, insulin receptor. CHROMOSOME 8 CLA... 3. LOCUS Igf2r locus, insulin-like growth factor II receptor. ... A sample entry is as follows: -------------------------------------------------------------------------- LOCUS Insr locus, insulin receptor. CHROMOSOME 8 CLASSES Receptors TEXT Insr locus, insulin receptor, Chr 8. The transmembrane allosteric enzyme which acts as an insulin receptor is composed of alpha and beta subunits. Both are thought to be derived through the cleavage of a common proreceptor precursor. When insulin interacts with its binding site on the extracellular alpha subunit, a cytoplasmic tyrosine kinase domain in the beta subunit is activated (3). The Insr gene in the mouse has been localized to the proximal end of Chr 8, using somatic cell hybrids (4) and two interspecific backcrosses (1, 2). See also the insulin-like growth factors (Igf-) and their receptors. REFERENCES 1. Ceci, J.D., M.L. Justice, L.F. Lock, N.A. Jenkins, and N.G. Copeland. 1990. An interspecific backcross linkage map of mouse Chromosome 8. Genomics 6:72-79. 2. Howard, T.A., J.M. Rochelle, A.M. Saunders, and M.F. Seldin. 1991. A linkage map of mouse Chromosome 8: further definition of the syntenic relationship between mouse Chromosome 8 and human Chromosomes 8, 16 and 19. Genomics 10:207-213. 3. Sibley, E., T. Kastelic, T.J. Kelly, and M.D. Lane. 1989. Characterization of the mouse insulin receptor gene promoter. Proc. Natl. Acad. Sci. USA 86:9732-9736. 4. Wang, L.-M., A.M. Killary, X.-E. Fang, S. K. Parriott, P.A.Lalley, G.I. Bell, and A.Y. Sakaguchi. 1988. Chromosome assignment of mouse insulin, colony stimulating factor 1, and low-density lipoprotein receptors. Genomics 3:172-175. UPDATED Wed May 13 14:59:40 EDT 1992 TAG Insr ---------------------------------------------------------------------- If you would simply like to browse through the Maps select: --> 2. Browse through the Chromosomes/ And you will see: --> 1. Chromosome 1/ 2. Chromosome 2/ 3. Chromosome 3/ 4. Chromosome 4/ 5. Chromosome 5/ 6. Chromosome 6/ 7. Chromosome 7/ 8. Chromosome 8/ 9. Chromosome 9/ 10. Chromosome 10/ 11. Chromosome 11/ 12. Chromosome 12/ 13. Chromosome 13/ 14. Chromosome 14/ 15. Chromosome 15/ 16. Chromosome 16/ 17. Chromosome 17/ 18. Chromosome 18/ 19. Chromosome 19/ 20. Chromosome X/ 21. Chromosome Y/ Now select the Chromosome that you are interested in browsing lets try Chromosome 1 - you will see: --> 1. Overview of Chromosome 1 2. Expanded View 1 (Region 5-7) 3. Expanded View 2 (Region 10-11) 4. Expanded View 3 (Region 15-21) 5. Expanded View 4 (Region 23-30) 6. Expanded View 5 (Region 31-40) 7. Expanded View 6 (Region 41-47) 8. Expanded View 7 (Region 48-54) 9. Expanded View 8 (Region 55-59) 10. Expanded View 9 (Region 60-68) 11. Expanded View 10 (Region 69-77) 12. Expanded View 11 (Region 79-81) 13. Expanded View 12 (Region 82-87) If you select "Overview of Chromosome 1" you will see a simple map containing some loci and with a number scale running down the left side of the map: | 10 | | 20 | | 30 | | 40 | | 50 | | 60 | | 70 | | 80 | | 90 | | 100| | | Use the numbers to define the Region where you would like to see an Expanded view of the map - which will show all the loci present in that section. ============================================================================== If you've never heard of gopher, don't worry - it's free and on the net. Write me a note if you'd like information on how to get started. To view the maps in the Encyclopedia you need to be able to display images. Many of the gopher clients will work just fine - a few hints: If you're using a Mac - go get the latest version of Turbogopher (earlier versions had trouble launching linked images). If you're using the DOS client (PCGopher III) - you'll need to download the image and view it seperately - one of those fun quirks about DOS, no memory and no multitasking. ============================================================================== The Encyclopedia of the Mouse Genome is built and maintained at The Jackson Laboratory in Bar Harbor Maine. For further information about the Encyclopedia contact davidnaman@jax.org at the Jackson Laboratory. The Gopher version of the Encyclopedia has been created by Dan Jacobson at Johns Hopkins University. Happy Searching, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-software@net.bio.net Wed Jun 02 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!xlink.net!math.fu-berlin.de!news.th-darmstadt.de!oc2.oc.chemie.th-darmstadt.de!martin From: martin@oc2.oc.chemie.th-darmstadt.de (Martin Kroeker) Newsgroups: bionet.software Subject: Re: Molbiol & Linux? Message-ID: <1ukc2gINNmku@rs2.hrz.th-darmstadt.de> Date: 3 Jun 93 08:17:20 GMT References: Distribution: bionet Organization: Technical University Darmstadt, Germany Lines: 28 NNTP-Posting-Host: oc2.oc.chemie.th-darmstadt.de In article ajb@s-crim1.dl.ac.uk (Alan Bleasby) writes: > >Rather than say `x,y & z' (wrt the question "which molbiol apps have been >ported to Linux) it'd probably be better to ask which haven't. >Providing the C source is available its a relatively easy task to port. > >There is no FORTRAN compiler for Linux (mercifully) so GCG isn't an Bah. Flame bait. We have this kind of argument on comp.lang.fortran every six weeks or so. Please do not start it here too. > >Linux sometimes gets schizophrenic about whether or not its SysV or BSD It is supposed to be(come) POSIX compliant with some BSD and SYSV extensions. > >Summary: If the program is written in (e.g.) C, PASCAL or LISP its > easily ported (generally). If its written in FORTRAN then there's > an f2c (FORTRAN to C) program which might help(?) f2c makes a very reliable gcc front end. I have successfully compiled several thousand lines of code (e.g. MOPAC, GROMOS, RIBBON, ORTEP). Regards, Martin -- Dipl.-Ing. Martin Kroeker kroeker@oc1.oc.chemie.th-darmstadt.de Inst. f. Organ. Chemie martin@oc2.oc.chemie.th-darmstadt.de Univ. (TH) Darmstadt db7p@mvs.hrz.th-darmstadt.de Germany (in real life: ) From owner-software@net.bio.net Wed Jun 02 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!usc!cs.utexas.edu!swrinde!network.ucsd.edu!munnari.oz.au!newsroom.utas.edu.au!medicalsc49h112.med.utas.edu.au!user From: Sun.Bin@anat.utas.edu.au (SUN BIN) Newsgroups: bionet.software Subject: wanted: software for dendritic pattern recognition Message-ID: Date: 3 Jun 93 07:08:42 GMT Sender: news@newsroom.utas.edu.au Followup-To: bionet.software Organization: UNI TAS Lines: 15 I AM INTERESTED IN ANY IBM OR MAC SOFTWARE THAT ENABLES THE RECOGNITION OF DENDRITIC MORPHOLOGICAL PATTERNS ACCORDING TO STANDARD CRITERIA (eg. number, length and thickness of first, second or third dendrites, coefficients obtained from the combination of all these data, volume occupied by the totality of the dendritic tree and other measurable features etc). CAN ANY ONE GIVE ME SOME ADVICE ABOUT THIS? THANK YOU IN ADVANCE. SUN BIN DEPT OF ANATOMY UNIVERSITY OF TASMANIA GPO BOX 252C TAS AUSTRALIA 7001 emai: Sun.Bin@anat.utas.edu.au From owner-software@net.bio.net Wed Jun 02 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!math.ohio-state.edu!sol.ctr.columbia.edu!news.kei.com!ub!newserve!sarah!albnyvms.bitnet!BOBREJ From: bobrej@albnyvms.bitnet (Robert Rej) Newsgroups: sci.med,sci.bio,bionet.software,sci.physics Subject: Re: Bibliographic software comparison? Message-ID: <1993Jun3.112911.6961@sarah.albany.edu> Date: 3 Jun 93 11:29:11 GMT References: <1ugbb2$2pi@max.physics.sunysb.edu> Sender: news@sarah.albany.edu (News Administrator) Reply-To: bobrej@albnyvms.bitnet Organization: University of Albany, SUNY Lines: 20 Xref: biosci sci.med:15904 sci.bio:3551 bionet.software:5154 sci.physics:17087 In article <1ugbb2$2pi@max.physics.sunysb.edu>, mhollowa@ic.sunysb.edu (Michael Holloway) writes: >We're thinking of buying Reference Manager for Windows (~$375 with discount) >but we're a poor lab and would appreciate hearing from anyone who has had >experience with other DOS system bibliographic software. Is there one that >stands out? Are there any that are real dogs? Is anyone out there using >Reference Manager? I'll summarize any E-mail and post if warrented. We evaluated several programs in our lab a few years ago and selected Reference Manager (DOS V3.xx or 4.xx). We're up to V5.05 and very happy with it; there have been few problems, usually associated with a newer version of WordPerfect or of our CDROM Medline (CD+) system. Tech support is super, amongst the best. I, too, was thinking of the Windows version but am unwilling to sacrifice the speed of the DOS version (real fast even on a 386DX/20). -Bob ____________________________________________________________________ bobrej@uacsc1.albany.edu Robert Rej - SUNY Albany Scarpia got the point! ____________________________________________________________________ From owner-software@net.bio.net Wed Jun 02 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!howland.reston.ans.net!agate!doc.ic.ac.uk!pipex!uknet!mcsun!news.funet.fi!funic!nic.funet.fi!csc.fi!harper From: Rob.Harper@csc.fi (Rob Harper) Newsgroups: bionet.software Subject: Winsock (Hgopher) Message-ID: <199306031215.AA18402@csc.fi> Date: 3 Jun 93 12:15:45 GMT Sender: root@nic.funet.fi (The FUnny NET guru) Organization: Finnish University & Research Network Lines: 72 >Xref: funic comp.protocols.nfs:5524 comp.protocols.tcp-ip.ibmpc:13666 alt.gopher:1561 comp.infosystems.gopher:4436 >Newsgroups: comp.protocols.nfs,comp.protocols.tcp-ip.ibmpc,alt.gopher,comp.infosystems.gopher >Path: funic!news.funet.fi!sunic!mcsun!uknet!pipex!doc.ic.ac.uk!cc.ic.ac.uk!mjh >From: mjh@cc.ic.ac.uk ( ) >Subject: Announcing Win3.1 Winsock and PC/NFS Gopher Client Beta 1.0 (HGOPHER) >Message-ID: <1993Jun3.114019.22771@cc.ic.ac.uk> >Nntp-Posting-Host: rimmer >Organization: Imperial College >Date: Thu, 3 Jun 93 11:40:18 BST >Lines: 60 ANNOUNCING THE AVAILABILITY OF HGOPHER WITH WINSOCK A Gopher Client For Windows 3.1 Version Beta 1.0 The Windows 3.1 PC NFS Gopher client that I recently announced (about two weeks ago) has now been converted to run using a WINSOCK compatible DLL. As the product seems to be fairly stable I have moved from an alpha release to the first Beta release. Some bugs have been fixed since the Alpha version. In addition I have change the name of the product since just "gopher" seemed a little too generic. For want of anything better its now called Hampson's Gopher or just plain HGOPHER. To all the people who helped me Alpha test the Winsock version a BIG THANK YOU. And to all the people who asked to be Alpha testers - I am sorry if I did not get back to you personally but there were quite a lot of you and I was busy sorting out the problems the first Alpha testers found. Features * Bookmarks * bookmark Editing (New this release) * DNS capability * Vendor name lookup * Text, image, telnet, tn3270 capability (providing you have other public domain or PC NFS products) * Index capability * copy to file capability * No CSO support yet * No Sound support yet * No PostScript support yet (although I looks like it does) * No MIME support yet Installation Available for ANON FTP from lister.cc.ic.ac.uk Change to directory pub/wingopher and collect the files:- readme.txt hgopher.exe [WINSOCK Version] (Binary mode required) hngopher.exe [PC NFS Only Version] (Binary mode required) Then read the readme.txt file Martyn Hampson -- ------------------------------------------------------------------------ Martyn Hampson m.hampson@ic.ac.uk lmperial College Computer Centre. ------------------------------------------------------------------------- From owner-software@net.bio.net Wed Jun 02 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!usc!howland.reston.ans.net!ux1.cso.uiuc.edu!news.cso.uiuc.edu!lwalsh From: lwalsh@nemo (Laura L. Walsh) Newsgroups: bionet.software,bionet.xtallography,bionet.general Subject: Annotated PDB Listing Message-ID: Date: 3 Jun 93 16:17:01 GMT Sender: usenet@news.cso.uiuc.edu (Net Noise owner) Organization: University of Illinois at Urbana Lines: 28 Xref: biosci bionet.software:5156 bionet.xtallography:310 bionet.general:5059 The most recent version of my annotated list of PDB files is now available for anonymous ftp from kekule.osc.edu in the directory /pub/chemistry/pdbdoc as the file pdb_file_list.jan.93 (216426 bytes). This file contains condensed information about the available X-ray structures and their quality. The file seq_groups.jan.93 (56033 bytes) is also present in the same directory. This file was obtained by running the BLAST program on the whole PDB database (including prerelease entries) to detect homologies between protein sequences. The details on the contents of the files and methodology are given at the beginning of each file. The files are available from anonymous ftp: ftp kekule.osc.edu (or ftp 128.146.36.48) Login: anonymous Passwd: kekule ftp> cd /pub/chemistry/pdbdoc ftp> get pdb_file_list.jan.93 ftp> seq_groups.jan.93 ftp> quit Laura Walsh Laura Lynn Walsh (lwalsh@nemo.life.uiuc.edu) (217) 244-2894 Beckman Inst., Univ. of IL * 405 N. Mathews Ave. * Urbana, IL 61801, USA From owner-software@net.bio.net Wed Jun 02 23:00:00 1993 Path: biosci!daresbury!daresbury!ajt From: ajt@rri.sari.ac.uk (Tony Travis) Newsgroups: bionet.software Subject: Re: Molbiol & Linux? Message-ID: <1993Jun3.173528.7635@gserv1.dl.ac.uk> Date: 3 Jun 93 17:12:43 GMT References: <9363094801.MIN-LPKAa08786.bionet-news@uk.ac.daresbury> Sender: list-admin@daresbury.ac.uk Reply-To: ajt@rri.sari.ac.uk Distribution: bionet Organization: Rowett Research Institute Lines: 33 Apparently-To: X-Newsreader: TIN [version 1.1 PL7] Martin Kroeker (martin@de.th-darmstadt.chemie.oc.oc2) wrote: : [...] : f2c makes a very reliable gcc front end. I have successfully compiled several : thousand lines of code (e.g. MOPAC, GROMOS, RIBBON, ORTEP). I've used both f2c and p2c which translate fortran or pascal to C respectively. Their stated objectives are to provide a means of compiling an equivalent program on platforms that do not have a native fortran or pascal compiler available (or it is too expensive). They do this job very well, but the code they produce is HORRENDOUS and not intended to be seen by human programmers! There are other programs available like BSD "struct" which 'structures' fortran into quite good ratfor. This is rather different and f2c or p2c are not good at it!! It is important to consider what the objective of translating from one programming language to another is. After all, mixed language compilation is straight-forward on most systems (including DOS) as long as you observe the parameter passing conventions and know the correspondence between types in the two languages. Personally, I structure fortran programs into ratfor so I can understand the algorithms. I expect a public domain fortran de-spagg program would do the same, but the only one I know about is "tidy" which is limited. Are there any *good* free fortran 'improvers' available? 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 Wed Jun 02 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!haven.umd.edu!umd5.umd.edu!comb15.umd.edu!Belas From: Belas@mbimail.umd.edu (Bob Belas) Newsgroups: bionet.software Subject: Re: Winsock (Hgopher) Message-ID: Date: 3 Jun 93 19:59:35 GMT References: <199306031215.AA18402@csc.fi> Organization: Center of Marine Biotechnology Lines: 50 NNTP-Posting-Host: comb15.umd.edu In article <199306031215.AA18402@csc.fi> Rob.Harper@csc.fi (Rob Harper) writes: >Newsgroups: bionet.software >Path: hecate.umd.edu!umd5.umd.edu!haven.umd.edu!darwin.sura.net!spool.mu.edu!agate!doc.ic.ac.uk!pipex!uknet!mcsun!news.funet.fi!funic!nic.funet.fi!csc.fi!harper >From: Rob.Harper@csc.fi (Rob Harper) >Subject: Winsock (Hgopher) >Message-ID: <199306031215.AA18402@csc.fi> >Sender: root@nic.funet.fi (The FUnny NET guru) >Organization: Finnish University & Research Network >Date: Thu, 3 Jun 1993 15:15:45 +0300 >Lines: 72 > >>Xref: funic comp.protocols.nfs:5524 comp.protocols.tcp-ip.ibmpc:13666 alt.gopher:1561 comp.infosystems.gopher:4436 >>Newsgroups: comp.protocols.nfs,comp.protocols.tcp-ip.ibmpc,alt.gopher,comp.infosystems.gopher >>Path: funic!news.funet.fi!sunic!mcsun!uknet!pipex!doc.ic.ac.uk!cc.ic.ac.uk!mjh >>From: mjh@cc.ic.ac.uk ( ) >>Subject: Announcing Win3.1 Winsock and PC/NFS Gopher Client Beta 1.0 (HGOPHER) >>Message-ID: <1993Jun3.114019.22771@cc.ic.ac.uk> >>Nntp-Posting-Host: rimmer >>Organization: Imperial College >>Date: Thu, 3 Jun 93 11:40:18 BST >>Lines: 60 > > ANNOUNCING THE AVAILABILITY OF HGOPHER > WITH WINSOCK > > A Gopher Client For Windows 3.1 Version Beta 1.0 > >The Windows 3.1 PC NFS Gopher client that I recently announced >(about two weeks ago) has now been converted to run using a >WINSOCK compatible DLL. ^^^^^^^^^^^^^^^^^^^^^^^?? What is WINSOCK? Would someone provide a bit more explanation of this software? Bob ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ "Now imagine a Moebius vortex inside a spherical constant, and you've ~~ ~~ got my cosmology." Frank Zappa, 1992. ~~ ~~ ~~ ~~ Bob (Belas@mbimail.umd.edu) ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-software@net.bio.net Wed Jun 02 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uknet!bnr.co.uk!bnrgate!nott!torn!utnut!cs.utexas.edu!usc!sol.ctr.columbia.edu!news.columbia.edu!cunixb.cc.columbia.edu!stone From: stone@cunixb.cc.columbia.edu (Glenn Stone) Newsgroups: sci.med,sci.bio,bionet.software,sci.physics Subject: Re: Bibliographic software comparison? Message-ID: <1993Jun3.165023.2193@news.columbia.edu> Date: 3 Jun 93 16:50:23 GMT References: <1ugbb2$2pi@max.physics.sunysb.edu> Sender: usenet@news.columbia.edu (The Network News) Reply-To: stone@cunixb.cc.columbia.edu (Glenn Stone) Organization: Columbia University Lines: 20 Xref: biosci sci.med:15947 sci.bio:3562 bionet.software:5158 sci.physics:17117 Nntp-Posting-Host: cunixb.cc.columbia.edu In article <1ugbb2$2pi@max.physics.sunysb.edu> mhollowa@ic.sunysb.edu (Michael Holloway) writes: >We're thinking of buying Reference Manager for Windows (~$375 with discount) >but we're a poor lab and would appreciate hearing from anyone who has had >experience with other DOS system bibliographic software. Is there one that There is a great reference manager called BIB that only costs $75, but it's mainly oriented towards social scientists -- it has built-in journal formats for something like 40 journals in anthro, sociology, political science, geography. But it has the advantage of being extremely easy to use (menu-driven). They're at BIB Software P.O. Box 7904 Missoula, MT 59807 ------------------------------------------------------------------------- Glenn Davis Stone BITNET: stone@cunixf Columbia University INTERNET: stone@columbia.edu ------------------------------------------------------------------------- From owner-software@net.bio.net Wed Jun 02 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!ux1.cso.uiuc.edu!news.cso.uiuc.edu!phylo!smith From: smith@phylo.life.uiuc.edu (Steven Smith) Newsgroups: bionet.software Subject: Future development of GDE Keywords: GDE Message-ID: Date: 3 Jun 93 23:22:17 GMT Sender: usenet@news.cso.uiuc.edu (Net Noise owner) Organization: University of Illinois at Urbana Lines: 55 Notice to all GDE users: After a brief break, I am back to doing development on GDE. I hope to get version 2.2 out shortly, and then begin working toward 3.0. I would like to start soliciting ideas about the 3.0 version. The one key issue to be addressed is whether or not it should be moved from XView (openlook) to Motif. The reason for this discussion comes from Sun's official adoption of Motif as part of the COSE agreement with IBM, HP, and USL. The benefits of such a move would be portability, and long term(?) compatability to other software running under X. The down side would be that this would take a tremendous amount of effort (read time) when no new functionality would be added. It might even be the case that some functionality would be lost at least for the immediate future. Sun has insured support of XView for the forseeable future, and is taking steps to simplify it's operation under mwm. The second issue to be raised is that of joint development. Thanks to the efforts of Tim Littlejohn at UMontreal, now seems like the perfect time to solicit assistance from the community in implementing some of the new features that people would like added to GDE. There is an ongoing discussion on the MegaGopher at U. Montreal about features that people would like to see added to GDE. I am aware of many places that have already made additions through the .GDEmenus file, and external functions. I also have submissions for modifications to the core editor that are folded in for the 2.2 release. Tim and I would like to propose a standard method of submitting additions to GDE to the mega-gopher for eventual inclusion in the released version. External functions (in whatever language) would be submitted in source form, along with a Makefile for compilation, a GDEmenus addition file, and a help file. In this manner, a directory of additions can be maintained which people can pick and choose as to whether or not they want a given addition in their own installation. As time progresses, additions would migrate into the release. A perfect example of such a submission would be Don Gilbert's latest version of ReadSeq. Source code additions to the core tools should be submitted as diff files from the original, latest source code tree. This would involve a bit more manipulation to work into the local versions. After a sufficient period of testing, the new additions would be folded into the released version. By doing things this way, people can benefit from developments as fast as possible. Yet there will be time for testing to insure reliability of additions, and development would not be under the oppressive control of one flakey software engineer (namely me). Comments are always appreciated. Email can be send to me at smith@nucleus.harvard.edu (dont know how for how long), or smiths@megasun.bch.umontreal.ca. Please Cc: all suggestions to gde@megasun.bch.umontreal.ca. I would like to thank everyone for their support and suggestions, and I hope that we can all help GDE to grow in the necessary directions for the future. Sincerely, Steven Smith From owner-software@net.bio.net Thu Jun 03 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!haven.umd.edu!umd5.umd.edu!hjpatt-91.umd.edu!user From: de19@umail.umd.edu (Dana S Emery) Newsgroups: bionet.software Subject: Re: Actually Hardware breakdown of Mac SE Message-ID: Date: 4 Jun 93 02:59:54 GMT References: <9306011537.AA11511@beloit.edu> Followup-To: bionet.software Distribution: bionet Organization: personal Lines: 24 NNTP-Posting-Host: hjpatt-91.umd.edu In article <9306011537.AA11511@beloit.edu>, jonesbb@BELOIT.EDU (Ben Jones) wrote: > > The fact that the hard drive and the internal floppy disk went out at the > same time suggests that neither may be at fault, but rather that the mother > board has failed. I admit, I hadnt considered that, but we dont know that they went out together. Guess a PS voltage check is in order, followed by an external floppy based boot-check. Hopefully this guy has access to a techie freind or a service center. > Don't buy a new drive until an Apple tech runs Mac > diagnostics on the unit. I wouldnt necessarily say that, functional scsi hard drives port well enough to other units given external cases, but it is her kroner and her decision to make. -- Dana S Emery From owner-software@net.bio.net Thu Jun 03 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!gatech!swrinde!cs.utexas.edu!utnut!torn!nott!bnrgate!bnr.co.uk!demon!visigoth.demon.co.uk!user From: pettsj@visigoth.demon.co.uk (James Petts) Newsgroups: bionet.software,comp.sys.mac.apps Subject: PharmK Program Message-ID: Date: 4 Jun 93 12:59:56 GMT Sender: news@demon.co.uk Followup-To: bionet.software,comp.sys.mac.apps Organization: No Affiliation Lines: 13 Xref: biosci bionet.software:5166 comp.sys.mac.apps:14745 Nntp-Posting-Host: visigoth.demon.co.uk I read in J. Pharm. Sci, 82(5) about a program for pharmacokinetic modelling program for the Mac called PharmK. Does anybody have any info about getting hold of a copy? ===> James Petts <=== ========================================================================= pettsj@visigoth.demon.co.uk ..oo000oo.. PGP 2.X key on the servers ========================================================================= I feel that if a person can't communicate, the very least he can do is shut up. -- Tom Lehrer ========================================================================= From owner-software@net.bio.net Thu Jun 03 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!usc!elroy.jpl.nasa.gov!swrinde!network.ucsd.edu!teetot.acusd.edu!thor From: thor@teetot.acusd.edu Newsgroups: bionet.software Subject: MacLade Message-ID: <1993Jun3.233100.15703@teetot.acusd.edu> Date: 3 Jun 93 23:31:00 GMT Distribution: usa Organization: usd Lines: 6 Does anyone know where I can get info on MacLade? Thanks, thor@teetot.acusd.edu -- From owner-software@net.bio.net Thu Jun 03 23:00:00 1993 Path: biosci!CSC.FI!Rob.Harper From: Rob.Harper@CSC.FI (Rob Harper) Newsgroups: bionet.software Subject: Xmosaic 1.1 Message-ID: <199306041023.AA01396@csc.fi> Date: 4 Jun 93 10:23:47 GMT Sender: daemon@net.bio.net Lines: 32 >Newsgroups: comp.infosystems.www >Path: funic!news.funet.fi!sunic!pipex!bnr.co.uk!bnrgate!nott!torn!howland.reston.ans.net!ux1.cso.uiuc.edu!news.cso.uiuc.edu!128.174.5.61!marca >From: marca@ncsa.uiuc.edu (Marc Andreessen) >Subject: Mosaic 1.1 prerelease 3 available for testing >Date: Fri, 4 Jun 1993 09:43:00 GMT >Message-ID: >Sender: usenet@news.cso.uiuc.edu (Net Noise owner) >X-Md4-Signature: f36687d59961ad02545e42b37a1ac136 >Organization: Nat'l Center for Supercomputing Applications >Lines: 20 Brave (and not so brave; it's pretty stable) souls can try out Mosaic 1.1, prerelease 3... file://ftp.ncsa.uiuc.edu/Mosaic/beta/xmosaic-1.1-pre3.tar.Z .../xmosaic-sun.Z .../xmosaic-sun-lresolv.Z .../xmosaic-sgi.Z .../xmosaic-ibm.Z If no coredumps or nuclear detonations are reported within 24-48 hours, it'll be kicked out of the nest as official release 1.1. Thanks much in advance for any feedback, Marc -- Marc Andreessen Software Development Group National Center for Supercomputing Applications marca@ncsa.uiuc.edu From owner-software@net.bio.net Thu Jun 03 23:00:00 1993 Path: biosci!CMU.UNIGE.CH!DLOWRY From: DLOWRY@CMU.UNIGE.CH (DOROTHY LOWRY) Newsgroups: bionet.software Subject: X on the PC - Summary of responses Message-ID: <01GYZ9BDNXOY0006L8@cmu.unige.ch> Date: 4 Jun 93 11:39:39 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 224 SUMMARY OF X (WINDOWS) FOR THE PC ------------------------------- A while ago (May 1993) I posted a message to bionet.software asking "So how do you let the SUN know that you are running X-windows"; it was basically a 2-part question - the first part dealt with what kind of software you can run on your PC to make it an X client. The second part dealt with how, once you have X running on your local computer, to tell a remote computer that you are running X so that you can use X on the remote. I received a TON of help, and, am looking forward to implementing it. I am embarrased to admit that I haven't had time to play with X yet but I have had some mail from other people who wanted to know what I'd found out. Therefore, I am summarizing all the responses I got (for my reference and yours) and I hope that I managed to find all the responses (please excuse me if you posted something/sent me something and I neglected to include it). Again, to everyone who responded, THANK YOU! I'm going to divide this summary into 3 parts: 1] An introduction to X - from Lyle Wiedeman 2] How to make the SUN (or whatever) know that you are running X. 3] X client programs for the PC - where to get them and some comments. As for me, I think I'm going to try out LINUX for myself and see if I can get it to work with everything we've got (PC/TCP, Novell and an insistence on running MS-Windows) and I might investigate DesQView/X since it is supposed to run both Windows and DOS already and I am not sure that Linux runs Windows. Regards, Dorothy ============================================================================== Dorothy Lowry - Graduate Student dlowry@cmu.unige.ch Dept. of Medical Biochemistry University of Geneva, Switzerland ============================================================================ PART 1: An introduction to X From: IN%"wiedeman@uci.edu" "Lyle Wiedeman" 15-MAY-1993 16:58:03.29 To: IN%"dlowry@cmu.unige.ch" CC: Subj: "Basic" question > And for my real and BASIC question/comment - if you are RUNNING > X-windows on a SUN, and the sequence analysis software, whatever, > is on ANOTHER SUN, how do you tell the second SUN that you are > running X windows? > > Do you need to rlogin or is telneting OK (sorry about my ignorance > but I haven't got access to a SUN workstation myself - this is so > I can tell the lucky people who HAVE got one, but are running > VT100 emulations to connect anywhere else!). If you haven't used X, it is little wonder this question puzzles you. You'll need to grasp some basic X concepts. An X server is a program which maintains a screen (a monitor); it controls who has the right to open windows on a given machine (screen, monitor). An X client is any program which can run under X (like your sequence analysis software). The screen it draws upon is sometimes the monitor attached to the computer it is running on, but the beauty of X is that this "client" program can open a window and draw on any screen (server) on the network. Most programs (clients), if they are DESIGNED to support X will look at the Unix environment for a variable called DISPLAY which indicates the machine which your X server is running on, and will then try to open a window on that machine's screen. So, to run a program on one machine and see the display on another, you need to do two things: tell the server (the machine you are sitting at) that the other machine is permitted to open windows -- with the xhost command. Then tell the machine you're running the client on where you want it to draw by setting the DISPLAY variable. It makes no difference at all how you communicate to the remote (client) machine; telnet and rlogin are equally useful. Lyle Wiedeman Office of Academic Computing wiedeman@uci.edu Univ. Calif. Irvine wiedeman@UCI.BITNET Irvine, CA 92717 (714) 856-8718 FAX (714) 725-2069 ============================================================================ PART 2: How do you make the SUN (or whatever) know that you are an X client From: IN%"wrp@cyclops.micr.virginia.edu" "Bill Pearson" 11-MAY-1993 14:25:16.96 Let's say "darwin" has your software, and "mendel" is your local xterminal. You have several options. The easiest is to: rlogin darwin setenv DISPLAY mendel:0.0 A functional alternative, which you could put on a menu, would be: rsh darwin /usr/X11/bin/xterm -display=mendel:0.0 -font=fixed I do this all the time. Bill Pearson ----------------------------------------------------------------------------------- From: IN%"noran!ringo!sjohnson@uunet.UU.NET" " (Scott Johnson)" 11-MAY-1993 15:15:56.94 If you want any X application to run on one machine and display on another, connected via a network, you have several possibilities. If you are running a command or shell tool: rlogin setenv DISPLAY :0 or rlogin -display :0 or rsh -display :0 I these don't work you have other problems and need to talk to your software vendor, if you have support. ----------------------------------------------------------------------------------- From: IN%"'/RFC-822=baillie(a)sfu.ca/'@cosine-gw.infn.it" 11-MAY-1993 18:35:44.34 Set your machine to accept X-win input by typing xhost + go to the other machine, BUT before starting the application, type setenv DISPLAY yourmachinename:0 start application Should work fine dave baillie dbaillie@trog.mbb.sfu.ca ---------------------------------------------------------------------------- From: robison@biosun.harvard.edu This is the sort of question I am constantly asking [sic]. 0) Sit at your machine :-) 1) Telnet or rlogin to the 2nd machine (either will do) 2) SETENV DISPLAY ipaddress:0 where ipaddress is the ipnumber or name for your node (such as biosun.harvard.edu) Sit back and enjoy!! I usually have aliases for all the machines I frequently use as displays which do the SETENV DISPLAY step (alias dmito "SETENV DISPLAY mito.harvard.edu:0" will make "dmito" a command to activate "mito.harvard.edu" as my display server). [HE FOLLOWED THIS WITH:] Oops, I forgot step 0.5 in my previous post. 0.5) xhost +otheripaddress where otheripaddress is the address of the machine which you will be accessing via telnet/rlogin. Again, I usually alias these things. For example, the following will cause "xmito" to launch a new command-tool window and rlogin to mito.harvard.edu. The window will display "mito" as its title (linebreak between the two lines inserted for clarity -- don't type it in this way): alias xmito "host +mito.harvard.edu;cmdtool -title mito -e rlogin mito.harvard.edu &" Once your in, you just have to do the "SETENV DISPLAY" step and you're going! Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@biosun.harvard.edu ============================================================================ Part 3: X client programs for the PC - where to get them and some comments PLEASE NOTE: ROB HARPER SENT ME AN ENTIRE SUMMARY OF ALL AVAILABLE X CLIENT PROGRAMS FOR THE PC. IT IS TOO LONG TO INCLUDE HERE BUT IF YOU WOULD LIKE A COPY OF IT I WILL SEND IT TOO YOU (send me (Dorothy Lowry) email at dlowry@cmu.unige.ch). From: IN%"22313TCN@msu.edu" "Thomas_C.Newman" 11-MAY-1993 14:11:21.95 In regards to X-windows on a PC. I have been running Quarterdeck's Desqview/X for the last 6 months and am quite pleased. You need at least 8 mb of RAM, 16 is better of course, but I can run more than 9 windows at once. You can even run windows in a window, but it is extremely slow. The program cost $250 for the PC package and another $100-200 for the network manager. Hope this helps, Tom Newman ----------------------------------------------------------------------------------- From: IN%"shawn@aragorn.ori.org" " (-Shawn Boles-)" 11-MAY-1993 21:13:47.92 With respect to your q re: xwindows for dos - Quarterdeck software claims an x window facility for their dos product. I have not used it but others who have say that it behaves reasonably..look in any pc mag for Quaterdeck ads. hope this helps... ----------------------------------------------------------------------------------- From: IN%"nenno@rhrk.uni-kl.de" "Mario Nenno" 17-MAY-1993 14:10:03.16 I don't know whether it works with PC/TCP AND Novell, but I know of two COMMERCIAL products for making x-windows on PCs: PC-Xview (for DOS) XVision (for Windows 3.x) Both work with PC/FTP (at least on our PCs). It's not much, but I hope it helps a little bit further. Sincelry Mario Nenno ----------------------------------------------------------------------------------- From: IN%"maalouf@proline.rowland.org" "George J. Maalouf" 14-MAY-1993 01:11:35.98 I strongly recommend using MIT-X11R5/TWM insted of openwindows/olwm. ==============================END OF SUMMARY========================================== From owner-software@net.bio.net Thu Jun 03 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!gibbs From: gibbs@husc4.harvard.edu (James Gibbs) Newsgroups: bionet.software Subject: Re: Actually Hardware breakdown of Mac SE Message-ID: Date: 4 Jun 93 17:44:39 GMT References: <1993May30.103028.11781@nomina.lu.se> Lines: 44 Nntp-Posting-Host: husc4.harvard.edu Lars.Snogerup@plantbio.lu.se (El Supremo) writes: >Dear netters! >A good friend of mine has mixed up my knowledge of how to use a macintosh >with the knowledge of what makes it work, so he dumped a mac se in my lap. >The problem is as follows; The computer has a Apple HD20 and a 800k >floppy drive and a SpeedCard. When booting the symbol with a disk and a >question mark appears, and if you put in a systemdisk in the druve it >dosen t help. I managed to start up the computer via an external >diskdrive, the icon for the hard disk do not appear on the desktop, If >you insert a disk in the internal diskdrive, you get the message that it >is not formatted, if you let it try to formatt the disk you get message >that the formatting failed. >When booting you can hear the hard disk starting and then stopping, so i >opend the macine and looked, when you boot the motor start in one >direction and then the other and then stops. You seem to have gotten a lot of bad responses to your problem in this thread. o It is very rare for more than one component to die at the same time. o I'm sure you didn't want to be told to build a funeral pyre. o When the motherboard goes, the drive doesn't behave as yours did. o As you told us, you already tried to boot off floppies. o blah, blah, blah. :) Apple had a problem with some HD20s made by Sony. It sounds clearly to me by your description that this is the problem. I had the same problem. At one point, Apple was replacing HD20s with HD40s for free. You can call an Apple dealer to find out if your friend's serial number matches the defective lots. The problem is stiction, by the way; the drive sticks on startup. Sometimes a sharp rap to the side of the case will free the disk. The sticking can vary with weather, too. I doubt if Apple is still fixing this for free, but in the meantime, you can disconnect the power supply to the internal hard disk drive (the thin wires with the white plastic plug) so that you will be able to boot off a floppy. If you unplug the entire HD20, the mac will no longer be internally terminated properly. I would suggest a new external (or internal) hard drive though. Hope this helps. Jim gibbs@husc4.harvard.edu From owner-software@net.bio.net Thu Jun 03 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.software Subject: Re: MacLade Message-ID: <1993Jun4.143714.25620@welchgate.welch.jhu.edu> Date: 4 Jun 93 14:37:14 GMT References: <1993Jun3.233100.15703@teetot.acusd.edu> Distribution: usa Organization: Johns Hopkins Univ. Welch Medical Library Lines: 49 In article <1993Jun3.233100.15703@teetot.acusd.edu> thor@teetot.acusd.edu writes: > Does anyone know where I can get info on MacLade? > >Thanks, >thor@teetot.acusd.edu >-- A clip from the Phylip documentation: ------ MacClade was written by Wayne Maddison and David Maddison of the University of Arizona. All distribution is by Sinauer Associates, Sunderland Massachusetts 01375, USA. Their phone number is: (413) 665 3722, FAX: (413) 665 7292. A disk with program, help file, and example data files, plus book (which has about 100 pages of intro to phylogenetic theory, and 250 pages of program instructions), is $75 U.S. ($40 for the book alone). Site licenses also available. An earlier and less capable Version 2 (which for example cannot read nucleic acid sequences and has fewer features for discrete characters) is also available by anonymous ftp(/gopher) ------ If you want to obtain the earlier version or a demo version of MacClade 3.0 point your gopher client at merlot .welch.jhu.edu and select the following: --> 13. Search Databases at Hopkins (Vectors, Promoters, NRL-3D, EST, OMIM../ --> 15. Search BOING (Bio Oriented INternet Gophers) And search for - macclade* And you will see: --> 1. macclade21.hqx. 2. macclade30_demo.hqx. 3. macclade.hqx. Number 1 is the old (not nearly so powerful) version and Number 2 is a demo version of MacClade 3.0. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-software@net.bio.net Thu Jun 03 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!ux1.cso.uiuc.edu!moe.ksu.ksu.edu!crcnis1.unl.edu!cse!price From: price@cse.unl.edu (Chad Price) Newsgroups: bionet.software Subject: Re: X on the PC - Summary of responses Message-ID: <1univdINNp39@crcnis1.unl.edu> Date: 4 Jun 93 13:33:33 GMT References: <01GYZ9BDNXOY0006L8@cmu.unige.ch> Distribution: bionet Organization: University of Nebraska--Lincoln Lines: 20 NNTP-Posting-Host: cse.unl.edu Minor corrections: the program running on your PC is the X-Server, NOT the client. The client program is the one running on the remote machine. Addition: Under OS/2, IBM has produced TCP/IP for OS/2 which includes (at minor extra cost) an NFS module, and an X-Server called PMX. I use PMX and am quite happy with it. OS/2 with TCP/IP and Netware requestor for OS/2 provides all of the connectivity I could possibly want, including allowing my PC to become an Internet node in its own right - send/receive mail directly, FTP to and from the OS/2 machine, mount drives from remote systems, telnet directly from hte OS/2 prompt and still run DOS programs simultaneously. Highly recommended! chad chad@windsurf.unmmc.edu (the OS/2 box) price@cse.unl.edu (the Unix machine where I read news) From owner-software@net.bio.net Thu Jun 03 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!darwin.sura.net!news-feed-1.peachnet.edu!umn.edu!gaia.ucs.orst.edu!ava.bcc.orst.edu!masrelia From: masrelia@ava.bcc.orst.edu (Malin Masreliez) Newsgroups: bionet.software Subject: SmartTerm 240 or a program that branches to a microcomputer OS? Message-ID: <1uojap$e57@gaia.ucs.orst.edu> Date: 4 Jun 93 22:45:45 GMT Organization: Biological Computing Consortium, OSU Lines: 16 NNTP-Posting-Host: ava.bcc.orst.edu Hello All- I've heard that there is a program called SmartTerm out in netland somewhere which enables PC users to exit a UNIX session with GCG initiallized and reenter without having to reinitiallize GCG (ie. typing "gcg" and waiting). If this program exists, does anyone know where I could get it? Thanks in advance- Malin Masreliez --------------------------------------------------------------------------------Malin Masreliez masrelia@ava.bcc.orst.edu "I haven't met a genome I didn't like." Biocomputing support Oregon State University ________________________________________________________________________________ From owner-software@net.bio.net Thu Jun 03 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!gatech!rutgers!mbcl!verwaerde From: verwaerde@mbcl.rutgers.edu Newsgroups: bionet.software Subject: Mac seqeunce analysis package. Message-ID: <2593.2c0e2aa8@mbcl.rutgers.edu> Date: 3 Jun 93 20:45:27 GMT Lines: 11 Hello, I bet this is a FAQ, sorry to bother: I'm willing to buy a sequnce analysis software package for Macintosh. I know Macdnasis; is there any equivalent of PCgene for the mac ? What are the other packages available ? (prizes and char.) In brief what's the best deal ? :-) Thanx for your answers Phil Verwaerde From owner-software@net.bio.net Thu Jun 03 23:00:00 1993 Path: biosci!uwm.edu!spool.mu.edu!howland.reston.ans.net!wupost!uunet!world!jbk From: jbk@world.std.com (Jeffrey B Kane) Newsgroups: bionet.software,comp.sys.mac.apps Subject: Re: PharmK Program Message-ID: Date: 4 Jun 93 23:23:46 GMT References: Organization: The World Public Access UNIX, Brookline, MA Lines: 15 Xref: biosci bionet.software:5171 comp.sys.mac.apps:14789 if you hear anything about this program, let me know. Jeffrey ====================================== Jeffrey Kane, MD Kane Biomedical Systems Boston, MA Internet jbk@world.std.com Compuserve 74206,640 AppleLink D0738 [Don't take life too seriously... it's not like anyone gets out of it alive.] From owner-software@net.bio.net Fri Jun 04 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!news.dfn.de!xlink.net!news.belwue.de!softserv.zdv.uni-tuebingen.de!studserv!zxmkr08 From: zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: Mac seqeunce analysis package. Message-ID: Date: 5 Jun 93 14:24:49 GMT References: <2593.2c0e2aa8@mbcl.rutgers.edu> Organization: InterNetNews at ZDV Uni-Tuebingen Lines: 18 NNTP-Posting-Host: studserv.zdv.uni-tuebingen.de In <2593.2c0e2aa8@mbcl.rutgers.edu> verwaerde@mbcl.rutgers.edu writes: >I bet this is a FAQ, sorry to bother: I'm willing to buy a sequnce analysis >software package for Macintosh. I know Macdnasis; is there any equivalent of >PCgene for the mac ? >What are the other packages available ? (prizes and char.) There is a quite exhaustive review by Harry Mangalam on the net (I sent it to the original poster by email, but you will find it by searching the old bionet.software issues with gopher) which is nicely updated by an article in the May issue of TIBS (also by HM). --Cornelius. -- /* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen */ /* email: krasel@studserv.zdv.uni-tuebingen.de */ /* "People are DNA's way of making more DNA." (R. Dawkins / anonymous) */ From owner-software@net.bio.net Fri Jun 04 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!uknet!comlab.ox.ac.uk!kieffer From: kieffer@bioch.ox.ac.uk (Bruno Kieffer) Newsgroups: bionet.software Subject: RIBBONS Message-ID: <1993Jun5.165732.5774@nmrf.bioch.ox.ac.uk> Date: 5 Jun 93 16:57:32 GMT Organization: Department of Biochemistry, University of Oxford Lines: 13 Originator: kieffer@nmrf.ocms Dear all, Where does one acquire RIBBONS from ? Or rather: from where does one acquire RIBBONS? Also I know you can get MIDAS (or is it MIDAS-plus?) form UCSF, but to whom should I address my query/order? My supervisor wants fancy pictures.... Same old story... Bruno Kieffer kieffer@bioch.ox.ac.uk Biochemistry Dpt. Oxford University From owner-software@net.bio.net Fri Jun 04 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!news.Vanderbilt.Edu!NewsWatcher!user From: beckwf@ctrvax.vanderbilt.edu (Warren Beck) Newsgroups: bionet.software Subject: Re: RIBBONS Message-ID: Date: 5 Jun 93 23:16:55 GMT References: <1993Jun5.165732.5774@nmrf.bioch.ox.ac.uk> Sender: news@news.vanderbilt.edu Followup-To: bionet.software Organization: Vanderbilt U., Dept. of Chemistry Lines: 9 Nntp-Posting-Host: 129.59.16.239 In article <1993Jun5.165732.5774@nmrf.bioch.ox.ac.uk>, kieffer@bioch.ox.ac.uk (Bruno Kieffer) wrote: > Where does one acquire RIBBONS from ? Or rather: from where does one acquire > RIBBONS? Also I know you can get MIDAS (or is it MIDAS-plus?) form UCSF, but to > whom should I address my query/order? > > My supervisor wants fancy pictures.... Same old story... > Norma Belfer (norma@cgl.ucsf.edu) coordinates distribution of Midas-Plus. From owner-software@net.bio.net Fri Jun 04 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc8.harvard.edu!chandoni From: chandoni@husc8.harvard.edu (John-Marc Chandonia) Newsgroups: bionet.software Subject: Re: X on the PC - Summary of responses Message-ID: <1993Jun5.133331.24713@husc3.harvard.edu> Date: 5 Jun 93 17:33:31 GMT References: <1univdINNp39@crcnis1.unl.edu> Reply-To: chandoni@husc8.harvard.edu Distribution: bionet Lines: 23 Nntp-Posting-Host: husc8.harvard.edu Originator: chandoni@husc8.harvard.edu In article <1univdINNp39@crcnis1.unl.edu>, price@cse.unl.edu (Chad Price) writes: > Under OS/2, IBM has produced TCP/IP for OS/2 which includes (at minor extra > cost) an NFS module, and an X-Server called PMX. I use PMX and am quite happy > with it. > > OS/2 with TCP/IP and Netware requestor for OS/2 provides all of the > connectivity I could possibly want, including allowing my PC to become an > Internet node in its own right - send/receive mail directly, FTP to and from > the OS/2 machine, mount drives from remote systems, telnet directly from hte > OS/2 prompt and still run DOS programs simultaneously. Highly recommended! I second this recommendation! Actually, you don't need the Netware requestor to do TCP/IP; it works over ethernet or slip also. There is also freely available, PM-based, gopher client and server software. IBM is supposedly working on an upgrade to their TCP/IP package that includes a very nice PM-based newsreader also. JMC -- chandoni@husc8.harvard.edu | I will not yell fire in a crowded classroom John-Marc Chandonia | I will not yell fire in a crowded classroom Graduate Biophysics Program | I will not yell fire in a crowded classroom Harvard University | I will not yell fire ... From owner-software@net.bio.net Fri Jun 04 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!ux1.cso.uiuc.edu!uwm.edu!psuvax1!psuvm!x03 From: X03@psuvm.psu.edu Newsgroups: bionet.software Subject: Computer modeling packages on all platforms?? Message-ID: <93156.160432X03@psuvm.psu.edu> Date: 5 Jun 93 20:04:32 GMT Organization: Penn State University Lines: 8 I wonder if someone familiar with computer modeling of biological systems (protein, DNA) can summerize all currently available packages, the strength and weakness, which platforms (PC, Mac, unix boxes (IBM, HP, SGI, Sun...)), Thanks. Xiaowu Chen Penn State From owner-software@net.bio.net Sat Jun 05 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!wupost!darwin.sura.net!haven.umd.edu!umd5.umd.edu!hjpatt-91.umd.edu!user From: de19@umail.umd.edu (Dana S Emery) Newsgroups: bionet.software Subject: Re: MacLade Message-ID: Date: 6 Jun 93 03:53:23 GMT References: <1993Jun3.233100.15703@teetot.acusd.edu> <1993Jun4.143714.25620@welchgate.welch.jhu.edu> Followup-To: bionet.software Distribution: usa Organization: personal Lines: 25 NNTP-Posting-Host: hjpatt-91.umd.edu In article <1993Jun4.143714.25620@welchgate.welch.jhu.edu>, danj@welchgate.welch.jhu.edu (Dan Jacobson) wrote: > > In article <1993Jun3.233100.15703@teetot.acusd.edu> thor@teetot.acusd.edu writes: > > Does anyone know where I can get info on MacLade? > $75 U.S. ($40 for the book alone). Site licenses > also available. recent shipping charge on a single copy was $5.30, so that is $80.30 total. If you are interested in MacClade, you may also be interested in PAUP, they complement each other for some forms of analysis. PAUP 3.1 is available (source source) from University of Illinois/INHS Mary Lou Williamson Illinois Natural History Survey, Center for Biodiversity Champaign IL 61820 recent cost was $100, no charge for shipping. -- Dana S Emery From owner-software@net.bio.net Sat Jun 05 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!news.funet.fi!news.tele.fi!uunet!europa.eng.gtefsd.com!howland.reston.ans.net!math.ohio-state.edu!caen!destroyer!cs.ubc.ca!alberta!kakwa.ucs.ualberta.ca!acs.ucalgary.ca!najafi From: najafi@enel.ucalgary.ca (Mohammed Kazam Najafi Koopai) Newsgroups: bionet.software Subject: Cell Imaging System Message-ID: <93Jun02.182145.12787@acs.ucalgary.ca> Date: 2 Jun 93 18:21:45 GMT Organization: ECE Department, U. of Calgary, Calgary, Alberta, Canada Lines: 53 Nntp-Posting-Host: eneli.enel.ucalgary.ca Hi everybody, I am working on a project that involves biological cell image analysis. Our application requires a real time image processing system that, given the microscopic images of the experimented cell, outputs the centroid position and orientation of the cell. This information is then used to measure DiElectroPhoresis characteristics of the cell. The system contains a microscope which is focused on the cells floating in a transparent chamber. A CCD camera grabs the microscopic image at the rate of 30 frames/second. An image processing block is needed to get the image and calculates the centroid of the floating cell at the same rate. The orientation of the cell is also required to be found. The orientation of the cell is needed to measure the rotational speed of the cell. In our application, there are many cases in which the cell is spinning in its place and the spinning rate is desired. Currently, an image processing hardware made by Matrox Company, Quebec, Canada (Imager-AT 1987) together with a software is being used. However, the following difficulties in our system have been encountered so far: - Although the spherical cells are chosen for this experiments, the cell images obtained are not always spherical. The non- uniform density of the inner part of the cell is the main reason for this appearance. This appearance causes faulty detections of the centroid position. The image analysis system has to reconstruct the real shape of the cell before centroid detection. - The process is not fast enough to detect quick cell movements. - The frames with multiple cells yield erroneous centroid position. The system cannot distinguish between the cells. We might have to use a faster hardware. An alternative solution to this problem can be using Analog Position Sensor ICs. But I do not know of the ICs available or where to start looking for these ICs. I would appreciate if anybody can help me or give some pointers in this regard. If you know of anybody working on a similar project please let me know. Please send me E_mail at the following address: najafi@enel.ucalgary.ca Thank you in advance. Kazem Najafi From owner-software@net.bio.net Sat Jun 05 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!math.ohio-state.edu!wupost!gumby!destroyer!news.itd.umich.edu!geneva.csmil.umich.edu!cash From: cash@geneva.csmil.umich.edu (Howard Cash) Newsgroups: sci.med,sci.bio,bionet.software,sci.physics Subject: Re: Bibliographic software comparison? Keywords: n Message-ID: <1utpmd$iaj@terminator.rs.itd.umich.edu> Date: 6 Jun 93 22:05:01 GMT References: <1ugbb2$2pi@max.physics.sunysb.edu> <1uit55$no2@umd5.umd.edu> Organization: Cognitive Science and Machine Intelligence Lab, U. of MIichigan Lines: 11 Xref: biosci sci.med:16189 sci.bio:3624 bionet.software:5180 sci.physics:17281 NNTP-Posting-Host: geneva.csmil.umich.edu I agree, EndNote from Personal Bibliographic Software is your best bet. But here's the hot tip: SEE IF YOU INSTITUTION ALREADY HAS A SITE LICENSE DISCOUNT. It becomes very cheap that way, but if you buy through one of those general software catalogues you will have no way to find out if you're eligable for the cheap deal. Give them a call at 313-996-1580 (I don't have their fax number handy). Hobie (Views are my own. I have no connection with Personal Bibliographic Software other than being very satisfied with my dealings with the company.) From owner-software@net.bio.net Sat Jun 05 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!haven.umd.edu!umd5.umd.edu!hjpatt-91.umd.edu!user From: de19@umail.umd.edu (Dana S Emery) Newsgroups: bionet.software Subject: Re: Actually Hardware breakdown of Mac SE Message-ID: Date: 6 Jun 93 04:33:01 GMT References: <1993May30.103028.11781@nomina.lu.se> Followup-To: bionet.software Organization: personal Lines: 394 NNTP-Posting-Host: hjpatt-91.umd.edu In article , gibbs@husc4.harvard.edu (James Gibbs) wrote: > Apple had a problem with some HD20s made by Sony. It sounds clearly to me > by your description that this is the problem. I had the same problem. At > one point, Apple was replacing HD20s with HD40s for free. I saved the following posting from comp.sys.mac.hardware. Thanks to peter for his repost of it. Thanks to werner for the orignal posting. ************************** start of repost ********************************** I saved the following from the net some time ago. Hope this helps, Peter -- Peter Orban National Research Council of Canada Internet: orban@nrcamt.ime.nrc.ca *************************** start of enclosed message *********************** [ After MODE32, this is another gutsy move in which Apple tries to "come clean" from a problem (most certainly) not anticipated, and most definitely prevented, had the right people had any inkling of it. But in the eyes of many hardware-literate people I know, the hard disks problem was known to exist, and reason not to purchase, LONG before Apple started to show signs of recognizing/admitting to it. To summarize what I understand the 2 service notes (sent out to guide Apple's certified techs) to say: Effective until Aug 15, 1993, a customer receives a free replacement 40meg drive if he has a 20meg or 40meg drive which displays "stiction" failure symptoms (in SE, SE-30, IIx, IIcs, IIci or IIfx) and the drive is either less than 4 years old *OR* is Model Number SRD2040. This could be either the drive which came installed in the Mac or a later add-on or replacement drive) Customers who had their HD replaced at a Certified Apple dealer before Aug 16, 1991 OUT OF WARRANTY (and thus paid for the replacement) can obtain reimbursement by submitting a claim to Apple by Feb 29, 1992. [ But I know of no hardware- literate Mac-owner experiencing this problem, who was willing to replace one BAD drive, with another (overpriced) one from the same company ...;-) I think the underlying assumption here also is, that any Apple Certified Tech doing repairs after Aug 16 would not have charged any customer for repairs qualifying to be done at no cost to the customer - but I wonder...] Symptoms which qualify under this program are: 1) STICTION [indicated by the drive failing to spin up after having been powered down] 2) HEAD CRASHES [indicated by a scraping noise (metallic, getting louder over time) at spinup] In the first notice, SOFT ERRORS are also mentioned (noticeable by the disk going in and out of seek mode) but the second 'clarification notice' states that this is no longer a symptom "acceptable to qualify, since soft errors cannot (usually) be detected by customers, since, in general, soft errors are not detectable. but a customer CAN detect a head crash" (which, eventually, WILL result). Personally, I consider this a bit of a cop-out, as I have seen drives that, before dying, seem to get stuck in seek mode with increasing frequency, and when copying large number of files on or off the disk from the Finder, with increasing frequency "file corruption" causes the copy to fail. This diminishes the use of the drive (when not trusted, one avoids using it, when alternatives are present), more frequent (but less trusted) back-ups (hopefully, at least ;-)... ...so what everyone (both Apple and customers) really need is a WIDELY AVAILABLE DIAGNOSTIC PROGRAM!!! while there may be no reliable way for most user to recognize soft errors, one would think that a diagnostic program run overnight should be able to log soft-errors (and I think some third-party disk formatters actually are capable of doing exactly that). I've seen drives dying slowly and suddenly, die completely or come back to life for many additional months only to die again... (I've had drives which repeatedly came back to life when taken on the bouncy ride to the shop ...)... Are users expected to bet their work and data on flaky drives, simply because they are not completely dead yet?!? I am quite sure that the hardware engineer who wrote up the "trouble symptoms" initially, thought he would be able to recognize soft errors when present, so why not the Apple Tech (or a hardware diagnostic program which SHOULD be part of the software package delivered to EVERY user with EVERY Mac in the first place ?!?) Well, that was my reaction and related opinions, anyway, mine, all mine. I enclose the original notes from Apple below both as reference and to be fair. please form your own opinion. Do I sound unhappy?!? Well, the best deserves most being improved still... ---Werner ] --------------- SERVICE NOTICE: 20MB/40MB HARD DRIVE REPAIR EXTENSION PROGRAM ( Copyright 1991, Apple Computer Inc.) OVERVIEW We have discovered that a certain batch of half-height internal 3.5" 20MB and 40MB hard drives and some external 3.5" 20MB and 40MB drives may have been subjected to disk media contamination. These drives may experience a number of different symptoms, as fully described later on in this notice. To address this problem, Apple is offering a 20MB/40MB Hard Drive Repair Extension Program for customers and Service Providers with drives manufactured four years ago or later that meet all the criteria below. A new drive, P/N 661-1629, has been substituted for the problem drives. DRIVE IDENTIFICATION INFORMATION * Definition of 20MB/40MB Symptoms * Stiction problems: Platter does not spin up after drive has been powered down for period of time. * Head crashes: Drive may or may not mount, and data may be corrupted. * Soft errors: Disk continually goes in and out of seek mode. * Model and Serial Number The affected 20MB and 40MB drives were manufactured in Macintosh( SE, Macintosh SE/30, Macintosh II, Macintosh IIx, Macintosh IIcx/IIci, and Macintosh IIfx computers. The problem also affects some external 3.5" 20MB and 40MB configurations. Additionally, these drives were used as Service repair modules under P/N 661-0612 (20MB) and P/N 661-0464 (40MB). Because of the problem, all new and existing orders for 20MB drives (P/N 661-0612) will automatically receive a 40MB drive (P/N 661-1629). If you have any questions regarding qualification of a failed 20MB or 40MB drive, contact Technical Operations for further clarification. * How To Identify Affected 40MB Drives 1) Symptoms of affected drives (one or more of the following): * Stiction problems * Head crashes * Soft errors 2) Serial number indicating the drive is less than four years old. See the chart below for qualifying dates and serial numbers. 3) Model number: SRD2040 * How To Identify Affected 20MB Drives 1) Symptoms of affected drives (one or more of the following): * Stiction problems * Head crashes * Soft errors 2) Model number: SRD2020 (Note: All drives with this model number are eligible throughout the life of this program. Serial number matching is not required.) RETURNING AND REPLACING HARD DRIVES * Customer Repair The program covers free replacement of a customerUs qualified failed 20MB (P/N 661-0612) or 40MB (P/N 661-0464) hard drive until August 15, 1993. In return, the customer will receive a 40MB hard drive (P/N 661-1629). Guidelines for Submitting Repair Claims Use the following guidelines for determining how to fill out the Warranty information area of an Apple Authorized Transaction Form when From owner-software@net.bio.net Sat Jun 05 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!bogus.sura.net!jhunix.hcf.jhu.edu!fmsrl7!destroyer!news.itd.umich.edu!geneva.csmil.umich.edu!cash From: cash@geneva.csmil.umich.edu (Howard Cash) Newsgroups: sci.med,sci.bio,bionet.software,sci.physics Subject: Re: Bibliographic software comparison? Keywords: n Message-ID: <1utqa2$id8@terminator.rs.itd.umich.edu> Date: 6 Jun 93 22:15:30 GMT References: <1ugbb2$2pi@max.physics.sunysb.edu> <1uit55$no2@umd5.umd.edu> Organization: Cognitive Science and Machine Intelligence Lab, U. of Michigan Lines: 11 Xref: biosci sci.med:16192 sci.bio:3625 bionet.software:5181 sci.physics:17282 NNTP-Posting-Host: geneva.csmil.umich.edu I agree, ProCite from Personal Bibliographic Software is your best bet. But here's the hot tip: SEE IF YOU INSTITUTION ALREADY HAS A SITE LICENSE DISCOUNT. It becomes very cheap that way, but if you buy through one of those general software catalogues you will have no way to find out if you're eligable for the cheap deal. Give them a call at 313-996-1580 (I don't have their fax number handy). Hobie (Views are my own. I have no connection with Personal Bibliographic Software other than being very satisfied with my dealings with the company.) From owner-software@net.bio.net Sun Jun 06 23:00:00 1993 Path: biosci!ICBR.IFAS.UFL.EDU!SJJ From: SJJ@ICBR.IFAS.UFL.EDU ("JONG, SONG-MUH J") Newsgroups: bionet.software Subject: GOPHER problem Message-ID: <9306070014.AA08500@net.bio.net> Date: 7 Jun 93 00:52:00 GMT Sender: news@net.bio.net Distribution: bionet Lines: 18 Hello, netters, I recently obtained the PC Gopher III program included in the slipdisk package. The GOPHER works like a charm, even faster than the one on our VMS machine. I could never imagine a PC can function as a GOPHER server like that! Anyway, the GOPHER works great except for one obvious problem: Sometimes, the program aborts when I ask it to save a file. Can anyone tell me what could be the reason for that abortion? Thanks for any suggestion! Song-Muh Jong University of Florida sjj@icbr.ifas.ufl.edu (Internet) sjj@ufbiot (BITNET) From owner-software@net.bio.net Sun Jun 06 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!gatech!rutgers!sun-barr!sh.wide!wnoc-kyo!kuis!kudpc!sakura.kudpc.kyoto-u.ac.jp!e50044 From: e50044@sakura.kudpc.kyoto-u.ac.jp (Shuji_Kaneko) Newsgroups: bionet.software Subject: Keyboard Publishing Co. Message-ID: <1993Jun7.092421.11889@kudpc.kyoto-u.ac.jp> Date: 7 Jun 93 09:24:21 GMT Sender: news@kudpc.kyoto-u.ac.jp Organization: Dept Pharmacol, Facul Pharm Sci, Kyoto Univ, Kyoto, Japan Lines: 11 Originator: e50044@sakura.kudpc.kyoto-u.ac.jp Nntp-Posting-Host: sakura.kudpc.kyoto-u.ac.jp Does anybody out there know the address of 'Keyboard Publishing Co.' ? I would like to purchase a copy of 'Pharmacology TextStack' which was reviewed in the March issue of Trends in Pharmacological Sciences (vol.14, No.3, p.105, 1993). Thanks in advance. -- Shuji Kaneko, Ph.D. skaneko@ddbj.nig.ac.jp Associate Professor NCC00506@niftyserve.or.jp Department of Pharmacology / Faculty of Pharmaceutical Sciences Kyoto University / Kyoto 606-01 / Japan From owner-software@net.bio.net Sun Jun 06 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!wupost!uunet!psgrain!ee.und.ac.za!hippo.ru.ac.za!ford.ee.up.ac.za!zeno.up.ac.za!bio1 From: bio1@navi.up.ac.za (Fourie Joubert) Newsgroups: bionet.software Subject: DNAGUI & Linux? Message-ID: Date: 7 Jun 93 09:22:39 GMT Organization: University of Pretoria Lines: 21 NNTP-Posting-Host: zeno.up.ac.za Hi If anyone has DNAGUI working in Linux, I would really like to know what changes they had to make? I am new to C, very new to Linux, and quite desperate to get an Image Analysis sytem running. When trying to "make", I get a wide range of compiler warnings and a few serious compiler errors. I am using SLS Linux and I seem to have all the necessary X-libs. Any help would be greatly appreciated! __________________________________________________________________________ _/_/_/_/ _/_/_/_/_/ Fourie Joubert _/ _/ Department of Biochemistry _/ _/ University of Pretoria _/_/_/_/ _/ South Africa _/ _/ bio1@navi.up.ac.za _/ _/_/_/_/ Disclaimer: "Fourie who?" __________________________________________________________________________ From owner-software@net.bio.net Sun Jun 06 23:00:00 1993 Path: biosci!SASK.USASK.CA!LEES From: LEES@SASK.USASK.CA Newsgroups: bionet.software Subject: Help needed Message-ID: <01GZ3I0CYCKO94FL48@SKYCAT.USask.CA> Date: 7 Jun 93 18:33:04 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 Hello, It will be very appreciated if anyone let me know how to find DNA Sequences Alignment Programs for PC as sharewares or Public Domains. Thanks very much. Lee e-mail: lees@skyfox.usask.ca (Internet) From owner-software@net.bio.net Sun Jun 06 23:00:00 1993 Path: biosci!daresbury!news!ajb From: ajb@s-crim1.dl.ac.uk (Alan Bleasby) Newsgroups: bionet.software Subject: Re: Windows DotPlot Message-ID: Date: 8 Jun 93 03:33:52 GMT References: <1993Jun7.142842.9539@gserv1.dl.ac.uk> Distribution: bionet Organization: SERC Daresbury Laboratory, Warrington, UK Lines: 34 NNTP-Posting-Host: s-crim1.dl.ac.uk In-reply-to: r.nakisa@ic.ac.uk's message of Mon, 7 Jun 1993 15:05:12 GMT Ramin says, >If you're going to get the program from seqnet (s-ind2...) then don't get >the program in the /dos directory because the zip file is corrupted. The >uncorrupted version is the the /incoming directory and has length 83,248 >bytes rather than 82,920 bytes Files on this ftp server are moved to appropriate directories and then deleted from `incoming'. Thanks for a nice piece of software Ramin but the first I've heard of this was reading the BIOSCI note. I'd make a plea to people submitting s/w & data to `incoming' directories to email the ftp-server manager (in this case me: ajb@s-crim1.daresbury.ac.uk) to say it's there, where it should be moved and contact directly if there are any problems. I'm not sure where the original problem was (certainly not lack of disc space and it's difficult to corrupt a file using `cp' :-). Nevertheless the program is now available on s-ind2.daresbury.ac.uk in the dos software directory (again) Thanks again Ramin. I wish more people would contribute software. Rgds Alan Bleasby BIOSCI Africa/Asia/Europe SERC(?) Daresbury Laboratory Warrington WA4 4AD UK Email: ajb@s-crim1.dl.ac.uk From owner-software@net.bio.net Sun Jun 06 23:00:00 1993 Path: biosci!AUDREY.LMF.ORG!jim From: jim@AUDREY.LMF.ORG (Jim Gale) Newsgroups: bionet.software Subject: PCR primer software Message-ID: <9306071647.AA24849@audrey.lmf.org> Date: 7 Jun 93 16:47:17 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 11 To PCR users I am intrested in PCR primer design software, if there is already a FAQ, please let me know. If not, I am fimilar with NBI's Oligo and Clonetech's primer detective. Would anyone offer any opinions on these programs, or on any other software that is available for PC (Dos or windows). I am looking for the most robust program available...degenerate PCR, RT-PCR, LCR, Sequencing primers, multiplex-PCR, etc.... Thanks for your input Jim From owner-software@net.bio.net Sun Jun 06 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!pipex!uknet!daresbury!daresbury!news From: r.nakisa@ic.ac.uk ((Ramin Charles Nakisa) ramin) Newsgroups: bionet.software Subject: Windows DotPlot Message-ID: <1993Jun7.142842.9539@gserv1.dl.ac.uk> Date: 7 Jun 93 15:05:12 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 29 Original-To: bio-soft@uk.ac.daresbury, methods@uk.ac.daresbury X-Popmail-Charset: British > It's here, it's ACE, (it's free), it's DOTPLOT for Windows! WinDot seems popular, but several have had probs finding the windot.zip file. Here are the addresses and directories of kosher windot files, which I have checked by ftping them and using pkunzip -t. Name IP Number Directory ~~~~ ~~~~~~~~~ ~~~~~~~~~ ftp.bchs.uh.edu 129.7.2.16 /pub/gene-server/dos/windot.zip fly.bio.indiana.edu 129.79.224.25 /Incoming/windot.zip s-ind2.dl.ac.uk 148.79.64.4 /incoming/windot.zip If you're going to get the program from seqnet (s-ind2...) then don't get the program in the /dos directory because the zip file is corrupted. The uncorrupted version is the the /incoming directory and has length 83,248 bytes rather than 82,920 bytes. Someone has been abusing Uncle Dan's /incoming directory, so now it's write- only. And Uncle Don's got a separate copy of the Windows version of readseq which now spanks under Windows because I compiled it with the Microsoft QuickWin library. The file is /Incoming/winseq.zip, but if you get a copy of windot.zip it's in there too. /--------------------------------------------------------------------------\ < Ramin Charles Nakisa, "She walks in beauty Tel: 071 589-5111 x 6729 > > Biophysics Section, As the night of FAX: 071 589-0191 < < The Blackett Lab, starry skies and EMAIL: > > Imperial College, cloudless climes..." ramin@ic.ac.uk < < London SW7 2BZ. mbrcn@seqnet.dl.ac.uk > \--------------------------------------------------------------------------/ From owner-software@net.bio.net Sun Jun 06 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!magnus.acs.ohio-state.edu!usenet.ins.cwru.edu!axa12-slip.cwru.edu!ashok From: ashok@biochemistry.cwru.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Re: GOPHER problem Message-ID: Date: 7 Jun 93 15:20:40 GMT References: <9306070014.AA08500@net.bio.net> Distribution: bionet Organization: Department of Biochemistry, Case Western Reserve University Lines: 23 NNTP-Posting-Host: axa12-slip.dialin.cwru.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev Final Beta] In article <9306070014.AA08500@net.bio.net> SJJ@ICBR.IFAS.UFL.EDU ("JONG, SONG-MUH J") writes: >Hello, netters, >I recently obtained the PC Gopher III program included in the >slipdisk package. The GOPHER works like a charm, even faster than >the one on our VMS machine. I could never imagine a PC can function >as a GOPHER server like that! PC Gopher III is a Gopher *client*. There are two DOS based Gopher servers available, one of which is quite versatile and KA9Q based, and maintained by myself. The Gopher server code was from Chris McNeil (cmcneil@mta.ca), while I have added numerous changes (enhancements?) to the SMTP, TCP, POP3, POP2 and FTP code. It is available from biochemistry.bioc.cwru.edu in /pub/pop3serv. Ashok -- Ashok Aiyar Mail: ashok@biochemistry.cwru.edu Department of Biochemistry Tel: (216) 368-3300 CWRU School of Medicine, Cleveland, Ohio Fax: (216) 368-4544 From owner-software@net.bio.net Sun Jun 06 23:00:00 1993 Path: biosci!CUHHCA.HHMI.COLUMBIA.EDU!system From: system@CUHHCA.HHMI.COLUMBIA.EDU (Phil Bourne) Newsgroups: bionet.software Subject: PDBlib v1.0 - C++ Class Library Representing Macromolecular Structure Message-ID: <9306072220.AA13457@cuhhca.hhmi.columbia.EDU> Date: 7 Jun 93 22:20:51 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 94 PDBlib Version 1.0 ------------------ What is PDBlib? --------------- PDBlib is a class library written in C++ for modeling a macromolecular structure at the level of detail (excluding symmetry information) found in a Protein Data Back (PDB) file. A class is supplied to read a PDB file into a PDBlib representation. This class is independent of the actual representation and other forms of input, for example from a relational database like SESAM, are possible. The library is made extensible by a close coupling between intrinsic and external classes. By writing only to the external classes you will remain compliant with future versions of the library. What do I get? -------------- bin: executable files. include: PDBLib header files that should not be altered by library users in general. include_ext: user extensible header files. lib: PDBLib library file. examples: Example source and header files. What don't I get? ---------------- You don't get source code. This is a temporary situation while we attempt to centralize bug fixes and additions to the library. If you find this situation unworkable source code is available by signing a copyright agreement which is available with the distribution. How do I use it? ---------------- Three examples are included for you to see how to use the library: o example.C demonstrates the utilities of the class library; o XDrawProtein.C is a simply drawing program that accesses a PDB file through the class library and displays a static view of the protein in a window; o PDBview will render a PDB file using only X/Motif; no special graphics hardware or software is needed. How do I get it? ---------------- Via anonymous ftp from cuhhca.hhmi.columbia.edu (128.59.98.1) in the directory pub/programs/PDB/PDBlib On what platforms is it available? ---------------------------------- PDBLib.1.0.SGI.tar.Z Compressed tar file of PDB object classes library and header files for SGI. AT&T C++ release 2.1 & 3.0 compatible. PDBLib.1.0.Sun.tar.Z Compressed tar file of PDB object classes library and header files for Sun Sparc station. AT&T C++ release 2.1 & 3.0 compatible. PDBLib.1.0.Cvx.tar.Z Compressed tar file of PDB object classes library and header files for Convex. AT&T C++ release 2.1 compatible. PDBLib.1.0.Alpha.tar.Z Compressed tar file of PDB object classes library and header files for Dec 3000 (Alpha AXP) with OSF1. Dec C++ (cxx) release 1.2 compatible. What about future versions? --------------------------- Version 2.0 (in 2-3 months) will contain support for crystallographic symmetry and use of templates as found in C++ AT&T v3.0 and beyond. Version 3.0 (in 1 year) will contain support for the macromolecular Crystallographic Information File (CIF) format to be adopted by the PDB. Who do I contact? ----------------- Address specific programming questions on PDBlib to Weider Chang, the author of most of the code (weider@cuhhca.hhmi.columbia.edu). Address questions concerning PDBview to Ilya Shindyalov (shindyal@cuhhca.hhmi.columbia.edu) Address general comments, criticisms, questions about future directions etc. to Phil Bourne (system@cuhhca.hhmi.columbia.edu). Phil Bourne June 7,1993 This work was supported by NSF grant IRI-9116798 with special thanks to Drs Maria Zemankova and John Wooley. From owner-software@net.bio.net Sun Jun 06 23:00:00 1993 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!howland.reston.ans.net!newsserver.jvnc.net!synapse.bms.com!riversend.bms.com!user From: Roberts_D@BMS.COM (Dan Roberts) Newsgroups: bionet.software Subject: Helical wheels in 3D?? Message-ID: Date: 7 Jun 93 17:57:45 GMT Sender: news@synapse.bms.com Followup-To: bionet.software Organization: Bristol-Myers-Squibb Research Lines: 11 I have been using the PLOTA helical wheel program to generate helical wheels. I was wondering if there is a way to represent these wheels in a quasi 3-D format. The problem is that when working with seven at once I quickly get confused with the spatial relationships btw. each seperate wheel..Thanks....Dan Dan Roberts BRISTOL-MYERS-SQUIBB PHARM. RES. CENTER Cardio-Vascular Biochem Dept. PRINCETON, NEW JERSEY U.S.A. PLANET EARTH, MILKY-WAY GALAXY <<<>>>Roberts_D@BMS.COM From owner-software@net.bio.net Mon Jun 07 23:00:00 1993 Path: biosci!KUDZU.CNIDR.ORG!kgamiel From: kgamiel@KUDZU.CNIDR.ORG (by way of mangalam@salk-sc2.sdsc.edu (Harry Mangalam)) Newsgroups: bionet.software Subject: WAIS Manager 3.0 for Windows! Message-ID: <9306081940.AA06785@molly.sdsc.edu> Date: 8 Jun 93 20:44:22 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 62 Upgrade announcement... WAIS Manager 3.0 by Kevin Gamiel 6/8/93 representing MCNC CNIDR and UNC-Chapel Hill Features/Enhancements - Winsock compliant (see note on Winsock below). - Multi-format handling capability. If a returned document has more than 1 type associated with it, a dialog appears displaying the available types. - Relevance feedback. Adds ability to ask "show me more like this". - New interface with Toolbar for quick access. - Dedicated Directory of Servers button. Location - sunsite.unc.edu pub/micro/pc-stuff/ms-windows/winsock/apps/waisman3.zip - ftp.cnidr.org pub/NIDR.tools/wais/pc/windows/waisman3.zip Installing WAIS Manager 1) Copy WAISMAN3.ZIP to an appropriate directory 2) Execute PKUNZIP.EXE -d WAISMAN3.ZIP. A subdirectory named WAISMAN3 will be created containing the files indicated in RELEASE.WRI. Also, a subdirectory named WAIS_SRC will be created and several .src files will be copied there. 3) From the Windows Program Manager, select 'File', 'New'. 4) Select 'Group Item' and create a group named "WAIS Manager 3.0" 5) Again select 'File', 'New'. 6) Select 'Program Item' and enter the following information: Description: WAIS Manager 3.0 Command Line: \WAISMAN3\TBOOK.EXE WAISMAN3.TBK Working Dir: \WAISMAN3 Shortcut: None * Set icon to \world.ico" 7) Double click on the icon and start WAISing! More on Winsock If you're not using Winsock, you're missing the boat in a big way. Ask your vendor for more info. Some vendors are providing the base service on a trial basis. Ftp to sunsite.unc.edu and get one of the packages from pub/micro/pc-stuff/ms-windows/winsock/packages. ---------------------------------------------------------------------- Kevin Gamiel - KEVIN.GAMIEL@CNIDR.ORG MCNC CNIDR - 919-248-1499 Proud charter member of Tar Heel Information Services - "Nothing but net!" ----------------------------------------------------------------------- From owner-software@net.bio.net Mon Jun 07 23:00:00 1993 Path: biosci!CONCH.SENOD.UWF.EDU!hhuang From: hhuang@CONCH.SENOD.UWF.EDU (Hong Huang) Newsgroups: bionet.software Subject: Help about protein database. Message-ID: <9306080059.AA25947@conch.senod.uwf.edu> Date: 8 Jun 93 00:59:15 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 Hello friends: I'm currently a computer science graduate student and going to have a project forcusing on the 3D structure of protein and the Amino Acid sequence. Would anybody be so kind to tell me about: (1). the protein structure databases (PIR, PDB, GenBank...) and their contents (primary, secondary, or ternary structure), and data format. (2). the existing shareware for modeling the protein 3D structure. (3). the possibility of predicting the protein 3D structure from amino acid sequence. or where can I find the answers. Please send any suggestion or answer to: hhuang@conch.senod.uwf.edu Thanks in advance. hhuang. From owner-software@net.bio.net Mon Jun 07 23:00:00 1993 Path: biosci!CU.NIH.GOV!CZJ From: CZJ@CU.NIH.GOV Newsgroups: bionet.software Subject: Re: Help about protein database. Message-ID: <9306081345.AA12019@net.bio.net> Date: 8 Jun 93 13:40:47 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 63 > MAIL VIA INTERNET FROM BIOSCI-REQUEST@net.bio.net MONDAY 06/07/93 9:00:57 P.M. > > Received: from CU.NIH.GOV by NIHCU (Mailer) id 6930; > Mon, 07 Jun 93 21:00:57 EDT > Received: from NET.BIO.NET by CU.NIH.GOV > with TCP; Mon, 7 Jun 93 21:01:22 EDT > Received: by net.bio.net (5.65/IG-2.0) > id AA11591; Mon, 7 Jun 93 18:00:03 -0700 > Received: from trivia.coginst.uwf.edu by net.bio.net (5.65/IG-2.0) with SMTP > id AA11570; Mon, 7 Jun 93 17:59:53 -0700 > Received: from conch.senod.uwf.edu by trivia.coginst.uwf.edu (5.64/A/UX-3.00) > id AA25975; Mon, 7 Jun 93 20:02:06 CDT > Received: from scallop.senod.uwf.edu.senod.uwf.edu by conch.senod.uwf.edu (4.1/SMI-4.0) > id AA25947; Mon, 7 Jun 93 19:59:15 CDT > Date: Mon, 7 Jun 93 19:59:15 CDT > From: hhuang@conch.senod.uwf.edu (Hong Huang) > Message-Id: <9306080059.AA25947@conch.senod.uwf.edu> > To: bio-soft@net.bio.net > Subject: Help about protein database. > > Hello friends: > > I'm currently a computer science graduate student and going to have a project > forcusing on the 3D structure of protein and the Amino Acid sequence. Would > anybody be so kind to tell me about: > > (1). the protein structure databases (PIR, PDB, GenBank...) and their > contents (primary, secondary, or ternary structure), and data format. > (2). the existing shareware for modeling the protein 3D structure. > (3). the possibility of predicting the protein 3D structure from amino > acid sequence. > > or where can I find the answers. Please send any suggestion or answer to: > > hhuang@conch.senod.uwf.edu > > Thanks in advance. > > hhuang. > Good luck. There are a number of things out there. The best book for a basic understanding of Protein Structure remains the book by Dickerson and Geis. Check your library. It is about 20 years old, but the concepts have not changed that much. I would also recommend the Protein Society. They distribute a program called kinemage for modeling protein structures and the journal contains graphics on a disk. Membership for students is quite reasonable. Address for info on membership: The Protein Society 9650 Rockville Pike Bethesda, MD 20852-3998 Tel: (301) 530-7120 FAX: (301) 530-7049 Jim Cassatt From owner-software@net.bio.net Mon Jun 07 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!howland.reston.ans.net!noc.near.net!news.cs.brandeis.edu!lau From: lau@auriga.rose.brandeis.edu (frankie t. k. lau) Newsgroups: bionet.software Subject: Protein c++ library/src from Steve Brenner? Message-ID: Date: 8 Jun 93 21:22:22 GMT Sender: news@news.cs.brandeis.edu (USENET News System) Organization: Brandeis University Lines: 12 hi all, I remember Steve Brenner had posted his library written in C++ about protein, etc. I wrote to him via email but mail bounced. If you happened to know more about this, pls enlighten me. or give me a functional email address for Dr. Brenner (MRC, Cambridge??) so that I can ask. email: lau@tammy.harvard.edu -Frankie From owner-software@net.bio.net Mon Jun 07 23:00:00 1993 Path: biosci!NET.BIO.NET!web!ceniai.cu!ingen.cu!carmas From: web!ceniai.cu!ingen.cu!carmas@NET.BIO.NET (Carlos Israel Armas) Newsgroups: bionet.software Subject: where is Charon package? Message-ID: Date: 4 Jun 93 23:02:50 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 16 hi netters! Just a ftp related question: I need to know where is located the package Charon which works with Pmail, serving as a gateway between UNIX and Netware mail systems. Someone told me it's on omnigate.clarkson.edu, but I do not know the exact subdirectory. Any help will be highly appreciated. thanks a lot. carlos -- carlos armas carmas%ingen@web.apc.org network manager automation division center of genetic engineering & biotechnology pobox 6162 havana, cuba voice: 537 218200 fax: 537 218070 From owner-software@net.bio.net Tue Jun 08 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!caen!batcomputer!munnari.oz.au!ariel.ucs.unimelb.EDU.AU!ucsvc.ucs.unimelb.edu.au!lugb!NewsWatcher!user From: genmjw@lure.latrobe.edu.au (Matthew Wakefield) Newsgroups: bionet.software Subject: RNA structure analysis Message-ID: Date: 9 Jun 93 07:59:42 GMT Sender: news@lugb.latrobe.edu.au (USENET News System) Followup-To: bionet.software Organization: LaTrobe University, Australia Lines: 3 Does anyone know of a good RNA structure program for the Mac or Vax that will cope with a 17Kb RNA molecule. This RNA is ment to be functional and I would like to compare the stuctures found in several species. From owner-software@net.bio.net Tue Jun 08 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!news.tele.fi!news.funet.fi!funic!convex!harper From: harper@convex.csc.FI (Rob Harper) Newsgroups: bionet.software Subject: Re: where is Charon package? Message-ID: <1993Jun9.060328.22127@nic.funet.fi> Date: 9 Jun 93 06:03:28 GMT References: Sender: usenet@nic.funet.fi Distribution: bionet Organization: Finnish Academic and Research Network Project - FUNET Lines: 24 Nntp-Posting-Host: convex.csc.fi In web!ceniai.cu!ingen.cu!carmas@NET.BIO.NET (Carlos Israel Armas) writes: >hi netters! >Just a ftp related question: >I need to know where is located the package Charon which works with >Pmail, serving as a gateway between UNIX and Netware mail systems. >Someone told me it's on omnigate.clarkson.edu, but I do not >know the exact subdirectory. >Any help will be highly appreciated. >thanks a lot. >carlos Try barnacle.erc.clarkson.edu in directory /contrib or cs.dal.ca in directory /pub/comp.archives or pinus.slu.se in directory /msdos.nfs.sunet.se/network/mail Rob "at your service" Harper -- Rob Harper E-mail: harper@convex.csc.fi Center for Scientific Computing Molbio/software: harper@nic.funet.fi Tietotie 6, P.O. Box 405 Telephone: +358 0 457 2076 SF-02101 Espoo Finland Fax: +358 0 457 2302 From owner-software@net.bio.net Tue Jun 08 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uknet!pavo.csi.cam.ac.uk!nntp-serv.cam.ac.uk!seb1005 From: seb1005@mbfs.bio.cam.ac.uk (Steven Brenner) Newsgroups: bionet.software Subject: Re: Protein c++ library/src from Steve Brenner? Message-ID: Date: 9 Jun 93 00:34:53 GMT References: Sender: news@infodev.cam.ac.uk (USENET news) Organization: U of Cambridge, England Lines: 26 In-Reply-To: lau@auriga.rose.brandeis.edu's message of Tue, 8 Jun 1993 21:22:22 GMT Nntp-Posting-Host: mbfs.bio.cam.ac.uk In article , lau@auriga.rose.brandeis.edu (frankie t. k. lau) writes: > hi all, > I remember Steve Brenner had posted his library written in > C++ about protein, etc. > I wrote to him via email but mail bounced. Sorry! > If you happened to know more about this, pls enlighten me. The problem was that my newsreader was (for reasons unknown to me) was stripping off the "mbfs" from my machine's email address. I've now fixed the problem. The correct address is: seb1005@mbfs.bio.cam.ac.uk. -Steve -- Steven E. Brenner | Internet seb1005@mbfs.bio.cam.ac.uk Department of Biochemistry | JANET seb1005@uk.ac.cam.bio.mbfs University of Cambridge | Laboratory +44 223 333671 Tennis Court Road | Home +44 223 314964 Cambridge CB2 1QW, UK | Lab Fax +44 223 333345 From owner-software@net.bio.net Tue Jun 08 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!rc1!is1e!rgordon From: rgordon@is1e.vub.ac.be (Gordon-Beresford Roland) Newsgroups: bionet.software Subject: Macromolecule Visualization Under X Keywords: Macromolecule 3D structure Message-ID: <2107@rc1.vub.ac.be> Date: 9 Jun 93 08:24:51 GMT Sender: news@rc1.vub.ac.be Organization: Brussels Free Universities (VUB/ULB), Belgium Lines: 28 I already found the Holly Graal, so now ... I'm looking for a public domain program which could display the 3D structure of a molecule (essentially proteins) with a "reasonable" interactivity. Furthermore I would like it to run on a Silcon Graphics machine (-> color display) but also on remote X terminals (-> Black & White display). I discarded the following programs : PDBView: Real X program. Nice, but much too slowwww. MULTI: Better but, as it uses the GL protocol, i can't send the result to an X terminal. (GL = Silicon Graphics proprietary protocol for graphic handling. ) Furthermore MULTI somehow forbids further use of any program requiring GL ! (Including login window) (I have a 4D/35GT, I have not really tried to solve this problem, no time) Have you any idea ? Thank You. ---------------------------------------------------- Roland M.H. GORDON-BERESFORD Unite de Conformation des Macromolecules Biologiques Universite Libre de Bruxelles Avenue Paul HEGER, CP 160-16 B-1050 Bruxelles Belgique tel: +32 2 648 52 00 fax: +32 2 648 89 54 e-mail: rgordon@ucmb.ulb.ac.be ---------------------------------------------------- From owner-software@net.bio.net Tue Jun 08 23:00:00 1993 Path: biosci!TAYLORU.EDU!JHMOORE From: JHMOORE@TAYLORU.EDU Newsgroups: bionet.software Subject: ENVIRONMENTAL SCIENCE Message-ID: <01GZ6M10SD0K9FM8QA@tayloru.edu> Date: 9 Jun 93 22:58:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 31 Fellow Internet comrades, I am looking for software that could be used in environmental education. Our School of Environmental Sciences (ES) has develop an Environmental Science Education degree (ESE sometimes called EASY). The School of ES is also in the early development stages of Environmental Science Education for Elementary Majors. Is there a specific source of software, or could some of the Environmental Experts in the audience suggest any. The software that I am interested in would be used by both the undergraduates and faculty for teaching. Also, I am interested in software that could be used by the elementary and secondary schools that would be visiting our ES facility. These could be authoring tools as well as specific environmental programs. Please forward any information to me directly. My Internet address is: JHMOORE@TAYLORU.EDU Thank you in advance! ---------------------------------------------------------------- Dr. John M. Moore Assistant Professor of Biology and Computer Science Taylor University 500 W. Reade Ave Upland, IN 46989 Voice: 317-998-4994 FAX: 317-998-4980 ---------------------------------------------------------------- From owner-software@net.bio.net Tue Jun 08 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!news.funet.fi!funic!nic.funet.fi!csc.fi!harper From: Rob.Harper@csc.fi (Rob Harper) Newsgroups: bionet.software Subject: CELLO Beta 0.1 Message-ID: <199306090723.AA11304@csc.fi> Date: 9 Jun 93 07:23:34 GMT Sender: root@nic.funet.fi (The FUnny NET guru) Organization: Finnish University & Research Network Lines: 109 OK you want to get on to the WEB from DOS. Well here is the first attempt... it is a beta so do your best. %%%%%%%%%%%%%%%%%%%%%%%%% CLIP %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% (Cross-posted to many lists and groups. Please forgive necessary duplications) Folks: This is an announcement of Beta Release 0.1 of Cello, a multipurpose Net browser for Microsoft Windows 3.1 Features: --WWW(HTTP/HTML) browser, with user-configurable colors and fonts. --Full-featured Gopher (though unfortunately not yet Gopher+) client, including a hyper-ized CSO which permits (sorta dumb) SMTP mailing. --Transparent access (via WWW) to FTP, HyTelNet, Telnet, etc. etc. ad infinitum. --Graphics and PostScript viewing and sound playing via MSWindows Associations...feature, using add-on, shareware viewers such as SNDTOOL, GV057, and the Windows version of GhostScript. --Ad-hoc Telnet, FTP, and Gopher sessions. --SLIP/PPP support with dialup scripting language. --Supports wide range of LAN configurations via Distinct TCP/IP runtime stack. Things you should know: -- Hardware: Cello needs a Windows 3.1-capable machine with enhanced mode and (preferably) swapping enabled. It is hungry for extended RAM. -- Software: Cello depends (for now...we're working on a Winsock version) on the Distinct TCP/IP runtime stack. The LII has licensed the use of a runtime version of this software for use by US academic institutions for a period of one year, starting June 1, after which we will renegotiate the license. Commercial organizations and non-academic users are strongly urged to contact Distinct directly at mktg.distinct.com. The Distinct software adds enormous functionality to the package, including SLIP/PPP support with scripting, and configuration for many types of LAN and networking layers. We are working on a Winsock version which will be available without restriction later this summer. --How to get it: FTP to fatty.law.cornell.edu, the /pub/LII/Cello subdirectory. The distribution is in multiple files. At a minimum, you will need README.1ST, which contains unpacking instructions. CELLO.ZIP, which contains the executable and Help application DIS.ZIP, which contains the runtime stack. Optionally, you should also get: VIEWERS.ZIP, which contains a graphics viewer and sound player for use with Cello. GSWIN.ZIP, which contains the Windows version of GhostScript. PLEASE NOTE that fatty is but an humble little Sparc and you can bring it to its knees fairly easily, so if you have another source for the GhostScript stuff please spare me and everyone else by going to the alternate source; the file is 2+ MB. Installation: Installation is performed by following the instructions in README.1ST, then using the online help. Additional support is available from a listserv list called appropriately enough CELLO-L. To subscribe, send a message to listserv@fatty.law.cornell.edu with the one-liner: sub cello-l your full name in the body of the message. cello-l is watched by the developer and by a few folks who graciously assisted in alpha testing and who know more about the software's treacherous behavior than its author; the listowner is Will Sadler at Indiana University Law School. We are also working on an archive of installation hints and tricks. Please try to take it easy on comp.infosystems.www; Tim already has too much to deal with (grin). Who'n'heck are these guys?: The Legal Information Institute, operating under the auspices of the Cornell Law School, is an entity set up to distribute legal information in hypertextual form by various means, including the Net. Since there wasn't a Web client for the platform used most by lawyers and legal academics, we took it into our (ill-advised) heads to write one. This is it, almost. For further information: lii@fatty.law.cornell.edu. Regards, Tb. Thomas R. Bruce Thomas_Bruce@cornell.edu Legal Information Institute Cornell Law School From owner-software@net.bio.net Tue Jun 08 23:00:00 1993 Path: biosci!SCRI.FSU.EDU!STRELETS From: STRELETS@SCRI.FSU.EDU Newsgroups: bionet.software Subject: Free domain reference database shell for PC: Seqanalref variant Message-ID: <930609093340.20202427@scri.fsu.edu> Date: 9 Jun 93 13:33:40 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 30 SAGITTARIUS SEQANALREF Personal Reference DataBank ************************************************** SAGITTARIUS Personal Reference DataBank is a dialog shell for object-oriented compression, storage and manipulation of reference database information with orientation on MS DOS PC-compartibles (at least 286 required) with installed hard disk optimisators (like Hyperdisk, Ncache, Smartdrive and others). This particular variant is oriented on SEQANALREF databases compiled by A.Bairoch. Dialog data shell includes following main possibilities: - selection of references to bank buffer by - dictionary-defined record for specified informational field (title, journal, author, keyword) - user-defined context in specified informational field (title, journal, author, keyword) - set of dictionary-defined records for main informational field (author, keyword) - reference abstract (non)perfect match with user-defined short context - store and retrieve buffer content (reference numbers) between sessions - output user-specified (buffer) reference data to disk files SAGITTARIUS SEQANALR Personal Reference DataBank is available by anonymous FTP from: - FTP.SCRI.FSU.EDU, directory pub/genetics/seqanalr/ From owner-software@net.bio.net Tue Jun 08 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!mcsun!uknet!pipex!zaphod.crihan.fr!univ-lyon1.fr!scsing.switch.ch!xlink.net!howland.reston.ans.net!gatech!emory!sol.ctr.columbia.edu!news.columbia.edu!cunixa.cc.columbia.edu!df35 From: df35@cunixa.cc.columbia.edu (David Fleischer) Newsgroups: bionet.software Subject: Internal/external email gate? Message-ID: <1993Jun9.134441.5107@news.columbia.edu> Date: 9 Jun 93 13:44:41 GMT Sender: usenet@news.columbia.edu (The Network News) Reply-To: df35@cunixa.cc.columbia.edu (David Fleischer) Organization: Columbia University Lines: 4 Nntp-Posting-Host: cunixa.cc.columbia.edu I am looking for a program (DOS BASED) to interface between a LAN email system like WP Office and external mail systems like Internet or Compuserve or MCI mail. It would poll external systems, log on, retrieve and send mail, reformat incoming and outgoing mail to conform to both systems, and generally make