From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!uwm.edu!rutgers!mcclb0.med.nyu.edu!sci.wfeb.edu!macrides From: macrides@sci.wfeb.edu Newsgroups: bionet.software Subject: Re: bionet.miscellaneous Message-ID: <1993Apr1.120000.107@wfeb2> Date: 1 Apr 93 16:00:00 GMT References: <1993Mar29.085959.18390@comp.bioz.unibas.ch> Organization: Worcester Fndn. for Exptl. Biol. Lines: 37 In article <1993Mar29.085959.18390@comp.bioz.unibas.ch>, doelz@comp.bioz.unibas.ch (Reinhard Doelz) writes: >[...] > I agree that it would be good to have a better 'sorted' environment. > In particular, the following interest groups could be valuable if > we can only afford running them : > > bionet.software.avail - those for asking for and discussing > availability, > as well as announcing software > * MODERATED * > bionet.software.system - general inquiries how to manage > biocomputing sw > > bionet.software.misc - all other stuff not fitting to the > other bionet.software newsgroups. > > > In particular, a group which discusses availability issues is most > needed in my view, and should be moderated. If this thread gets enough > discussion we could dare to raise a call for discussion on it. >[...] I don't think there's a serious problem w.r.t. volume or junk for those accessing bionet.software via news readers, but I suspect those with email subsciptions, and those who check this group primarily for announcements of software releases and upgrades, would greatly appreciate the creation of a bionet.software.avail and corresponding email list. Hopefully, it would become the place where all of the biology-related software archives and software developers post announcements of new software or upgrades. Fote ========================================================================= Foteos Macrides Worcester Foundation for Experimental Biology MACRIDES@SCI.WFEB.EDU 222 Maple Avenue, Shrewsbury, MA 01545 ========================================================================= From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.software Subject: Re: Molbio Software Standard Message-ID: <1993Apr2.081120.23403@comp.bioz.unibas.ch> Date: 2 Apr 93 08:11:20 GMT References: <1993Apr1.215716.5202@gserv1.dl.ac.uk> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Distribution: bionet Organization: EMBnet Switzerland [BASEL] Lines: 78 Nntp-Posting-Host: biox.embnet.unibas.ch In article <1993Apr1.215716.5202@gserv1.dl.ac.uk>, r.nakisa@ic.ac.uk ((Ramin Charles Nakisa) ramin) writes: |> |> Here is an outline to discuss: |> |> * The source is written in C. C really is very portable and as an added |> bonus it allows us to use Don Gilbert's amazing ureadseq module to |> read and write sequences in all the standard formats. This would also |> allow us to build up a standard library of functions, so that we don't |> have to re-invent the wheel with every program. say _ANSI C_ and POSIX system calls. Never use dedicated tricks like memory mapping, byte-order dependent routines, and system-specific binary data setups. |> |> * It should work when compiled for MS-DOS, Windows (quickwin), Macintosh |> (simple window format?), UNIX and X. |> quite ambitious. You MUST include a text interface, and I would also want to have the VMS operating system in there. It would be great if people would read a style guide to avoid spagetti code. An API below the UI needs to be defined and then you can put all you want on top. |> * It must be able to read and write all the standard sequence formats. |> Why? A reasonabpe input API is sufficient to have all sequences imported easily. Think about future sequence formats, which would need to be read also. |> * There should be a standard interface. The most portable interface is |> one that consists of only printf and scanf. A standard graphic |> interface would be very difficult to define in a platform-independent |> way. Compiler's can usually produce basic windows for windowing |> operating systems eg. the quickwin library on the MS C/C++ 7.0 compiler. |> Hoppla. You're putting things upside down if you were talking windows up in the definition. A reasonable API with structures defined for parameter transmission to the code can well live with complex I/O statements if it is only modular enough. |> * It should offer sensible default parameters when possible, and |> use standard command-line switches. |> How to use these on a Mac? :-) |> * Graphic output should be in at least two formats: Postscript and HPGL |> Again, if a meta language can be agreed on, the output is only a driver which needs to be plugged in. Make sure that the API on the output side is defined and it isn't a problem no longer. |> * All source should be included and beautified. |> |> This might kill you. Who is really interested in getting source? If it works, it's fine. No need to fiddle with the compilesr of bersion X.Y.Z, patchlevel 1425 (but make sure that you have the XXX product disbled). Copyright procedures become significantly more important, and if there is a reasobable object library (so that you can link to) I would be satisfied. |> If you have ever used particularly good/bad molbio software then here is |> your chance to have a say before it's written! You have forgotten the networks. The furure will be much more client/server computing than you can currently imagine. -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!perrier!sundvall From: sundvall@perrier.embnet.se (Mats Sundvall) Newsgroups: bionet.software Subject: Re: The Entrez CD-ROM and the Government Pr Message-ID: <1ph8u9INNp15@buzz.bmc.uu.se> Date: 2 Apr 93 11:44:09 GMT References: Reply-To: sundvall@perrier.embnet.se Organization: EMBNet Project Sweden Lines: 11 NNTP-Posting-Host: perrier.embnet.se >It turns out that the staff at NCBI are totally unlike those at the GPO. I >received an e-mail response to the above net message from Dennis at NCBI the >same day. Next morning, Rose Marie called and this morning I received a >Fed Ex package containing a copy of Entrez. Wow! Thanks guys. So, whats the deal for the rest of us? We did send a check a long time ago. We have just seen the little note that told us to wait. How long? Mats Sundvall University of Uppsala Sweden From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.software Subject: Re: Massively Parallel Applications in Sequence Analysis Message-ID: <1993Apr2.075945.22969@comp.bioz.unibas.ch> Date: 2 Apr 93 07:59:45 GMT References: <1p6q49INNe18@s-crim1.dl.ac.uk> <1peuciINNicd@s-crim1.dl.ac.uk> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Distribution: bionet Organization: EMBnet Switzerland [BASEL] Lines: 49 Nntp-Posting-Host: biox.embnet.unibas.ch In article <1peuciINNicd@s-crim1.dl.ac.uk>, mbpcr@s-crim1.dl.ac.uk (A. Parsons) writes: |> The question I originally asked also had the caveat (which noone to date has |> commented on) "How much longer can we do WITHOUT data parallel solutions for |> searching the masses of data being generated by the HGMP?" |> Sorry for playing devil's advocate but I would say that the individual site can live long without a parallel computer. The database providers might like to have one, which they can use effectively. The biocomputer sites might need one (if they can afford to abandon the safe tracks and develop, maintain, and optimize own hardware/software solutions). You might have seen the discussion on the suspected contaminations reported in human cDNA libraries (Science, issue of previous week). In order to run thousands of sequences vs. EMBl, SWISSPROT, GENBANK, PIR we used a Silicon Graphics Cluster, containing 2 Indigos, a Crimson, and a 2-Processor Power series. It took about two to three weeks elapsed time on this setup, where the machines were also used for development work, molecular modelling, and general GCG usage. Now if you have such a problem of running 10000 fasta and blast jobs, how often do you need the results `yesterday` ? How often do you have these giantic questions at all? If you run these analysis, the 'granularity' as given in the fact that you run each sequence after another is sufficient to dissipate it amongst machines. You might want to have a parallel version if you have a multi-processor machine but the real idea is that the effort to manage, and maintain, a pvm installation is tedious on the long run. A Hierarchical Access System is perfect enough - you distribute single jobs across the net and keep using the 'established' software. This is alos beneficious due to the fact that the experience with the parameters and the search results is generally higher with fasta or blast-type of searches than with special algorithms. Last point coming into mind is that the question on 'similarity' is differently asked at database providers rather than end users. A reasona- ble check of a database annotator is to look for identities, maybe figure out alleles, but not weak homologies as most of the end users are interes- ted in. This is explicitly not talking on the 'biocomputers' who search the needle in the hey (no pun intended - just to scale the effort right). Those guys might not be able to live without monsters in the future. -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: Rob.Harper@csc.fi (Rob Harper) Newsgroups: bionet.software Subject: Simtel20 uploads for March Message-ID: <1993Apr2.081940.11541@gserv1.dl.ac.uk> Date: 2 Apr 93 08:19:46 GMT Sender: harper@fi.csc Distribution: bionet Lines: 474 Original-To: bio-soft@uk.ac.daresbury File PD1:UPLOADS.MAR Created: Apr. 1, 1993 NOTE: This file is also available in comma-delimited format as SIM9303.IDX MSDOS FILES UPLOADED TO WSMR-SIMTEL20.ARMY.MIL during the month of March 1993 NOTE: Type B is Binary; Type A is ASCII Filename Type Length Date Description ============================================== Directory PD1: 4DMK402.ZIP B 11650 930331 Update file for 4DOS 4.01 utility disk users 4DOS402D.ZIP B 262145 930331 Manual for 4DOS 4.02 COMMAND.COM replacement 4DOS402P.ZIP B 310863 930331 4DOS 4.02 Programs and auxiliary files 4DOS402U.ZIP B 175545 930331 4DOS 4.02 update for registered 4.01d users 4DUPD402.ZIP B 7562 930331 List of what's new in 4DOS 4.02 4SIGHT13.ZIP B 7314 930304 tcsh-like & windowed 4DOS filename completion Directory PD1: AM91.ZIP B 222157 930322 ArcMaster front-end/convrt for ARC/ARJ/LZH/ZIP ARCID102.ZIP B 19962 930314 Identifies archive types by file signature AT780D.ZIP B 109719 930322 Archive shell for ARC/LZH/PAK/PKA/LBR/ZOO/ZIP RV249.ZIP B 27151 930322 Archive lister for ZIP/ARJ/LZH/ZOO/PAK/ARC etc RVS110.ZIP B 50642 930322 RVS-RView: View/extract contents of archives SHEZ89.ZIP B 224529 930318 Shell interface to ZIP/ARJ/LZH/ZOO/ARC/SQZ/PAK Directory PD1: 80X0393.ZIP B 172490 930328 ASM snippet collection from 80XXX FidoNet echo TBONES07.ZIP B 37888 930305 Skeletal ASM programs for programming TSRs Directory PD1: AA-51.ZIP B 167571 930320 Astronomical almanac - sun moon planets stars DE118I.ZIP B 185587 930320 N-body numerical integration of moon & planets SKYIMG1.ZIP B 1048378 930306 Planetary/Lunar GIF images for SkyMap v1.2 SKYMAP12.ZIP B 244063 930306 SkyMap v1.2 Win3.1 Planetarium program+docs Directory PD1: GEOTOL.ZIP B 31420 930308 GD&T made easy for AutoCAD R12 Directory PD1: MS-ASK.ZIP B 3428 930303 Ask user for input in a batch file. w/ASM src TSBAT42.ZIP B 100448 930302 Collection of useful batch files by Timo Salmi WAITER.ZIP B 11459 930306 Batutl: Counts down, allowing user to bail out Directory PD1: FMQT131U.ZIP B 52695 930315 Quoter for 'FM' BBS FrontDoor Message Editor GCHAT140.ZIP B 35679 930318 Generic BBS Chat v1.40. DESQview aware, free PCBEM103.ZIP B 35143 930322 Multiple event manager for PCBoard BBS WCAT26A.ZIP B 445278 930317 Working demo of Wildcat BBS, part A. 921103 WCAT26B.ZIP B 360679 930317 Working demo of Wildcat BBS, part B. 921103 Directory PD1: BID200.ZIP B 56806 930318 BBS Information Door v2.00 new user help Directory PD1: VIDBOOK0.ZIP B 1604730 930325 Graphic GIFs&viewer Bible Study - Romans 1:20 VIDBOOK1.ZIP B 1783585 930325 Graphic GIFs&viewer Bible Study - Isaiah 30:26 Directory PD1: BVIEW1_0.ZIP B 46621 930325 BView v1.0: Binary or hex file viewer/editor Directory PD1: MNUBT300.ZIP B 36494 930305 Select from multi configs w/booting, (VGA req) Directory PD1: ACTLIB11.ZIP B 150258 930302 General purpose libraries C/C++ programmers LINGU11A.ZIP B 28031 930317 Easy multi-language support for C programs ODOORS41.ZIP B 424685 930318 C library for creating professional BBS doors PCL4C34.ZIP B 71564 930322 Asynchronous communications library for C Directory PD1: BCAD100.ZIP B 315374 930319 BCAD v1.0 CAD/CAM editor, VGA/286/386/486 EASYTRAX.ZIP B 496079 930318 Protel's powerful PCB layout, freeware version LASI411A.ZIP B 302597 930318 LASI v4.11 IC layout CAD prgm: unzip in \lasi4 LASI411B.ZIP B 331388 930318 LASI v4.11 IC layout CAD prgm: unzip in \lasi4 LASI411C.ZIP B 279701 930318 LASI v4.11 IC layout CAD prgm: unzip in \lasi4 LASIDEMO.ZIP B 22424 930318 LASI v4.1 DEMO drawing: unzip in \lasi4\demo TMC101.ZIP B 138128 930331 TextModeCad: CAD system in text mode envirnmnt Directory PD1: RSC300.ZIP B 65164 930301 Resident Scientific Expression Calculator v3.0 Directory PD1: TORG311.ZIP B 174878 930329 Organic chemistry ID of unknowns simulator Directory PD1: CLTAB100.ZIP B 7031 930304 Align your Clipper (Summer/5.0) programs CL_CLK10.ZIP B 6447 930325 Clock for Clipper 5.0, with Clipper source NFLIB21.ZIP B 208840 930325 Nanforum Toolkit v2.1, docs/library/NG, 1/2 NFSRC21.ZIP B 361267 930325 Nanforum Toolkit v2.1, src code/Make file, 2/2 Directory PD1: GZIP107.ZIP B 49053 930322 GNUzip: Unix compress/uncompress replacement Directory PD1: TSR100JE.ZIP B 75319 930324 TSR class for Borland C++ (with source) Directory PD1: CDS300D.ZIP B 57902 930321 CD Catalog with browse & search. Mouse Support CEM063.ZIP B 218777 930310 Records cemetery tombstone inscriptions CEQPT37B.ZIP B 165371 930323 Database for equipment service/usage histories CINVT55C.ZIP B 164615 930323 Inventory pgm for tracking store stock/orders COLLCT21.ZIP B 369801 930326 CollectorMate v2.1: Database for collectors TCARD28.ZIP B 268321 930301 Small business employee punch card. Log in/out TIMTBL01.ZIP B 186429 930325 Timetable printer saves data to Paradox tables Directory PD1: DDJ9211.ZIP B 991669 930303 Dr. Dobbs Journal mag listings, Nov. 1992 Directory PD1: DEM-FAQ.ZIP B 12755 930305 Frequently Asked Questions for Demacs Directory PD1: CSAP312.ZIP B 31639 930322 Sorts disk directory, removes deleted entries FFF42.ZIP B 118886 930318 Derr's FileFinder 4.2, performs fuzzy search Directory PD1: DCF40F.ZIP B 67511 930314 Very fast 1-pass diskette copy utility FLEXP250.ZIP B 189086 930331 Flexibak Plus: Hard disk backup w/compression KG_DF105.ZIP B 5291 930316 Disk Free: Disk free/used as % of total, w/src MACSEE22.ZIP B 54701 930325 Read/write Macintosh disks on PC. DOS & WIN3.x TCPY200.ZIP B 54509 930325 Fast multi-volume file copy program WDATIDE.ZIP B 122573 930317 Western Digital hard disk utility, from WD BBS Directory PD1: DESKU110.ZIP B 234104 930322 File, font, mouse and more utilities for DV/X Directory PD1: BOXER50A.ZIP B 296096 930302 Boxer5.0a Editor:mouse,undo,mult files&windows SEDIT100.ZIP B 319647 930314 Easy to use text editor with spelling check TMED160A.ZIP B 9672 930331 Small TSR memory editor and key macro VDE165A.ZIP B 152333 930321 Meyer's small, fast, WordStar-like text editor Directory PD1: ACLOCKMP.ZIP B 363411 930315 Animated Clock: Teach kids to tell time AMDCM1A.ZIP B 226417 930315 Animated multiplication/division game, 1 of 2 AMDCM1B.ZIP B 407270 930315 Animated multiplication/division game, 2 of 2 AMEM20.ZIP B 266091 930315 Animated Memory Game: aids kids' memory skills Directory PD1: DAUBWAVE.ZIP B 45610 930303 Wavelet analysis program, w/C source Directory PD1: AUTFTP12.ZIP B 18779 930306 Auto get files from OAK using SIMDIR+NSCA FTP CDROM.INF A 806 930327 Where to obtain SIMTEL20 files on CD-ROM CHANGES.DOC A 1156 930329 Details on SIMTEL20's change to ZIP 2.0 format DOWNLOAD.INF A 2829 930327 How to get SIMTEL20 files via telephone modem MAILSERV.INF A 3119 930322 List of e-mail servers offering SIMTEL20 files OAKFTP01.ZIP B 2544 930331 Unix script to auto-ftp MS-DOS files from OAK QUICKREF.LST A 3901 930331 Quick reference list to SIMTEL20's MSDOS dirs SIMIBM.HDR A 815 930327 SIMIBM.IDX header file for PC-File+ use SIMIBM.ZIP B 299379 930331 Comma-delim list of all MSDOS files w/descrip. SIMLIST.ZIP B 292846 930331 Text format list of all MSDOS files w/descrip. Directory PD1: DLCPMV23.ZIP B 26067 930323 BSD Unix-style file copying/moving utilities EXECUT10.ZIP B 8140 930325 Archive files with common extentions. (w/src) HFM318.ZIP B 342215 930318 Filemanager/archive shell,compares 2 dir lists UUDO12.ZIP B 19370 930331 Multi-file/multi-part 'smart' uudecoder UUEXE521.ZIP B 33438 930315 R.E. Marks' fast multi-section UU/XX EN/DEcode Directory PD1: DEBTFR30.ZIP B 194655 930326 Home mortgage mgr, calculate/record payments STCKT700.ZIP B 370442 930318 Stock Trader v7.00: Stock history, buy, sell Directory PD1: MCHEF_1A.ZIP B 279829 930309 Recipe, diet & meal management tool. Part 1of2 MCHEF_1B.ZIP B 307611 930309 Recipe, diet & meal management tool. Part 2of2 Directory PD1: ILMP9303.ZIP B 78100 930307 GEnieLamp IBM Online Magazine (Mar 1993) Directory PD1: VPIC60.ZIP B 248433 930322 GIF/MAC/PCX/ColorRix pics view/convrt, EGA/VGA Directory PD1: RCS55AS.ZIP B 201450 930331 Revision Control System for text files, source RCS55AX.ZIP B 193001 930331 Revision Control System for text files EXE/doc Directory PD1: GRPHCA22.ZIP B 256733 930309 Interactive scientific plotting program, v2.2 Directory PD1: CBOOK.ZIP B 159565 930331 Holloway's VGA+mouse coloring book for kids CHIARO10.ZIP B 127870 930319 Chiaro Suite of image utilities release 1.0 DISP125.ZIP B 266563 930329 Display/convert images with different formats MAKAMESS.ZIP B 445810 930331 VGA graphical message maker/presenter. Req 386 SVGAKT31.ZIP B 318358 930307 SuperVGA test kit lib. Supports most SuperVGAs UVESA31.ZIP B 21525 930307 Universal VESA TSR for most SuperVGA cards Directory PD1: FRGLOD10.ZIP B 14327 930329 Hams: Yaesu FRG100 sw-rcvr channel data progmr JVFAX51.ZIP B 318153 930304 Ham Radio FAX and SSTV program version 5.1 Directory PD1: DART1G.ZIP B 230550 930303 Hypertext file viewer and launcher, w/editor HLPDK21.ZIP B 251303 930329 DOS/Windows hypertext Help development kit Directory PD1: ASP6302.ZIP B 532493 930315 Association of Shareware Professionals catalog FAQP9305.ZIP B 49813 930317 comp.os.msdos.programmer FAQ from Usenet FTPLIST.ZIP B 6880 From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!news-feed-1.peachnet.edu!umn.edu!msus1.msus.edu!TIGGER.STCLOUD.MSUS.EDU!Q00023 From: q00023@TIGGER.STCLOUD.MSUS.EDU Newsgroups: bionet.software Subject: Hydrophobicity of amino acid chain determination Message-ID: <1993Apr1.221826.2929@msus1.msus.edu> Date: 2 Apr 93 04:18:26 GMT Reply-To: q00023@TIGGER.STCLOUD.MSUS.EDU Organization: ST. CLOUD STATE UNIVERSITY, ST. CLOUD, MN Lines: 8 Nntp-Posting-Host: tigger.stcloud.msus.edu Dear netters, I would like to know if there are any shareware of determining hydrophobicity of a amino acid chain. I would appreciate anyone who reply to my request. Thanks in advance, Gabriel Cheung St.Cloud State University Biotechnology & Biochemistry From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!LAKE.SCAR.UTORONTO.CA!chan From: chan@LAKE.SCAR.UTORONTO.CA (Leslie Chan) Newsgroups: bionet.software Subject: reading Postscript file Message-ID: <9304020242.AA08898@lake.scar.utoronto.ca> Date: 2 Apr 93 02:42:52 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 8 Hello all, I downloaded why I thought was a plain text file via anonymous FTP but it turned out to be a postscript file. I use Word on a Macintosh but I can't seem to convert the file to readable form. Any suggestions would be greatly appreciated. Leslie Chan Chan@lake.scar.utoronto.ca From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.software Subject: Re: free or cheap homology programs Message-ID: <1993Apr2.165452.8767@welchgate.welch.jhu.edu> Date: 2 Apr 93 16:54:52 GMT References: <1pe5u4INNbe5@uniwa.uwa.edu.au> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 23 In article <1pe5u4INNbe5@uniwa.uwa.edu.au> robert@arbo.microbiol.uwa.oz.au (Robert Coelen) writes: > > >Hi, > >Can anyone tell me which of the major Nucleic Acid database >interrogation programs, available for Unix boxes, are FOC or relatively >cheap for a university environment ?? > > FastA and Blast are two of the more common ones - both are available for free by anonymous ftp. FastA from virginia.edu in the pub/fasta/ directory. Blast from ncbi.nlm.nih.gov in the pub/blast directory. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!gatech!usenet.ufl.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.software Subject: Re: DNA analysis software for Macintosh Message-ID: <1993Apr2.164849.8015@welchgate.welch.jhu.edu> Date: 2 Apr 93 16:48:49 GMT References: <1993Mar31.144114.3097@ucbeh.san.uc.edu> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 42 In article <1993Mar31.144114.3097@ucbeh.san.uc.edu> craftdl@ucbeh.san.uc.edu writes: >I am in need of an inexpensive DNA analysis software program for the Macintosh. >The program should be able to do sequence comparisons, restriction enzyme >analysis, translations, etc. I realize there are excellent programs available >for the Macintosh;however, graduate students on a limited budget cannot afford >these expensive programs. This problem is compounded when your department is >basically PC oriented and cannot purchase a program for the Mac. If anyone has >suggestions or knows of inexpensive programs, please mail me at >CRAFTDL@ucbeh.san.uc.edu Sounds like what you're looking for is Don Gilbert's SeqApp - available by gopher or anonymous ftp at ftp.bio.indiana.edu - a little clip from the readme is as follows: SeqApp is a biological sequence editor and analysis program for Macintosh computers. It includes links to network services and external analysis programs. Features include multiple sequence alignment editor single sequence editor window read and write several sequence file formats easy hand alignment features including colored bases and sliding automatic multiple sequence alignment thru Clustal external app automatic gel fragment alignment to contigs thru exernal app consensus,reverse,complement,degap operations restriction maps dot plots translate dna to/from protein using various codon tables automatic preference saving internet send mail, read mail internet gopher, information retreival including genbank. internet sequence analysis services user-definable links to external analysis programs and more Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software Subject: Re: Molbio Software Standard Message-ID: <1pggn0$amq@overload.lbl.gov> Date: 2 Apr 93 04:50:40 GMT References: <1993Apr1.215716.5202@gserv1.dl.ac.uk> <1993Apr1.223703.13177@alw.nih.gov> Organization: Dendrome, A Genome Database for Forest Trees Lines: 25 NNTP-Posting-Host: s27w007.pswfs.gov Go for it guys. While you biologists are standardizing and writing the software standard we programmers will be standardizing the meaning of locus, gene, allele, wild-type, species, homology, germplasm, site, map, mutation, pathogen and trait. Then we will tell you the common format for segregation data that is self-descriptive with regard to the pedigree, type of cross, and ploidy. Next we will tell you how to name your probes and libraries. By that time you should just about have come to terms with small, medium, huge and obese memory models for MessyDos, resource forks in Macs, record types in VMS, concurrent record updates, non-deterministic operating systems and the deadly embrace. If you guys keep thinking of programmers as lab techs we're not going to get anywhere. Captiously, --bks -- Bradley K. Sherman, Dendrome Project Institute of Forest Genetics, USDA Forest Service P.O. Box 245, Berkeley, CA, 94701, USA Phone: 510-559-6437 FAX: -6440 Internet: bks@s27w007.pswfs.gov From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!UM.CC.UMICH.EDU!Doug.Eernisse From: Doug.Eernisse@UM.CC.UMICH.EDU Newsgroups: bionet.software Subject: Cladistics Programs for Dos/Unix? Message-ID: <21617704@um.cc.umich.edu> Date: 2 Apr 93 16:01:08 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 33 Just to clarify Carol Bult's recent comments: > The DOS-based cladistics program I use is Hennig86 which was written > by Steve Farris. The program cost is modest, ~ $50.00 (U.S.), but I'm not >-sure how > Steve is handling the distribution of the program because he no longer > lives in the US. Hennig86 is obtained by sending a check to: Dr. A. Kluge Museum of Zoology Univ. of Michigan Ann Arbor, MI 48109 Cost is $50 plus $5 or $10 for shipping and diskette, etc., depending on whether the order is from U.S. or not, respectively. >My understanding is that he is working on a > Windows version of PAUP, but it will probably be awhile before that is > ready for distribution. The non-Mac version of PAUP, which might be released soon or perhaps not, does not depend on Windows. The Mac version 3.1 will soon be released. The old MS-DOS/mainframe version is truly obsolete and should not be used (unless you don't care whether or not you find the minimum length trees). As Carol mentioned, Phylip is available and is free (Joe, have you got it working on microwave ovens yet? ;-) --virtually all platforms--does other things besides parsimony searches Doug Eernisse Doug_Ee@um.cc.umich.edu From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!BENGAL.TIGR.ORG!bult From: bult@BENGAL.TIGR.ORG (Carol Bult) Newsgroups: bionet.software Subject: Cladistics Programs for Dos/Unix? Message-ID: <9304021419.AA03907@bengal.tigr.org> Date: 2 Apr 93 14:19:25 GMT References: <9304012321.AA21694@net.bio.net> Sender: daemon@net.bio.net Distribution: bionet Lines: 58 Rober Guralnick asked about cladistic analysis programs for DOS/Win or UNIX. The DOS-based cladistics program I use is Hennig86 which was written by Steve Farris. The program cost is modest, ~ $50.00 (U.S.), but I'm not sure how Steve is handling the distribution of the program because he no longer lives in the US. He is working on a new version which I think he plans on releasing this summer at the Hennig Meetings (August 9-13, Fullerton, CA.). Kevin Nixon (Cornell University) has written a program called CLADOS which is file compatible with Hennig86. I haven't used the program yet, so I'm not sure what its capabilities are. You might want to contact Keven to find out more about his program: Dr. Kevin C. Nixon LH Bailey Hortorium Cornell, University Ithaca, NY 14853 Again, the cost is modest (last I heard, it was $50). There is an old, old DOS version of PAUP (Phylogenetic Analysis Using Parsimony, by David Swofford), but I'm not even sure if David distributes it anymore. My understanding is that he is working on a Windows version of PAUP, but it will probably be awhile before that is ready for distribution. Joe Felsenstein distributes the C source code for his program, PHYLIP, via anonymous FTP. He just released version 3.5. It's free and can run on 386 or 486 PCs or UNIX. The FTP site is: evolution.genetics.washington.edu (IP 128.95.12.41) If you can't access the files via FTP, you can send him several diskettes (call him first to find out how many you would need to send) and he'll send you the program that way. Joe's address is: Dr. Joe Felsenstein Dept. of Genetics Univ of Washington Seattle, WA 98195 Good luck.. Carol ___________________________________________________________________ Carol Bult, Ph.D. bult@tigr.org The Institute for Genomic Research 932 Clopper Road voice: 301-869-9056 Gaithersburg, MD 20878 fax: 301-869-9423 ___________________________________________________________________ From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.software Subject: Re: Cladistics Programs for Dos/Unix? Message-ID: <1993Apr2.170342.9976@welchgate.welch.jhu.edu> Date: 2 Apr 93 17:03:42 GMT References: <1pftdd$l30@agate.berkeley.edu> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 25 In article <1pftdd$l30@agate.berkeley.edu> robg@fossil.Berkeley.EDU (Robert Guralnick) writes: >Hi all - > > Quick question... Any decent relatively inexpensive or free (!!!!) >cladistic analysis program out there for either DOS/Win3.1 or Unix based >environments. Thanks. > Joe Felsenstein's PHYLIP is a *very* extensive phylogeny package with versions for Unix, VMS, DOS, Mac ... PHYLIP comes with *lots* of documentation and is all available for free by anonymous ftp from evolution.genetics.washington.edu in the pub/ directory. The documentation also contains a list of other phylogeny packages available from others. Paup, by David Swofford, is a good phylogeny package that costs about $50. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!WSUVMS1.CSC.WSU.EDU!THOMPSON From: THOMPSON@WSUVMS1.CSC.WSU.EDU (Steve Thompson: VADMS genetics) Newsgroups: bionet.software Subject: PostScript and Mac MS Word Message-ID: <930402104012.20203d51@BOBCAT.CSC.WSU.EDU> Date: 2 Apr 93 18:40:12 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 46 Hello Leslie and the rest of the bio-soft world - Leslie Chan in message <9304020242.AA08898@lake.scar.utoronto.ca> wrote: >Hello all, >I downloaded why {what} I thought was a plain text file via anonymous FTP but >it turned out to be a postscript file. I use Word on a Macintosh but I >can't seem to convert the file to readable form. Any suggestions would >be greatly appreciated. > >Leslie Chan >Chan@lake.scar.utoronto.ca Using ONLY MS Word on a Mac, the only way that I know of {who knows how many others there really are 8-)} to interpret actual postscript is by selecting ALL of the PostScript text with your mouse and then using the Style options in one of your menus {I'm sorry but I am not sitting at my Mac now so I can't describe the actual menu entry names} such that the selected text is converted to Word's special PostScript Style. This converts it into a special reserved format which Apple LaserWriters recognize as being true PostScript rather than just ASCI. Then print that file to your Laserwriter from within word. Other ways which do not use Word include the Apple LaserWriter Utility which can download ASCI PostScript files to a Laserwriter printer for interpretation and the public domain package GhostScript which can allow onscreen previewing of most PostScript files. These topics have been covered several times within this newgroup and summaries are available by Gopher through IUBIO. What "I" would like to be able to figure out is how to accurately position and rescale EPSF files within an MS WORD document. It may not be possible but I keep trying. I know it should be possible within "fancier" layout and graphics packages such as PageMaker and Canvas but my {and our program's} empty pockets preclude that route. G'day All, Steve T Steven M. Thompson Consultant in Molecular Genetics and Sequence Analysis VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory Washington State University, Pullman, WA 99164-1224, USA AT&Tnet: (509) 335-0533 or 335-3179 FAX: (509) 335-0540 BITnet: THOMPSON@WSUVMS1 or STEVET@WSUVM1 INTERnet: THOMPSON@wsuvms1.csc.wsu.edu From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!LIBRARY.CATAWBA.EDU!scoggin From: scoggin@LIBRARY.CATAWBA.EDU (Dr. Steve Coggin) Newsgroups: bionet.software Subject: (none) Message-ID: <55677.scoggin@library.catawba.edu> Date: 2 Apr 93 19:27:54 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 1 Subscribe bio-software Steve Coggin From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!agate!spool.mu.edu!uwm.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.software Subject: Re: Hydrophobicity of amino acid chain determination Message-ID: <1993Apr2.171833.11305@welchgate.welch.jhu.edu> Date: 2 Apr 93 17:18:33 GMT References: <1993Apr1.221826.2929@msus1.msus.edu> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 19 In article <1993Apr1.221826.2929@msus1.msus.edu> q00023@TIGGER.STCLOUD.MSUS.EDU writes: >Dear netters, > I would like to know if there are any shareware of determining hydrophobicity of a amino acid chain. I would appreciate anyone who reply to my request. > There are several available, any paricular machine/OS your looking for? For DOS there's Prograph by (Kay Hofmann), and seqaid. For the Mac there's PLOTA ..... Prograph and PLOTA are available by gopher and anonymous ftp from (among others) felix.embl-heidelberg.de. Seqaid is available by gopher and anonymous ftp from (among others) ftp.bio.indiana.edu. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-software@net.bio.net Thu Apr 01 23:00:00 1993 Path: biosci!CU.NIH.GOV!CZJ From: CZJ@CU.NIH.GOV Newsgroups: bionet.software Subject: Re: Hydrophobicity of amino acid chain determination Message-ID: <9304021657.AA00747@net.bio.net> Date: 2 Apr 93 15:38:28 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 36 > MAIL VIA INTERNET FROM BIOSCI-REQUEST@net.bio.net THURSDAY 04/01/93 11:21:34 P.M. > > Received: from CU.NIH.GOV by NIHCU (Mailer) id 1152; > Thu, 01 Apr 93 23:21:34 EST > Received: from NET.BIO.NET by CU.NIH.GOV > with TCP; Thu, 1 Apr 93 23:22:59 EST > Received: by net.bio.net (5.65/IG-2.0) > id AA06272; Thu, 1 Apr 93 20:23:27 -0800 > Received: by net.bio.net (5.65/IG-2.0) > id AA06268; Thu, 1 Apr 93 20:23:26 -0800 > Message-Id: <9304020423.AA06268@net.bio.net> > To: bio-soft@net.bio.net > From: q00023@TIGGER.STCLOUD.MSUS.EDU > Subject: Hydrophobicity of amino acid chain determination > Date: 2 Apr 93 04:18:26 GMT > Reply-To: q00023@TIGGER.STCLOUD.MSUS.EDU > Nntp-Posting-Host: tigger.stcloud.msus.edu > > Dear netters, > I would like to know if there are any shareware of determining hydrophobicity of a amino acid chain. I would appreciate anyone who reply to my request. > > Thanks in advance, > > Gabriel Cheung > St.Cloud State University > Biotechnology & Biochemistry > > Profilegraph writen by Kay Hofman has that information in an easy to use format. It can be obtained fromt he embl file server and other ftp sites. Jim Cassatt From owner-software@net.bio.net Fri Apr 02 23:00:00 1993 Path: biosci!agate!spool.mu.edu!uunet!decwrl!concert!rock!taco!csemail.cropsci.ncsu.edu!samodena From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena) Newsgroups: bionet.software Subject: Re: The Entrez CD-ROM and the Government Printing Office (US) Message-ID: <1993Apr2.224449.15497@ncsu.edu> Date: 2 Apr 93 22:44:49 GMT References: Sender: news@ncsu.edu (USENET News System) Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620 Lines: 24 In article rhughes@ucsd.edu (Richard J. Hughes) writes: >Has anyone else been having trouble ordering the Entrez CD-ROM from the US >Government Printing Office? I have had plenty of difficulty. >..... >When you call the Gov't Printing Office, you are put on hold for a long >time. When someone finally answers, the audio is so faint as to be almost >indiscernable (maybe 5 dB above background). Please post the GPO phone number: I want to take a crack at that system. ;^) Steve --- +------------------------------------------------------------------+ | In person: Steve Modena AB4EL | | On phone: (919) 515-5328 | | At e-mail: nmodena@unity.ncsu.edu | | samodena@csemail.cropsci.ncsu.edu | | [ either email address is read each day ] | | By snail: Crop Sci Dept, Box 7620, NCSU, Raleigh, NC 27695 | +------------------------------------------------------------------+ Lighten UP! It's just a computer doing that to you. (c) OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO From owner-software@net.bio.net Fri Apr 02 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!swrinde!zaphod.mps.ohio-state.edu!wupost!spool.mu.edu!uunet!psinntp!newstand.syr.edu!SUVM.SYR.EDU!DRPORTER From: DRPORTER@SUVM.SYR.EDU (Brad Porter) Newsgroups: bionet.software Subject: Population modeling software in the works... Message-ID: <16BA412030.DRPORTER@SUVM.SYR.EDU> Date: 3 Apr 93 01:46:15 GMT Organization: Syracuse University Lines: 15 This isn't an official announcement or anything, but I thought I'd inform you of some biological software currently being developed. The project I'm currently working on is a matrix modeling program for Windows 3.1. While the project is still in the works, it will include numerous graphical representations of the model, eigen value extraction, and a variable projection matrix (complete with the ability to calculate matrix values as functions of N). By posting this message, I'm really just trying to get a feel of how many out there would be interested in the software when it's done. The package is scheduled to be in beta form by May. Additional information can be obtained by emailing either myself (I'm just the software engineer, though), or Brian Underwood (the project director) at the addresses listed: Dr. Brian Underwood: deer@suvm.acs.syr.edu Brad Porter: drporter@suvm.acs.syr.edu -Brad Porter From owner-software@net.bio.net Fri Apr 02 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!agate!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.software Subject: Re: Molbio Software Standard Message-ID: <1pl38j$9jh@overload.lbl.gov> Date: 3 Apr 93 22:31:47 GMT References: <1993Apr1.215716.5202@gserv1.dl.ac.uk> <1993Apr1.223703.13177@alw.nih.gov> <1pggn0$amq@overload.lbl.gov> Organization: Dendrome, A Genome Database for Forest Trees Lines: 32 NNTP-Posting-Host: s27w007.pswfs.gov In article <1pggn0$amq@overload.lbl.gov> bks@s27w007.pswfs.gov (Bradley K. Sherman) writes: > ... >If you guys keep thinking of programmers as lab techs we're not going >to get anywhere. > ... First of all, let me apologize for my intemperate remarks and especially to lab techs without whom I could not do my work. Writing software for researchers is a difficult proposition. It is very common for a single successful run of a program to be the last use of that program! It is often the case that a simple graph or picture is the culmination of hundreds of hours of moving data from one form to another, filtering out noise, and applying a special purpose mathematical transform -- often some arcane algorithm thought up by Gauss after one too many Schnapps on a chilly night in 1843 and never before implemented in any form more concrete than a doctoral dissertation. By the time the software is cast into a robust form, thoroughly vetted and outfitted with its direct manipulation interface for Curses, Windows , Windows NT, Mac, OS/2, OpenLook, NeXtStep Motif, VMS, ... and then retested for window manager idiosyncrasies the problem it solves may be of no interest. --bks -- Bradley K. Sherman, Dendrome Project Institute of Forest Genetics, USDA Forest Service P.O. Box 245, Berkeley, CA, 94701, USA Phone: 510-559-6437 FAX: -6440 Internet: bks@s27w007.pswfs.gov From owner-software@net.bio.net Fri Apr 02 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!network.ucsd.edu!dialin1-32-1.extern.ucsd.edu!rhughes From: rhughes@ucsd.edu (Richard J. Hughes) Newsgroups: bionet.software Subject: Re: The Entrez CD-ROM and the Government Printing Office (US) Message-ID: Date: 3 Apr 93 06:56:44 GMT References: <1993Apr2.224449.15497@ncsu.edu> Organization: ucsd.edu Lines: 62 NNTP-Posting-Host: dialin1-32-1.extern.ucsd.edu In article <1993Apr2.224449.15497@ncsu.edu> samodena@csemail.cropsci.ncsu.edu (S. A. Modena) writes: >Please post the GPO phone number: I want to take a crack at that system. Their voice phone number is (202) 783-3238, although this might not do you a whole lot of good. This is what our secretary had to say: -----------------------------Forwarded ---------------------------------- From: Andrina Marshall Date: 3/29/93 4:45PM To: Richard Hughes Receipt Requested Subject: Superintendent of Documents Fiasco ------------------------------------------------------------------------- Per your request please find below a brief description of this morning's events regarding my interaction with the vendor - Superintendent of Documents. I phoned the Superintendent of Documents this morning starting at 8AM, and after 5 or 6 attempts of busy signals finally got through and spoke to a TECHNICIAN. After explaining to the TECHNICIAN that I spoke to a woman in the ORDERS DEPT. on March 18th asking her to send us an invoice for the subscription to Entry on CD-ROM because the university will not issue a check without an invoice, this TECHNICIAN said I should speak to the ORDERS DEPT. again. After being transferred to the ORDERS DEPT., I repeated the information adding that the woman said she would send out the invoice that day. The ORDERS DEPT. representative then stated I should speak to CUSTOMER SERVICE. After being transferred to CUSTOMER SERVICE, I repeated the information and was told I should speak to the INVOICING DEPT. After being transferred to the INVOICING DEPT, I repeated the information and was told I should speak to a TECHNICIAN. I was then transferred back to the original gentleman I spoke with to begin with - the TECHNICIAN, and was told the invoice had PROBABLY been processed in their system but could take up to 3 or 4 weeks. I stated that NOONE told this to me on March 18th, and that in fact the woman in the ORDERS DEPT. stated she would get the invoice out to me that day. Last, I requested an invoice to be faxed, but was told "they don't do that anymore". I hope this helps. GOOD LUCK. ------------------------------------------------------------------------- Yes, you will need it. Richard +------------------------------------------------------------------------+ | Dr. Richard J. Hughes rhughes@ucsd.edu | | Department of Pharmacology <> | | University of California at San Diego Tel (619) 534-2298 | | La Jolla, CA 92093-0636 FAX (619) 534-7461 | +------------------------------------------------------------------------+ From owner-software@net.bio.net Fri Apr 02 23:00:00 1993 Path: biosci!agate!spool.mu.edu!uunet!mcsun!dxcern!hprd26a!tonko From: tonko@hprd26a.cern.ch (Tonko Ljubicic) Newsgroups: bionet.software Subject: Free EMBL-database query/search software ? Message-ID: Date: 3 Apr 93 13:08:13 GMT Sender: news@dxcern.cern.ch (USENET News System) Organization: CERN European Lab for Particle Physics Lines: 12 Does anybody know of a free (or cheap) EMBL database searching software ? In the manner of CD-SEQ from the EMBL CD for instance. Preferably for DOS (Windows?) and Unix (X11?). -- Tonko -- ljubicic@dxcern.cern.ch ljubicic@cernvm.bitnet tonko@hprd26a.cern.ch Ante Tonko Ljubicic Division PPE CERN (European Laboratory for Particle Physics) 1211 Geneve 23 Switzerland From owner-software@net.bio.net Fri Apr 02 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: Re. EMBL File Server Message-ID: <9304031516.AA25128@net.bio.net> Date: 3 Apr 93 15:01:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 461 From: tonko@hprd26a.cern.ch (Tonko Ljubicic) Subject: Free EMBL-database query/search software ? Date: 3 Apr 93 13:08:13 GMT tonko@hprd26a.cern.ch (Tonko Ljubicic) wrote: >Does anybody know of a free (or cheap) EMBL database searching >software ? In the manner of CD-SEQ from the EMBL CD for instance. >Preferably for DOS (Windows?) and Unix (X11?). Here is a newsletter from EMBL: From: NETHELP@EMBL-Heidelberg.DE Subject: EMBL File Server Newsletter No. 9, Dec. 4th 1992 Date: 4 Dec 92 11:03:17 GMT ------------------------------------------------------------------------------ | EMBL FILE SERVER News Number 9, December 4th 1992 | | | | European Molecular Biology Laboratory, Data Library & Computer Group, | | Postfach 10.2209, 6900 Heidelberg, Germany. | | Tel: +49 6221 387258 | | E-mail: NetHelp@EMBL-Heidelberg.DE Fax: +49 6221 387519 | ------------------------------------------------------------------------------ Contents: <1> Introduction <2> Improvement of EMBL's Internet connectivity <3> Anonymous FTP services - alternative sites <4> New mail server command <5> Updates to data collections <6> Updates to software collection <7> Other updates <8> Summary of directories on the file server <9> Getting started ? <10> Network addresses at EMBL <1> Introduction ------------ The EMBL File Server is a facility available on the EMBL computing system for external users to request files by electronic mail, anonymous FTP or Gopher. The service is free. <2> Improvement of EMBL's Internet connectivity ------------------------------------------- Recently there has been a improvement in EMBL's Internet connection which results in considerably faster access to our anonymous FTP server and to our Gopher server, and also a quicker response to e-mail file server requests. Please note that the FTP and Gopher servers both run on FTP.EMBL-Heidelberg.DE (192.54.41.33) Do not use the host name EMBL-Heidelberg.DE <3> Anonymous FTP services - alternative sites (a) The anonymous FTP archives at EMBL are mirrored by an FTP server managed by the Israeli EMBnet national node (INN) at the Weizmann Institute. Internet address: sunbcd.weizmann.ac.il (b) Complete copies of the EMBL quarterly releases are also available by anonymous FTP from: - Swiss EMBnet Node, Biozentrum der Universitaet Basel (Switzerland) Internet address: bioftp.unibas.ch [131.152.8.1] Maintained by Reinhard Doelz (doelz@comp.bioz.unibas.ch) Plain ASCII flat files. See the file DESCRIPTION in the top level directory for more information, also on other formats of data. - Department of Molecular Biology Massachusetts General Hospital Internet address: amber.mgh.harvard.edu [132.183.190.26] Maintained by Mike Cherry (CHERRY@Frodo.MGH.Harvard.EDU) Compressed EMBL flat files. See the 000readme.txt file in the EMBL directory for more information, also on other formats of data. <4> New mail server command ----------------------- The SIZE command was added to the set of commands recognised by the EMBL e-mail server. Because some mailer systems have a maximum file size limitation the EMBL mail server splits large files into parts. The default size of these packets is 95K but can be changed with the SIZE command. E.g. SIZE 30 would change the packet size to 30K, whereas SIZE 500 would set it to 500K. Note, however, that uuencoded files are stored in individual parts of 90K each on our server, so changing the packet size to larger values will have no effect on them. <5> Updates to Data Collections ------------------------------------ New databases have been added to the file server recently: (a) Steven Henikoff's BLOCKS database Henikoff, S. and Henikoff, J. G. (1991) Automated assembly of protein blocks for database searching. Nucleic Acids Res. 19, 6565-6572. E-mail server: directory BLOCKS Anonymous ftp: /pub/databases/blocks (b) A database of CpG islands in the human genome (CPGISLE) Larsen, F., Gundersen, G., Lopez, L. and Prydz, H. (1992) CpG island as Gene Markers in the Human Genome. Genomics 13, 1095-1107. E-mail server: directory CPGISLE Anonymous ftp: /pub/databases/cpgisle (c) A database of protein kinase catalytic domains (PKCDD) provided by S.K. Hanks, A.M. Quinn and T. Hunter, Salk Institute. E-mail server: directory PKCDD Anonymous ftp: /pub/databases/pkcdd (d) Pre-release data from the Brookhaven Protein Data Bank (PDB) are now available in addition to the full releases. E-mail server: directory PROTEINDATA <6> Updates to Software Collection ------------------------------ Here is a list of new (N) molecular biological programs or updates (U): The full path specifications for these files on the EMBL ftp server are shown in square brackets. DOS: ---- AUTHORIN.UAA (N) Sequence data submission tool (Intelligenetics/DDBJ/EMBL/GenBank) [/pub/software/dos/authorin.uaa to authorin.uaf] CODONS.UUE (N) Codon usage analysis (A. Lloyd and P. Sharp) [/pub/software/dos/codons.uue] CREGEX.C (U) Conversion of PROSITE to Prosearch format v1.2 (J. Leunissen) [/pub/software/dos/cregex.c] DOTPLOT.UUE (N) Dot plot analysis (R> Nakisa) [/pub/software/dos/dotplot.uue] ESEE.UAA (U) Multiple sequence alignment editor v1.09e (E. Cabot) [/pub/software/dos/esee.uaa to esee.uac] FASTMAP.UAA (N) Approx. multipoint lod score calculation (D. Curtis) [/pub/software/dos/fastmap.uaa to fastmap.uac] GEPASI.UAA (N) Modelling of metabolic pathways (P. Mendes) [/pub/software/dos/gepasi.uaa to gepasi.uai] MACAW105.UAA (U) Multiple sequence editor v1.05 (G. Schuler) [/pub/software/dos/macaw105.uaa and macaw105.uab] PEDRAW14.UAA (U) Pedigree drawing program v1.4 (D. Curtis) [/pub/software/dos/pedraw14.uaa to pedraw14.uae] RAMHA.UAA (N) Monte Carlo simulation of random mutagenesis synthetic cDNA (D. Siderovski) [/pub/software/dos/ramha.uaa and ramha.uab] SAR2PCIT.UUE (N) Conversion of SeqAnalRef to ProCite format (E. Sonnhammer) [/pub/software/dos/sar2pcit.uue] SORFIND.UAA (N) Prediction of exons in vertebrate genomic DNA (G. Hutchinson) [/pub/software/dos/sorfind.uaa and sorfind.uab] TRBBS.UAA (N) File exchange program for automated fluorescent DNA sequencer data (I. Consani) [/pub/software/dos/trbbs.uaa and trbbs.uab] Mac: ---- AUTHORIN.HQX (N) Sequence data submission tool (Intelligenetics/DDBJ/EMBL/GenBank) [/pub/software/mac/authorin.hqx] DATAMINDER.HQX (N) Data management tools for molecular biologists (K. Usdin) From owner-software@net.bio.net Sun Apr 04 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!wupost!uunet!utcsri!utnut!torn!pulp.cs.laurentian.ca!abigail From: abigail@ramsey.cs.laurentian.ca (Shawn Abigail) Newsgroups: bionet.software Subject: Complete (small) genome wanted Summary: Complete (small) genome wanted Keywords: genome Message-ID: <1993Apr5.040245.25101@ramsey.cs.laurentian.ca> Date: 5 Apr 93 04:02:45 GMT Organization: Dept. of Computer Science, Laurentian University, Sudbury, ON Lines: 14 Work is proceeding on a small gene analysis program I am working on. With the package, I would like to include the entire sequenced genome of some organism (one that has a small genome). I was thinking that phage T4 might fit the bill. Anyway, does anybody know where I could ftp such a thing (perhaps in GenBank format). I do not have any other software running on our mainframe, and I do not have access to a cd-rom (i.e. I have no way of searching the entire GenBank library). If anyone knows where I could ftp some small but completely sequenced genome (and only that genome), please send me some email. Thanks. Shawn Abigail abigail@ramsey.cs.laurentian.ca From owner-software@net.bio.net Sun Apr 04 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: r.nakisa@ic.ac.uk ((Ramin Charles Nakisa) ramin) Newsgroups: bionet.software Subject: Re: Molbio Software Standard Message-ID: <1993Apr5.173120.6378@gserv1.dl.ac.uk> Date: 5 Apr 93 18:31:20 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 37 Original-To: bio-soft@uk.ac.daresbury X-Popmail-Charset: British Bradley K. Sherman writes > It is very common for a single successful run of a program > to be the last use of that program! It is often the case that > a simple graph or picture is the culmination of hundreds of hours > of moving data from one form to another, filtering out > noise, and applying a special purpose mathematical transform > -- often some arcane algorithm thought up by Gauss after one > too many Schnapps on a chilly night in 1843 and never before > implemented in any form more concrete than a doctoral dissertation. > > By the time the software is cast into a robust form, thoroughly > vetted and outfitted with its direct manipulation interface > for Curses, Windows , Windows NT, Mac, OS/2, OpenLook, NeXtStep > Motif, VMS, ... and then retested for window manager idiosyncrasies > the problem it solves may be of no interest. From my experience with molbio software, it is usually the same programs that are used repeatedly, such as translation, ORF detection, restriction analysis and so on. If there were a library of standard routines to carry out these manipulations with a simple, consistent interface it would be much easier to write and use multi-platform software. Of course there are always Sherman's gaussian outliers 8-), programs which are used only once, but even these would be easier to develop given a standard library. Having established a standard, it becomes easier to assemble several programs by different authors into a single package as Don Gilbert has done for the Mac. I think such a package would be worthwhile, and although it may not please all of the people all of the time, it would please most of the people some of the time. /--------------------------------------------------------------------------\ < 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 Apr 04 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!hsdndev!nmr-z!Frodo.MGH.Harvard.EDU!CHERRY From: cherry@Frodo.MGH.Harvard.EDU Newsgroups: bionet.software Subject: Re: ACEDB Workshop in Boston, July 28-31 Message-ID: <1993Apr5.171506.4296@nmr-z.mgh.harvard.edu> Date: 5 Apr 93 17:15:06 GMT References: <930405095700.20608caf@Frodo.MGH.Harvard.EDU> Sender: usenet@nmr-z.mgh.harvard.edu (User for USENET news postings) Reply-To: cherry@Frodo.MGH.Harvard.EDU Distribution: bionet Organization: Dept Molecular Biology, Massachusetts General Hospital Lines: 6 Nntp-Posting-Host: frodo.mgh.harvard.edu >> Otto Rieter, DKFZ, Heidelberg, Germany My apologies to Otto for mispelling his name. The correct spelling is Ritter. Mike From owner-software@net.bio.net Sun Apr 04 23:00:00 1993 Path: biosci!FRODO.MGH.HARVARD.EDU!CHERRY From: CHERRY@FRODO.MGH.HARVARD.EDU (Mike Cherry 726-5955) Newsgroups: bionet.software Subject: ACEDB Workshop in Boston, July 28-31 Message-ID: <930405095700.20608caf@Frodo.MGH.Harvard.EDU> Date: 5 Apr 93 13:57:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 85 A C E D B D E V E L O P E R ' S W O R K S H O P July 29-31, 1993 Massachusetts General Hospital Boston, Massachusetts A workshop for developers and curators of the ACEDB genome database software will be held at Massachusetts General Hospital in downtown Boston July 29-31, 1993. The goal of this meeting is to promote interaction between the many groups that are currently developing genome databases using the ACEDB software. ACEDB was developed by Richard Durbin and Jean Thierry-Mieg for use by the C. elegans genome effort. Currently many groups have found the ACEDB user interface and database to be very useful in providing a wide variety of genome related information. A very partial list of the current projects using the ACEDB software includes C. elegans, Arabidopsis, human, Drosophila, wheat and pine tree genome efforts. There is no registration fee for this workshop. However, space is limited to 60 people so please notify us of your interest. We will also notify you of the final details. A block of rooms has been reserved at a hotel across the street from the meeting site. The rate is $105 per night for either single or double occupancy. If you wish to reserve a room at this hotel and are in the US call Holiday Inn at 800-HOLIDAY and give the convention code MOL. If you are calling from outside the US you'll need to dial direct to +617-742-7630 and mention the Department of Molecular Biology meeting. Details for the meals have not been finalized but we anticipate breakfast, lunch and perhaps one dinner will be provided at no charge. A number of workstations will be available for live demonstrations during the formal sessions as well as during discussion periods. A tentative list of topics that will be included in the agenda are: ACEDB Database and Interface: o Data models and design o Query interface o Metadata o Data verification o Images o Physical and Genetic Map tools ACEDB Community: o Updates on how various groups are using ACEDB o Species specific enhancements o Novel Graphic Displays o Costumization o Discussion of future directions and needs Additional Topics: o data entry/editing o analysis tools New Developments: o new Client/Server for ACEDB o Otto Rieter's Relational/ACEDB link o Interactions of ACEDB with remote sequence databases o LBL Enhancements A partial list of speakers: Richard Durbin, MRC-LMB, Cambridge, UK Jean Thierry-Mieg, CNRS, Montpellier, France Susanne Lewis, LBL, Berkeley, California John McCarthy, LBL, Berkeley, California Otto Rieter, DKFZ, Heidelberg, Germany Sam Cartinhour, MGH, Boston, Massachusetts Mike Cherry, MGH, Boston, Massachusetts Please contact us with any questions and please let me know if you plan to attend. The meeting room can only hold a limited number of people and we are organizing a small network of workstations for demonstrations. Mike Cherry and Sam Cartinhour Department of Molecular Biology Massachusetts General Hospital Boston, MA 02114 FAX: +617-726-6893 Internet: curator@frodo.mgh.harvard.edu From owner-software@net.bio.net Sun Apr 04 23:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!noc.near.net!uunet!mcsun!dxcern!hprd26a!tonko From: tonko@hprd26a.cern.ch (Tonko Ljubicic) Newsgroups: bionet.software Subject: Re: Free EMBL-database query/search software ? Message-ID: Date: 5 Apr 93 15:25:01 GMT References: Sender: news@dxcern.cern.ch (USENET News System) Organization: CERN European Lab for Particle Physics Lines: 35 In tonko@hprd26a.cern.ch (Tonko Ljubicic) writes: >Does anybody know of a free (or cheap) EMBL database searching >software ? In the manner of CD-SEQ from the EMBL CD for instance. >Preferably for DOS (Windows?) and Unix (X11?). I'm new to this "bionet software" world so let me please rephrase my question since the responses I got were too general... The question is : Does somebody have any experience/opinions/recommendations about the freely available EMBL-database search/query tools ? ------ Is anybody out there using any of them ? Or everybody uses the mail-server ? Eh ? I _KNOW_ about the EMBL ftp server, but from the 1-liners in the help/doc files I can't find any package that would compile and run on a general Unix workstation with a general C compiler. Of course, I can try to hack some of these packages to make them run on my system(s) but is it worth the trouble ? Is there any generally accepted tool ? -- Tonko -- ljubicic@dxcern.cern.ch ljubicic@cernvm.bitnet tonko@hprd26a.cern.ch Ante Tonko Ljubicic Division PPE CERN (European Laboratory for Particle Physics) 1211 Geneve 23 Switzerland From owner-software@net.bio.net Sun Apr 04 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: s.fraser@ic.ac.uk Newsgroups: bionet.software Subject: Software for analysis of electrophoretic data Message-ID: <1993Apr5.083350.27298@gserv1.dl.ac.uk> Date: 5 Apr 93 09:33:57 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 22 Original-To: bio-soft@uk.ac.daresbury (bio-soft newsgroup) X-Mailer: ELM [version 2.3 PL3] I have already posed this question to the InfoMac digest, so apologies to those of you who have seen it already. However, I had little helpful response last time, so hope you people in this newsgroup can help me. I am looking for some software, preferably in the public domain or shareware, for the analysis of data from electro- phoresis, to run on a Macintosh computer. The package BioSys, which runs on DOS, VMS etc. does most of the required analyses (such as calculations of genetic distance and heterozygosity, and clustering), but is there a more friendly Macintosh alternative? Please respond directly to me, and I will summarize to the newsgroup. Simon Fraser Centre for Population Biology Imperial College at Silwood Park UK s.fraser@ic.ac.uk From owner-software@net.bio.net Sun Apr 04 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!zaphod.mps.ohio-state.edu!caen!uvaarpa!murdoch!darwin.clas.Virginia.EDU!rbm8p From: rbm8p@Virginia.EDU (Rick MacDonald) Newsgroups: bionet.software,bionet.xtallography Subject: SAXS software sought Message-ID: Date: 5 Apr 93 15:30:21 GMT Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia Lines: 15 Xref: biosci bionet.software:4721 bionet.xtallography:243 Originator: rbm8p@darwin.clas.Virginia.EDU I seek SAXS software. Would some kind soul who is familiar with current methods in small-angle x-ray scattering data analysis point me toward software that implements "Moore's method" or some other recipe for computing a radial distribution of distances from solution scattering data? What do SAXS spectroscopists use? In the absence of software, comments on the implementing the transform (Intensity ---> spherically averaged density) would be much appreciated. Rick From owner-software@net.bio.net Sun Apr 04 23:00:00 1993 Path: biosci!WITSVMA.WITS.AC.ZA!047NAIL From: 047NAIL@WITSVMA.WITS.AC.ZA (Paul Nailand) Newsgroups: bionet.software Subject: DOS molecular virology software Message-ID: <9304051213.AA20024@net.bio.net> Date: 5 Apr 93 12:13:16 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 21 I apologise for the second posting of this message but I am trying to help some university colleagues locate appropriate software and have had to ask them to refine their needs. They follow below, any suggestions etc etc etc will be most appreciated. ----- "We have about 40 computers, all 386 and beyond, connected in a Novell v3.11 network. Our molecular virology projects at the moment are mostly concerned with the molecular epidemilogy of Polio, Hepatitis B and HIV in South Africa. We have developed or are developing in house PCR tests for these as well as many other viruses including HCV. So we are interested in primer selection, comparison of local sequences with published data, dendrogram drawing and the like. Restriction enzyme sites within the PCR fragments we produce and analysis of several subtypes simultaneously is also of interest." -- Sheila Bouwer, National Institute of Virology ----- Thankyou Paul Nailand University of the Witwatersrand Email: 047nail@witsvma.wits.ac.za From owner-software@net.bio.net Mon Apr 05 23:00:00 1993 Path: biosci!daresbury!keele!uknet!pipex!uunet!utcsri!utnut!torn!pulp.cs.laurentian.ca!abigail From: abigail@ramsey.cs.laurentian.ca (Shawn Abigail) Newsgroups: bionet.software Subject: Genetic Codes Summary: Genetic Codes Keywords: genetic code Message-ID: <1993Apr6.151333.5307@ramsey.cs.laurentian.ca> Date: 6 Apr 93 15:13:33 GMT Organization: Dept. of Computer Science, Laurentian University, Sudbury, ON Lines: 13 I downloaded the list of genetic codes (SGC0, SGC1, etc), but I have one question. Do all of the codes listed recognize AUG as an initiation codon? Some of the codes do not list any initiation codons (does this mean AUG is accepted?), some list alternate initiation codons (does this mean that AUG is also acceptable?) and some list alternates and AUG (this really confuses me, because I would not expect to see AUG listed if it was implied). Thanks for any help you can provide, because there is nobody here at my university that can help me with this. Shawn Abigail abigail@ramsey.cs.laurentian.ca From owner-software@net.bio.net Mon Apr 05 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!haven.umd.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.software Subject: Re: Complete (small) genome wanted Keywords: genome Message-ID: <1993Apr5.143855.8829@welchgate.welch.jhu.edu> Date: 5 Apr 93 14:38:55 GMT References: <1993Apr5.040245.25101@ramsey.cs.laurentian.ca> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 40 In article <1993Apr5.040245.25101@ramsey.cs.laurentian.ca> abigail@ramsey.cs.laurentian.ca (Shawn Abigail) writes: > >Work is proceeding on a small gene analysis program I am working on. >With the package, I would like to include the entire sequenced genome >of some organism (one that has a small genome). I was thinking >that phage T4 might fit the bill. Anyway, does anybody know where >I could ftp such a thing (perhaps in GenBank format). I do not >have any other software running on our mainframe, and I do not have >access to a cd-rom (i.e. I have no way of searching the entire GenBank >library). If anyone knows where I could ftp some small but completely >sequenced genome (and only that genome), please send me some email. >Thanks. > A gopher search of genbank for: complete and genome yields *lots* of (too many) candidates for you. If you want a phage genome a search for: complete and genome and phage yields about 6 complete genomes for you, ranging in size from 3.5 kb (Bacteriophage MS2) to 46.6 kb (Bacteriophage lambda). A search for complete and genome and bacteriophage will yield a few more genomes in the same size range. If you don't know what gopher is don't worry it's free and on the net, write me a note if you need information on how to get started with gopher. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-software@net.bio.net Mon Apr 05 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.software Subject: Re: Free EMBL-database query/search software ? Message-ID: <1993Apr6.060708.4535@comp.bioz.unibas.ch> Date: 6 Apr 93 06:07:08 GMT References: Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 38 Nntp-Posting-Host: biox.embnet.unibas.ch In article , tonko@hprd26a.cern.ch (Tonko Ljubicic) writes: |> |> Does somebody have any experience/opinions/recommendations about |> the freely available EMBL-database search/query tools ? |> As I responded to you privately already, there is a lot of software out there which you can use. Amos Bairoch has assembled a very useful list of Molecular Biology Archives and Mailservers which is available on many FTP sites (at ours, it is in /info). With respect to query systems, the Sequence Retrieval Software (SRS), copyrighted by Thure Etzold, is just going into Beta testing. ATLAS from the PIR International as distributed on their CD should also run on UNIX. |> Is anybody out there using any of them ? Or everybody uses the |> mail-server ? Eh ? I already offered to you the services of the Swiss National EMBnet node. Nodes of the European Molecular Biology Network (EMBnet) are prepared to answer questions of this kind specifically and detailed. |> these packages to make them run on my system(s) but is it worth |> the trouble ? Maybe you enlighten the audience what your UNIX is like. Unfortunately, UNIX comes in so many flavours that you might fight very hard in hacking your code if you got a rare brand. -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- From owner-software@net.bio.net Mon Apr 05 23:00:00 1993 Path: biosci!news.miami.edu!usenet.ufl.edu!usenet.cis.ufl.edu!caen!zaphod.mps.ohio-state.edu!usc!usc!not-for-mail From: mhess@neuroblast.hsc.usc.edu (Mark A. Hess) Newsgroups: bionet.software Subject: Predicting RNA hairpins Summary: Finding single most stable RNA hairpin Keywords: RNA/secondary structure Message-ID: <1pqnskINN763@neuroblast.hsc.usc.edu> Date: 6 Apr 93 01:54:28 GMT Sender: nntp@neuroblast.hsc.usc.edu Organization: University of Southern California, Los Angeles, CA Lines: 9 NNTP-Posting-Host: neuroblast.hsc.usc.edu I'm looking for software that will find the single most stable stem-loop in an RNA sequence. I have tried the (M)FOLD programs of Dr. M. Zuker, but they don't really do this. The structures consist of many weak hairpins, the sum of which yields a modest negative free energy for my sequences. I've also tried a program called stem-loop and fed the individual hairpins to FOLD. This proved too time consuming (hundreds of stem-loops are found) and the structures are weak. I'd prefer to systematically search for all single hairpins in the range of say, -15 to -20 kcal/mol free energy-about 30% less stable than the aggregate structures. Thanks in advance for any help. Mark A. Hess mhess@hsc.usc.edu From owner-software@net.bio.net Mon Apr 05 23:00:00 1993 Path: biosci!TOURS.INRA.FR!jdacheux From: jdacheux@TOURS.INRA.FR (Jean-Louis.Dacheux) Newsgroups: bionet.software Subject: registration Message-ID: <9304061608.AA07199@tours.tours.inra.fr> Date: 6 Apr 93 16:08:54 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 7 I am interesting to receive regularly informations about the News Bio-soft. What is the procedure to follow to do that? Jean-Louis Dacheux. Lab Physiology of Reproduction INRA 37380 Monnaie France. Thanks you From owner-software@net.bio.net Tue Apr 06 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!haven.umd.edu!darwin.sura.net!paladin.american.edu!howland.reston.ans.net!zaphod.mps.ohio-state.edu!sdd.hp.com!decwrl!decwrl!csus.edu!news.ucdavis.edu!hamlet.ucdavis.edu!ez005587 From: ez005587@hamlet.ucdavis.edu (David J. Meyer) Newsgroups: bionet.software Subject: Data acquisition and analysis Message-ID: Date: 7 Apr 93 18:13:35 GMT Sender: usenet@ucdavis.edu Organization: University of California, Davis Lines: 18 X-Newsreader: Tin 1.1 PL3 Hello, netters! I am looking for some help with analysis of chromatographic profiles. 1) I have a number of chart recordings which I would like to import into some type of program which will allow me to integrate user-defined peaks. I am aware of some programs able to do this, but would like to hear from users about the capabilities of different packages. I would prefer packages for the Mac. 2) I would like to connect an old 286 to our FPLC to avoid such problems in the future. Some of the commercial packages designed *specifically* to do this seem a bit pricey. What's the best way to do this for less money? Thanks in advance! David J. Meyer djmeyer@ucdavis.edu From owner-software@net.bio.net Tue Apr 06 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!wupost!bcserv!eric From: eric@bcserv.wustl.edu (Hugo (Eric)) Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Bionet faq in Win3.1 help format, suggestions solicited Keywords: FAQ, helpfiles, hypertext Message-ID: Date: 7 Apr 93 13:20:57 GMT Organization: Washington University in Saint Louis, MO USA Lines: 13 Xref: biosci bionet.molbio.methds-reagnts:4992 bionet.software:4729 NNTP-Posting-Host: bcserv.wustl.edu Dear Bionetters, I am in the process of compiling various articles from USENET bionet newsgroups into a Windows 3.1 help file. Before I get too involved I'm soliciting opinions from the Net as to what would be most valuable to include. If you have any suggestions please email me. When I get a preliminary help file done I'll make it freely available to whoever would like it. Thanks for any feedback, Eric ;-) -- Eric R. Hugo, Postdoctoral Research Associate |eric@bcserv.wustl.edu Dept. of Biochemistry and Molecular Biophysics| Washington University School of Medicine | Box 8231, St. Louis, MO 63110_________________| (314) 362-3342 From owner-software@net.bio.net Tue Apr 06 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!zaphod.mps.ohio-state.edu!moe.ksu.ksu.edu!kuhub.cc.ukans.edu!husc-news.harvard.edu!husc.harvard.edu!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.software Subject: Re: Genetic Codes Keywords: genetic code Message-ID: Date: 7 Apr 93 12:57:25 GMT References: <1993Apr6.151333.5307@ramsey.cs.laurentian.ca> Lines: 42 Nntp-Posting-Host: husc10.harvard.edu abigail@ramsey.cs.laurentian.ca (Shawn Abigail) writes: >I downloaded the list of genetic codes (SGC0, SGC1, etc), but I have >one question. Do all of the codes listed recognize AUG as an >initiation codon? Some of the codes do not list any initiation >codons (does this mean AUG is accepted?), some list alternate >initiation codons (does this mean that AUG is also acceptable?) and >some list alternates and AUG (this really confuses me, because I >would not expect to see AUG listed if it was implied). Thanks for >any help you can provide, because there is nobody here at my university >that can help me with this. >Shawn Abigail >abigail@ramsey.cs.laurentian.ca I don't have a reference for this (and I need one too!) but the general rules are: 1) Eukaryote nuclei use only AUG, translated as Met. 2) Bacteria use AUG mostly, but GUG, CUG, and UUG sometimes. It is always translated to fMet. 3) Some mitochondria use a whole host of initiators, but still translate them to Met. 4) Chloroplast genes use AUG translated as Met, but in some cases the AUG is created through RNA editing. Any corrections/additions/expansions will be appreciated -- I'm doing this all from (error-prone) memory. It's sort of a wierd place to look, and they have some subtle errors, but one place that has these listed is the documentation for NCBI's ASN.1 Tool Library, available via FTP from ncbi.nlm.nih.gov. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@biosun.harvard.edu From owner-software@net.bio.net Tue Apr 06 23:00:00 1993 Path: biosci!ITSA.UCSF.EDU!jharper From: jharper@ITSA.UCSF.EDU (M. Jane Harper) Newsgroups: bionet.software Subject: statistics packages for Windows Message-ID: <9304070321.AA15646@itsa.ucsf.EDU> Date: 7 Apr 93 03:21:46 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 11 I'd be curious to see what the bioscientists on the Net have found useful in the way of statistics packages, especially those which run under Windows. Our campus statisticians are good at formulas but not really computer mavens, and make funny faces when I say "But I'm running Windows ..." :-) Any input would be valued. Jane Harper Doctoral Student, Neuroscience/Nursing University of California at San Francisco jharper@itsa.ucsf.edu From owner-software@net.bio.net Tue Apr 06 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!noc.near.net!howland.reston.ans.net!zaphod.mps.ohio-state.edu!saimiri.primate.wisc.edu!usenet.coe.montana.edu!news.u.washington.edu!news.u.washington.edu!news From: mparker@fred.fhcrc.org (Michael Parker) Newsgroups: bionet.software Subject: Searching protein database by size Message-ID: <1pv0umINNqn4@shelley.u.washington.edu> Date: 7 Apr 93 16:53:42 GMT Organization: FHCRC Lines: 3 NNTP-Posting-Host: 140.107.32.73 X-UserAgent: Nuntius v1.1.1d13 X-XXDate: Wed, 7 Apr 93 08:55:40 GMT I want to find all yeast sequences in the protein database and translated nucleic acid database over 150 Kd to 200Kd. Anyone know of a way to do this? From owner-software@net.bio.net Tue Apr 06 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: mbg@mrc-lmb.cam.ac.uk (Gerstein "M.") Newsgroups: bionet.software Subject: Does a Program for Characterizing Grooves on Protein Surfaces Exist? Message-ID: <1993Apr7.131920.5938@gserv1.dl.ac.uk> Date: 7 Apr 93 18:21:52 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 8 Original-To: bio-software@uk.ac.daresbury Does a program for characterizing grooves on protein surfaces exist? That is, does anyone know of program which takes a list of atomic coordinates and gives as output an indication of whether an atom exposed on the surface is deep in a groove or sticking out into solution? A simple surface area calculation (i.e. Lee & Richards) is not sufficient. mark gerstein (mbg@mrc-lmb.cam.ac.uk) From owner-software@net.bio.net Tue Apr 06 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!natinst.com!news.dell.com!swrinde!sdd.hp.com!zaphod.mps.ohio-state.edu!moe.ksu.ksu.edu!usenet-feed.umr.edu!cnews From: snayar@next3.cs.umr.edu (Sanjay Nayar) Newsgroups: bionet.software Subject: Paper by Kececioglu and Myers Keywords: fragmen assembly Message-ID: <1993Apr7.184738.29190@umr.edu> Date: 7 Apr 93 18:47:38 GMT Sender: cnews@umr.edu (UMR Usenet News Post) Reply-To: snayar@cs.umr.edu Organization: University of Missouri-Rolla, Missouri's Technological University Lines: 13 Nntp-Posting-Host: next9.cs.umr.edu I am looking for the follwing paper, or a complete reference to it. If someone could email me either, it would be appreciated very much. Kececioglu, J. and Myers E.W. (1989). "A robust and automatic fragment assembly system." Thanks in advance, -- Sanjay Nayar | As often as a study is cultivated by narrow University of Missouri-Rolla| minds, they will draw from it narrow snayar@cs.umr.edu | conclusions. From owner-software@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!TIFRVAX.BITNET!SMITRA From: SMITRA@TIFRVAX.BITNET Newsgroups: bionet.software Subject: SUB CANCELLATION Message-ID: <01GWS1KZIQCW0006TT@tifrvax.tifr.res.in> Date: 8 Apr 93 13:13:25 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 4 F7 ID LIKE MY SUBSCRIPTION TO THE BIOSOFT NEWSGROUP CANCELLED. THANKS, ROMIT From owner-software@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!ICGEB.TRIESTE.IT!pongor From: pongor@ICGEB.TRIESTE.IT (Sandor Pongor) Newsgroups: bionet.software Subject: ICGEB/EMBnet Course: Computers in Molecular Biology Message-ID: <9304081256.AA05187@icgeb.trieste.it> Date: 8 Apr 93 12:57:54 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 118 Practical Course "Computer Methods in Molecular Biology" International Centre for Genetic Engineering and Biotechnology 14-23 July 1993, Trieste-Italy Co-sponsored by ICGEB and EMBnet/BRIDGE Organizer: Sandor Pongor, ICGEB Trieste, Italy Faculty: Amos Bairoch, University of Geneva, Geneva, Switzerland Dennis Benson, NCBI-NIH, Bethesda, USA Martin Bishop, Medical Research Council, HGMP, Cambridge, UK Miklos Cserzo, Institute of Enzymology, Budapest, Hungary Reinhard Doelz, Biozentrum, Basel, Switzerland David Judge, University of Cambridge, Cambridge, UK Jack Leunissen, University of Nijmegen, The Netherlands Peter Rice, EMBL, Heidelberg, Germany Cecilia Saccone, University of Bari, Bari, Italy Gyorgy Simon, ICGEB Trieste, Italy Topics: Introduction to Computer Operating Systems Computer Communications, Networking, File Transfer, Electronic Mail, Bulletin Boards Molecular Biology Databases Sequence Homology Searches, Alignments Multiple Alignment, PCR Primer Design Sequence Patterns, Distant Protein Homologies Molecular Evolution: Quantitative and Qualitative Aspects Genome Projects Registration is limited to 30 participants. Prerequisites: Participants must have a basic knowledge of biochemistry and molecular biology, a basic familiarity with computer uses and a need for DNA or protein sequence analysis for their ongoing research. In order to apply, submit the below participation form via e-mail, FAX or normal mail to Ms. Diana Viti, ICGEB, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757333, Fax: +39-40-226555, Telex: 460396 ICGEBT I, Email: viti@icgeb.trieste.it Closing date for applications 31 May 1993. ICGEB will provide accommodation and local hospitality to participants from ICGEB Member Countries. Travel to and from Trieste will normally be borne by the participants. There is no registration fee. ICGEB MEMBER COUNTRIES: Afghanistan, Algeria, Argentina, Bhutan, Bolivia, Brazil, Bulgaria, Chile, China, Colombia, Congo, Costa Rica, Croatia, Cuba, Ecuador, Egypt, Greece, Hungary, India, Indonesia, Iran, Iraq, Italy, Kuwait, Mauritania, Mauritius, Mexico, Morocco, Nigeria, Pakistan, Panama, Peru, Poland, Russia, Senegal, Sri Lanka, Sudan, Syria, Thailand, Trinidad & Tobago, Tunisia, Turkey, Venezuela, Viet Nam, Yugoslavia, Zaire --- Cut here --- ___________________________________________________________________________ INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY MEETINGS * COURSES * WORKSHOPS PARTICIPATION FORM (viti@icgeb.trieste.it) ___________________________________________________________________________ MEETING/COURSE/WORKSHOP.TITLE COMPUTER METHODS IN MOLECULAR BIOLOGY, 14-23 JULY, 1993 ___________________________________________________________________________ DATES............| LOCATION.........| ___________________________________________________________________________ SURNAME..........| FIRSTNAME........| SEX..............| DATE.OF.BIRTH....| AGE..............| COUNTRY.OF.BIRTH.| NATIONALITY......| ___________________________________________________________________________ FULL.BUSINESS.ADDRESS ___________________________________________________________________________ TELEPHONE.NUMBER.| FAX.NUMBER.......| TELEX.NUMBER.....| E-MAIL.ADDRESS...| ___________________________________________________________________________ HOW.WILL.YOUR.RESEARCH.BENEFIT.BY.YOUR.PARTICIPATION.IN.THE.MEETING/COURSE/ WORKSHOP.(NO.MORE.THAN.5.LINES.OF.TEXT) ___________________________________________________________________________ RESEARCH.AREA.OF.INTEREST ___________________________________________________________________________ PRESENT.POSITION ___________________________________________________________________________ ACADEMIC.QUALIFICATIONS.(DEGREE/YEAR/INSTITUTE) ___________________________________________________________________________ INSTITUTES.OF.WORK.SINCE.FORMAL.EDUCATION ___________________________________________________________________________ FELLOWSHIPS.HELD ___________________________________________________________________________ PREVIOUSLY.ATTENDED.ICGEB.MEETINGS/COURSES/WORKSHOPS ___________________________________________________________________________ SHORT.LIST.OF.RELEVANT.PUBLICATIONS ___________________________________________________________________________ From owner-software@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!gatech!emory!emoryu1!emoryu1.cc.emory.edu From: bcresas@emoryu1.cc.emory.edu (Scott Sammons) Newsgroups: bionet.software,bit.listserv.info-gcg Subject: Looking for menu shells for UNIX GCG? Keywords: GCG Message-ID: <2586@emoryu1.cc.emory.edu> Date: 8 Apr 93 16:16:02 GMT Sender: news@emory.edu Reply-To: bcresas@emoryu1.cc.emory.edu Followup-To: bionet.software Organization: Emory University, Atlanta GA, Biomolecular Computing Resource Lines: 11 Xref: biosci bionet.software:4743 Nntp-Posting-Host: emoryu1.cc.emory.edu Has anyone written any menu shells for the GCG UNIX version? I know there are several for VMS, but I haven't found any for UNIX. Scott A. Sammons ============================================================================== | Scott A. Sammons (404) 727-2780 | | Emory University FAX: (404) 727-3659 | | Biomolecular Computing Resource | | 3025 Rollins Research Center | | Atlanta, GA 30322 Internet: bcresas@emoryu1.cc.emory.edu | ============================================================================== From owner-software@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!spool.mu.edu!agate!garnet.berkeley.edu!southbay From: southbay@garnet.berkeley.edu Newsgroups: bionet.software,biz.comp.software Subject: Short Courses on Software Testing & Metrics Message-ID: <1q1npk$i93@agate.berkeley.edu> Date: 8 Apr 93 17:35:48 GMT Organization: University of California, Berkeley Lines: 37 Xref: biosci bionet.software:4742 NNTP-Posting-Host: garnet.berkeley.edu U.C. Berkeley Continuing Education in Engineering Announces 2 Short Courses in Software Testing and Metrics Software Testing (April 19-21, 1993) This intensive three-day course covers both the current industrial practices and advanced technologies available to successfully implement and sustain an improved software testing program. The advanced software testing technologies discussed are intended to encourage the planning of future enhancements to software test programs. Lecturers: Warren Harrison, Ph.D., Paul W. Oman, Ph.D., Mark Wiley Software Metrics (April 22-23, 1993) Measurement is an essential part of improving the software development process. Measurement facilitates the objective characterization and baselining of an organizations current software assets, as well as providing a method to characterize its evolution and improvement. This course covers both the theoretical foundations of measurement and software metrics, as well as their application to improve and characterize the software development process. Lecturers: Gene Miluk, M.S., Warren Harrison, Ph.D. For more information (complete course descriptions, outlines, instructor bios, etc.) contact: Harvey Stern U.C. Berkeley Extension/Southbay 800 El Camino Real Ste. 150 Menlo Park, CA 94025 Tel: (415) 323-8141 Fax: (415) 323-1438 From owner-software@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!natinst.com!news.dell.com!swrinde!zaphod.mps.ohio-state.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.software Subject: Re: Looking for the program Gene Jockey. Thanks! Keywords: gene, jockey, mac Message-ID: <1993Apr8.171416.1032@welchgate.welch.jhu.edu> Date: 8 Apr 93 17:14:16 GMT References: <47549@sdcc12.ucsd.edu> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 107 In article <47549@sdcc12.ucsd.edu> ericg@jeeves.ucsd.edu (Eric Geerdes) writes: >Greetings from San Diego, > >We're trying to find info on the program Gene Jockey. > >Don't know if it is public domain or not--but we do know it's >for the Mac. > >Thanks for any help you might come up with. > >-Eric >UCSD Biology Computer Services >ericg@ucsd.edu > Gene Jockey is commercial - I'm including a little information below. You can find a demo version of this program by gopher or anonymous ftp from several sites - one of them being ftp.bio.indiana.edu in the molbio/mac directory. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu -------------------- GeneJockey A program for editing, manipulating and analysing nucleic acid and protein sequences DEMO VERSION. Please note that the demo version will not save or print sequences (it can, however print this 'Read Me' window). The global clipboard is disabled, so data cannot be transferred into or out of the program. The demo version can open only GeneJockey files and Genbank files (NOT text files, DNA inspector files or IBI Pustell files). The communications routines are also disabled. None of these restrictions apply to the full version. Introduction GeneJockey is a program for the Apple Macintosh which makes full use of the machine's WIMP interface. Nucleic acid and protein sequences can be entered from the keyboard or imported as files in other formats (Currently the program can read or write nucleic acid files in the format of Textco's DNA Inspector and IBI's Pustell programs. Text files corresponding to other formats can be read, and Genbank files in Macintosh format can be opened ). The program displays both sequence data and annotations in the same window, and permits multiple windows to be open (up to 30) so that sequences can be assembled from several sources by standard Macintosh editing techniques. Sequences entered by hand may be verified by re-typing or by having the machine read the sequence back, using sampled sounds rather than speech synthesis for clarity. Standard procedures for manipulating sequences are provided : both types of sequence may be reversed, and nucleic acid sequences may be complemented, inverted or translated to protein. In each case a new window is opened to contain the modified sequence, the original remaining unchanged. Basic database searching facilities are provided, and you may search your own GeneJockey files or Genbank files or both at once. You may search the comments section of the files with keywords entered at the keyboard, or search the sequence sections using the sequence currently displayed in the front window. In either case, the program makes a crude estimate of the time required to complete the search before starting. Standard search facilities are provided for searching a single sequence with a short sub-sequence, and the availability of wild card characters allows consensus sequences to be searched for. Sequence analysis commands include : Align:(Simple - display the sequences in the two top windows aligned so that the longest possible single match is obtained, or Exhaustive - stretch the sequences where necessary to display as much homology as possible between them). In either case the displayed sequences remain fully editable, enabling sequence fragments read from sequencing gels to be adjusted to obtain the best contig in the simplest possible manner. Matrix : Dot-plot matrix between two sequences. Reading Frames - Display all open reading frames longer than a threshold length, optionally starting only at a start codon and reading both strands of the nucleic acid. Selected areas of open reading frame can then be translated to protein. Hydropathicity Plot : The hydropathicity profile of protein sequences may be displayed using either Kyte and Doolittle or Hopp and Woods methods. Sequence Information : Displays base counts, molecular weights etc for both a selected section of sequence and for the entire sequence. Restriction Analysis : The program contains recognition sequences for about 400 restriction enzymes (You can change these and add more if necessary). DNA sequences may be analysed using a preselected list of restriction enzymes drawn from these, and the results displayed in text form either as individual digests, as a multiple digest, or as a graphic map. The program can automatically select those enzymes which can cut (or not cut) within a selected section of the sequence. Requirements The program requires a minimum of a Macintosh Plus. In order to make use of the Genbank sequence database a hard disk is required, and since this database currently occupies about 30 Mbyte a large disk is necessary if you want to have the whole of Genbank available. If the program is to be used for extensive database searching a faster machine is recommended to reduce waiting time. ------ From owner-software@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!wupost!howland.reston.ans.net!agate!dog.ee.lbl.gov!network.ucsd.edu!sdcc12!jeeves!ericg From: ericg@jeeves.ucsd.edu (Eric Geerdes) Newsgroups: bionet.software Subject: Looking for the program Gene Jockey. Thanks! Keywords: gene, jockey, mac Message-ID: <47549@sdcc12.ucsd.edu> Date: 8 Apr 93 16:12:00 GMT Sender: news@sdcc12.ucsd.edu Lines: 12 Nntp-Posting-Host: jeeves.ucsd.edu Greetings from San Diego, We're trying to find info on the program Gene Jockey. Don't know if it is public domain or not--but we do know it's for the Mac. Thanks for any help you might come up with. -Eric UCSD Biology Computer Services ericg@ucsd.edu From owner-software@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!wupost!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.software Subject: Re: Paper by Kececioglu and Myers Message-ID: <1993Apr8.150213.14816@welchgate.welch.jhu.edu> Date: 8 Apr 93 15:02:13 GMT References: <1993Apr7.184738.29190@umr.edu> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 69 In article ksuiter@acpub.duke.edu (Karl A. Suiter) writes: >In article <1993Apr7.184738.29190@umr.edu>, snayar@next3.cs.umr.edu (Sanjay >Nayar) wrote: >> >> >> I am looking for the follwing paper, or a complete reference to it. >> If someone could email me either, it would be appreciated very much. >> >> Kececioglu, J. and Myers E.W. (1989). "A robust and automatic >> fragment assembly system." >> >> Thanks in advance, > >Sanjay, > > I searched our library reference database here at Duke (it goes back to >1988) and it found no references for Kececioglu and Meyers together, >although there were a number of papers published by each author separately >on the subject of fragment alignment. > >You can track down these references in your library yourself instead of >relying on the net to do your work for you :-) My guess is that Sanjay tried and couldn't find it and *then* asked for help that was beyond his local resources. The request was quite specific - it wasn't one of those - "please send me all references on cancer" requests. I too have come to the conclusion that the paper doesn't exist as I couldn't find it in a host of bibliographic databases :-(. It may have been a poster at a meeting or some such item that might be mentioned or even referenced but not appear in the general literature - it's hard to tell without knowing more about where he found the partial citation. At any rate he can call Myers and ask him because a little gopher searching tells me: A clip from Myers Grant abstract: ----- -PROJECT NUMBER......5 R01 LM04960-05 PRINCIPAL INVESTIGATOR MYERS, EUGENE W JR UNIVERSITY OF ARIZONA GOULD-SIMPSON BLDG TUCSON, AZ 85721 PERFORMING ORGANIZATION: UNIVERSITY OF ARIZONA TITLE Efficient software for the analysis of biosequences ----- And his phone number PHONE: (602) 621-6612 And email: meyers@cs.arizona.edu or gene@cheltenham.cs.arizona.edu Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-software@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!zaphod.mps.ohio-state.edu!usc!elroy.jpl.nasa.gov!news.claremont.edu!cgsvax.claremont.edu!goldsmig From: goldsmig@cgsvax.claremont.edu Newsgroups: bionet.software Subject: Microscopy HW and SW Request Message-ID: <1993Apr8.072711.1@cgsvax.claremont.edu> Date: 8 Apr 93 15:27:11 GMT Sender: news@news.claremont.edu (The News System) Organization: The Claremont Graduate School Lines: 11 I am seeking information on sources of hardware and software required to capture images taken from microscope slides in any type of DOS compatible digital format. I would also appreciate sources of used microscopes (although I realize that this is probably not the best news group for such a posting). I need to keep the costs as low as possible because this is in support of a personal avocation (the study of local native flora and fauna) and because my resources are quite limited. Thank you in advance for any help you might provide. George Goldsmith From owner-software@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!wupost!howland.reston.ans.net!gatech!concert!duke!news.duke.edu!hurston.zoo.duke.edu!user From: ksuiter@acpub.duke.edu (Karl A. Suiter) Newsgroups: bionet.software Subject: Re: Paper by Kececioglu and Myers Message-ID: Date: 8 Apr 93 13:37:44 GMT References: <1993Apr7.184738.29190@umr.edu> Sender: news@news.duke.edu Followup-To: bionet.software Organization: Duke University Lines: 32 Nntp-Posting-Host: hurston.zoo.duke.edu In article <1993Apr7.184738.29190@umr.edu>, snayar@next3.cs.umr.edu (Sanjay Nayar) wrote: > > > I am looking for the follwing paper, or a complete reference to it. > If someone could email me either, it would be appreciated very much. > > Kececioglu, J. and Myers E.W. (1989). "A robust and automatic > fragment assembly system." > > Thanks in advance, Sanjay, I searched our library reference database here at Duke (it goes back to 1988) and it found no references for Kececioglu and Meyers together, although there were a number of papers published by each author separately on the subject of fragment alignment. You can track down these references in your library yourself instead of relying on the net to do your work for you :-) Karl --- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= | Karl A. Suiter, Duke University, Zoology Dept., Durham, NC 27706 | |=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=| | Voice: (919) 684-2251 | INTERNET: ksuiter@acpub.duke.edu | | FAX: (919) 684-6168 | COMPUSERV: 72701,3543@compserv.com | =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-software@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!usc!howland.reston.ans.net!newsserver.jvnc.net!yale.edu!news.yale.edu!YaleVM.YCC.Yale.Edu!MCKMICP From: MCKMICP@YaleVM.YCC.Yale.Edu (Michael McKenna) Newsgroups: bionet.software Subject: Superfamily Phylogenetics Message-ID: <16BA9133D2.MCKMICP@YaleVM.YCC.Yale.Edu> Date: 8 Apr 93 01:53:21 GMT Sender: news@news.yale.edu (USENET News System) Organization: Yale University Lines: 20 Nntp-Posting-Host: yalevm.ycc.yale.edu I would like to generate a phylogenetic tree of the lipocalin# superfamily. These sequences are very distantly related, if at# all, but share a number of common general characteristics, including# a signal peptide, several pairs of cysteine residues, and a # molecular weight between 15 and 20 kD. They also share a common # function; the transport and delivery of hydrophobic molecules# through an aqueous environment. Several of these molecules have # had their structures solved, and there is a compelling uniformity# to their structure, even though the identity is very low at the# primary level, often on the order of 20%.# # I have discovered a number of potential lipocalins in the antennae of# Drosophila melanogaster which belong to the family of odorant-binding# proteins. My question is- Is it possible to generate a phylogeny from# sequence data when only dubious connections can be made with various # allignment algorithms. Most of the programs I have seen can do a # resonable job with clearly related molecules. I suspect it can't# be done reasonably in this particular case. Any suggestions?# # Thanks, Mike McKenna MCKMICP@YALEVM.YCC.Yale.edu From owner-software@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!CSHL.ORG!peters From: peters@CSHL.ORG (Bobbie Peters - CSHL Computer Center) Newsgroups: bionet.software Subject: Auto ftp of databanks Message-ID: <9304082002.AA18810@phage.cshl.org> Date: 8 Apr 93 20:02:13 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 23 Hello, We are trying to set up a system to download the weekly/daily updates of the various databanks (GB, EMBL, PIR, SP) so we can translate them into IntelliGenetics on the SUN. IG's TOIGSF program shouldn't have any problem doing the translations, but getting the databanks is another thing. Does anyone have a UNIX program already written to go get the databanks at a specific time at night - maybe with something that will check to be sure it is the right update to the release I have loaded? I am sure I am not the only one to try to do this & I just don't want to reinvent the wheel. Thanks !! Bobbie Peters User Liaison v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v Cold Spring Harbor Laboratory Voice: (516) 367-8390 Box 100 Fax: (516) 367-9576 1 Bungtown Road Internet: Cold Spring Harbor, NY 11724-2213, USA (or theiss@...) ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ From owner-software@net.bio.net Wed Apr 07 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: GORTI@SBBIOVM.EARN (Guillermo Orti) Newsgroups: bionet.software Subject: subscribe Message-ID: <1993Apr8.185626.27979@gserv1.dl.ac.uk> Date: 8 Apr 93 18:43:34 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 1 Original-To: bio-software@UK.AC.DARESBURY please subscribe Guillermo Orti to the list (GORTI@SBBIOVM) From owner-software@net.bio.net Thu Apr 08 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!swrinde!zaphod.mps.ohio-state.edu!howland.reston.ans.net!agate!netsys!pagesat!news.cerf.net!network.ucsd.edu!sdcc12!jeeves!ericg From: ericg@jeeves.ucsd.edu (Eric Geerdes) Newsgroups: bionet.software Subject: Re: Looking for the program Gene Jockey. Thanks! Summary: Here's a sample of responses... Thanks again folks! Keywords: gene, jockey, mac Message-ID: <47604@sdcc12.ucsd.edu> Date: 9 Apr 93 15:55:44 GMT References: <47549@sdcc12.ucsd.edu> Sender: news@sdcc12.ucsd.edu Lines: 73 Nntp-Posting-Host: jeeves.ucsd.edu ******************************************************************* Here is a sample of the responses to my post. What a Group!... ******************************************************************* At 1:15 PM 4/8/93 -0400, Doug.Eernisse@um.cc.umich.edu wrote: >Eric, > It is commercial but I believe there is a partly functional >demo version around. Have you checked ftp.bio.indiana.edu in ^^^^^^^^^^^^^^^^^^^ >the /molbio/mac directory? It is fast and has some interesting >capabilities as I recollect. > >Doug Eernisse ********************************** THE DEMO IS THERE JUST AS HE SAID. ********************************** At 3:23 PM 4/9/93 +0200, Kirk Schnorr wrote: >I have used GeneJockey and have found it to be one of the best integrated >DNA analysis program I have worked with. It is available from an English >software firm called Biosoft, 22 Hills Road Cambridge, CB2 1JP >I am surprized no one has mentioned the package until now. One reason may >be that you have to pay for it. If I recall it is about 500 German marks. > They will send a demo version if asked. The demo version is the best way >to assess the program. > >Kirk SCHNORR >... At 10:17 AM 4/9/93 -0400, genecodes@aol.com wrote: >Hi Eric, >... >If you are looking for Mac software, you should take a look at Sequencher >from Gene Codes. I know there are some people at UCSD who are doing >a reasonable ammount of DNA sequencing. ... There was a short review of >Sequencher in the December issue of MacWorld (p. 274). > >Send me your surface mail address and I'll see that someone sends you a >demo kit. Sequencher is not as broad an application as Gene Jockey or >the GCG package on the Vax, but it covers sequencing technology in depth, >is extremely well designed and easy to use, and is technically way ahead >of the other commercial packages on the market. >... >Howard Cash [ contact genecodes@aol.com for more info ] At 1:31 PM 4/9/93 +0948, Rod Bonfiglioli wrote: > >... > the prograsm is mareketed by a firm in cambridge, UK. the firm will send you >a crippled demo that is absolutely useless and wont really show you anything the >program will do,. i got a copy of this crippled demo disk, and got very little >idea what the program would do, so i didnt bother buying it. best of luck >though. if no-one else on the net sends you the adress of the firm (i cant >think of it off the top top top of my head...) get back to me and i will find >the address for you. > >rod > >-- >Rod Bonfiglioli, Waite Agricultural Research Institute, >University of Adelaide, South Australia. >e-mail rbonfigl@waite.adelaide.edu.au Bye ---------------------------------------------------------------------------- Eric Geerdes x48927 /x48560 * To keep a snorer from snoring... Biology Computer Services/MILL * When snorer sleeps, put whipped cream UCSD * in their hand--then tickle their face. ---------------------------------------------------------------------------- From owner-software@net.bio.net Thu Apr 08 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!zaphod.mps.ohio-state.edu!pacific.mps.ohio-state.edu!ohstpy!miavx1!miamiu!fdong From: FDONG@MIAMIU.BITNET Newsgroups: bionet.software Subject: ARE THERE ANY METHODS TO DOWNLOAD A FILE FROM GCG? Message-ID: <93098.162556FDONG@MIAMIU.BITNET> Date: 8 Apr 93 20:25:56 GMT References: <2586@emoryu1.cc.emory.edu> Organization: Miami University - Miami Computing and Information Service Lines: 7 HELLO, NETTERS; CAN ANYONE TELL ME HOW TO DOWNLOAD A FILE FROM GCG OR FROM THIS SYSTEM? I TRY TO DOWNLOAD A FILE FROM GCG AND PRINT IT ON THE LP-PRINT , BOTH ARE NOT DONE. ANY INFORMATION IS HIGHLY APPRECIATED. FROM FDONG@MIAMIU.ACS.MUOHIO.EDU. From owner-software@net.bio.net Thu Apr 08 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!wupost!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: SEQApp Program Questions-Help Needed- Message-ID: Date: 9 Apr 93 12:08:32 GMT Sender: news@synapse.bms.com Followup-To: bionet.software Organization: Bristol-Myers-Squibb Research Lines: 17 I have just gotten a copy of SEQAPP and I am having trouble setting up the mail set up addresses. I guess in the Box labeled "Your Mail address' I would put In the Send Mail host box I would put and in the Post-Office user@Host I have no Idea what to put!!..And what is the postoffice pswd??? I asked our computer network guru and he didnt know either...Can anybody help me out???..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 Fri Apr 09 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!zaphod.mps.ohio-state.edu!uwm.edu!linac!att!princeton!tcp9kip37.princeton.edu!Gould From: Gould@pucc.princeton.edu (Grant Gould) Newsgroups: bionet.software Subject: BIOLAB BBS Message-ID: <1993Apr9.145051.1659@Princeton.EDU> Date: 9 Apr 93 14:50:51 GMT Sender: news@Princeton.EDU (USENET News System) Organization: none Lines: 5 X-Xxmessage-Id: Originator: news@nimaster X-Xxdate: Fri, 9 Apr 93 10:49:25 GMT Nntp-Posting-Host: tcp9kip37.princeton.edu X-Useragent: Nuntius v1.1.1d17 Hey, I've got a piece of literature here that claims there's a BIOLAB BBS at biolab.bio.ilstu.edu login as newuser. Yet NCSATelnet claims it doesn't exist. The sysop (sysop@biolab.bio.ilstu.edu) doesn't exist according to Pegasus. Can anyone give me a hint in this direction? Is Biolab bbs down for some reason? From owner-software@net.bio.net Fri Apr 09 23:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software Subject: Re: The Entrez CD-ROM and the Government Printing Office (US) Message-ID: Date: 10 Apr 93 04:25:27 GMT References: Organization: BIOSCI International Newsgroups for Biology Lines: 47 rhughes@ucsd.edu (Richard J. Hughes) writes: >Has anyone else been having trouble ordering the Entrez CD-ROM from the US >Government Printing Office? I have had plenty of difficulty. >I initially faxed an order, waited, received no response and faxed a >query. Still no reponse. Thanks to help from the Net, I managed to locate >their voice telephone number. I had in fact sent the faxes to the correct >telephone number but they had been ignored because they didn't include a >check (?...but that's what they said). I wonder why they even have a FAX >number. >When you call the Gov't Printing Office, you are put on hold for a long >time. When someone finally answers, the audio is so faint as to be almost >indiscernable (maybe 5 dB above background). I and one of our secretaries >have called them on four separate occasions and have made very little >headway. The audio always borders on the inaudible and whoever you speak to >passes the buck (and you) to someone else. You can just tell that they >aren't interested in selling you this CD-ROM. >Turns out that they won't send out the goods without prepayment. UCSD >P.O.'s aren't good enough. But UCSD can't generate a P.O. number without an >invoice. The Gov't printing office doesn't want to send invoices without >the goods. Catch 22. >**<>** >It ticks me off that I'm paying taxes to support these bozos in a job >that they don't give a damn about. >**<>** >Maybe the best thing to do is not to order from them. That way maybe the >Gov't won't be able to justify paying all those bozos to jerk us around. >Richard Tsk, tsk (silence). This is doubly sad because Yuki Abe who worked very hard in her former role handling GenBank orders at IG is now out looking for a job .... such are the ways of the world 8-(. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-software@net.bio.net Fri Apr 09 23:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software Subject: Re: The Entrez CD-ROM and the Government Printing Office (US) Message-ID: Date: 10 Apr 93 05:02:33 GMT References: Organization: BIOSCI International Newsgroups for Biology Lines: 51 rhughes@ucsd.edu (Richard J. Hughes) writes: >It turns out that the staff at NCBI are totally unlike those at the GPO. I >received an e-mail response to the above net message from Dennis at NCBI the >same day. Next morning, Rose Marie called and this morning I received a >Fed Ex package containing a copy of Entrez. Wow! Thanks guys. >The folks who work at NCBI are clearly a different breed than those who work >at GPO. I should have known that already, I guess. Greg Schuler >promptly sent me a copy of the manual for his fantastic MACAW program. All >I had to do was ask. >Richard J. Hughes I have the highest regards for Dennis Benson and others at NCBI. They have many talented people working there and Dennis has been a personal friend for over five years. I also want to point out one small fact in your statement above: > I received an e-mail response to the above net message *** While the GenBank contract was ebbing away, I stood up repeatedly at a number of GenBank advisor meetings and argued that all major government-sponsored projects should have an associated newsgroup to ensure that they remain responsive to the public. This advice did not always fall on sympathetic ears ....... You have just provided **yet another** example of why this remains true, and why the network has such an important role to play in biology. The next time that someone tries to tell you that the BIOSCI newsgroups are full of worthless garbage, please be sure to remind them of your experience. I think that we can put up with the occasional flame wars and sometimes bruised egos in exchange for the benefits like this. I survived five years of public potshots first as manager of the BIONET National Computer Resource for Molecular Biology and later as GenBank Manager, and I believe that others can too. Posters should be civil, of course, and I have always advocated contacting the private help addresses before going public, but the newsgroups can serve as a forum when other routes fail. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-software@net.bio.net Fri Apr 09 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!cs.utexas.edu!cactus.org!wixer!pagesat!news.cerf.net!network.ucsd.edu!sdcc12!jeeves!ericg From: ericg@jeeves.ucsd.edu (Eric Geerdes) Newsgroups: bionet.software Subject: Re: Looking for the program Gene Jockey. Thanks! Summary: Here's a sample of responses... Thanks again folks! Keywords: gene, jockey, mac Message-ID: <47604@sdcc16.Tcsd.edu> Date: 9 Apr 93 15:55:44 GMT References: <47549@sdcc12.ucsd.edu> Sender: news@sdcc12.ucsd.edu Lines: 73 Nntp-Posting-Host: jeeves.ucsd.edu ******************************************************************* Here is a sample of the responses to my post. What a Group!... ******************************************************************* At 1:15 PM 4/8/93 -0400, Doug.Eernisse@um.cc.umich.edu wrote: >Eric, > It is commercial but I believe there is a partly functional >demo version around. Have you checked ftp.bio.indiana.edu in ^^^^^^^^^^^^^^^^^^^ >the /molbio/mac directory? It is fast and has some interesting >capabilities as I recollect. > >Doug Eernisse ********************************** THE DEMO IS THERE JUST AS HE SAID. ********************************** At 3:23 PM 4/9/93 +0200, Kirk Schnorr wrote: >I have used GeneJockey and have found it to be one of the best integrated >DNA analysis program I have worked with. It is available from an English >software firm called Biosoft, 22 Hills Road Cambridge, CB2 1JP >I am surprized no one has mentioned the package until now. One reason may >be that you have to pay for it. If I recall it is about 500 German marks. > They will send a demo version if asked. The demo version is the best way >to assess the program. > >Kirk SCHNORR >... At 10:17 AM 4/9/93 -0400, genecodes@aol.com wrote: >Hi Eric, >... >If you are looking for Mac software, you should take a look at Sequencher >from Gene Codes. I know there are some people at UCSD who are doing >a reasonable ammount of DNA sequencing. ... There was a short review of >Sequencher in the December issue of MacWorld (p. 274). > >Send me your surface mail address and I'll see that someone sends you a >demo kit. Sequencher is not as broad an application as Gene Jockey or >the GCG package on the Vax, but it covers sequencing technology in depth, >is extremely well designed and easy to use, and is technically way ahead >of the other commercial packages on the market. >... >Howard Cash [ contact genecodes@aol.com for more info ] At 1:31 PM 4/9/93 +0948, Rod Bonfiglioli wrote: > >... > the prograsm is mareketed by a firm in cambridge, UK. the firm will send you >a crippled demo that is absolutely useless and wont really show you anything the >program will do,. i got a copy of this crippled demo disk, and got very little >idea what the program would do, so i didnt bother buying it. best of luck >though. if no-one else on the net sends you the adress of the firm (i cant >think of it off the top top top of my head...) get back to me and i will find >the address for you. > >rod > >-- >Rod Bonfiglioli, Waite Agricultural Research Institute, >University of Adelaide, South Australia. >e-mail rbonfigl@waite.adelaide.edu.au Bye ---------------------------------------------------------------------------- Eric Geerdes x48927 /x48560 * To keep a snorer from snoring... Biology Computer Services/MILL * When snorer sleeps, put whipped cream UCSD * in their hand--then tickle their face. ---------------------------------------------------------------------------- From owner-software@net.bio.net Fri Apr 09 23:00:00 1993 Path: biosci!NET.BIO.NET!web!ingen.cu!scorpio.cu!carmas From: web!ingen.cu!scorpio.cu!carmas@NET.BIO.NET (Carlos I. Armas) Newsgroups: bionet.software Subject: ftruncate() function? Message-ID: <9304090203.AA06071@scorpio.cu> Date: 9 Apr 93 02:03:58 GMT Sender: daemon@net.bio.net Reply-To: carmas%ingen@web.apc.org Distribution: bionet Organization: Center of Genetic Engineering & Biotechnology Lines: 12 hi all! I would appreciate if somebody tell me which function performs in UNIX ISC 3.0 ( C language) the same task than ftruncate() on UNIX BSD. any suggestion or advise will be welcome. thanks in advance! carlos -- carlos armas email: carmas%ingen@web.apc.org network manager automation division center of genetic engineering & biotechnology p.o.box 6162 havana, cuba From owner-software@net.bio.net Fri Apr 09 23:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software Subject: Re: bionet.miscellaneous Keywords: progress, productive, elegant Message-ID: Date: 10 Apr 93 04:04:38 GMT References: <1993Mar29.085959.18390@comp.bioz.unibas.ch> Organization: BIOSCI International Newsgroups for Biology Lines: 35 doelz@comp.bioz.unibas.ch (Reinhard Doelz) writes: >In article , darrenp@dibbler.cs.monash.edu.au (Daz) writes: >|> I propose we rename this newsgroup to somehting like bionet.misc or >|> bionet.irrelevant. >|> >I agree that it would be good to have a better 'sorted' environment. >In particular, the following interest groups could be valuable if >we can only afford running them : >bionet.software.avail - those for asking for and discussing > availability, > as well as announcing software > * MODERATED * >bionet.software.system - general inquiries how to manage > biocomputing sw >bionet.software.misc - all other stuff not fitting to the > other bionet.software newsgroups. >In particular, a group which discusses availability issues is most >needed in my view, and should be moderated. If this thread gets enough >discussion we could dare to raise a call for discussion on it. Seems like this thread died out after a few messages. If someone wants to put together a formal proposal, I'll be waiting. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-software@net.bio.net Fri Apr 09 23:00:00 1993 Path: biosci!uwm.edu!wupost!emory!sol.ctr.columbia.edu!ira.uka.de!news.belwue.de!softserv.zdv.uni-tuebingen.de!studserv!zxmkr08 From: zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: BIOLAB BBS Message-ID: Date: 10 Apr 93 18:47:38 GMT References: <1993Apr9.145051.1659@Princeton.EDU> Organization: InterNetNews at ZDV Uni-Tuebingen Lines: 100 NNTP-Posting-Host: studserv.zdv.uni-tuebingen.de In <1993Apr9.145051.1659@Princeton.EDU> Grant Gould writes: >Hey, I've got a piece of literature here that claims there's a BIOLAB BBS >at biolab.bio.ilstu.edu login as newuser. Yet NCSATelnet claims it >doesn't exist. NCSA Telnet is right :-) With a little help of nslookup, I found that there is a domain ilstu.edu. It contains the following subdomains: > ls ilstu.edu [rs6000.cmp.ilstu.edu] Host or domain name Internet address ilstu server = rs6000.cmp.ilstu.edu rs6000 138.87.1.2 ilstu server = uxc.cso.uiuc.edu uxc 128.174.5.50 ilstu server = iugate.ucs.indiana.edu iugate 129.79.1.9 ilstu 138.87.1.2 uh server = rs6000.cmp.ilstu.edu rs6000 138.87.1.2 uh server = uxc.cso.uiuc.edu uxc 128.174.5.50 uh server = iugate.ucs.indiana.edu iugate 129.79.1.9 smtplink 138.87.1.111 aca server = rs6000.cmp.ilstu.edu rs6000 138.87.1.2 aca server = uxc.cso.uiuc.edu uxc 128.174.5.50 aca server = iugate.ucs.indiana.edu iugate 129.79.1.9 phy server = protein.phy.ilstu.edu protein 138.87.129.3 phy server = rs6000.cmp.ilstu.edu rs6000 138.87.1.2 phy server = uxc.cso.uiuc.edu uxc 128.174.5.50 phy server = iugate.ucs.indiana.edu iugate 129.79.1.9 phy 138.87.129.4 math server = spider.math.ilstu.edu spider 138.87.132.21 math server = rs6000.cmp.ilstu.edu rs6000 138.87.1.2 math server = uxc.cso.uiuc.edu uxc 128.174.5.50 math server = iugate.ucs.indiana.edu iugate 129.79.1.9 ir server = rs6000.cmp.ilstu.edu rs6000 138.87.1.2 ir server = uxc.cso.uiuc.edu uxc 128.174.5.50 ir server = iugate.ucs.indiana.edu iugate 129.79.1.9 it server = rs6000.cmp.ilstu.edu rs6000