From owner-software@net.bio.net Sun Oct 01 23:00:00 1995 Path: biosci!PWINET.UPJ.COM!RVDESHP0 From: RVDESHP0@PWINET.UPJ.COM Newsgroups: bionet.software Subject: Re: [Q]-EXCELL-how to... Date: 2 Oct 1995 12:15:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: <06fed120@pwinet.upj.com> NNTP-Posting-Host: net.bio.net Let's say you have 50 numeric values in column A starting from row 1 and ending in row 50 (A1 to A50) of an Excel spreadsheet, and you want to multiply all with a constant factor (say 100). Go to a new column (let's say column B), and in row B1, type the following : =A1*76 It is very important that you start with an "=" sign. Hit the "return" key once. Then, go back and click into cell B1, keep the "shift" key pressed, and click into the cell - B50. This should select all the cells from B1 to B50. Go to the "Edit" menu, and select "fill down" (on a Mac, you can do this by pressing "command D". AND THERE YOU GO ! All the values in cells A1 to A50 will be multiplied by 100, and the results will be entered into cells B1 to B50. I hope, this helps. Let me know if you need any more help. Good luck. Rajendra V. Deshpande, Ph.D. Molecular Biology Research The Upjohn Company Kalamazoo, MI 49007 e-mail : RVDESHP0@pwinet.upj.com ______________________________ Reply Separator _________________________________ Subject: [Q]-EXCELL-how to... Author: Ivo Wiesner at INTERNET Date: 9/29/95 7:11 PM Hello Netters out there! need your kind help in: how to multiply all figures at once by a factor (let say *100) within a spreadsheet in Excell ver.4.0??? I have already no idea how to get it work.... ThanX much in adv. for reply. Ivo Wiesner ************* *IVO WIESNER* ************************************************************** *SURFACE MAIL: | E-MAIL: * *Institute of Plant | nfix@bf.jcu.cz * *Molecular Biology | (full time Unix system server) * *Czech Academy of Sciences | ivow@gen.umbr.cas cz * *Branisovska 31 | (home-table Linux @ DOS systems)* *Ceske Budejovice *********************************** *CZ 370 05 |PHONE: | * *Czech Republic |+42-38-47755| * ********************************|FAX: | * *the only way for this Universe |+42-38-41475| * * is love ! | | * ************************************************************** From owner-software@net.bio.net Sun Oct 01 23:00:00 1995 Path: biosci!ihnp4.ucsd.edu!agate!newsxfer.itd.umich.edu!tank.news.pipex.net!pipex!uknet!bhamcs!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.software Subject: NAOMI Version 2.2 Date: 2 Oct 1995 13:55:27 GMT Organization: University of Oxford Lines: 68 Message-ID: <44or0f$ju5@news.ox.ac.uk> NNTP-Posting-Host: nmrz.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.software NAOMI - Version Upgrade Announcement (Please note, NAOMI is provided at zero charge for academic use) (e-mail contact smb@bioch.ox.ac.uk) _____________________________________________________________________________ The computer program NAOMI Version 2.2 is available _now_ from the NAOMI Web site at: http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html or via anonymous ftp from: nmrz.ocms.ox.ac.uk in directory pub/smb/naomi/ Users of versions older than 2.10 will need new license keys to allow the upgrade to work (please contact the author in this case). _____________________________________________________________________________ Upgrade features : solvent accessibility, symmetry operations, disulphide bonds, new side-chain modelling commands, new molscript output options e.g. see the illustrations on the Cytokines Web: http://www.ocms.ox.ac.uk/~smb/cyt_web/ Fixes of minor bugs in key residues and molscript output commands. _____________________________________________________________________________ What is NAOMI? NAOMI is an easy-to-use, state-of-the-art computer program which is aimed at both specialist and non-specialist researchers who make use of three-dimensional structures of proteins in their work. It has hundreds of users Worldwide. Some facilities offered by the program for working with structure include: automatic 'key' residue identification automatic hydrophobic core/packing analysis automatic hydrogen bonds main-chain and side-chain identification (including high quality energy calculations) automatic secondary structure (helix, strand and turn) classification using fuzzy logic automatic supersecondary structure classification (beta-hairpin loops) conformational parameters: phi,psi,chi1,chi2,chi3,chi4,chi5 etc solvent accessibility (both absolute and percentage) calculations automatic identification of disulphide bonds, salt bridges, chain-breaks side-chain modelling and manipulation applying symmetry operators automatic structure repair (building in missing atoms) NMR structure refinement module interfaces to graphics programs (MOLSCRIPT (and thus Raster3D), INSIGHT, QUANTA to allow automatic preparation of figures More details are available on the Web site. NB NAOMI currently works only on Silicon Graphics workstations running IRIX 5.* _____________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry, | \>> | University of Oxford, Oxford, UK. | \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ |____________________________________________________________________________ From owner-software@net.bio.net Sun Oct 01 23:00:00 1995 Path: biosci!agate!msunews!harbinger.cc.monash.edu.au!bunyip.cc.uq.oz.au!news.qut.edu.au!SCI_LIF_PGS_PRG From: a.liedloff@qut.edu.au (Adam Liedloff) Newsgroups: bionet.software Subject: Sequence Editors and genetic Distance Calculators Date: 2 Oct 1995 02:36:41 GMT Organization: Queensland University of Technology, Australia Lines: 24 Distribution: world Message-ID: <44nj7p$pa9@stork.qut.edu.au> NNTP-Posting-Host: 131.181.38.88 Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: News Xpress Version 1.0 Beta #3 Hi all, Recently we were asked to develop a user friendly (Windows based) program to manipulate nucleotide sequences and calculate genetic distance measures, such as Nst and Gst. Our project has grown and we are now looking at developing the program further. We are going to include Fst and Nei's genetic distance as well as base frequencies, transition/transversion ratios, amino acid sequence and longest repeated sub-sequence analysis. My question is therefore does anyone have any suggestions for other procedures which would be useful in such a program. We are especially interseted in graphical data display and the methods most commonly used. Any input would be appreciated, please email p.mayes@qut.edu.au Thanks. From owner-software@net.bio.net Sun Oct 01 23:00:00 1995 Path: biosci!daresbury!hgmp.mrc.ac.uk!news From: Christopher Spry Newsgroups: bionet.software Subject: Re: WebCutter now in Sweden Date: 2 Oct 1995 12:07:29 GMT Organization: St. George's Hospital Medical School Lines: 28 Message-ID: <44okm1$5ae@mercury.hgmp.mrc.ac.uk> References: NNTP-Posting-Host: sprysgi.sghms.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX 5.3 IP22) X-URL: news:maxwell-0210950027430001@branford-college-node.net.yale.edu Internet access to many hosts is often very poor. For example this host was unusable from here on Mon Oct 2 at 13:04:26 BST 1995. %traceroute www.medkem.gu.se traceroute to rna.medkem.gu.se (130.241.76.38), 30 hops max, 40 byte packets 1 route1.sghms.ac.uk (192.153.12.2) 4 ms 2 ms 2 ms 2 193.61.71.65 (193.61.71.65) 4 ms 3 ms 4 ms 3 eu-gw.ja.net (193.63.94.2) 4 ms 103 ms 112 ms 4 gw.linx.ja.net (193.62.157.14) 4 ms 7 ms 6 ms 5 UK-s0.dante.bt.net (194.72.26.197) 55 ms * 72 ms 6 * 194.72.7.4 (194.72.7.4) 58 ms * 7 NL-s1-0.eurocore.bt.net (194.72.24.134) 156 ms * * 8 SE-s0.dante.bt.net (194.72.24.10) 253 ms 249 ms * 9 NORDUnet-s0.dante.bt.net (194.72.26.50) 264 ms 291 ms 258 ms 10 * * lower-gw.sunet.se (192.36.148.197) 285 ms 11 * * gbg34-gw.sunet.se (193.10.85.18) 257 ms 12 * * * 13 med-bmb-gw.gu.se (130.241.80.2) 235 ms 265 ms 252 ms 14 rna.medkem.gu.se (130.241.76.38) 266 ms * * Does anyone know who I should contact about this poor service? -- Christopher Spry. cspry@sghms.ac.uk St. George's Hospital Medical School London SW17 0RE, U.K. Phone +44 181-725 2990; Fax +44 181-725 5821 HREF=http://sprysgi.sghms.ac.uk/~cspry/cspry.htmls From owner-software@net.bio.net Sun Oct 01 23:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!oleane!tank.news.pipex.net!pipex!news.sprintlink.net!in1.uu.net!noc.near.net!usenet.uchc.edu!usenet From: Les Loew Newsgroups: bionet.software Subject: CBIT Software Date: 2 Oct 1995 13:13:24 GMT Organization: Univ of CT Health Center Lines: 35 Message-ID: <44oohk$m2n@threed.uchc.edu> NNTP-Posting-Host: volt.uchc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.software The Center for Biomedical Imaging Technology has available a number of SGI software applications that have been developed for use with our Zeiss and Biorad confocal microscopes as well as a number of digtal imaging widefield systems. We felt that these may be of use to others and are now making them available via anonymous ftp. They include: RatioView: a simple image analysis package that is especially convenient for calcium, pH, or membrane potential distribution in single cells by dual wavelength ratio imaging. A tutorial is included in our web site. CBITRender: a 3D visualization environment including a raytracer. Both single processor and distributed multiprocessor (running under LINDA) versions are available. Imgview3D: utilities for creating and visualizing 3D datasets with the SGI Imagevision library. BioRad Library: an extension to the ImageVision Library permitting it to automatically read the BioRad .pic fileformat. The software can all be found on the web at http://panda.uchc.edu/htbit/ and following the thread under "Imaging Research and Development". While you are there, please learn about the other activities at CBIT. -- Les Loew Professor of Physiology Director, Center for Biomedical Imaging Technology University of Connecticut Health Center Farmington, CT 06030-1507 Tel. 203-679-3568 FAX 203-679-1269 Best E-mail les@volt.uchc.edu CBIT URL http://panda.uchc.edu/htbit/ From owner-software@net.bio.net Sun Oct 01 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!in1.uu.net!satisfied.apocalypse.org!news2.near.net!news3.near.net!sol.caps.maine.edu!dartvax.dartmouth.edu!usenet From: bob.gross@dartmouth.edu (Bob Gross) Newsgroups: bionet.software Subject: Re: Ram doubler software needed! Date: 2 Oct 1995 21:41:27 GMT Organization: Dartmouth College Lines: 8 Sender: Robert.H.Gross@dartmouth.edu Message-ID: <44pma7$qiu@dartvax.dartmouth.edu> References: <442m3j$nh0@ixnews3.ix.netcom.com> <44hjgq$1108@news.cuny.edu> NNTP-Posting-Host: at-1-sn-41.dartmouth.edu X-Newsreader: InterNews 1.2d5@dartmouth.edu RAM Doubler software is commercially available from Connectix Corp. It is illegal to give it away. Bob Gross email: bob.gross@dartmouth.edu Director, Computational Biology Center phone: 603-646-2059 Dept. Biological Sciences FAX: 603-646-1347 Dartmouth College, 6044 Gilman Hanover, New Hampshire 03755 USA From owner-software@net.bio.net Sun Oct 01 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!swrinde!cs.utexas.edu!news.sprintlink.net!simtel!zombie.ncsc.mil!cs.umd.edu!haven.umd.edu!purdue!oitnews.harvard.edu!yale!yale!news.ycc.yale.edu!branford-college-node.net.yale.edu!user From: maxwell@minerva.cis.yale.edu (Max Heiman) Newsgroups: bionet.software Subject: WebCutter now in Sweden Date: Mon, 02 Oct 1995 00:27:43 -0700 Organization: Yale University Lines: 27 Message-ID: NNTP-Posting-Host: 130.132.110.159 Webcutter, a free on-line utility to restriction map DNA sequences, has just been mirrored in Sweden thanks to the generosity of Dr. Tore Samuelsson of the University of Goteburg. Webcutter is available now for free and public use at http://firstmarket.com/firstmarket/cutter and http://www.medkem.gu.se/cutter For those of you unfamiliar with the program, Webcutter is software you run through your favorite WWW browser. It differs from other restriction mapping programs primarily in its use of existing internet resources. For example, it features: * Automatic sequence search-and-input from NCBI's GenBank * Monthly enzyme database updates from New England Bio Labs' REBASE * Easy-to-use, customizable digests * World-wide accessibility via internet Webcutter eliminates the need to copy-and-paste your sequence from the GenBank, and hassle of your software's enzyme database becoming outdated. If you have any questions about or difficulties with Webcutter, please contact me at maxwell@minerva.cis.yale.edu Enjoy!, MH From owner-software@net.bio.net Sun Oct 01 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!news.sprintlink.net!howland.reston.ans.net!newsserver.jvnc.net!synapse.bms.com!NewsWatcher!user From: watson_j@bms.com (A. John Watson) Newsgroups: bionet.software Subject: Re: OLIGO, Is there any new version? Date: Mon, 02 Oct 1995 14:37:39 -0300 Organization: Bristol-Myers Squibb Lines: 27 Message-ID: References: <446d69$eod@gate.sinica.edu.tw> NNTP-Posting-Host: 140.176.107.223 In article <446d69$eod@gate.sinica.edu.tw>, Hsien-wei Peng wrote: > Is there any NEW version of the OLIGO primer designing software? > > Where can I download it or buy one? > > Thank for your answering!! There is a version 5.0 for Windows (I just got a demo disk), and, as I understand it, a new Macintosh version (6.0), which I believe will be released either late this year or early next year. The new Mac version is supposed to be similar to Windows ver. 5.0. Oligo is available from National Biosciences Inc. (800) 747-4362. I am not affiliated, etc, etc. John ---------------- John Watson watson_j@bms.com --------------------------------------------------------------------- "If you're not part of the solution, you're part of the precipitate." --------------------------------------------------------------------- From owner-software@net.bio.net Sun Oct 01 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!wizard.pn.com!Germany.EU.net!EU.net!uunet!in2.uu.net!news.texoma.com!usenet From: Kenneth Ramsey Newsgroups: bionet.software Subject: Re: probe/primer design software Date: 2 Oct 1995 22:22:53 GMT Organization: Texoma Pathology Associates/Micro Gene Lines: 8 Message-ID: <44pont$pqq@mercury.texoma.com> References: NNTP-Posting-Host: ppp41.texoma.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) To: bz1t-isgr@asahi-net.or.jp Have you tried a program called BLAST? The government branch that maintains Entrave and Gen Bank recommends it. I, myself, use Mac Vector for that type of work, but it is for the Mac. I don't know if Kodak has a Windows version or not. Their phone number (voice) is 1-800-225-5352, (fax) 1-800-879-4979. Ken Ramsey From owner-software@net.bio.net Mon Oct 02 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!gatech!concert!ecsgate!newton.uncg.edu!hamlet!b_lee2 From: "Bin . Lee" Newsgroups: bionet.software,bionet.software.source Subject: Disassembly program for PC Date: Mon, 2 Oct 1995 20:37:58 -0400 Organization: The University of North Carolina at Greensboro Lines: 17 Message-ID: NNTP-Posting-Host: hamlet.uncg.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: b_lee2@hamlet Hi, guys: Any one know any good disassembly program for PC, if I can get any shareware from the Net, that will be super, otherwise, please tell me where I can get some commericial products. Please also tell me any good hex edit. Please send email. Thanx in advance. Cheers From owner-software@net.bio.net Mon Oct 02 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!swrinde!gatech!news.sprintlink.net!moonbeam.aecom.yu.edu!usenet From: Sergey Levin Newsgroups: bionet.software Subject: PI prediction program Date: 3 Oct 1995 02:56:24 GMT Organization: Albert Einstein College of Medicine Lines: 282 Message-ID: <44q8oo$ptt@moonbeam.aecom.yu.edu> NNTP-Posting-Host: zonker.bioc.aecom.yu.edu Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="-------------------------------23861016217768" X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP17) X-URL: file:/dtelico/people/slevin/POLINA/predict_pi/predict_pi.post This is a multi-part message in MIME format. ---------------------------------23861016217768 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Some time ago I saw a person asking for a program to predict PI of a peptide. Here is some code which does that. -- & !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!S!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!S!!!!!!!S!!!!!!!!!!! | [Ca++] | [##|##] <-| Sergey "The Shmul" Levin | |_ _ V _ | Albert Einstein College Of Medicine | PFUS->###s_/m\_P_/m\ | Department of Anatomy and Structural Biology | ###< \_/ \_/ | 1300 Morris Park Avenue, Bronx, New York 10461| #### | Ulmann building 905 | phosphodiesterase phone (718) 430 4064 | Parafusin - a member of PGM e-mail slevin@telico.bioc.aecom.yu.edu | superfamily ============================================================================= ---------------------------------23861016217768 Content-Transfer-Encoding: 7bit Content-Type: text/plain /***********************************************************************/ /* I just thought that there might be a use for something like this */ /* among protein people. I presonally used it to analyze transmembrane */ /* protein sequences. Programm contents and use is described below */ /* */ /* PROGRAMM: predict_pi */ /* */ /* FILE format: 1 letter amino acid code, all in 1 line */ /* */ /* FUNCTION: predicts overall theoretical pI of a protein sequence */ /* using a really dumb algorythm described below. Also, using this */ /* algorythm, it produces a file with a graph of floating frame of */ /* 10 AA pI values ( pI of AAi to AAi+10), which will be used for */ /* allocation of imporatnt streches in the protein. */ /* */ /* ALGORYTHM: we calculate the summary charge of the peptide by adding */ /* a fractional charge for each AA and recieve a "theoretical */ /* titration curve. Afterwords we solve the root of the function by */ /* bisection. If you can figure out a better way to solve this */ /* function, do not hesitate to chage it. */ /* */ /* COMMENTS: This might also be usefull for aligning distantly-related */ /* protein sequences and possibly, fishing out folds from the PDB. */ /* I will check on that further on. Also, sometimes it is nice to know */ /* the overall theoretical PI of the protein. I have used it to find */ /* stabilizing "post"-membrane loops in a Ca++ chanell sequence. */ /* */ /* USE: Compile (on anything you want: ANSI C). Give name of sequence */ /* file at the command line. */ /* */ /* AUTHORS AND RIGHTS: This programm is a part of a POLINA package */ /* POLINA = Protein Oriented LINear Analysis . The entire package will */ /* be out later (let me debug it and polish some things. Program */ /* written by Sergey Levin, Copyleft 1995 Me at PM :). */ /* I DO NOT!!!! */ /* CARE WHAT YOU USE IT FOR, PUBLISH AND MODIFY ALL YOU WANT :). */ /* just write me a quick e-mail if you find any use for this programm.*/ /* I am just curious. email: slevin@telico.bioc.aecom.yu.edu */ /***********************************************************************/ #include #include #define ITERATIONS 3000 #define AMINO_ACIDS 24 /* the 3 letter code Gly Ala Val Leu Ile Met Cys Ser Thr Asn Gln Asp Glu Lys Arg His Phe Tyr Trp Pro del*/ char aminos[AMINO_ACIDS]="gavlimcstnqdekrhfywp- "; /* the 1 letter code g a v l i m c s t n q d e k r h f y w p NT CT */ int charge_table[AMINO_ACIDS]={0, 0, 0, 0, 0, 0,-1, 0, 0, 0, 0,-1,-1,+1,+1,+1, 0,-1, 0, 0, +1, -1 }; /* the 1 letter code g a v l i m c s t n q d e k r h f y w p NT CT */ float pK_table[AMINO_ACIDS]={0, 0, 0, 0, 0, 0, 8.3, 0, 0, 0, 0, 3.9, 4.1, 10.7, 12.5, 6.0, 0, 10.1, 0, 0, 9.9, 2.9 }; int sequence[10000]; int end; int amino2int(char); float pI_peptide(int protein[10000], int n ); void titr_curve(); /*******************************************************/ /*Main file: parcing of command line and function calls*/ /*******************************************************/ void main(int argc, char *argv[]) { if(argc<2) { printf("\nPOLINA> PREDICT_PI: Error. Use: [name]

[OUT]\n"); exit(0); } read_in(argv[1]); printf("\n POLINA> PREDICT_PI: Protein %s\n", argv[1]); printf("\n POLINA> PREDICT_PI: Overall pI=%f\n", pI_peptide(sequence, end)); pI_frame( 9, "pi.out"); printf("\nPOLINA> PREDICT_PI: Wrote pI results to %c\n",argv[4]); } /******************************************************/ /* Read in the protein sequence from a file given on */ /* command line. There should be NO OTHER CHARACTERS */ /* in the sequence file. Modify function as you wish */ /* to accomodate different formats of sequence files. */ /******************************************************/ read_in(char *filename) { FILE *f; char ch; int i, temp; if((f=fopen(filename,"r"))==NULL) { printf("\nPOLINA> PREDICT_PI: Error opening file: %s\n",filename); exit(1); } while(ch!='\n' && !feof(f)) { fscanf(f, "%c", &ch); sequence[i]= amino2int(ch); i++; } end=i-2; fclose(f); } /*****************************************************/ /*Converts aminoacid letter code into numerical value*/ /*using the given table. slevin, 1994 */ /*****************************************************/ int amino2int(char amino) { int i; for(i=0; i<=24; i++) { if(amino==aminos[i]) return i; if(amino=='\n') return 24; } fprintf(stderr,"\nPOLINA> PREDICT_PI: Amino acid '%c'does not exist" , amino); return 24; } /**********************************************************/ /* Floating frame of pI of a protein. */ /**********************************************************/ void pI_frame(int frame, char *filename) { FILE *f; int temp[10]; int i, j, k; f=fopen(filename,"w"); for(i=0; i+frame<=end; i++) { for(j=0; j<=frame; j++) temp[j]=sequence[i+j]; fprintf( f, "%i , %f\n",i, pI_peptide(temp, frame )); } fclose(f); } /******************************************************/ /*The basic formula for charge of a protein is derived*/ /*from Henderixon-Hasselbach equation */ /* */ /* pH = pK + log([base]/[acid]) */ /* */ /* and fractional charge Q=1/(1+[base]/[acid]) */ /* */ /* Charge = Summ(Charge of sidechain*1/1+10^q(ph+pK)) */ /* */ /******************************************************/ float protein_charge(float pH, int protein[], int n) { float charge=0; int i; float base_acid; for(i=0; i<=n; i++) { if(i==0) { base_acid=powf(10, (pH - pK_table[23])); charge += 1 / (1+base_acid); } if(i==n) { base_acid=powf(10, -(pH - pK_table[24])); charge += -1 / (1+base_acid); } if( charge_table[protein[i]] == +1 ) { base_acid=powf(10, (pH - pK_table[protein[i]])); charge += 1 / (1+base_acid); } if( charge_table[protein[i]] == -1 ) { base_acid=powf(10, -(pH - pK_table[protein[i]])); charge += -1 / (1+base_acid); } else charge+=0; } return charge; } /*************************************************************/ /*This is a bisection method for finding roots to a function */ /*notice that here function is RIGHT AWAY the "protein_charge*/ /*function. Root returned is pI of the given sequence */ /* If you are not good at numerical analysis, I would advise */ /* you not to modify this function */ /*************************************************************/ float pI_peptide( int protein[1000], int n) { int i; float dx, fu, fmid, xmid, root; float brack1=1.5,brack2=13.5, xacc=0.0001; fu=protein_charge(brack1, sequence, n); fmid=protein_charge(brack2, sequence, n); root = fu < 0.0 ? (dx=brack2-brack1,brack1) : (dx=brack1-brack2,brack2); for (i=1; i<=ITERATIONS; i++) { fmid = protein_charge(xmid=root+(dx *= 0.5),protein, n); if (fmid <= 0.0) root=xmid; if (fabs(dx) < xacc || fmid == 0.0) return root; } } /*************************************************************************/ /*This functions outputs titration curve for the protein. Is not used in */ /* main. I used it for my presentations */ /*************************************************************************/ void titr_curve() { float i=0, I; while(i<13.5) { protein_charge(i, sequence, end); i+=0.1; } } ---------------------------------23861016217768-- From owner-software@net.bio.net Mon Oct 02 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!tank.news.pipex.net!pipex!warwick!bham!bhamcs!news.ox.ac.uk!news From: Ewan Birney Newsgroups: bionet.software Subject: Re: Sequence Editors and genetic Distance Calculators Date: 3 Oct 1995 17:53:09 GMT Organization: Oxford University Lines: 14 Message-ID: <44rta5$9b@news.ox.ac.uk> References: <44nj7p$pa9@stork.qut.edu.au> NNTP-Posting-Host: nmra.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 4.1.3 sun4m) To: a.liedloff@qut.edu.au X-URL: news:44nj7p$pa9@stork.qut.edu.au Re: What sort of things are useful for genetic distance calculations Does your program produce "trees" as an endpoint? if so then you should make sure you can export newhampshire style trees which means that funky programs such as treetool can use it, and more mundane programs like PairWise can also use them... And do you not consider protein sequences (in particular protein alignments) for distance measures? ewan birney (birney@molbiol.ox.ac.uk) From owner-software@net.bio.net Mon Oct 02 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!EU.net!sun4nl!Inter.NL.net!usenet From: R.Villerius@inter.nl.net (Roel Villerius) Newsgroups: bionet.software Subject: Microtox Date: Tue, 03 Oct 1995 19:17:24 GMT Organization: none Lines: 12 Message-ID: <44s5o5$ltv@altrade.nijmegen.inter.nl.net> NNTP-Posting-Host: asn99-12.assen.nl.net X-Newsreader: Forte Free Agent 1.0.82 Hello, I'm working on a program that makes it posible to read 3 sample's from a MICROTOX. It's a program for a open day where kid's can bring water with them and then the program gives the water a note. But I can't figure out with's characters the microtox send to the computer. Does anybody has a list of those characters an is able to send that list to me in a E-mail-message. My E-mail address is R.Villerius@inter.nl.net. From owner-software@net.bio.net Mon Oct 02 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!in2.uu.net!newsfeed.ACO.net!news.univie.ac.at!news-admin@univie.ac.at From: Yuri Koshelnick Newsgroups: bionet.software Subject: Wanted: software nice graphic representation of DNA Date: 3 Oct 1995 14:46:27 GMT Organization: Institute of Medical Physiology, Vienna University, Austria Lines: 7 Message-ID: <44ric3$1f90@ftp.univie.ac.at> NNTP-Posting-Host: cexp5.ephy.univie.ac.at Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) Can someone point me to a PC progam that is able to prepare a genomic DNA figure for puplication.I was using DNAstar but it does not fit my needs, because it is not possible to write intron and exon base letters in different sizes. Also the numbering of the promotor region with (minus) numbers and the numbering of the translated proteinsequence below the DNA sequence is not possible. From owner-software@net.bio.net Mon Oct 02 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!xlink.net!rz.uni-karlsruhe.de!news.uni-stuttgart.de!uni-regensburg.de!lrz-muenchen.de!fauern!winx03!wpxx02.toxi.uni-wuerzburg.de!krasel From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: WebCutter now in Sweden Date: 3 Oct 1995 14:20:42 GMT Organization: Dept. of Pharmacology, U Wuerzburg Lines: 19 Message-ID: <44rgrq$jdd@winx03.informatik.uni-wuerzburg.de> References: <44okm1$5ae@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [version 1.2 PL2] Christopher Spry (cspry@sghms.ac.uk) wrote: > Internet access to many hosts is often very poor. For example this host was unusable > from here on Mon Oct 2 at 13:04:26 BST 1995. [traceroute protocol deleted -- routing apparently occurs from the UK to the Netherlands, and from there to Sweden] I assume that BST means British Standard Time. Therefore, the usual approach would be to access the Swedish server either in the early morning or the late evening, when traffic is lower (morning sounds more promising). I am afraid that contacting anybody won't help much -- that's the way the Internet works. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Mon Oct 02 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: "Sergey V. Orlov" Newsgroups: bionet.software Subject: Re: Gene promoter software Date: 4 Oct 1995 00:05:19 +0100 Organization: l biochem iem Lines: 22 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <44sfjf$hui@mserv1.dl.ac.uk> References: <9510313370.~INN-BHBa00221.bionet-news@dl.ac.uk> MIME-Version: 1.0 Original-To: bio-soft@dl.ac.uk > Hi,everyone: > Does anybody knows that what software is available for finding gene- > promoter mortiff and boundary ? I know the `software prosite` is for protein > motiff, what is it for gene mortiff ? > Thanks in advance > > Rongrong Wu Hi, Rongrong. There is a program Promoter Scan designed by D. Prestridge. This program seek possible promoter sequences, estimating density of protein binding sites (cis-acting elements) ( see J.Mol.Biol. 249, N.5:923-932 (1995)). You can write D. Prestridge (e-mail: danpbiosci.umn.edu) and he will tell you ftp site with this program. Hope, it helps, Serge Orlov E-mail: serge@serge.stud.pu.ru .. From owner-software@net.bio.net Mon Oct 02 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!newsjunkie.ans.net!merlion.singnet.com.sg!lantana.singnet.com.sg!usenet From: emily@singnet.com.sg (emily) Newsgroups: bionet.software Subject: BEST INTERNET SOFTWARES Date: Tue, 03 Oct 1995 16:12:57 GMT Organization: Singapore Telecom Internet Service Lines: 2 Message-ID: <44rnus$5mr@lantana.singnet.com.sg> NNTP-Posting-Host: ts900-1529.singnet.com.sg X-Newsreader: Forte Free Agent 1.0.82 I am looking for the good internet softwares,any suggestion? From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!in2.uu.net!nntpgate.primenet.com!nntpdist.primenet.com!news.asu.edu!usenet From: jml@asu.edu (John M. Lynch) Newsgroups: bionet.software Subject: Randomized MANOVA Date: Tue, 03 Oct 1995 22:32:10 GMT Organization: Arizona State University Lines: 13 Message-ID: <44sds6$q8i@news.asu.edu> NNTP-Posting-Host: ppp1-02.inre.asu.edu X-Newsreader: Forte Free Agent 1.0.82 Hi there !!! I'm looking for software (preferably free/shareware) to do a randomized MANOVA on data. I know of Resampling Stats, but that only does univariate tests. The program would have to run in DOS. Any one out there with any leads? Cheers, John M. Lynch From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!simtel!harbinger.cc.monash.edu.au!phimr-04.med.monash.edu.au!TIM-M From: TIM-M@med.monash.edu.au (Tim Murphy) Newsgroups: bionet.software,bionet.software.source Subject: Re: Disassembly program for PC Date: Wed, 4 Oct 1995 00:54:04 GMT Organization: Monash University Lines: 16 Message-ID: References: NNTP-Posting-Host: phimr-04.med.monash.edu.au X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] NB: use email address in .sig ONLY (brain dead nwews reader) G'day folks "Bin . Lee" writes: >Hi, guys: >Any one know any good disassembly program for PC, if I can get any >shareware from the Net, that will be super, otherwise, please tell me >where I can get some commericial products. ASM86 is a shareware assembly/disasembly program that is rated very highly. It can be found in the SimTel msdos archives in the assemler area. Cheers! Ian From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!in1.uu.net!news.u.washington.edu!darwin.genetics.washington.edu!mlee From: mlee@darwin.genetics.washington.edu (Marty Lee) Newsgroups: bionet.software Subject: Strain Database Software Date: 4 Oct 1995 00:47:48 GMT Organization: University of Washington Genetics Lines: 20 Distribution: bionet Message-ID: <44sljk$9rg@nntp3.u.washington.edu> References: <9510313370.~INN-BHBa00221.bionet-news@dl.ac.uk> <44sfjf$hui@mserv1.dl.ac.uk> NNTP-Posting-Host: darwin.genetics.washington.edu Howdy, I'm writing from a lab specializing in streptococcus pathogenesis, and we have been freezing away wild type isolates, various mutants, transformants, etc for some time. We would like to keep track of these strains using either the Sun machines, (Unix), or on our Macs. We have looked into using dBase under Unix, but after getting into the nitty gritty it appears that dBase is quite a bog. I've previously used Filemaker Pro. That was easy but has all the limitations of a flat file manager. Does anybody know of a good strain database system? Please e-mail me (at the following address) and I will post the results in a weeks time. Thanks much, Marty Lee mlee@sol.chmc.org (or) mlee@genetics.washington.edu From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!in1.uu.net!mr.net!news.mr.net!timbuk.cray.com!equalizer!ihnp4.ucsd.edu!sdcc12.ucsd.edu!sdcc14!cabney From: cabney@sdcc14.ucsd.edu (Chuck Abney 7;^}) Newsgroups: bionet.software,comp.os.linux.misc Subject: porting SUN-gcg to Linux? Date: 4 Oct 1995 07:42:33 GMT Organization: University of California, San Diego Lines: 20 Message-ID: <44tdt9$cgq@sdcc12.ucsd.edu> NNTP-Posting-Host: sdcc14.ucsd.edu Xref: biosci bionet.software:13503 comp.os.linux.misc:72276 Is anyone familiar enough with gcc and SUN/Linux code rules to tell me if such a thing is feasible? Wouldn't it be cool to run gcg on your home computer? Is it just a matter of changing the directory references in the Makefile, or must the #ifdef lines in the source also be changed?? Mistakes?...sorry for my ignorance. I'm a biologist Jim, not a programmer! For all you who speak with numbers, gcg (Genetics Computer Group) is a collection of tools for manipulating DNA sequences. It has been recently ported to the UNIX platform and given a pretty (Tcl) face. Philanthropists and Linux lovers please correspond at cabney@ucsd.edu. -chuck -- G* My father compounded with my mother under the Dragon's Tail,*G E* and my nativity was under Ursa Major, *E N* so it follows that I am rough and lecherous. *N E* -Edmund, on the admirable evasion *I From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.tamu.edu!newshost.comco.com!news.texas.net!news.sprintlink.net!in2.uu.net!netnews.jhuapl.edu!aplcenmp!darwin.sura.net!aurora.LaTech.edu!news.ttu.edu!news From: Alan Neely Newsgroups: bionet.software Subject: Re: [Q]-EXCELL-how to... Date: 4 Oct 1995 16:37:22 GMT Organization: Texas Tech University H.S.C. Lines: 12 Message-ID: <44ud82$73u@hydra.acs.ttu.edu> References: <44hcs8$mk0@mserv1.dl.ac.uk> NNTP-Posting-Host: phy024.lubb.ttuhsc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) To: nfix@jcu.cz You can copy the whole spread sheet to the clippoboard and then "paste-special" and choose multiply. -- _____________________________________________ _____ Alan Neely, Ph.D. Texas Tech U. Health Sciences Center Lubbock TX, 79430 From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!ix.netcom.com!netnews From: dmbarc@ix.netcom.com (DMBARC ) Newsgroups: bionet.software Subject: Wanted: Hotline Software Information Date: 4 Oct 1995 15:47:38 GMT Organization: Netcom Lines: 5 Message-ID: <44uaaq$dcb@ixnews2.ix.netcom.com> NNTP-Posting-Host: ix-nyc7-20.ix.netcom.com X-NETCOM-Date: Wed Oct 04 8:47:38 AM PDT 1995 I am trying to find out who (if anyone) is still distributing the Hotline contact management software that was originally manufactured by General Information. I need it for Windows. Thanks, in advance, for any information! From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!sol.ctr.columbia.edu!news.mindlink.net!van-bc!fonorola!nntp.igs.net!usenet From: supertek@igs.net (Darrell Bigelow) Newsgroups: bionet.software Subject: Extract data from CANTAX program? Date: 4 Oct 1995 21:14:09 GMT Organization: IGS - Information Gateway Services Lines: 26 Message-ID: <44utf1$p8n@nntp.igs.net> NNTP-Posting-Host: supertek.igs.net Mime-Version: 1.0 X-Newsreader: WinVN 0.99.2 Hello out there... I'm an independent computer consultant, and am the owner of a small business called Supertek Computer Services. Recently, I was hired under contract by a client, that wishes to extract data from a CANTAX program and merge the data for approximately 100 clients (15 fields for each client), into a form letter, that can be sent out to each of them. Does anyone know any company (or otherwise) that might have a program that can do this? Of course we are willing to pay the $$$ needed for a such a program. If not, might you suggest perhaps methods of being able to do this without a lot of time consuming "cutting" and "pasting"? I have been in touch with SOFTKEY, the makers of the CANTAX program. They have informed me that they have DISCONTINUED the product, and neither sell it anymore, or have any technical support for the product. Any assistance would be sincerely appreciated. Regards, Darrell Bigelow From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!UTSPH.SPH.UTH.TMC.EDU!gsbs1032 From: gsbs1032@UTSPH.SPH.UTH.TMC.EDU Newsgroups: bionet.software Subject: Seeking postdoctoral position in sequence analysis Date: 4 Oct 1995 13:11:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <009975FC.F7F4F4F8.2866@utsph.sph.uth.tmc.edu> NNTP-Posting-Host: net.bio.net I am looking for a postdoctoral position in the US in sequence analysis, computational biology, phylogenetic analysis, and other areas of mathematical biology. The position is sought starting in the summer of 1996. I am a foreign student at the University of Texas at Houston with a strong background in sequence analysis, genetics and mathematical biology expecting to obtain a Ph.D. degree in May, 1996. Curriculum vitae, letters of reference, paper reprints and academic transcipts are available upon request. Please respond to gsbs1032@utsph.sph.uth.tmc.edu and sa95081@odin.mda.uth.tmc.edu From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!warwick!bham!usenet From: s.m.williams.bcm@bham.ac.uk (Steve) Newsgroups: bionet.software Subject: Re: Plasmid drawing for PC? Date: Wed, 04 Oct 1995 11:22:25 GMT Organization: The University of Birmingham, UK. Lines: 46 Message-ID: <44tsuo$75j@sun4.bham.ac.uk> References: <44rhde$5u6@surz03.HRZ.Uni-Marburg.DE> NNTP-Posting-Host: bcs177.bham.ac.uk X-Newsreader: Forte Free Agent 1.0.82 smueller@papin.HRZ.Uni-Marburg.DE (Mueller Steffen) wrote: >I'm searching for a plasmid drawing program working with Windows or OS/2. >Preferably Shareware. Is there any such program available (or do I have to >do it myself :-) ) >Thanx, > Steffen >-- >|-----------------------------------------------------------------------| >| Steffen Mueller, Molecular Genetics, Dep. Biology, University Marburg | >|-----------------------------------------------------------------------| >|smueller@mailer.uni-marburg.de steffen@molgen.biologie.uni-marburg.de| >|-----------------------------------------------------------------------| >|>>>>>>>>>>>> http://staff-www.uni-marburg.de/~smueller <<<<<<<<<<<<<<<<| >|-----------------------------------------------------------------------| Hi Steffen, The best package I've come across is VectorNTI. You can find the linkto the programme from on of my web pages. The URL for which is:- http://sun1.bham.ac.uk/s.m.williams.bcm/images/viewers.html Have fun, Steve \\\\ \\\\(o o) 8(o o)(_)Ooo ###########################################ooO##(_)###Ooo######### # # # E-Mail: S.M.WILLIAMS.BCM@bham.ac.uk # # # # WWW: http://sun1.bham.ac.uk/s.m.williams.bcm/home_page.html # # WWW: http://iptunix.bcm.bham.ac.uk/sjwb/sjwb.html # # # # Phone: (44)0121-415-5435 # # Fax: (44)0121-414-7366 # # # ################################################################## From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!usc!howland.reston.ans.net!swrinde!sdd.hp.com!hamblin.math.byu.edu!news.Arizona.EDU!usenet From: Soaring Bear Newsgroups: bionet.software Subject: Biosym's Apex QSAR program Date: 4 Oct 1995 23:23:01 GMT Organization: The University of Arizona Lines: 27 Message-ID: <44v50l$pda@news.ccit.arizona.edu> NNTP-Posting-Host: basie.pharm.arizona.edu Mime-Version: 1.0 X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.2 IP22) References: <44utf1$p8n@nntp.igs.net> X-URL: news:44utf1$p8n@nntp.igs.net Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Hello: Despite my posts to CCL & Dibug I have been unable to find a single satisfied user of Biosym's Apex QSAR software. I have received several emails from folks who tried and gave up. Is there anyone out there who is successfully using it? who has published? Please email me at: bear@ellington.pharm.arizona.edu thankyou -- _____ ____ * ___) * _ \ http://ellington.pharm.arizona.edu/~bear : (___ : |_) : Cyber-Chemist: cancer drug design topo-O O-topo \___ \ | _ < Molecular & Nutritional Biochemist 5'*. : : .***. ___) : | |_) : Herbs, Nutrition, Natural Dentistry | *. .* | | | (_____/oaring |____/ear@ellington.pharm.arizona.edu | | *. * | | | * UA New Pharmacy 404, Tucson 85721 3'.| DNA helix| * '***' '***' From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!howland.reston.ans.net!torn!nott!crc-news.doc.ca!netfs.dnd.ca!ub!newserve!news.cc.geneseo.edu!news From: john haynie Newsgroups: bionet.software Subject: Application to do simple pedigree diagrams Date: 4 Oct 1995 21:19:44 GMT Organization: biology/SUNY Geneseo Lines: 30 Message-ID: <44utpg$7fm@news.cc.geneseo.edu> NNTP-Posting-Host: mendel.bio.geneseo.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.software#44pma7$qiu@dartvax.dartmouth.edu I recently found myself in need of some pedigree diagrams in gif format for teaching purposes (see http://darwin.bio.geneseo.edu/Courses/Bio271/applications/answers/alopec ia.html for an example). I was able to make a bunch of symbols using a drawing program and then copy and attach the symbols to make the actual pedigrees. What a pain that was for even slightly complex pedigrees! Can anyone suggest a way to simplify this process. My needs are minimal so some megabucks commercial application is out of the question. I searched the Oakland virtual software library and surprisingly found nothing on pedigree. Is there a freeware or shareware ap that will do a little pedigree drawing given some data file or point and click instructions? Perhaps something that plugs into one of the standard drawing programs. I have access to PowerMac with the popular drawing programs as well as UNIX (SunOS 4.1.3). Could do it with PC if that's the only choice. Any suggestions appreciated. If interested, I'll post a summary of replies. Thanks, jlh -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- John Haynie | haynie@uno.cc.geneseo.edu Biology Dept/SUNY | http://darwin.bio.geneseo.edu/ Geneseo, NY 14454-1401 | From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!simtel!swidir.switch.ch!scsing.switch.ch!elna.ethz.ch!usenet From: Urs Braendle Newsgroups: bionet.software Subject: Fishers exact test for Windows Date: 4 Oct 1995 19:51:24 GMT Organization: Plant Pathology Lines: 13 Message-ID: <44uojs$mu8@elna.ethz.ch> NNTP-Posting-Host: braendle.slip.ethz.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.software#0684d6b0@pwinet.upj.com Does anyone know about a Windows version of the fabulous Fish6 program for the Macintosh? Thanks for any hint Urs Dr. Urs Braendle Phytomedicine/Pathology Swiss Federal Institute of Technology Zuerich From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.tamu.edu!newshost.comco.com!news.texas.net!news.sprintlink.net!in2.uu.net!cospo.osis.gov!naic.wpafb.af.mil!blackbird.afit.af.mil!zombie.ncsc.mil!cs.umd.edu!info.usuhs.mil!usenet From: Mika Salminen Newsgroups: bionet.software Subject: GDE 2.2a for DEC ALPHA OSF/1? Date: 4 Oct 1995 13:00:32 GMT Organization: Henry M Jackson Foundation Lines: 10 Message-ID: <44u0hg$2jp@info.usuhs.mil> NNTP-Posting-Host: 131.158.31.163 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.software We are heavy users of the excellent expandable GDE alignment enviroment opf Stephen Smith. We have been using the system on Sun Sparcs, but would like to start using DEC ALPHA powered machines running OSF/1. Does anyone out there know if has been ported to this system, and whether the bundled Treetool sofware also is included in such a port? Thank's in advance, Mika Salminen Henry M. Jackson Foundation From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!gatech!news.sprintlink.net!in2.uu.net!iglou!news From: ams@iglou.com Subject: Have your CAD drawings, programs, VHS video, photos, data, or sound put on CDROM !!! X-Nntp-Posting-Host: dp2-005.ppp.iglou.com Message-ID: Sender: news@iglou.com (News Administrator) Organization: IgLou Internet Services (1-800-436-4456) X-Newsreader: Forte Agent .99b.112 Date: Wed, 4 Oct 1995 20:33:42 GMT Lines: 57 >>> Advanced Media Solutions, Inc. <<< AMS@IGLOU.COM 1-502-935-0816 48 HOUR TURNAROUND (family photos, video, home inventory, catalogues, software backup, cad drawings, financial records, real estate, archiving or just anything that you want and with the added security of CD technology) With todays Media Technologies becoming more advanced and sophisticated, there are more choices and greater flexibility concerning your storage medium. Individuals now have a myriad of solutions for information dissemination, data storage and retrieval. AMS can provide your exacting needs via CD format. Compact Disk technology offers temperature, moisture ,magnetic and viral resistance; with the added benefits of 650 Mbyte storage (or 74 minutes video), random access and a 100 year shelf life. AMS offers these alternatives on KODAK PTHALOCYANINE Compact Disk: CUSTOM CD WE SUPPORT THE FOLLOWING CD ENCODING FORMATS WITH ISO9660/HIGH SIERRA AND APPLE HFS COMPAIBILIES IN SINGLE-VOLUME AND MULTI-VOLUME SESSIONS: RED BOOK (AUDIO) YELLOW BOOK MODE 1 (DATA) AND MODE 2 (IMAGING AND VIDEO) GREEN BOOK (CD-i) WHITE BOOK (MPEG-1 VIDEO, CD KARAOKE AND RealMagic) ORANGE BOOK PART 2 KODAK PHOTO CD MIXED MODE SYSTEM BACKUP SUPPORTING QIC-40, QIC-80, QIC-WIDE, 4MM DAT AND DC600 OCR SCANNING WITH CONVERSIONS TO POPULAR WORD PROCESSING APPLICATIONS MULTI-PLATFORM FILE CONVERSIONS MULTI-MEDIA PRESENTAIONS PHOTO AND TEXT IMAGING VIRUS SCANNING AND ERADICATION Volume discounts of 3 or more Silk screening of CD's is also available. Most applications average $100 US FOR MORE INFO... EMAIL AMS@IGLOU.COM PHONE (502) 935-0816 AMS PO BOX 58414 LOUISVILLE, KY 40268-0414 From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!news.cac.psu.edu!news.math.psu.edu!psuvax1!news.cc.swarthmore.edu!netnews.upenn.edu!news.drexel.edu!n1-2-202.macip.drexel.edu!user From: friedmrd@post.drexel.edu (Richard Friedman) Newsgroups: bionet.software Subject: Sequence aligment programs for the mac Date: Wed, 04 Oct 1995 10:28:13 -0400 Organization: Drexel University Lines: 14 Message-ID: NNTP-Posting-Host: n1-2-202.macip.drexel.edu Does anyone know of a program which will allow for DNA sequence alignment which can be used on the Mac? Thanks -- -Rich Friedman@mbcl.rutgers.edu or Friedmrd@post.drexel.edu or rfriedma@astro.temple.edu *********************************************************** * "This Genie gig has it's ups and `(:>)~\ * * downs -- PHENOMENAL COSMIC POWER, \ / * * itty-bitty living space." \___/ * *********************************************************** From owner-software@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!plug.news.pipex.net!pipex!oleane!jussieu.fr!pasteur.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!News.Uni-Marburg.DE!papin.HRZ.Uni-Marburg.DE!smueller From: smueller@papin.HRZ.Uni-Marburg.DE (Mueller Steffen) Newsgroups: bionet.software Subject: Plasmid drawing for PC? Date: 3 Oct 1995 14:30:06 GMT Organization: Hochschulrechenzentrum der Universitaet Marburg Lines: 16 Message-ID: <44rhde$5u6@surz03.HRZ.Uni-Marburg.DE> NNTP-Posting-Host: papin.hrz.uni-marburg.de X-Newsreader: TIN [version 1.2 PL2] I'm searching for a plasmid drawing program working with Windows or OS/2. Preferably Shareware. Is there any such program available (or do I have to do it myself :-) ) Thanx, Steffen -- |-----------------------------------------------------------------------| | Steffen Mueller, Molecular Genetics, Dep. Biology, University Marburg | |-----------------------------------------------------------------------| |smueller@mailer.uni-marburg.de steffen@molgen.biologie.uni-marburg.de| |-----------------------------------------------------------------------| |>>>>>>>>>>>> http://staff-www.uni-marburg.de/~smueller <<<<<<<<<<<<<<<<| |-----------------------------------------------------------------------| From owner-software@net.bio.net Wed Oct 04 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Sequence aligment programs for the mac Date: 5 Oct 1995 13:24:39 GMT Organization: Biology, Indiana University - Bloomington Lines: 7 Message-ID: <450man$b1s@usenet.ucs.indiana.edu> References: NNTP-Posting-Host: sunflower.bio.indiana.edu You may find SeqPup, a multiple sequence editor, handy for alignments. Use ClustalW with it for automatic alignments. Find SeqPup at ftp://iubio.bio.indiana.edu/molbio/seqpup/ - don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Oct 04 23:00:00 1995 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!swrinde!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!is.bbsrc.ac.uk!bcc.ac.uk!news From: dcurtis@hgmp.mrc.ac.uk (David Curtis) Subject: Re: Application to do simple pedigree diagrams Message-ID: <1995Oct5.121812.43796@ucl.ac.uk> Date: Thu, 5 Oct 1995 12:17:29 GMT References: <44utpg$7fm@news.cc.geneseo.edu> Organization: University College London X-Newsreader: Forte Free Agent 1.0.82 Lines: 21 john haynie wrote: >Can anyone suggest a way to simplify this process. My needs are minimal >so some megabucks commercial application is out of the question. I >searched the Oakland virtual software library and surprisingly found >nothing on pedigree. Is there a freeware or shareware ap that will do a >little pedigree drawing given some data file or point and click >instructions? Perhaps something that plugs into one of the standard >drawing programs. Try my PEDRAW program. It runs on a PC, and you get it from ftp.gene.ucl.ac.uk, in /pub/packages/dcurtis. BTW, this is practically a FAQ. Other people have drawn up lists of programs, I think Ellen Wijsman for one? Dave Curtis (dcurtis@hgmp.mrc.ac.uk) Institute of Psychiatry, London http://www.iop.bpmf.ac.uk/home/depts/psychmed/general/dcurtis/dcurtis.htm From owner-software@net.bio.net Wed Oct 04 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: GDE 2.2a for DEC ALPHA OSF/1 Date: 5 Oct 1995 13:22:10 GMT Organization: Biology, Indiana University - Bloomington Lines: 9 Message-ID: <450m62$at1@usenet.ucs.indiana.edu> References: <44u0j0$2jp@info.usuhs.mil> NNTP-Posting-Host: sunflower.bio.indiana.edu SeqPup, a multiple sequence editor, is not GDE, but it will run on DECs, Suns, other Unix XWindow as well as Mac and MSWindows. Find it at ftp://iubio.bio.indiana.edu/molbio/seqpup/ - don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Wed Oct 04 23:00:00 1995 Path: biosci!ihnp4.ucsd.edu!news1.ucsd.edu!sdcc14.ucsd.edu!cabney From: "Chuck Abney 7;^}" Newsgroups: bionet.software,comp.os.linux.misc Subject: Re: porting SUN-gcg to Linux? Date: Wed, 4 Oct 1995 19:29:04 -0700 Organization: The Avant-Garde of the Now, Ltd. Lines: 91 Message-ID: References: <199510042233.PAA22648@galaxy.ucr.edu> NNTP-Posting-Host: sdcc14.ucsd.edu Mime-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="67175506-869054091-812860144=:15853" In-Reply-To: <199510042233.PAA22648@galaxy.ucr.edu> Xref: biosci bionet.software:13517 comp.os.linux.misc:72298 This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. --67175506-869054091-812860144=:15853 Content-Type: TEXT/PLAIN; charset=US-ASCII Well, the text of the readme file indicates this is less than a full version, due to some features having VMS specific calls. Also, it kinda sounds like a beta product. Thanks for the encouragement... chuck G* My father compounded with my mother under the Dragon's Tail,*G E* and my nativity was under Ursa Major, *E N* so it follows that I am rough and lecherous. *N E* -Edmund, on the admirable evasion *I --67175506-869054091-812860144=:15853 Content-Type: TEXT/PLAIN; charset=US-ASCII; name="000readme.txt" Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: DQpJTlNUQUxMQVRJT04gUFJPQ0VEVVJFIEZPUiBFR0NHIFBST0dSQU1TIA0K LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLQ0KDQoo VU5JWCBWRVJTSU9OIDcuMikgDQoNCigxKSBUZWNobmljYWwgTm90ZSANCj09 PT09PT09PT09PT09PT09PQ0KDQpUaGVpICBwcm9ncmFtcyByZXNlbWJsZSB0 aGUgR0NHRU1CTCBwcm9ncmFtcyBzaW1pbGFyIHRvIHRoZSBvbmVzIGRpc3Ry aWJ1dGVkDQppbiB0aGUgNy4wIFZNUyBWZXJzaW9uIG9mIEdDRyB1bnN1cHBv cnRlZC5iY2suIFRoZXJlIGhhdmUgYmVlbiBzb21lIGVuaGFuY2UtDQptZW50 cyAgbWFkZSAgYnkgdGhlIGF1dGhvcnMgUGV0ZXIgUmljZSAoRU1CTCkgYW5k IFJvZHJpZ28gTG9wZXogKE9zbG8pLiBTb21lDQpwcm9ncmFtcyBhcmUgIG9t aXR0ZWQgIGR1ZSAgdG8gIFZNUyAgc3BlY2lmaWMgIGNhbGxzLCBhbmQgc29t ZSBoYXZlIG5vdCBiZWVuIA0KY29udmVydGVkIHN1Y2Nlc3NmdWxseSB5ZXQu IFJvZHJpZ28gTG9wZXogYW5kIEphY2sgTGV1bmlzc2VuIChOZWptZWdlbikg aGF2ZSANCmFjdGl2ZWx5ICBjb250cmlidXRlZCAgdG8gIHRoZSBVTklYIHBv cnQgZG9uZSBieSBSZWluaGFyZCBEb2VseiAoQmFzZWwpLiBUaGUgDQp2ZXJp ZmllZCBvcGVyYXRpbmcgc3lzdGVtcyBpbmNsdWRlDQoNCklSSVggNC4wLjEN CklSSVggNC4wLjQNCklSSVggNC4wLjUgICAgDQogICAgICAgICAgICAzLjEw IGNvbXBpbGVycyBvbiBJUklYIA0KDQpVTFRSSVggNC4yDQpVTFRSSVggNC4y QQ0KVUxUUklYIDQuMw0KDQpTVU4gT1MgNC4xLjINCg0KDQooMikgSW5zdGFs bGF0aW9uIG9mIHRoZSBzb2Z0d2FyZSANCj09PT09PT09PT09PT09PT09PT09 PT09PT09PT09PT09DQoNCkl0IGkgaXMgYXNzdW1lZCB0aGF0IHlvdSBsb2dn ZWQgaW4gYXMgc291cmNlIGNvZGUgbWFpbnRhaW5lciwgYW5kIGhhdmUgZXhl Y3UtDQp0ZWQgIGdjZyBhbmQgZ2Nnc3VwcG9ydC4gTmV4dCwgZ28gdG8gYSBm cmVlIGRpc2sgYW5kIGlzc3VlIHRoZSBmb2xsb3dpbmcgY29tLQ0KbWFuZHMu IFRoZSBlZ2NnIHByb2dyYW1zIHVzZSBhYm91dCAyMCBtYnl0ZSBvZiBkaXNr IHNwYWNlIGluIHRoZWlyIGZpbmFsIGNvbi0NCmZpZ3VyYXRpb24uIFRvIGJ1 aWxkIHRoZSBwcm9ncmFtcywgYSBzcGFjZSBvZiA2MCBNQnl0ZXMgaXMgcmVj b21tZWRlbmQuIA0KDQpJZiB5b3UgZG9uJ3QgYWxyZWFkeSBoYXZlIHRoZSBl Z2NnIHRyZWUgKExvb2sgaW4gJEdDR0NPUkVST09UL2djZ3Vuc3VwcG9ydGQp LCANCnVucGFjayB0aGUgZmlsZXMgd2l0aCANCg0KJSB1bmNvbXByZXNzIGVn Y2cudGFyLloNCiUgdGFyIC14dm9mIGVnY2cudGFyIA0KDQpOZXh0LCBnbyB0 byB0aGUgc3lzc2NyaXB0IGRpcmVjdG9yeSANCg0KJSBjZCBlZ2NnL2VnY2dj b3JlL3N5c3NjcmlwdA0KDQphbmQgbWFrZSB0aGUgbWFrZWZpbGUgd2l0aCB0 aGUgY29ycmVzcG9uZGluZyB0b1hYWCBjb21tYW5kIGZvciBYWFggPSANCnVs dHJpeCwgaXJpeCwgc3VuLiBFLmcuLCBpZiB5b3UgdXNlZCBhIFNpbGljb24g R3JhcGhpY3MsIGRvIGEgDQoNCiUgdG9pcml4IE1ha2VmaWxlLmdlbmVyaWMg PiBtYWtlZmlsZSANCg0KW05PVEU6IElmIHlvdSBhcmUgcnVubmluZyBTVU4g T1MgNC4xLjIgb3IgSVJJWCA0LjAuNCBwbGVhc2UgcmVhZCB0aGUgbWFrZWZp bGUgDQphbmQgZWRpdCBpdCBhY2NvcmRpbmdseSB0byByZWZsZWN0IHRoZSBu ZWNlc3NhcnkgY2hhbmdlcy5dDQoNCmFuZCBidWlsZCB0aGUgc3RhcnR1cCBm aWxlIA0KDQolIG1ha2Ugc3RhcnR1cA0KDQpUaGVuLCBzb3VyY2UgaXQgDQoN CiUgc291cmNlIC4uLy4uL2VnY2dzdGFydHVwDQoNCmFuZCAgbWFrZSAgdGhl ICAgZG9jdW1lbnRhdGlvbiAoV2hpY2ggYXNzdW1lcyB0aGF0IHlvdSB1c2Ug bHByIG9uIGEgUG9zdHNjcmlwdCANCnByaW50ZXIuSWYgeW91IGRvbid0IHlv dSBuZWVkIHRvIGVkaXQgdGhlIGZpbGUgbWFrZV9zb3VyY2UuY3NoIGFuZCBy ZXBsYWNlIHRoZSANCmxwciBjb21tYW5kIHdpdGggdGhlIHN1aXRhYmxlIG9u ZSwgZS5nLiBscHIgLVBwb3N0IGlmICdwb3N0JyBpcyB5b3VyIHByaW50ZXIp LiANCg0KJSBzb3VyY2UgbWFrZV9zb3VyY2UuY3NoIA0KDQpOZXh0LCBidWls ZCB0aGUgcGFja2FnZSANCg0KJSBtYWtlIGFsbCANCg0KYW5kIGFmdGVyIGhh dmluZyB0ZXN0ZWQgaXQsIGNsZWFuIHVwIHRoZSBkaXJlY3Rvcnkgd2l0aCAN Cg0KJSBtYWtlIGNsZWFuIA0KDQooMykgQ29uZmlndXJhdGlvbiANCj09PT09 PT09PT09PT09PT09DQoNCkluIG9yZGVyIHRvIG1ha2UgYWxsIHVzZXJzIHJ1 biB0aGUgc29mdHdhcmUsIGluc2VydCB0aGUgbGluZSANCg0Kc291cmNlIDx5 b3VyIHBhdGg+L2VnY2cvZWdjZ3N0YXJ0dXANCg0KaW50byB5b3VyIGdjZyBh bGlhc2luZyBzY3JpcHQuIFRoZSBvbi1saW5lIGRvY3VtZW50YXRpb24gd2ls bCBiZSBhY2Nlc3NpYmxlICBpbiANCnRoZSBjb21tYW5kIA0KDQplZ2VuaGVs cCANCg0KYW5kIHRoZSBwcm9ncmFtcyBhcmEgYWxsIGNhbGxhYmxlIGJ5IG5h bWUuIA0KDQoNCig0KSBDaGFuZ2VzIHdpdGggdGhlIG5leHQgcmVsZWFzZQ0K PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09IA0KDQpUaGUgcG9y dCBjb250YWlucyBzdGlsbCBzb21lIFZNUyByZW1haW5lcnMgc3VjaCBhcyBt aXhlZC1jYXNlIGZpbGVuYW1lcyAgYW5kICAkDQpjaGFyYWN0ZXJzLlRoZXNl IGFyZSBoYXJkIHRvIHRyYWNrIGFuZCBhbnkgaGludCBvbiBpdHMgcHJlc2Vu Y2UgaXMgYXBwcmVjaWF0ZWQuDQpBbGwgIHN1Z2dlc3Rpb25zLCAgYW5kICBo aW50cyAgIG9uICAgIG9kZGl0aWVzIG9mIFVOSVggaW1wbGVtZW50YXRpb24s IGFyZSBtb3N0IA0Kd2VsY29tZSBpZiBzZW50IHRvIHRoZSBhdXRob3JzIG9y IGVtYm5ldEBjb21wLmJpb3oudW5pYmFzLmNoLiBUaGFua3MuIA0KDQo= --67175506-869054091-812860144=:15853-- From owner-software@net.bio.net Wed Oct 04 23:00:00 1995 Path: biosci!PASTEUR.HJF.ORG!msalminen From: msalminen@PASTEUR.HJF.ORG (Mika Salminen) Newsgroups: bionet.software Subject: GDE 2.2a for DEC ALPHA OSF/1 Date: 4 Oct 1995 17:04:42 -0700 Organization: Henry M Jackson Foundation Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <44u0j0$2jp@info.usuhs.mil> NNTP-Posting-Host: net.bio.net We are heavy users of the excellent expandable GDE alignment enviroment opf Stephen Smith. We have been using the system on Sun Sparcs, but would like to start using DEC ALPHA powered machines running OSF/1. Does anyone out there know if has been ported to this system, and whether the bundled Treetool sofware also is included in such a port? Thank's in advance, Mika Salminen From owner-software@net.bio.net Wed Oct 04 23:00:00 1995 Path: biosci!agate!spool.mu.edu!torn!nott!nrcnet0.nrc.ca!ratilal From: "Christoph W. Sensen" Newsgroups: bionet.software Subject: BLAST and FASTA e-mail servers Date: 5 Oct 1995 22:36:52 GMT Organization: NRC Institute for Marine Biosciences Lines: 14 Message-ID: <451mm4$r83@nrcnet0.nrc.ca> NNTP-Posting-Host: ninja.imb.nrc.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 4.1.3_U1 sun4m) To: sensencw@ninja.imb.nrc.ca,gaasterl@mcs.anl.gov X-URL: news:bionet.software Dear netters, I am looking for alternatives for the BLAST server at NCBI and the FASTA server at EBI. Are there any other sites that mirror the two above? Christoph Sensen Institute for Marine Biosciences National Research Council of Canada 1411 Oxford Street Halifax, N.S. Canada B3H 3Z1 From owner-software@net.bio.net Wed Oct 04 23:00:00 1995 Path: biosci!daresbury!hgmp.mrc.ac.uk!sunsite.doc.ic.ac.uk!ipg.umds.ac.uk!newsadm From: Department of Craniofacial Development Newsgroups: bionet.software Subject: Re: Sequence aligment programs for the mac Date: 5 Oct 1995 20:45:58 GMT Organization: Department of Craniofacial Development Lines: 11 Message-ID: <451g66@news-ipg.umds.ac.uk> References: NNTP-Posting-Host: cfd-lab.umds.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: friedmrd@post.drexel.edu X-URL: news:friedmrd-0410951028130001@n1-2-202.macip.drexel.edu friedmrd@post.drexel.edu (Richard Friedman) wrote: >Does anyone know of a program which will allow for DNA sequence alignment >which can be used on the Mac? How about Greg Schuler's Macaw (at ) which handles up to about= 20-30 sequences very well. It's user friendly too. Nadeem From owner-software@net.bio.net Wed Oct 04 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!simtel!oleane!jussieu.fr!pasteur.fr!usenet From: Hassan Badrane Newsgroups: bionet.software Subject: Re: Sequence aligment programs for the mac Date: 5 Oct 1995 10:00:48 GMT Organization: Institut Pasteur Lines: 8 Message-ID: <450acg$d5f@montespan.pasteur.fr> References: NNTP-Posting-Host: hbadrane@mendel.sis.pasteur.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 4.1.3 sun4m) To: friedmrd@post.drexel.edu X-URL: news:friedmrd-0410951028130001@n1-2-202.macip.drexel.edu hi, ftp://ftp.embl-heidelberg.de/pub/software/mac/ you will find "align" and "clustalw". Hassan From owner-software@net.bio.net Wed Oct 04 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!xlink.net!news.dfn.de!news.embl-heidelberg.de!bioftp.unibas.ch!daresbury!hgmp.mrc.ac.uk!jclewley From: jclewley@hgmp.mrc.ac.uk (Dr. J.P. Clewley) Newsgroups: bionet.software Subject: Re: Sequence aligment programs for the mac Date: 5 Oct 1995 15:45:18 GMT Organization: UK HGMP Resource Centre Lines: 8 Message-ID: <450uie$sb9@mercury.hgmp.mrc.ac.uk> References: <450man$b1s@usenet.ucs.indiana.edu> NNTP-Posting-Host: tin.hgmp.mrc.ac.uk You might also want to look at MACAW ftp to ncbi.nlm.nih.gov Commercially, MegAlign of Lasegene (DNAStar) is good, or GeneJockey Jon Clewley From owner-software@net.bio.net Wed Oct 04 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!in1.uu.net!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!cronkite.ocis.temple.edu!usenet From: Joel Sheffield Newsgroups: bionet.software Subject: Re: Wanted Ramdoubler for PC Date: 5 Oct 1995 14:36:14 GMT Organization: Temple University, Academic Computer Services Lines: 13 Message-ID: <450qgu$bsd@cronkite.ocis.temple.edu> References: NNTP-Posting-Host: zeos4.chem.temple.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) I have used SoftRam, one of several commercial programs -I have seen it for sale for $US 29.95-59.95 (Quite a range!). I don't know exactly how much RAM it makes available, but it certainly has improved the performance of several programs.rewpero@dial.eunet.ch (Recupero Marco) wrote: >Hi, does anyone know where to go to get Ramdoubler? > >Doesn't it causes a lot of bugs or is that ok? > >Thank's > From owner-software@net.bio.net Wed Oct 04 23:00:00 1995 Path: biosci!cmb.bcm.tmc.edu!solovyev From: solovyev@cmb.bcm.tmc.edu (Victor V. Solovyev) Newsgroups: bionet.software Subject: New Drosophila/Nematode/Invertebrate Gene-Finder programs Date: 5 Oct 1995 12:37:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: <199510051936.OAA02623@ostrich.cellb.bcm.tmc.edu> NNTP-Posting-Host: net.bio.net New BCM Gene-Finder service: ========================================================================== FGENED, FEXD and DSPL Recognition of Ivertebrate (Drosophila/Nematode) gene structure ========================================================================== These three new program developed for analysis of Invertebrate sequences: the programs are similar with Gene-finder programs that were developed earlier for analysis of Human or Mammalian sequences. They work for Drosophila as well as for Nematode sequences. You can receive instruction about sequence format from WWW page FGENED -prediction of gene structure with assembling of potential exons FEXD - prediction of 5'-, internal and 3'- potential exons DSPL - prediction of splice sites Analysis of uncharacterized sequences and help files are available through WWW: http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html or by sending your file containing a sequence (the sequence format is described below) Weizmann Institute of Science Email services: services@bioinformatics.weizmann.ac.il (and soon will be available in University of Houston: service@bchs.uh.edu ) Examples: mail -s fgened services@bioinformatics.weizmann.ac.il < test.seq or mail -s fgened service@bchs.uh.edu < test.seq where test.seq a file with the sequence. The same for FEXD and DSPL programs. Questions:solovyev@cmb.bcm.tmc.edu =============================================================== The other services are =============================================================== FGENEH - search for Mammalian gene structure with exons assembling by dynamic programming FEXH - search for 5'-, internal and 3'-exons HEXON - search for internal exons HSPL - search for splice sites RNASPL - prediction exon-exon junctions in cDNA sequences CDSB - prediction of Bacterial coding regions HBR - recognition of human and bacterial sequences to test a library for E. coli contamination by sequencing example clones TSSG - recognition of human promoter regions (Ghosh/Prestridge motif data) TSSW - recognition of human promoter regions (Weingender motif data base) POLYAH - recognition of of 3'-end cleavage and polyadenilation region of human mRNA precursors FGENED - search for Invertebrate gene structure with exons assembling by dynamic programming FEXD - search for Invertebrate 5'-, internal and 3'-exons DSPL - search for Invertebrate splice sites SSP - prediction of a-helix and b-strand in globular proteins by segment-oriented approach. NSSP - prediction of a-helix and b-strand segments in globular proteins by nearest-neighbor algorithm. From owner-software@net.bio.net Thu Oct 05 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!in2.uu.net!panix!bloom-beacon.mit.edu!ai-lab!bronze.lcs.mit.edu!not-for-mail From: bw@bronze.lcs.mit.edu (Bruce Waldman) Newsgroups: bionet.software Subject: SigmaGel Date: 6 Oct 1995 05:46:31 -0400 Organization: MIT AI/LCS labs Lines: 9 Message-ID: <452ttn$89a@bronze.lcs.mit.edu> NNTP-Posting-Host: bronze.ai.mit.edu Is anyone using Jandel SigmaGel? I have the program but it crashes as soon as I load the first sample image that they provide. Jandel is unresponsive to my requests for assistance. Has anyone gotten this program to work? Thanks Bruce Waldman bw@gnu.ai.mit.edu From owner-software@net.bio.net Thu Oct 05 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!news00.sunet.se!sunic!sunic!sunic.sunet.se!news.uni-c.dk!news.daimi.aau.dk!biobase!nagstrup From: nagstrup@biobase.dk (Bent Nagstrup) Newsgroups: bionet.software,comp.os.linux.misc Subject: Re: porting SUN-gcg to Linux? Followup-To: bionet.software,comp.os.linux.misc Date: 6 Oct 1995 06:52:09 GMT Organization: The Danish BioBase Lines: 18 Message-ID: <452jmp$lrb@biovax.biobase.dk> References: <44tdt9$cgq@sdcc12.ucsd.edu> NNTP-Posting-Host: biobase.dk X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software:13530 comp.os.linux.misc:72493 Is the gcg-package freeware? Otherwise it might not be so cool... And, anyway the gcg programs are not worth so much without all the gigabytes of databases and very fast cpu's, so I really don't think it would be worth the bother to spend some months porting gcg to your '486sx with a 420 MB harddrive :) But please don't let that stop you: I also use Linux at home and I also think it's a neat idea, but maybe not practically possible... keep hacking! Bent -- /-------------------------------------------------------------------------\ | Bent Nagstrup Johansen | | Finger me for PGP v2.6.2i public key | | "if you outlaw privacy, only outlaws will have privacy" | \-------------------------------------------------------------------------/ From owner-software@net.bio.net Thu Oct 05 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!simtel!zombie.ncsc.mil!cs.umd.edu!haven.umd.edu!purdue!lerc.nasa.gov!magnus.acs.ohio-state.edu!cis.ohio-state.edu!nntp.sei.cmu.edu!bb3.andrew.cmu.edu!andrew.cmu.edu!ng10+ From: Nigel Goddard Newsgroups: bionet.software,bionet.jobs,bionet.neuroscience Subject: JOB: C/C++/Neuroscience/Scientific Computing Date: Fri, 6 Oct 1995 16:23:55 -0400 Organization: Pittsburgh Supercomputing Center, Carnegie Mellon, Pittsburgh, PA Lines: 53 Message-ID: <4kRN1PG00jW=1I_KAY@andrew.cmu.edu> NNTP-Posting-Host: po7.andrew.cmu.edu Xref: biosci bionet.software:13531 bionet.neuroscience:10600 Please do not forward this to other bboards, but you can forward it to selected individuals you think may be suitable. I'm looking for an experienced C/C++ programmer to work on "neural" software in a high-performance scientific computing environment. Almost all the work will be focused on parallel platforms: workstation clusters, massively parallel supercomputers and SMPs. The user community is scientists in neuroscience, psychology and other related disciplines. The full text of the job ad appears below. Respond to ngoddard@psc.edu. Nigel Goddard TITLE: Applications Programmer DEPARTMENT: Pittsburgh Supercomputing Center (PSC) SALARY RANGE: Negotiable STARTING RANGE: Negotiable FLSA STATUS: Exempt HOURS: Full-time The Pittsburgh Supercomputing Center (PSC) is currently seeking candidates for the position of Applications Programmer to participate in software development work within the Biomedical Applications Group of PSC. In addition to being a national center established by the National Science Foundation, the PSC is a National Institutes of Health sponsored research resource and has an extensive program of research and development of biomedical applications, including molecular modeling, protein and nucleic acid sequence analysis and neural science. This position is responsible for helping to develop software for the biomedical applications group at the Pittsburgh Supercomputing Center, particularly in the neural sciences area and with a focus on parallel applications. The position responsibilities will include writing original code as well as working with existing code, and the associated documentation and test routines. Examples of projects include: parallelization of the GENESIS neural simulation system; development of a database system for neural models and associated data; development of near real-time parallel image processing software for functional magnetic resonance imaging studies. QUALIFICATIONS: Bachelor of Science in Computer Science or Engineering or equivalent experience; two years of professional experience in developing large programs is highly desireable. Candidate should be proficient in C++ or C, and have working knowledge of FORTRAN and the ability to communicate effectively with co-workers and end users. It is highly desireable for the candidate to have experience working on group programming projects and experience with high performance computers or parallel programming environments. Experience programming with MPI, PVM and AVS and with neural network or computational neuroscience applications is highly desireable. This is a summary statement of the responsibilities and qualifications for this position. From owner-software@net.bio.net Fri Oct 06 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: DNA Format Conversion Date: 7 Oct 1995 03:28:37 GMT Organization: Biology, Indiana University - Bloomington Lines: 9 Message-ID: <454s55$qh2@usenet.ucs.indiana.edu> References: NNTP-Posting-Host: sunflower.bio.indiana.edu You can use Readseq on macs (a biosequence format converter), but i'd suggest using seqpup or seqapp instead, which include readseq. Here are addresses to fetch from: ftp://iubio.bio.indiana.edu/molbio/seqpup/ ftp://iubio.bio.indiana.edu/molbio/seqapp/ -- this one is older ftp://iubio.bio.indiana.edu/molbio/readseq/ -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Fri Oct 06 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!news10.sunet.se!news00.sunet.se!sunic!news.sprintlink.net!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts (Zoology)) Newsgroups: bionet.software Subject: Re: WINDOWS compiler for DLLs Date: 7 Oct 1995 10:00:04 GMT Organization: University of Cambridge, England Lines: 42 Distribution: bionet Message-ID: <455j34$afi@lyra.csx.cam.ac.uk> References: <44dmki$9q6@mserv1.dl.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk "Lorin Milescu" writes: > Hi ! > There is anyone knowing about a compiler for WINDOWS >to produce DLLs, from one of the following: C, Pascal, FORTRAN, >Basic etc., FREEWARE, except gcc compiler ? > Thanks. As far as I am aware there are *no* free or shareware compilers for Windows. A couple of BASIC interpreters but that's it. You will need to buy a commercial compiler. Here are the ones I know of: Language Compiler Windows95/WindowsNT Windows 3.x C Visual C++ 2 Yes No C Visual C++ 1 No Yes C Borland C++ Yes Yes C Watcom C++ Yes Yes C Symantec C++ Don't know Yes Pascal Turbo Pascal for Win No Yes Pascal Borland Pascal 7.0 No Yes Pascal Borland Delphi Not yet Yes FORTRAN Microsoft Fortran Don't know Yes Basic Visual Basic Not sure Yes Of these, the Borland compilers are the cheapest. As far as I am aware Visual Basic cannot create DLLs. I used Turbo Pascal for Windows for about three years and really liked it. I currently use the two Microsoft C++ compilers, which are both very good, especially the 32bit NT/Windows 95 version. The Borland C++ compilers are also very good. I haven't used the Watcom or Symantec products. Watcom has the advantage that in a single package you get all the compilers for DOS, Windows 3.x, Windows NT, and OS/2. If you only want to write stuff for 16 bit Windows, I would recommend Borland C++ 3.x (very cheap these days because it's so old) or Turbo Pascal for Windows (also very cheap because of its age). Creation of DLLs in TPW is trivially easy compared to doing it in C++. Regards, Tim. From owner-software@net.bio.net Fri Oct 06 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!torn!news.bc.net!rover.ucs.ualberta.ca!scanner.worldgate.com!umsedm.worldgate.com!user From: David_Frederiksen@ums.supernet.ab.ca (David Frederiksen) Newsgroups: bionet.software Subject: DNA Format Conversion Date: Fri, 06 Oct 1995 18:35:40 -0700 Organization: Sphincter Labs Inc. Lines: 9 Message-ID: NNTP-Posting-Host: umsedm.worldgate.com X-Newsreader: Yet Another NewsWatcher 2.0b30 Can anyone direct me to some MAC software that will convert Gene Bank formats to Phylip formats? I will use what ever is available ... anything but long hand transposition. David Frederiksen -- Have you hugged a tree today? From owner-software@net.bio.net Fri Oct 06 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!simtel!harbinger.cc.monash.edu.au!yoyo.aarnet.edu.au!news.adelaide.edu.au!mc-ii2.waite.adelaide.edu.au!user From: m-kamei@waite.adelaide.edu.au (Makoto Kamei) Newsgroups: bionet.software Subject: Re: DNA restriction analysis programming Date: Wed, 04 Oct 1995 13:25:04 +0930 Organization: The University of Adelaide Lines: 21 Distribution: world Message-ID: References: <446vqc$jl0@ns2-1.CC.Lehigh.EDU> <449n1k$d74@sparcserver.lrz-muenchen.de> NNTP-Posting-Host: mc-ii2.waite.adelaide.edu.au In article <449n1k$d74@sparcserver.lrz-muenchen.de>, salger@wap1.zi.biologie.uni-muenchen.de (Klaus Salger) wrote: >You could try Double Digester. You can get it from ftp.cs.yale.edu or >IUbio or many other sites. It's available for Sun and HP workstations >and for Macintosh. > Didn't work for Macintosh LC630 running System 7.5.1. I contacted the author but was told that he no longer has time to fix the bug. However, I also was told that this program works quite well if you are running pre-System 7.5 machines. Makoto -- Makoto Kamei Insect Molecular Biology Group Dept. of Crop Protection The Univ. of Adelaide Australia From owner-software@net.bio.net Fri Oct 06 23:00:00 1995 Newsgroups: bionet.software,comp.os.linux.misc Path: biosci!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: porting SUN-gcg to Linux? Message-ID: <1995Oct7.101820.10755@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <44tdt9$cgq@sdcc12.ucsd.edu> <452jmp$lrb@biovax.biobase.dk> Date: Sat, 7 Oct 1995 10:18:20 GMT Lines: 48 Xref: biosci bionet.software:13536 comp.os.linux.misc:72572 Bent Nagstrup (nagstrup@biobase.dk) wrote: : Is the gcg-package freeware? Otherwise it might not be so cool... The GCG package is *NOT* freeware. If you mount any copy you must have a license. It might be possible, convincing arguments provided, that license agreements can be made with the company to accomodate this special situation (This is plain speculation, and usual disclaimers apply; I don't work for them etc.) : And, anyway the gcg programs are not worth so much without all the gigabytes : of databases and very fast cpu's, so I really don't think it would be worth : the bother to spend some months porting gcg to your '486sx with a 420 MB : harddrive :) Disks are getting cheap these days. Missing disk space will only matter if you use non-SCSI hardware. CPU's are another issue but you can bare with a PC-type of performance if it is for single user entities - You might wait for a day or two but you'll make it. : But please don't let that stop you: I also use Linux at home and I also : think it's a neat idea, but maybe not practically possible... Another approach will be to use Solaris on the PC, and then (theoretically) it should work. However, question being, what do you gain? The software will continue to evolve and, unless you can convince the provider that they support your 'port', it will be a looser at the first problem or update you encounter. Do not forget that Fortran on Linux is still fairly young and GCG uses F77 at least partially to some extent. Linux is a good system if you use software which is either supported or made specifically for Linux. Given the restricted computational power, I would suggest a low-end workstation (for academics , 15k$ should be enough for a 'single user' 8GBytedisk/64MByte memory box) and this gets you the clean and smooth access to software which is supported, for no porting cost. You want do do it yourself, still? Consider your rating of personpower which you would apply if you want to get hired by someone. Experience provided, at least $200 per hour is the rate for good specialists. In only 100 hours you'll have assembled your workstation - that is less than half a year if you spent two hours of your free time each day (Sixpacks and coffee not counted). regards Reinhard -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| BioComputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-software@net.bio.net Fri Oct 06 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!news10.sunet.se!news00.sunet.se!sunic!news.sprintlink.net!simtel!swidir.switch.ch!scsing.switch.ch!news.belwue.de!News.Uni-Marburg.DE!papin.HRZ.Uni-Marburg.DE!klieber From: klieber@papin.HRZ.Uni-Marburg.DE (Hans-Georg Klieber) Newsgroups: bionet.software Subject: Re: SigmaGel Date: 7 Oct 1995 07:55:19 GMT Organization: Hochschulrechenzentrum der Universitaet Marburg Lines: 21 Message-ID: <455bp7$13c@surz03.HRZ.Uni-Marburg.DE> References: <452ttn$89a@bronze.lcs.mit.edu> NNTP-Posting-Host: papin.hrz.uni-marburg.de X-Newsreader: TIN [version 1.2 PL2] Bruce Waldman (bw@bronze.lcs.mit.edu) wrote: > Is anyone using Jandel SigmaGel? I have the program > but it crashes as soon as I load the first sample image > that they provide. Jandel is unresponsive to my requests > for assistance. Has anyone gotten this program to work? Dear Sir, I recently considered to by this software but haven't done so yet. I would be very interested to learn about your further experiences with Jandel and the functionality of the program. Regards, Hans-Georg --------------------------------------------------- Dr. Hans-Georg Klieber Institute for Physiology, University of Marburg Deutschhausstrasse 2, 35033 Marburg, Germany From owner-software@net.bio.net Fri Oct 06 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!pcnet.com!news.dfw.net!dfw.net!cnichols From: cnichols@dfw.net (Cary Nichols) Newsgroups: bionet.software Subject: Story Developer Elite --Writer's Software Date: 7 Oct 1995 17:54:00 GMT Organization: DFWNet -- Public Internet Access Lines: 64 Message-ID: <456ero$qdr@fnord> NNTP-Posting-Host: dfw.net X-Newsreader: TIN [version 1.2 PL2] Announcing new software for writers from The Writer's Notebook: (All are for Windows.) Story Developer Elite Story Developer Lite The Writer's Toolkit Story Developer Elite comes on four installation diskettes. It has a multi-document interface where the screens are available with just a mouse- or key-press, or menu-selectable, or icons. Screens include CharacterCards, PlotSummary, PlotCards, SceneCards, StoryNotes, ThemeCards, Multi-AddressBooks, Multi-PhoneBooks, Calendar, IdeaCards, AuthorsJournal, InterviewCards, ResourceCards, SubmissionCards, Text Editor, etc. You can connect to the programs of your own choice, and return back to SDE. You can arrange the sheets (screens) by Cascade, Layer, TileVertical, or TileHorizontal. Lots more options! Story Developer Elite is only $ 44.95 to internet subscribers (compares to programs costing hundreds of dollars). Story Developer Lite contains CharacterCards, PlotCards, SceneCards, ThemeCards, SettingCards, StoryCards, InterviewCards, SubmissionCards, IdeaCards, ResourceCards, AuthorsJournal, and NoteCards. Most screens allow unlimited typing within the text-boxes. SDL is for those of you who don't need the Multi-Adressbooks, Multi-phonebooks, or Calendar, etc. Story Developer Lite is only $34.95 to internet subscribers. The Writer's Toolkit consists of Character Generator, Story Generator, and NoteCards. You can switch between the three with just a mouse- or key-click. The Character Generator has button-tabs to the left of the screens. Screens are for Physical Traits, Personal Beliefs, Psychological Traits, Profession/Occupation, Family Background, Relationships, Music/Literature/Art, Education, Geographical, Experiences, Recreation, and Character Tags. The Story Generator has button-tabs to the left of the screens. Screens are for Title, Time Period, Locale, Description, Protagonist, Antagonist, Others, Background, Beginning, Middle, Ending, and Details. Both the CG & SG have unlimited-entry scrollable screens with text-boxes relating to each. (e.g., the Physical Traits screen contains boxes for entry of Age, Height, Weight, Eyes, Hair, IQ, Nationality, Skin Color, Facial Details, Body, Posture, Scars, Voice, etc.) The NoteCards allow unlimited typing, and as many cards as you like (Creation date is kept, so you can use the NoteCards as an Author's Journal, or for any other purpose you like). The Writer's Toolkit is only $ 34.95 to internet subscribers. ... OR GET ALL THREE FOR ONLY $ 59.95 !!! (internet subscribers only). ... or get any two for $ 49.95 (Magazine ads begin within the next couple of months with all three at higher prices.) To order products from The Writer's Notebook, send check or money-order made payable to Cary Nichols, to: Cary Nichols P.O. Box 20161 Ft. Worth, TX 76102-8161 To download a presentation of SDE: http://www.dfw.net/~cnichols/ or ftp: dfw.net/pub/users/sde/sde.zip Send e-mail to: cnichols@dfw.net From owner-software@net.bio.net Sat Oct 07 23:00:00 1995 Path: biosci!agate!spool.mu.edu!daily-planet.execpc.com!sundog.tiac.net!news.sprintlink.net!simtel!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-stuttgart.de!uni-regensburg.de!fauern!winx03!wpxx02.toxi.uni-wuerzburg.de!krasel From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: DNA Format Conversion Date: 7 Oct 1995 15:38:09 GMT Organization: Dept. of Pharmacology, U Wuerzburg Lines: 14 Message-ID: <4566t1$gpu@winx03.informatik.uni-wuerzburg.de> References: NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [version 1.2 PL2] David Frederiksen (David_Frederiksen@ums.supernet.ab.ca) wrote: > Can anyone direct me to some MAC software that will convert Gene Bank > formats to Phylip formats? I will use what ever is available ... anything > but long hand transposition. I think Don Gilbert has a Mac port of his Unix program readseq available at ftp.bio.indiana.edu. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Sat Oct 07 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!in2.uu.net!news.u.washington.edu!evolution.genetics.washington.edu!joe From: joe@evolution.genetics.washington.edu (Joe Felsenstein) Newsgroups: bionet.software Subject: Re: DNA Format Conversion Date: 8 Oct 1995 04:26:21 GMT Organization: University of Washington Genetics Lines: 18 Message-ID: <457jtd$pqg@nntp3.u.washington.edu> References: <4566t1$gpu@winx03.informatik.uni-wuerzburg.de> NNTP-Posting-Host: evolution.genetics.washington.edu Summary: Align them first! Keywords: DNA sequence formats, phylogenies, alignment In article <4566t1$gpu@winx03.informatik.uni-wuerzburg.de>, Cornelius Krasel wrote: >David Frederiksen (David_Frederiksen@ums.supernet.ab.ca) wrote: >> Can anyone direct me to some MAC software that will convert Gene Bank >> formats to Phylip formats? I will use what ever is available ... anything >> but long hand transposition. > >I think Don Gilbert has a Mac port of his Unix program readseq available >at ftp.bio.indiana.edu. Before goiing straight from GENBANK files to PHYLIP, you ought to align the sequences first, with something like ClustalW. Otherwise PHYLIP will be casually assuming that site 1 of one sequence is aligned with site 1 of annother. ----- Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41) Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA From owner-software@net.bio.net Sat Oct 07 23:00:00 1995 Path: biosci!agate!newsxfer.itd.umich.edu!chi-news.cic.net!news.jmls.edu!premier3.premier.net!news From: spcsinc@tyrell.net (Mark W. McBride, President) Newsgroups: bionet.software Subject: RDBMS with barcoding - Announce Date: Sun, 08 Oct 1995 16:12:35 GMT Organization: Scadinavian PC Systems, Inc. Lines: 47 Message-ID: <458tg9$bmr@premier3.premier.net> Reply-To: spcsinc@tyrell.net NNTP-Posting-Host: claitors.dialup.premier.net X-Newsreader: Forte Free Agent 1.0.82 Hello! All are invited to visit our web site and download a working trial version of SPCS PrimaBase(R) - a relational database management system for Windows that uniquely offers integrated barcode support and printing. It is free-form, fully relational, easy to set up and operate and fast. It operates on a 286 w/1MB RAM (NSTL verified) and flies on a 386. That's what we use in-house (no 486s or Pentiums) and I have more than half a million records flying through it. Full install space is about 2MB - not less powerful just tight code! And yes, you *can* print barcodes with the trial version. SPCS PrimaBase prints and supports: Full ASCII Code 39, Code 128, Interleaved 2 of 5, UPC-A, UPC-E, EAN-8, EAN-13 and US Postnet with Delivery Point. Single station and network versions supporting from 5 to 32 concurrently operating nodes are available. The trial version is network ready for 1-4 concurrently operating nodes. Hope to hear from you soon! Any questions, just write! Best, Mac ----------------------------------------------------------------------- |SCANDINAVIAN PC SYSTEMS, INC "Not high tech, | | Baton Rouge, La = 504-338-9580 not low tech, just | | 9 a.m.-5:30 p.m. Central M-F the *right* tech!" (R)| |-----------------------------------------------------------------------| |SPCS, Inc. is a Vietnam-era veteran operated small business. Est. 1985| |-----------------------------------------------------------------------| | WWW: http://www.tyrell.net/~spcsinc | E-Mail: spcsinc@tyrell.net| | Alternative WWW address: http://www.tyrell.net/~spcsinc/pageone.html | | Alternative E-mail address: mark.mcbride@sbaonline.gov | |-----------------------------------------------------------------------| | Snail mail to: SPCS, Inc., P.O. Box 3156, Baton Rouge LA 70821-3156 | |-----------------------------------------------------------------------| | Publishers of: John C. Dvorak's PC Crash Course and Survival Guide(tm)| | SPCS' PC Crash Course and Survival Guide (tm) for Windows | |Computer-based writing aids: Readability(tm) Plus & Corporate Voice(tm)| | SPCS PrimaBase(R) - Windows RDBMS uniquely offering barcode support! | ------------------------------³ºÞº³º³Û³ºÝ³ºÝ³³------------------------- NOTE: Demo disks on several of our products are available for download at our web site. If you attempt to get to our web site and are unable to access our pages, please let us know by return e-mail as quickly as possible so that we may correct the problem. Thank you for your interest and assistance! From owner-software@net.bio.net Sat Oct 07 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!usenet.eel.ufl.edu!news.ultranet.com!bigboote.WPI.EDU!news3.near.net!yale!yale.edu!news.ycc.yale.edu!branford-college-node.net.yale.edu!user From: maxwell@minerva.cis.yale.edu (Max Heiman) Newsgroups: bionet.software Subject: Re: WebCutter now in Sweden Date: Sun, 08 Oct 1995 01:53:16 -0700 Organization: Yale University Lines: 14 Message-ID: References: <44okm1$5ae@mercury.hgmp.mrc.ac.uk> <44rgrq$jdd@winx03.informatik.uni-wuerzburg.de> NNTP-Posting-Host: 130.132.110.157 I was wondering why so few users were taking advantage of the new webcutter mirror! Please email me at maxwell@minerva.cis.yale.edu if you don't get a response from it, or if you have any other problems, and I'll try to get things running right away. Please include in your message what time you tried to connect and exactly what happened (that is, were you able to reach the home page but not run the analysis, or could you not even reach the home page? Did your browser get stuck at "Contacting host..." or did it tell you something like "This server is busy or refusing connections."? Are you able to connect to the webcutter site at http://firstmarket/firstmarket/cutter?) Thanks a lot, and sorry for the inconvenience, MH From owner-software@net.bio.net Sun Oct 08 23:00:00 1995 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!newsfeed.internetmci.com!newsxfer.itd.umich.edu!uunet!in2.uu.net!news.connectnet.com!usenet From: billr@emsys.com (Bill Richardson) Newsgroups: bionet.software Subject: ANNOUNCE: Peachtree Support Center online Date: Mon, 09 Oct 1995 02:52:23 GMT Organization: CONNECTnet Internet Network Services (service provider) Lines: 10 Message-ID: <45a2pa$dn5@news.connectnet.com> NNTP-Posting-Host: emsys.com X-Newsreader: Forte Free Agent 1.0.82 CompTech, LTD announces the launch of their Peachtree Support Center online Website. The only authorized Peachtree Support Center in Wisconsin, CompTech provides online, telephone, and onsite technical support, as well as Peachtree authorized Training, for all Peachtree Software products. Check them out at: http://www.emsys.com/comptech/ From owner-software@net.bio.net Sun Oct 08 23:00:00 1995 Path: biosci!agate!news.ucdavis.edu!library.ucla.edu!info.ucla.edu!newsfeed.internetmci.com!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!news From: Christopher Spry Newsgroups: bionet.software Subject: Re: WebCutter now in Sweden Date: 9 Oct 1995 09:30:07 GMT Organization: St. George's Hospital Medical School Lines: 37 Message-ID: <45aq2v$619@mercury.hgmp.mrc.ac.uk> References: <44okm1$5ae@mercury.hgmp.mrc.ac.uk> <44rgrq$jdd@winx03.informatik.uni-wuerzburg.de> NNTP-Posting-Host: sprysgi.sghms.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX 5.3 IP22) To: maxwell@minerva.cis.yale.edu X-URL: news:maxwell-0810950153160001@branford-college-node.net.yale.edu maxwell@minerva.cis.yale.edu (Max Heiman) wrote: >I was wondering why so few users were taking advantage of the new >webcutter mirror! You may not have seen my posting. I think that there are serious problems with some of the European network services. My posting: ---------------- Internet access to many hosts is often very poor. For example this host was unusable from here on Mon Oct 2 at 13:04:26 BST 1995. %traceroute www.medkem.gu.se traceroute to rna.medkem.gu.se (130.241.76.38), 30 hops max, 40 byte packets 1 route1.sghms.ac.uk (192.153.12.2) 4 ms 2 ms 2 ms 2 193.61.71.65 (193.61.71.65) 4 ms 3 ms 4 ms 3 eu-gw.ja.net (193.63.94.2) 4 ms 103 ms 112 ms 4 gw.linx.ja.net (193.62.157.14) 4 ms 7 ms 6 ms 5 UK-s0.dante.bt.net (194.72.26.197) 55 ms * 72 ms 6 * 194.72.7.4 (194.72.7.4) 58 ms * 7 NL-s1-0.eurocore.bt.net (194.72.24.134) 156 ms * * 8 SE-s0.dante.bt.net (194.72.24.10) 253 ms 249 ms * 9 NORDUnet-s0.dante.bt.net (194.72.26.50) 264 ms 291 ms 258 ms 10 * * lower-gw.sunet.se (192.36.148.197) 285 ms 11 * * gbg34-gw.sunet.se (193.10.85.18) 257 ms 12 * * * 13 med-bmb-gw.gu.se (130.241.80.2) 235 ms 265 ms 252 ms 14 rna.medkem.gu.se (130.241.76.38) 266 ms * * Does anyone know who I should contact about this poor service? --------------------------------------- Christopher Spry. cspry@sghms.ac.uk From owner-software@net.bio.net Sun Oct 08 23:00:00 1995 Path: biosci!agate!spool.mu.edu!news.sol.net!daily-planet.execpc.com!news.moneng.mei.com!news.ecn.bgu.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!plug.news.pipex.net!pipex!dish.news.pipex.net!pipex!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!newshost.rpms.ac.uk!usenet From: Dr Mick Jones Newsgroups: bionet.software Subject: HELP: All MacUsers Date: 4 Oct 1995 10:46:16 GMT Organization: Virology, RPMS Lines: 38 Message-ID: <44tolo$9o@newshost.rpms.ac.uk> NNTP-Posting-Host: virol11.rpms.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.software HELP (Please). I have on my desk a Mac Centris 650 with 8Mb RAM, etc. and yesterday I upgraded my system software to 7.5 (using a CD version of the software). Everything seemed to load and work as expected. However, when I insert a floppy disk into the drive NOTHING. No floppy icon appears on the monitor screen. Desktop doesn't recognise the drive. If I use Norton Utilities to check the floppy disk, it eventually brings up the icon on screen, so that I can then access the files on the floppy as normal. However, if I eject the disk and then insert another one, I get the same problem; it is not recognised. Any suggestions gratefully received. Also does anybody know of another newsgroup where help can be obtained Does anybody knoe of an Apple email address for technical support (preferably in the UK or Europe)? Many thanks. Please reply to mjones@rpms.ac.uk Mick _____________________________________________________________________ Mick Jones Tel: 081-740-3328 (+44-81-740-3328) Department of Virology FAX: 081-743-8331 (+44-81-743-8331) RPMS, Du Cane Road Email: mjones@rpms.ac.uk London, W12 0NN, UK URL: http://www.rpms.ac.uk/rpms_home.html *********************************************************** "Smoke me a kipper, I'll be back for breakfast." Ace Rimmer (Red Dwarf) "Crackin' bit of toast, Gromit." Wallace (The Wrong Trousers) _____________________________________________________________________ From owner-software@net.bio.net Sun Oct 08 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!in1.uu.net!news.usa.net!port31.cos1-annex.usa.net!clvaivod From: clvaivod@super7.uccs.edu (Carla L. Vaivoda) Newsgroups: bionet.software Subject: COLORADO> Colorado Springs Software Roundtable Meeting Date: Mon, 9 Oct 1995 13:39:29 Organization: Colorado Springs Software Roundtable Lines: 19 Message-ID: NNTP-Posting-Host: port31.cos1-annex.usa.net Summary: COLORADO Software Roundtable Meeting Keywords: COLORADO Software Roundtable Meeting X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Tuesday, October 24, 1995: The Colorado Springs Software Roundtable will kick off its new season with a meeting/presentation on development and marketing strategies for Windows 95 applications. This will be apanel presentation led by Doug LeMaire of Bendata. If you are involved in software development and/or marketing you won't want to miss this meeting! Where: Embassy Suites Hotel 7290 Commerce Center Drive Colorado Springs, CO When: Tuesday, October 24, 1995 4:00pm - registration 4:30pm - program begins Cost: $15.00 non-members, free to Software Roundtable members. Register with CITTI before October 23 by calling 719-548-8245. Refreshments will be served - Cash Bar From owner-software@net.bio.net Sun Oct 08 23:00:00 1995 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.reston.ans.net!agate!msunews!netnews.upenn.edu!biochem.dental.upenn.edu!ellis From: ellis@biochem.dental.upenn.edu (Ellis Golub) Newsgroups: bionet.software Subject: Re: SigmaGel Date: 9 Oct 1995 00:52:43 GMT Organization: University of Pennsylvania Lines: 47 Distribution: world Message-ID: <459ror$s8c@netnews.upenn.edu> References: <452ttn$89a@bronze.lcs.mit.edu> <455bp7$13c@surz03.HRZ.Uni-Marburg.DE> NNTP-Posting-Host: biochem.dental.upenn.edu I was a beta tester of this software. When the last beta release crashed just as you suggest, I reported it to Jandel. They told me that some other beta testers had had similar problems, and they were investigating. After a long period of silence, I received the first production release with a letter thanking me for testing it. When I reported that this version crashed when I opened an image, Jandel told me it was the fault of my hardware, that only 1% of users experience this problem and they weren't interested anymore. As I have other software for this purpose, I simply uninstalled my copy. Until then, my experiences with Jandel had been quite positive. SigmaPlot is among the best scientific plotting packages available. I had heard that SigmaGel was selling well and was gining user acceptence. However, based on my experience, I'd make sure it works in my system before investing in it. In article <455bp7$13c@surz03.HRZ.Uni-Marburg.DE>, klieber@papin.HRZ.Uni-Marburg.DE (Hans-Georg Klieber) writes: |> |> Bruce Waldman (bw@bronze.lcs.mit.edu) wrote: |> > Is anyone using Jandel SigmaGel? I have the program |> > but it crashes as soon as I load the first sample image |> > that they provide. Jandel is unresponsive to my requests |> > for assistance. Has anyone gotten this program to work? |> |> Dear Sir, |> |> I recently considered to by this software but haven't |> done so yet. I would be very interested to learn |> about your further experiences with Jandel and |> the functionality of the program. |> |> Regards, |> Hans-Georg |> |> --------------------------------------------------- |> Dr. Hans-Georg Klieber |> Institute for Physiology, University of Marburg |> Deutschhausstrasse 2, 35033 Marburg, Germany -- ============================================================================== Ellis Golub Phone: (215) 898-4629 Biochemistry Department FAX: (215) 898-3695 University of Pennsylvania ellis@biochem.dental.upenn.edu School of Dental Medicine 4001 Spruce Street Philadelphia, PA 19104-6003 =============================================================================== From owner-software@net.bio.net Sun Oct 08 23:00:00 1995 Path: biosci!ARTSCI.WUSTL.EDU!mpion From: mpion@ARTSCI.WUSTL.EDU (Martin Pion) Newsgroups: bionet.software Subject: Re: HELP: All MacUsers Date: 9 Oct 1995 10:06:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 103 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Mick, I recently installed a larger HD into my accelerated Mac LCII and took the opportunity to upgrade the system to 7.5 via a CD-ROM. After apparently installing OK I experienced a serious problem - it quit unexpectedly when using MSWord v5.1a, and subsequently my HD icon disappeared from the desktop - but I eventually got it working again after a couple of days of trying every software test that seemed relevant. I can't say exactly what will work for you but here's a list of software tests & fixes, most of which I had tried to cure my problem: Tests & Fixes. 1. If you have anti-viral software running continuously, switch it off, delete the original program from your hard disk and try reinstalling it. The program may have got corrupted by the AV software during installation or while it was running. 2. Reboot your machine holding down the shift key to disable all system extensions (no icons should appear along the bottom of the main monitor). Does the problem disappear? If it does then you will need to try and identify which extension is causing the problem. 3. Rebuild the desktop database by holding down Option-Command through out startup. Rebuild desktop for every drive connected. 4. Try using Norton Utilities to verify that all your drives and respective partitions are sound. Sometimes DiskFirst Aid [which is supplied on a floppy disk called Disk Tools which comes with System 7.5, will find and fix a problem that Norton [or Central Point] will miss. You must run DiskFirst Aid from an external floppy to fix any problems found. 5. Update your driver, using the Apple HD SC Setup, which comes on the same Disk Tools disk. Note: If this program can't find your internal hard drive you must use the driver update software that came with your particular drive. 6. Hold down Option-Command-P-R while booting your Mac. Note that the machine will appear to boot twice. This resets the Parameter RAM and if there was anything wrong with it, the problem should now be cured. 7. Finally, the thing which really worked to cure MY problem was removing the MSWord Preferences document from the System Folder and trashing it! [8. Not relevant to this problem: Is the application causing problems running in enough memory? Check from the Finder that it has its required amount to run by starting it and check from About this Macintosh in the Apple Menu that it has an adequate partition when the problem occurs. Do not run any other applications other than the Finder.] N.B. I'm sending this to all on this newsgroup as a list you may find useful when you run into a Mac problem. Good luck! Martin. Martin Pion, Biosoft, PO Box 10938, Ferguson, MO 63135. Tel: 314 524 8029 Fax: 314 524 8129 Acknowledgement: This list is based on one originally compiled by Dr Philip L. Taylor author of GeneJockey and AssayZap, and provided to me to help an end-user of GeneJockey cure a problem. =========================================== At 10:46 AM 10/4/95, Dr Mick Jones wrote: >HELP (Please). > >I have on my desk a Mac Centris 650 with 8Mb RAM, etc. and yesterday I >upgraded my system software to 7.5 (using a CD version of the software). >Everything seemed to load and work as expected. > >However, when I insert a floppy disk into the drive NOTHING. No floppy >icon appears on the monitor screen. Desktop doesn't recognise the >drive. If I use Norton Utilities to check the floppy disk, it >eventually brings up the icon on screen, so that I can then access the >files on the floppy as normal. However, if I eject the disk and then >insert another one, I get the same problem; it is not recognised. > >Any suggestions gratefully received. > >Also does anybody know of another newsgroup where help can be obtained > >Does anybody knoe of an Apple email address for technical support >(preferably in the UK or Europe)? > >Many thanks. > >Please reply to mjones@rpms.ac.uk > >Mick > >_____________________________________________________________________ >Mick Jones Tel: 081-740-3328 (+44-81-740-3328) >Department of Virology FAX: 081-743-8331 (+44-81-743-8331) >RPMS, Du Cane Road Email: mjones@rpms.ac.uk >London, W12 0NN, UK URL: http://www.rpms.ac.uk/rpms_home.html >*********************************************************** >"Smoke me a kipper, I'll be back for breakfast." Ace Rimmer (Red >Dwarf) >"Crackin' bit of toast, Gromit." Wallace (The Wrong Trousers) >_____________________________________________________________________ From owner-software@net.bio.net Sun Oct 08 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!nntp.crl.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!sherlockholmes.chem.ualberta.ca!user From: Scott.Delinger@Ualberta.Ca (Scott L. Delinger) Newsgroups: bionet.software Subject: Re: Sequence aligment programs for the mac Date: Mon, 09 Oct 1995 10:21:39 -0600 Organization: U of Alberta, Department of Chemistry Lines: 14 Message-ID: References: NNTP-Posting-Host: sherlockholmes.chem.ualberta.ca X-Newsreader: Yet Another NewsWatcher 2.0.1 In article , friedmrd@post.drexel.edu (Richard Friedman) wrote: >Does anyone know of a program which will allow for DNA sequence alignment >which can be used on the Mac? You might look at Sequencher 3.0, commercial software from Gene Codes Corp, info@genecodes.com 313.769.7249 (Ann Arbor, Michigan, USA) -- Scott L. Delinger U of Alberta, Department of Chemistry Scott.Delinger@Ualberta.Ca From owner-software@net.bio.net Sun Oct 08 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!swrinde!tank.news.pipex.net!pipex!in2.uu.net!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!taurus.fccc.edu!news From: Vladimir Khazak Newsgroups: bionet.software Subject: Looking for DNA Strider Date: 9 Oct 1995 17:34:21 GMT Organization: Fox Chase Cancer Center Lines: 5 Message-ID: <45bmet$mq3@taurus.fccc.edu> NNTP-Posting-Host: scfuzzy.rm.fccc.edu I am trying to find out how to get DNA Strider program. Thanks, in advance, for any information! Ilya Serebriiskii From owner-software@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!uwm.edu!chi-news.cic.net!news.uiowa.edu!uunet!in1.uu.net!news.texoma.com!usenet From: Kenneth Ramsey Newsgroups: bionet.software Subject: Re: Sequence aligment programs for the mac Date: 10 Oct 1995 13:18:26 GMT Organization: Internet Texoma, Inc. Lines: 8 Message-ID: <45drr2$fr7@venus.texoma.com> References: NNTP-Posting-Host: ppp42.texoma.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.2N (Windows; I; 16bit) To: friedmrd-0410951028130001@n1-2-202.macip.drexel.edu You might also try MacVector. I use that software for my research and it has the capabilities of doing that. Use the 800 directory assistance to get a phone number for the company, look under Kodak Imaging. If you can't find the number drop me a note and I'll e-mail it to you. Ken Ramsey From owner-software@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!agate!news.ucdavis.edu!library.ucla.edu!newsfeed.internetmci.com!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!mail2news.demon.co.uk!ecmsel.demon.co.uk From: topjob Newsgroups: bionet.software Subject: C/C++, PC/Unix, Molecular Design, Oxford - ECM Selection Ltd Date: Tue, 10 Oct 95 12:21:59 GMT Organization: ECM SELECTION Lines: 31 Message-ID: <813327719snz@ecmsel.demon.co.uk> Reply-To: topjob@ecmsel.co.uk X-NNTP-Posting-Host: ecmsel.demon.co.uk X-Newsreader: Demon Internet Simple News v1.27 Path: ecmsel.demon.co.uk!topjob From: topjob@ecmsel.demon.co.uk To: mail2news@news.demon.co.uk Newsgroups: uk.jobs.offered Subject: Ref:n.3216 - C/C++,PC/Unix, Molecular Design, to#25000, OXFORD Message-ID:<1000n.3216@ecmsel.demon.co.uk> Date: Tue, 10 Oct 95 12:05:53 Reply to: topjob@ecmsel.co.uk Our client is one of Europe's leading developers of computer aided molecular design software and database management systems for use principally by companies in the fields of pharmaceutical and biotechnology research. They urgently seek a number of high calibre PC/Unix Analyst Programmers to work on the next generation of projects. With an excellent academic background, ideally to PhD level, in Chemistry, Physics, Material Science, Mathematics or similar, you will have solid skills in C or C++ , preferably within a commercial environment, or from a relevant academic background. These are ideal opportunities to join this exciting development environnment, working on technically challenging projects in pleasant, modern surroundings. -- Please contact us by Email (CV's Plain ASCII please!): topjob@ecmsel.co.uk ----- Alternatively snail, fax or phone: ECM SELECTION LTD, The Maltings, Burwell, Cambridge, CB5 0HB Tel: 01638 742244 Fax: 01638 743066 From owner-software@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!news.cac.psu.edu!news.math.psu.edu!chi-news.cic.net!news.uiowa.edu!uunet!in1.uu.net!news.texoma.com!usenet From: Kenneth Ramsey Newsgroups: bionet.software Subject: Re: Sequence aligment programs for the mac Date: 10 Oct 1995 13:15:47 GMT Organization: Internet Texoma, Inc. Lines: 8 Message-ID: <45drm3$fr7@venus.texoma.com> References: NNTP-Posting-Host: ppp42.texoma.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.2N (Windows; I; 16bit) To: friedmrd@post.drexel.edu,(Richard,Friedman) You might also try MacVector. I use that software for my research and it has the capabilities of doing that. Use the 800 directory assistance to get a phone number for the company, look under Kodak Imaging. If you can't find the number drop me a note and I'll e-mail it to you. Ken Ramsey From owner-software@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!uwm.edu!chi-news.cic.net!news.uiowa.edu!uunet!in1.uu.net!news.texoma.com!usenet From: Kenneth Ramsey Newsgroups: bionet.software Subject: Re: Sequence aligment programs for the mac Date: 10 Oct 1995 13:16:55 GMT Organization: Internet Texoma, Inc. Lines: 8 Message-ID: <45dro7$fr7@venus.texoma.com> References: NNTP-Posting-Host: ppp42.texoma.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.2N (Windows; I; 16bit) To: bionet.software You might also try MacVector. I use that software for my research and it has the capabilities of doing that. Use the 800 directory assistance to get a phone number for the company, look under Kodak Imaging. If you can't find the number drop me a note and I'll e-mail it to you. Ken Ramsey From owner-software@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!mail2news.demon.co.uk!ecmsel.demon.co.uk From: topjob Newsgroups: bionet.software Subject: C++ Analyst, Molecular Design, Oxford - ECM Selection Ltd Date: Tue, 10 Oct 95 12:32:10 GMT Organization: ECM SELECTION Lines: 31 Message-ID: <813328330snz@ecmsel.demon.co.uk> Reply-To: topjob@ecmsel.co.uk X-NNTP-Posting-Host: ecmsel.demon.co.uk X-Newsreader: Demon Internet Simple News v1.27 Path: ecmsel.demon.co.uk!topjob From: topjob@ecmsel.demon.co.uk To: mail2news@news.demon.co.uk Newsgroups: uk.jobs.offered Subject: Ref:n.4206 - C++ Analyst, Molecular Design, to#25000, OXFORD Message-ID:<1000n.4206@ecmsel.demon.co.uk> Date: Tue, 10 Oct 95 12:05:53 Reply to: topjob@ecmsel.co.uk Our client is at the leading edge of computer aided molecular design software and database management systems for the pharmaceutical and biotechnology industries. They currently seek a high calibre Analyst Programmer, ideally with knowledge of Quantum Chemistry and development experience on Macintosh platforms. You will have a strong academic background, ideally to PhD level, in a scientific or numerate subject with solid programming skills in C++, ideally within a commercial environment or from a relevant academic project. This is an ideal opportunity to develop your skills in this dynamic, technically challenging environment at the cutting edge of this high profile technology area. -- Please contact us by Email (CV's Plain ASCII please!): topjob@ecmsel.co.uk ----- Alternatively snail, fax or phone: ECM SELECTION LTD, The Maltings, Burwell, Cambridge, CB5 0HB Tel: 01638 742244 Fax: 01638 743066 From owner-software@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!WAM.UMD.EDU!qfang From: qfang@WAM.UMD.EDU (Fang Qingquan) Newsgroups: bionet.software Subject: Re: ANTHEPROT for Windows available! Date: 10 Oct 1995 08:42:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <45dvl3$bov@cri.ens-lyon.fr> NNTP-Posting-Host: net.bio.net Where is it? qfang@wam.umd.edu On 10 Oct 1995 deleage@bugatti.ibcp.fr wrote: > We are very pleased to announce the first release of ANTHEPROT for Windows. > It is a beta release and all comments and suggestions are welcome! > ANTHEPROT (ANalyze THE PROTeins) is a package designed for protein > sequence analysis. Up to now it was available on DOS and IBMrs6000. > This program allows to : > 1) Detect sites and signatures using the PROSITE database > 2) Provide an interface to the Fasta program. > 3) Provide an interface to CLUSTALV program > 4) Contain several secondary structure prediction > 5) Allows dot matrix plots. > 6) Interactive graphic still supported, clipboard access, color > printings, pseudo multitasking (long work run in background mode), > and many things more... > -- > ===================================================================== > # Institut de Biologie et Chimie des Proteines. UPR 412-CNRS # > # ***** ***** **** ***** Dr Gilbert Deleage # > # # # # # # # # 7, passage du Vercors # > # # ***** # # # 69367 Lyon Cedex 07,FRANCE # > # # # # # #**** Tel: (33) 72-72-26-47 # > # # # # # # # Fax: (33) 72-72-26-01 # > # ***** ****** **** # deleage@ibcp.fr # > ===================================================================== > > From owner-software@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!cri.ens-lyon.fr!bugatti.ibcp.fr!deleage From: deleage@bugatti.ibcp.fr (deleage@ibcp.fr) Newsgroups: bionet.software Subject: ANTHEPROT for Windows available! Date: 10 Oct 1995 15:18:38 GMT Organization: Institut de Biologie et Chimie des Proteines. CNRS-Lyon Lines: 12 Message-ID: <45e2se$euv@cri.ens-lyon.fr> NNTP-Posting-Host: bugatti.ibcp.fr X-Newsreader: TIN [version 1.2 PL1] The anonymous ftp site is ibcp.fr Also available through http://www.ibcp.fr -- ===================================================================== # Institut de Biologie et Chimie des Proteines. UPR 412-CNRS # # ***** ***** **** ***** Dr Gilbert Deleage # # # # # # # # # 7, passage du Vercors # # # ***** # # # 69367 Lyon Cedex 07,FRANCE # # # # # # #**** Tel: (33) 72-72-26-47 # # # # # # # # Fax: (33) 72-72-26-01 # # ***** ****** **** # deleage@ibcp.fr # ===================================================================== From owner-software@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!bcm.tmc.edu!pendragon.jsc.nasa.gov!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!uwvax!newssinet!news.nc.u-tokyo.ac.jp!tkyex1.phys.s.u-tokyo.ac.jp!news.tisn.ad.jp!crick!news.nih.go.jp!jun From: jun@nih.go.jp (Jun Ishikawa) Newsgroups: bionet.software Subject: Re: DNA Format Conversion Date: 10 Oct 1995 09:43:16 GMT Organization: National Institutes of Health (NIH) Tokyo, Japan Lines: 15 Message-ID: References: NNTP-Posting-Host: crick.nih.go.jp Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII In-reply-to: David_Frederiksen@ums.supernet.ab.ca's message of 07 Oct 1995 10:35:40 +0900 In article David_Frederiksen@ums.supernet.ab.ca (David Frederiksen) writes: > Can anyone direct me to some MAC software that will convert Gene Bank > formats to Phylip formats? I will use what ever is available ... anything > but long hand transposition. Try following URL: http://www.nih.go.jp/~jun/htdocs/research/readseq.html Good luck! -- Jun Ishikawa, Ph.D. National Institute of Health (jun@nih.go.jp) Dept. of Bioactive Molecules From owner-software@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!mail2news.demon.co.uk!ecmsel.demon.co.uk From: topjob Newsgroups: bionet.software Subject: C/C++, Molecular Biology, Oxford - ECM Selection LTd Date: Tue, 10 Oct 95 12:44:08 GMT Organization: ECM SELECTION Lines: 31 Message-ID: <813329048snz@ecmsel.demon.co.uk> Reply-To: topjob@ecmsel.co.uk X-NNTP-Posting-Host: ecmsel.demon.co.uk X-Newsreader: Demon Internet Simple News v1.27 Path: ecmsel.demon.co.uk!topjob From: topjob@ecmsel.demon.co.uk To: mail2news@news.demon.co.uk Newsgroups: uk.jobs.offered Subject: Ref:n.4210 - C/C++, Molecular Biology, to#30000, OXFORD Message-ID:<1000n.4210@ecmsel.demon.co.uk> Date: Tue, 10 Oct 95 12:05:53 Reply to: topjob@ecmsel.co.uk This is an outstanding, new opportunity to develop your project management skills with one of Europe's leading developers of computer aided molecular design software and database management systems for companies in the fields of pharmaceutical and biotechnology research. You should have an excellent academic and employment background, ideally to PhD level, in a scientific or numerate subject with demonstrable project-leading experience, and fluency in C or C++ with a 'hands-on' approach. Your communication skills will be exemplary and you will be innovative and flexible in your approach. The role is not purely a management role and will require the successful candidates to be involved in design, coding and testing of the sof