From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!news.cs.umb.edu!ctc.com!news.pop.psu.edu!news.cac.psu.edu!newsserver.jvnc.net!yale.edu!xlink.net!scsing.switch.ch!swidir.switch.ch!cisun2000.unil.ch!pcisrec-c302.unil.ch!vjongene From: vjongene@isrec-sun1.unil.ch (Victor Jongeneel) Newsgroups: bionet.software,sci.image.processing Subject: Analysis of BioRad confocal Z-series Message-ID: Date: 2 Dec 93 17:00:12 GMT Organization: Ludwig Institute for Cancer Research Lines: 19 Xref: biosci bionet.software:6621 sci.image.processing:4560 NNTP-Posting-Host: pcisrec-c302.unil.ch X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Hello Netters! Sorry if my question qualifies as a FAQ. We are generating many confocal "slices" through biological samples (Z series) using a BioRad system. Reconstitution of 3D objects from these serial slices is currently done using the BioRad sofware on a PC clone, thus painfully slow and not very good. As we will acquire an SGI graphics station (Indigo2 with all the goodies), we would like to move the analysis to this machine. To do this, we have found two apparently suitable programs so far: VoxelView, supposedly very good but also expensive, and Synu from Steve Lamont, a little more limited but also almost free. I would appreciate hearing about any experiences collected with these two packages, and even more about other possibilities. Thanks to all! Victor J. From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!pipex!sunic!trane.uninett.no!news.eunet.no!nuug!news.eunet.fi!funic!nic.funet.fi!csc.fi!harper From: Rob.Harper@csc.fi (Rob Harper) Newsgroups: bionet.software Subject: NCSA Mosaic for the Macintosh 1.0.1 Message-ID: <199311250918.AA13808@csc.fi> Date: 25 Nov 93 09:18:55 GMT Sender: root@nic.funet.fi (The FUnny NET guru) Organization: Finnish Academic and Research Network Project - FUNET Lines: 74 >Path: funic!news.funet.fi!sunic!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!garfield.ncsa.uiuc.edu!user >From: kims@ncsa.uiuc.edu (Kim Stephenson) >Newsgroups: comp.infosystems.www >Subject: NCSA Mosaic for the Macintosh 1.0.1 >Followup-To: comp.infosystems.www >Date: 24 Nov 1993 23:53:34 GMT >Organization: National Center for Supercomputing Applications >Lines: 61 >Message-ID: >NNTP-Posting-Host: garfield.ncsa.uiuc.edu NCSA is proud to announce the 1.0.1 release of NCSA Mosaic for the Macintosh. 1.0.1 was released Wednesday, November 24, 1993 at 3:35 pm (central time). NCSA Mosaic is an application that allows the user to easily access networked information from all over the world with the click of a button. The Internet is the primary source of networked information to the University and scientific communities. Services to access this information are rapidly being created. A few examples of the services currently available are Gopher, WAIS, World Wide Web, FTP, Usenet News, Telnet, and Archie. NCSA Mosaic is designed to provide transparent, seamless access to nearly all of these information sources and services. In addition it gives the user a mechanism to retrieve and display a wide variety of data types. These types include text, images, movies, sound and scientific data. NCSA Mosaic for the Macintosh can be download via anonymous ftp from ftp.ncsa.uiuc.edu directory Mac/Mosaic. The bugs and improvements of 1.0.1 release: For a complete list of features check the Macintosh home page. New Features.......... - Speed. Mosaic is significantly faster now, especially if you have fast network. - Domain names are cashed if you are using MacTCP 2.0+, resulting in faster downloads - "Open URL..." menu item is active even if there are no documents open. - HTTP 0.9 loading option. Because of incompatibilities between protocols this option has been added. If you are having problems with HTTP 0.9 server, switch this option on before loading documents from it. An example of this is http://slacvm.slac.stanford.edu:5080/FIND/spires. - Images stored in the cache are loaded automatically, even if "Auto-load images" option is off. - Inline images will be loaded to disk if "Load to disk" option is on. - The cache can be flushed from the menu. - Images are dithered on machines without color Quickdraw. Bugs............... - Mosaic would not start up unless a printer was chosen. - " HTML entity is now recognized. - redirected URLs (in HTTP 1.0 protocol) work for all protocols. - Memory problems have been fixed. Mosaic will run well in 2 megabytes. - Nested numbered lists are now always numbered correctly. - Text files are single-spaced. - All the files (even the last one) are listed in the FTP directories. Please send any questions, comments, bugs or suggestions to mosaic-mac@ncsa.uiuc.edu NCSA Mosaic for the Mac Development Team. Aleks Totic, Tom Redman, Kim Stephenson & Mike McCool University of Illinois National Center for Supercomputing Applications 152 CAB 605 E. Springfield Champaign, IL 61820 From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!europa.eng.gtefsd.com!darwin.sura.net!gwu.edu!unix1.circ.gwu.edu!not-for-mail From: wilesm@unix1.circ.gwu.edu (Marc Wiles) Newsgroups: bionet.software,bionet.cellbiol Subject: Re: Looking for morphometry software Message-ID: <2d0qrq$a4t@unix1.circ.gwu.edu> Date: 24 Nov 93 23:31:06 GMT References: <1993Nov24.221031.6107@rhrk.uni-kl.de> Organization: The George Washington University Lines: 6 Xref: biosci bionet.software:6619 bionet.cellbiol:188 NNTP-Posting-Host: 128.164.127.253 You may want to check out Jandel Scientifics software products. They support tablets, etc. I'm not sure what their current release products include, but I've used JAVA, SigmaScan and related programs in the past. Alternatives might include, for pre-digitized images, VOXL-view from Bio-Rad. Marc From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!biosci!VAXTM1.RTPNC.EPA.GOV!SREGO%NARVAX From: SREGO%NARVAX@VAXTM1.RTPNC.EPA.GOV Newsgroups: bionet.software Subject: (none) Message-ID: <01H5RVU0NCW28WXBGT@epavax.rtpnc.epa.gov> Date: 26 Nov 93 19:17:28 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 2 Please place me on the Bio-Soft mailing list. Thank you. Steve Rego From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!olivea!biosci!scri.scot-agric-res-inst.ac.uk!cepgl From: cepgl@scri.scot-agric-res-inst.ac.uk (Graham Lewis) Newsgroups: bionet.software Subject: Reading QPro .WQ1 files Message-ID: <21070.9311261633@scri.sari.ac.uk> Date: 26 Nov 93 16:33:15 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 20 Hello evrybody, We currently store weather data using a PC based data manipulation program called Power-system. We have some models written in a pascal dialect thst run within Power-system, reading the weather data files directly. Unfortunately this makes the models non-portable (unless you also have Power-system. Also, Power-system is a bit olde Worlde in its user interface. I have rewritten the models in Borlands Turbo Pascal to take weather data as ASCII files. We are considering changing the way we manage the weather data by storing the data as spreadsheets using Borlands Quatro Pro. I would like my Turbo pascal programs to read Quatro Pro spreadsheet files directly (without first converting them to ASCII. Does anybody know how I do this? What I suppose I am asking is ; What is the format of a Quatro Pro spreadsheet file? Graham The Scottish Crop Research Institute Invergowrie Dundee Voice : 0382 563731 extn 2515 \|/ \|/ \|/ \|/ \|/ \|/ \|/ \|/ email : cepgl@uk.ac.sari.scri ----------------------------------- From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!nih-csl!jowens.nci.nih.gov!jow From: jow@helix.nih.gov (Jim Owens) Newsgroups: bionet.software Subject: Blast and fasta, what's the difference? Message-ID: <1993Nov24.200507.14929@alw.nih.gov> Date: 24 Nov 93 20:05:07 GMT Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: NIH, Lab of Genetics Lines: 33 X-Xxmessage-Id: X-Xxdate: Wed, 24 Nov 93 20: 06:59 GMT X-Useragent: Nuntius v1.1.2 Recently some coworkers have been sequencing some cDNAs derived from differential display analysis so they are likely to come up with some unknown sequences. We have three ways to proceed in searching the sequence databases: 1) Blast on the (US) National Library of Medicine computer (blast@ncbi.nlm.nih.gov) 2) fasta on the GCG package on a local UNIX machine 3) MacVector search of a database on a local Macintosh A preliminary Blast search with the first 30 bases of sequence of a differential display product there was a nearly perfect match to a cockroach protein. However, after 100 more bases was added to the unknown cDNA, the Blast search came up with several other hits with lesser matches, but the cockroach cDNA was not among them. A fasta search came up with a different collection of hits. Why did the Blast search lose the cockroach sequence when the length of the query sequence was changed, even though none of the new hits gave as many bases matched? What are the differences in output due to? What are the differences between fast and BLAST and the Pustell matrix (used by MacVector)? Explanations I have read are either too technical or so simple that the differences are unclear. Is there a FAQ for laymen that explains the difference between a local and global homology search? Or explains the advantages and disadvantages of BLAST vs. fasta searches? Thanks in advance. Jim Owens ____________________________________________________ The Secretary denies any knowledge of my activities. From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!wupost!monsanto.com!c0_s2_async_7.monsanto.com!user From: rcwieg@ccmail.monsanto.com (Roger Wiegand) Newsgroups: bionet.software Subject: Re: Sequencher vs Applied Biosystems Message-ID: Date: 26 Nov 93 00:09:29 GMT References: <93322.213551IRVK@MAINE.MAINE.EDU> Sender: news@tin.monsanto.com (USENET News System) Followup-To: bionet.software Organization: Monsanto/Searle Molecular Genetics Lines: 11 Sequencher ought to be a better program at about 10X the cost*!! How about comparing apples and apples? (note I've not used either one "for real" yet and am not commenting on their relative merit) *6-10 user packod seqed vs a 5 user network licenceof sequencher -- Thanks, Roger Wiegand rcwieg@ccmail.monsanto.com From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!hearst.acc.Virginia.EDU!murdoch!dayhoff.med.Virginia.EDU!wrp From: wrp@dayhoff.med.Virginia.EDU (William R. Pearson) Newsgroups: bionet.software,bionet.molbio.embldatabank,bionet.molbio.genbank Subject: Fasta updates Message-ID: Date: 25 Nov 93 19:56:47 GMT Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia Lines: 9 Xref: biosci bionet.software:6625 bionet.molbio.embldatabank:263 bionet.molbio.genbank:1456 New versions of the FASTA package of programs are available from "virginia.EDU" in pub/fasta/fasta16c24b.shar(.Z) and pub/fasta/beta/fasta16c31a.shar(.Z). The programs have been belatedly modified to read the current EMBL format and the beta/fasta16c31.shar program has been more extensively tested (and corrected) to work with the NCBI BLASTP/N formats. Bill Pearson From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!xlink.net!fauern!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: ABI Inherit software/hardware Message-ID: <2d2sspINNcvp@sat.ipp-garching.mpg.de> Date: 25 Nov 93 18:18:01 GMT References: Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 27 NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.1 PL8] Harry Mangalam (mangalam@uci.edu) wrote: : In article , : jasons@perrier.embnet.se (jason stewart) wrote: : > I began hearing about the ABI Inherit system which was to come with a Sun : > and another box stuffed full of Fast Data Finder chips for doing homology : > searching/sequence alignment. They were having a problem with finding a : > service rep. here in Europe so it never seems to have taken off over on : > this side of the ocean. This sounds quite similar to the system which will be installed here by another (not our) group. I was told today that it comes with a SparcStation 10 and would be able to run a FASTA in 20 seconds :-) Maybe that answers Harry's question: : [...] the rep : couldn't tell me what the advantages were over BLAST/fasta. I can't see : anyone spending that kind of $ on such a specialized piece of hardware [...] The system will be installed in December or January. --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3975 */ /* "People are DNA's way of making more DNA." (R. Dawkins/anonymous) */ From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!wupost!waikato!aukuni.ac.nz!kiwi!deepserv!nick From: nick@deepserv.kiwi.gen.nz (Nick Warburton) Newsgroups: bionet.software Subject: Help, Labtutor address ?? Message-ID: <42746.328932250@deepserv.kiwi.gen.nz> Date: 25 Nov 93 11:52:26 GMT Organization: Deep Thought NZ, Auckland, New Zealand Lines: 19 X-Newsreader: Tin 1.1 PL4 From: adrianw@deepthnk.kiwi.gen.nz (Adrian Walden) Organization: Deep Thought NZ Date: Tue, 23 Nov 1993 08:25:55 NZ Subject: Help, Labtutor address ?? Please forward this message to bionet.software ,Internet Message follows: Macworld September 1993 contains a review of a hypercard stack called Labtutor 2.0. This product was developed at Stanford University and is now produced by a company called J K Eaton. Can somebody please advise me of their address (email or postal). Thanks. Adrian. - Adrian _/_/_/ _/_/_/_/ Adrian Walden _/ _/ _/ Deep Thought BBS, Auckland, New Zealand _/ _/ _/ A FirstClass(tm) Macintosh GUI BBS _/_/_/ _/ Internet: adrianw@deepthought.kiwi.gen.nz From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!caen!msuinfo!via-annex1-2.cl.msu.edu From: Bloksber@pilot.msu.edu (Leonard N. Bloksberg) Newsgroups: bionet.software Subject: Re: Blast and fasta, what's the difference? Message-ID: <19931125000921.Bloksber@via-annex1-2.cl.msu.edu> Date: 25 Nov 93 05:09:00 GMT References: <1993Nov24.200507.14929@alw.nih.gov> Organization: Michigan State University Lines: 22 NNTP-Posting-Host: via-annex1-2.cl.msu.edu X-Newsreader: FTPNuz (DOS) v1.0 In Article <1993Nov24.200507.14929@alw.nih.gov> "Jim Owens " says: > > 1) Blast on the (US) National Library of Medicine computer > (blast@ncbi.nlm.nih.gov) > 2) fasta on the GCG package on a local UNIX machine > 3) MacVector search of a database on a local Macintosh > > Is there a FAQ for laymen that explains the advantages and disadvantages > of BLAST vs. fasta searches? > > Thanks in advance. > > Jim Owens > ____________________________________________________ > The Secretary denies any knowledge of my activities. > I have the exact same setup, and would like to know the same answer. Please post a summary or email me the answer you get. Thanks. Leonard N. Bloksberg Bloksber@pilot.msu.edu . . From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!spool.mu.edu!olivea!decwrl!decwrl!tribune.usask.ca!canopus.cc.umanitoba.ca!mizar.cc.umanitoba.ca!frist From: frist@ccu.umanitoba.ca Newsgroups: bionet.software Subject: Re: DNA restriction analysis in PASCAL Message-ID: Date: 26 Nov 93 20:21:56 GMT References: <1993Nov24.163243.5916@genes.icgeb.trieste.it> Sender: news@ccu.umanitoba.ca Organization: University of Manitoba, Winnipeg, Manitoba, Canada Lines: 36 Nntp-Posting-Host: castor.cc.umanitoba.ca In article <1993Nov24.163243.5916@genes.icgeb.trieste.it> oberto@genes.icgeb.trieste.it (Jacques Oberto) writes: >Hi All: > >Does anybody have PASCAL source code to do restriction >enzyme analysis of a DNA sequence? >Any help or pointer welcome. >Thanks > >Jacques. > > >-- >Jacques Oberto The following programs are available as both Pascal Source and executables, for both DOS and Unix, as part of the FSAP package: INTREST - interactive restriction site search BACHREST - batch " " " ; now works with REBASE DIGEST - given output file from BACHREST, allows user to predict multiple enzyme digest patterns, for complete or partial digests All programs are available by anonymous FTP to the directory 'psgendb' at ftp.cc.umanitoba.ca. See README in this directory for more information. =============================================================================== Brian Fristensky | Department of Plant Science | A question is like a knife that slices University of Manitoba | through the stage backdrop and gives us Winnipeg, MB R3T 2N2 CANADA | a look at what lies hidden behind. frist@cc.umanitoba.ca | Office phone: 204-474-6085 | Milan Kundera, THE UNBEARABLE LIGHTNESS FAX: 204-261-5732 | OF BEING =============================================================================== From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!olivea!spool.mu.edu!darwin.sura.net!news.gdb.org!dev.gdb.org!danj From: danj@dev.gdb.org (Dan Jacobson) Newsgroups: bionet.software Subject: Re: PDB files for non-proteins Keywords: pdb, data, molecular coordinates, molecules Message-ID: <1993Dec2.171508.26948@news.gdb.org> Date: 2 Dec 93 17:15:08 GMT References: <2dbt53$q1f@clarknet.clark.net> Sender: news@news.gdb.org Organization: The Johns Hopkins University - Genome Data Base (GDB) Lines: 68 Nntp-Posting-Host: dev.gdb.org In article <2dbt53$q1f@clarknet.clark.net> chinatom@clark.net (Tom Wiens) writes: >Does anyone know of an online data source similar to the Protein Data Bank, >which provides xyz coordinates for molecules other than proteins (e.g., >organics or simple inorganic compounds), making possible the modelling of >their physical structure? > > The database that your looking for is probably the Cambridge Structural Database (CSD). Below is a brief description of the Database and some people to contact for more information on accessing it. There's also the NDB (Nucleic Acid Database) which is a 3D structure database for Nucleic Acid based molecules - ie DNA ... You can access this by gopher at ndb.rutgers.edu path=1/etc/ndb_link_files Best of luck, Dan Jacobson danj@mail.gdb.org ----------- The CSD contains the most comprehensive collection of evaluated crystallographic data in the world. Data for about 80,000 organic and organometallic crystal structures were included in the CSD as of January, 1991. Atomic coordinates, chemical connectivity tables, bibliographic data fields including reference sources for the data, and coordinates for chemical structure diagrams for each molecule are part of the system.... About 8000 new crystal structures will be added to the data base yearly. The contact in the U.K. is: Dr. Olga Kennard C.C.D.C. University Chemical Laboratory Lensfield Road Cambridge, CB2 1EW U.K. [011-44] 223-336409 A contact in the U.S. is probably: Investigator: Charles L Coulter Sponsor : National Institute of Health National Center for Research Resour Biomedical Research Technology Program Westwood Bldg Rm 8A15 Bethesda, MD 20892 Phone : (301) 496-9840 or William Duax Medical Foundation of Buffalo, Inc. 73 High Street Buffalo, NY 14203 Phone: (716) 856-9600 email: acamjv%mfb@ubvms.bitnet From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!europa.eng.gtefsd.com!emory!nigel.msen.com!yale.edu!newsserver.jvnc.net!news.cac.psu.edu!psuvm!imeg From: IMEG@psuvm.psu.edu Newsgroups: bionet.software Subject: MEGA: Mol. Evol. Gen. Analysis. Info Message-ID: <93336.092725IMEG@psuvm.psu.edu> Date: 2 Dec 93 14:27:25 GMT Expires: 31 Jan 94 00:00:00 GMT Organization: Penn State University Lines: 286 This document contains many pages, including 1. Cover letter 2. Order form (We no longer accept purchase orders) 3. Hardware and software requirements 4. Program upgrade policy 5. Functions in MEGA MEGA version 1.0, 1.01 September, 1993 To whom it may concern: A computer software called MEGA: Molecular Evolutionary Genetics Analysis has been developed. This software is for facilitating statistical studies of molecular evolution by using IBM compatible personal computers. It contains various methods of estimating evolutionary distances and three different methods of phylogenetic inference (UPGMA, neighbor-joining, and maximum parsimony) with either a standard-error test or a bootstrap test of topological differences. For the maximum parsimony method, new algorithms of the branch-and-bound and heuristic searches are implemented. MEGA also computes basic statistical quantities such as nucleotide and amino acid frequencies, transition/transversion bias, codon usage frequencies, number of variable sites, etc. In addition, advance on- screen sequence data and phylogenetic tree editors are included. Integrated and interactive designs, on-line context-sensitive helps, text-file editor, and other unique features make it easy to use MEGA. MEGA version 1.0 is distributed with a nominal fee to defray the cost of producing the user manual (140 pp.) and diskettes, and the mailing and handling expenses (see enclosed order form). However, for anyone who is unable to pay the fee for some reason, it will be provided free of charge after receiving a letter explaining the circumstances. MEGA will not be sent by electronic-mail because the accompanying manual cannot be included in this case. Technical questions and other inquires about MEGA should be directed to the senior author of the software. Please include your electronic-mail address, if any. Sincerely yours, Sudhir Kumar Koichiro Tamura Masatoshi Nei Telephone: (814) 863-7334 FAX: (814) 863-7336 E-mail: imeg@psuvm, imeg@psuvm.psu.edu MEGA ORDER FORM Cost* ----------------------------------------------------------------- Program No Charge User manual, diskette, shipping, and handling $ 15.00 For shipment outside North America add $10.00 _________ (We will use first class airmail) TOTAL _________ ----------------------------------------------------------------- * This cost can be waived if the circumstances for the inability to pay (e.g., lack of hard currencies in some countries) are explained. Diskette type desired: Please specify: [ ] 3.5" Diskette (1.44MB) [ ] DOS Version ...... [ ] 5.25" Diskette (1.2MB) [ ] Computer system... [ ] other (specify).... [ ] Do you use windows? Yes/No All orders must be prepaid in U.S. dollars. Return this form together with a check or money order payable to Penn State University at the following address. Purchase orders will not be accepted. Joyce White Institute of Molecular Evolutionary Genetics The Pennsylvania State University 328 Mueller Laboratory University Park, PA 16802 USA Telephone: (814)-863-7334 Fax: (814)-863-7336 E-mail: IMEG@PSUVM.PSU.edu, IMEG@PSUVM About the user: Name: ____________________________________________ Address: ____________________________________________ ____________________________________________ ____________________________________________ Telephone: _____________________ Fax: _________________ E-Mail: ____________________________________________ --------Hardware and Software------ IBM and IBM-compatible PCs, XTs, ATs, etc. Color/monochrome monitors. 640KB RAM memory. DOS version 3.3 or later. Hard disk with 2MB free. No extended or expanded memory required. No graphics adapters required. No math-chip required. Supports the keyboard as well as the mouse (not essential). ------- Program upgrade policy ---- Since MEGA is in its first version, there may be many software bugs in the program. We are considering to provide registered users a version where bugs reported in version 1.0 and 1.01 will be fixed. As you may notice from the order form, we are just trying to recover the cost of distributing MEGA only. So we are not in a position to provide many upgrades. In any case, we do not plan to include new methods in MEGA soon (for at least one year), and therefore the questions about upgrades may not be so pressing at this moment. -------Functions in MEGA------- Input Input data: DNA sequences RNA sequences Amino acid sequences Distance matrices Input formats: Interleaved sequences Non-interleaved sequences Upper-triangular distance matrix Lower-triangular distance matrix Choice of: Alignment gap symbol Missing-information site symbol Identical site symbol In-memory data editing features Selection: Desired OTUs Domains of sequences Individual sites and codons Codon positions Exclude/include missing information sites Exclude/include alignment gap sites Edit OTU labels Restore OTU labels Sequence data presentation Highlight: Variable sites Parsimony-informative sites Two-fold redundant sites Four-fold redundant sites Translate: Translation of nucleotide sequences into amino acid sequences Output: Formats: MEGA PAUP PHYLIP Publication Data subsets: Only variable sites Only parsimony-informative sites Amino acid sequences translated Codon positions Sequence statistics: Nucleotide and amino acid frequencies Nucleotide pair frequencies in pairwise comparisons Insertion-deletion frequencies Codon usage frequencies Relative synonymous codon usage (RSCU) values Variable sites in overlapping segments Variable sites in nonoverlapping segments Distance estimation Nucleotide substitutions Quantities: Number of nucleotide differences Nucleotide substitutions Transitional substitutions Transversional substitutions Transition/transversion ratio Distance measures: p-distance Jukes-Cantor distance Kimura 2-parameter distance Tajima-Nei distance Tamura distance Tamura-Nei distance Gamma distances Jukes-Cantor model Kimura 2-parameter model Tamura-Nei model Synonymous-nonsynonymous substitutions Genetic code tables: "Universal" Mammalian mitochondrial Drosophila mitochondrial Yeast mitochondrial Computation: Synonymous substitutions Nonsynonymous substitutions Average distances for all pairwise comparisons and standard errors Amino acid substitutions Distance measurers: Number of amino acid differences p-distance Poisson-correction distance Gamma distance Distance output: Control on: Page size Precision for distance output Distance q standard error formats Tree building and test Methods: Neighbor-joining (NJ) UPGMA Maximum parsimony (MP): Branch-and-bound search Heuristic search Statistical Tests: Bootstrap test: Neighbor-joining UPGMA Branch length test: Neighbor-joining Phylogeny editing: Tree re-rooting Swapping and flipping branches Consensus tree Condensed tree Phylogeny printing: Various printers Multiple page printouts Choice of fonts Choice of orientation Choice of page size Tree preview General functions File browsing File editing Exiting to DOS temporarily Context-sensitive Helps Error messages From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!math.fu-berlin.de!news.dfn.de!uni-muenster.de!uni-muenster.de!haebler From: haebler@uni-muenster.de (Marcus Haebler) Newsgroups: bionet.software Subject: Molecule Design Program for X11 Message-ID: <2dkqpj$1atn@obelix.uni-muenster.de> Date: 2 Dec 93 13:32:35 GMT Organization: Westf. Wilh.-Universitaet Muenster, Germany Lines: 17 NNTP-Posting-Host: urix6.uni-muenster.de Hi, I have found a hint that there was a free Molecule Designer for X. Can someone tell me where I can find the stuff? Thanx, Marcus -- ********************************************************************** * Marcus Haebler * Internet: haebler@uni-muenster.de * * Althausweg 29 * You can also contact me via IRC. * * 48159 Muenster * Drop me a note at Noteserv@service.de * * Germany * Nickname: D_Gently (Mostly Harmless) * ********************************************************************** From owner-software@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!parc!decwrl!ames!agate!howland.reston.ans.net!cs.utexas.edu!uunet!biosys!timb@apldbio.com From: timb@apldbio.com (Tim Burcham) Newsgroups: bionet.software Subject: Re: ABI Inherit software/hardware Message-ID: <693@biosys.apldbio.COM> Date: 1 Dec 93 15:34:58 GMT References: Sender: news@biosys.apldbio.COM Reply-To: timb@apldbio.com Followup-To: Re: ABI Inherit software/hardwre Organization: Applied Biosystems, Inc. Lines: 29 Harry writes: >See: The Journal of NIH Research, Vol 5, No 10, p 81-82 for one (not very >complementary) view of it. I saw one at a local meeting but the rep >couldn't tell me what the advantages were over BLAST/fasta. I can't see >anyone spending that kind of $ on such a specialized piece of hardware - >well I guess I can - they built the B2, the space shuttle, and several >billions worth of aircraft carriers. > I won't comment on most of this (I'm obviously biased ;-), but the article cited should be considered an ADVERTISEMENT, not a research article. Look for a response in an upcoming issue of Journal of NIH Research. The INHERIT system used in the study was PRE-RELEASE TEST VERSION. INHERIT is now undergoing it's fourth iteration since that test version was released. The current iteration includes a MAJOR HARDWARE CHANGE from the test system that was reviewed in Journal of NIH Research. I sorry you didn't get a good demo. Look into Journal of NIH Research and their editorial policies. You will probably be as disgusted as I was... ----------------------------------------------------------------------------- Tim Burcham Data Products R&D timb@apldbio.com Applied Biosystems (415)570-6667 850 Lincoln Centre Dr (800)874-9868 Foster City, CA 94404 From owner-software@net.bio.net Thu Dec 02 22:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software Subject: IMPORTANT!!! - BIOSCI at net.bio.net off-line this ENTIRE WEEKEND!! Message-ID: Date: 3 Dec 93 00:32:37 GMT Organization: BIOSCI International Newsgroups for Biology Lines: 26 We are aware of continuing problems with duplicated messages and are taking the BIOSCI system off-line from 5 PM Friday, 6 DEC, until Monday AM. The message duplication is caused by a relatively infrequent but recurring file corruption problem that we have been experiencing with our news message tracking database. We will be doing a news system software upgrade over the weekend. All BIOSCI services including e-mail, news, WAIS, Gopher, FTP archive access, etc. will be inaccessible over the weekend, so here is your chance to take a short break from e-mail overload 8-). I am going to post this note to several of the more popular groups to ensure that as many readers as possible see it. My apologies if you subscribe to several of these groups by e-mail - you will get one copy for each group that you receive. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-software@net.bio.net Thu Dec 02 22:00:00 1993 Path: biosci!CUCIS.CIS.COLUMBIA.EDU!ciminoj From: ciminoj@CUCIS.CIS.COLUMBIA.EDU (James Cimino) Newsgroups: bionet.software Subject: Medical Informatics Fellowship Message-ID: <9312031623.AA142254@cucis.cis.columbia.edu> Date: 3 Dec 93 16:23:07 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 63 Training Program in Medical Informatics The Columbia University Center for Medical Informatics invites applications for fellowships in medical informatics starting in July, 1994. The goal of the program is to train medical informatics scientists for careers as productive researchers and teachers. The fellowship is funded by the National Library of Medicine, an agency of the National Institutes of Health, and is open to U.S. citizens or permanent residents with an M.D. or Ph.D. degree. The Center is located at the Columbia-Presbyterian Medical Center in New York City. Columbia University is an equal opportunity employer and takes affirmative action. Women and minorities are especially encouraged to apply. The Center for Medical Informatics has fourteen faculty members with diverse backgrounds and an active research program. Areas of special interest include clinical information system development, clinical decision support, computer-based learning, database design, natural language processing, medical vocabularies, medical knowledge representation, information retrieval strategies, physician data entry, genome mapping, molecular modeling, and high performance computing and communication. The Center has close ties and joint appointments with the Departments of Computer Science, Biochemistry, Medicine, Radiology, and Pathology and the Schools of Dentistry, Nursing and Epidemiology. Opportunities also exist in the areas of computer applications in medical librarianship and computer aided learning. A particular strength of the Center is the ability to provide research opportunities in the context of working production systems. We are seeking applicants who want a "hands on" experience while carrying out innovative research and mastering a strong curriculum. Notable features of our environment include the Integrated Academic Information Management System (IAIMS) Phase III implementation funded by the National Library of Medicine, the full partnership of the Columbia University Health Sciences Library in IAIMS and in the Center for Medical Informatics, and close collaborative relationships with basic and clinical science departments. The training program includes a stipend and tuition support for course work in medical informatics, computer science, evaluation study design, and biostatistics. Educational programs will be individualized to address the needs and directions of each fellow. In addition, each fellow will be expected to develop, conduct, and report on an original research project. Opportunities exist for a masters and PhD degrees in Medical Informatics. Support for each fellow will be for three years in most cases. Stipends are available and are in keeping with NIH post-doctoral guidelines. Fellows who wish to maintain their clinical skills will be given opportunities to do so. Applicants should send a letter of not more than two pages describing their background, relevant experience, and motivation; transcripts from medical or graduate school and from college; and a curriculum vita. Letters of reference from three referees should be sent under separate cover. Application materials should be sent to James J. Cimino, M.D., Atchley Pavilion 1310, 161 Fort Washington Avenue, New York, NY 10032. Additional information may be obtained by calling Dr. Cimino at 212- 305-8127 or by e- mail to ciminoj@cucis.cis.columbia.edu. From owner-software@net.bio.net Thu Dec 02 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!news.claremont.edu!nntp-server.caltech.edu!seqvax.caltech.edu!mathog From: mathog@seqvax.caltech.edu (David Mathog) Newsgroups: bionet.software Subject: PDBtoGCG (for VMS) Message-ID: <2DEC199314460760@seqvax.caltech.edu> Date: 2 Dec 93 22:46:00 GMT Organization: Division of Biolgy, CALTECH Lines: 221 NNTP-Posting-Host: seqvax.bio.caltech.edu News-Software: VAX/VMS VNEWS 1.41 Sometimes users insist on having the sequences out of PDB files (even though most of these can be retrieved from other databases). It's a bit of a pain to do manually, so here are a short script and a program it uses that carry out this conversion automatically. It only works on protein sequences, and then only if the sequence(s) are properly recorded in the SEQRES records (so sue me). Each strand's sequence is placed in a separate file. The script is DCL, but the equivalent sh or csh shouldn't be too tough. (Yes, the GCG conversion code could be put into hackem.for - feel free if you think that it's worth the effort.) No guarantees, warranties, or etc :-)! David Mathog mathog@seqvax.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech ******* PDBtoGCG.COM ***************************************************** $! *************************************************************** $! PDBTOGCG.COM $! $! Command procedure to convert PDB sequence(s) to GCG sequence(s). $! It will accept the name of the PDB file as a parameter, otherwise $! it prompts for it. $! This only works for PROTEIN sequences! $! $! Be sure to modify the RUN HACKEM line to match your site! $! $! David Mathog, CalTech Biology, 1-DEC-1993 $! ************************************************************ $ $ on control_y then goto terminate $ ws := "write sys$output" $ iq := inquire/nopunctuation $ $ if (P1 .eqs."") $then $ iq pdbfile "Name of the PDB file to convert to GCG sequence format " $ if pdbfile .nes. "" then goto okpdbname $ ws "Message from PDBtoGCG:" $ ws "Cannot convert unless you supply the name of a PDB file!" $ ws "Conversion aborted" $ stop $else $ pdbfile = P1 $endif $okpdbname: $! $ open/write tfil killmepdbtogcg.com $ write tfil "$run gcgexrun:hackem" $ write tfil PDBFILE $ close tfil $ @killmepdbtogcg.com/out=nla0: $ delete killmepdbtogcg.com. $! $ define/user sys$output nla0: $ reformat/threeintoone/protein/default hackem*.pep $ purge hackem*.pep $! $! now rename them $! $! extract the root part of the name for constructing the final output $! file's name $! $ file = F$SEARCH(PDBFILE) $ root = f$parse(FILE,,,"NAME") ! root name of sequence $! $! rename any and all output files $! $count = 0 $TOP: $ file = F$SEARCH("HACKEM*.PEP") $ if(file .eqs. "")then goto byebye $ count = count + 1 $ chunk = F$PARSE(FILE,,,"NAME") $ chunk = chunk - "HACKEM" $ chunk := "''ROOT'''chunk'.PEP" $ rename 'file' 'chunk' $ ws "Sequence ''count' in file ''chunk'" $ goto TOP $! $BYEBYE: $ delete hackem.out. $ if count .eq. 0 $ then $ ws "PDBtoGCG: WARNING: no sequences were found in ''PDBFILE'" $ else $ ws "PDBtoGCG: Extracted ''COUNT' sequences from ''PDBFILE'" $ endif $! $terminate: *********** hackem.for ************************************************* C HACKEM.FOR C C 1-DEC-1993, David Mathog, biology division, Caltech C C *Incredibly* simple minded program that takes a PDB file C and spits the SEQRES records out into separate files for C each chain for further processing by GCG REFORMAT. C C Input: The name of the PDB file C Output: hackem.out C Number of Chains C Names of files = hackem.chain_id C hackem_1.pep C hackem_A.pep C hackem_2.pep etc. C C Note, if a chain has NO NAME there will be a space in the 12 C position. In this case, the single output sequence will be named C hackem.pep. C C C SEQRES line format is: C 6A1 SEQRES C I4 Serial # for current chain C 1X space C A1 Chain identifier (any symbol!) C 1X space C I4 Number of residues in this chain C 1X space C 13(1X,A3) Residue names, in three letter code format C C plus, sometimes, junk on the end C implicit none character*200 file,listof,outfile character*132 line character*1 chain integer*4 status,linelen,filelen,count,i,outlen logical OK c write(6,*)'Name of the PDB file to process: ' read(5,'(q,a)',iostat=status)filelen,file(1:filelen) if(status .ne. 0 .or. filelen .eq. 0)then write(6,*)'HACKEM: using default input file of HACKEMPDB' file = 'HACKEMPDB' filelen=9 end if c c open the input file c open(unit=10,file=file(1:filelen) 1 ,form='FORMATTED',carriagecontrol='LIST',status='OLD' 1 ,READONLY,iostat=status) if(status .ne. 0) 1 stop 'HACKEM: fatal error, could not open PDB file' c c scan it for SEQRES records c The initial chain value should NEVER occur in a PDB file! c ok = .true. chain = char(1) count = 0 c do while(ok) read(10,'(q,a)',iostat=status)linelen,line(1:linelen) if(status .eq. 0)then if(line(1:6) .eq. 'SEQRES')then if(chain .ne. line(12:12))then !new chain chain = line(12:12) count = count + 1 listof(count:count) = chain if(count.gt.0)close(11,dispose='SAVE') call makename(outfile,outlen,chain) open(unit=11,file=outfile(1:outlen) 1 ,form='FORMATTED',carriagecontrol='LIST',status='NEW' 1 ,iostat=status) if(status .ne. 0) 1 stop 'HACKEM: fatal error, could not open output file' write(11,'(a)')'Sequence of chain '//chain//' from ' 1 //file(1:filelen) write(11,'(a)')'..' end if if(linelen .gt. 70)linelen=70 write(11,'(a)')line(20:linelen) else if(count .ge. 1)ok = .false. end if else !possibly an error, but treat it like an EOF ok = .false. end if end do c c write out hacker.out - number of chains and names of files c if(count.ge.1)close(unit=11,dispose='SAVE') open(unit=11,file='hackem.out' 1 ,form='FORMATTED',carriagecontrol='LIST',status='NEW' 1 ,iostat=status) if(status .ne. 0) 1 stop 'HACKEM: fatal error, could not create "hackem.out"' write(11,'(I4)')count if(count.ge.1)then do i = 1, count call makename(outfile,outlen,listof(i:i)) write(11,'(a)')outfile(1:outlen) end do end if c close(unit=11,dispose='SAVE') c stop 'HACKEM: processing completed' end subroutine makename(file,flen,chain) implicit none character*200 file character*1 chain integer*4 flen if(chain .eq. ' ')then file = 'hackem.pep' flen = 10 else file = 'hackem_'//chain//'.pep' flen = 12 end if return end ***** that's all folks ****************************************************** From owner-software@net.bio.net Thu Dec 02 22:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software Subject: Re: ABI Inherit software/hardware Message-ID: Date: 3 Dec 93 06:00:18 GMT References: <693@biosys.apldbio.COM> Organization: BIOSCI International Newsgroups for Biology Lines: 66 timb@apldbio.com (Tim Burcham) writes: >Harry writes: >>See: The Journal of NIH Research, Vol 5, No 10, p 81-82 for one (not very (stuff deleted) >I won't comment on most of this (I'm obviously biased ;-), but the article >cited should be considered an ADVERTISEMENT, not a research article. (more stuff deleted) Tim, A couple of people are beginning to send me requests to formalize the guidelines for commercial discussions as has been done for job postings, and, in light of the increasing commercial presence on the net, I suppose it is getting time to do so. I realize from personal experience that it is hard to simply sit by and ignore flames thrown at one's products, but the tradition on the net has been for the commercial folks to stand aside and let the users discuss the pros and cons among themselves. On the other hand, I have clearly stated in the past that commercial companies can respond in a factual manner to questions about their products. Each one of these situations has many gray aspects, of course, but the one point that I do want everyone to be clear on is that commercial users should not take general requests for information (such as "I am looking for software that does X ...") as an opening to get some free air time. This is clearly not what you are doing above, but you are allowing yourself to get sucked into a flame war which you might be better off avoiding. A simple reply such as: "We believe there are inaccuracies in this article. A response to the article cited will be appearing in XXX." would be sufficient without comments about editorial policy, etc. Instead your use of text such as >I won't comment on most of this (I'm obviously biased ;-), but the article >cited should be considered an ADVERTISEMENT, not a research article. has prompted other private comments to me to the contrary including questions about the appropriateness of your message. As to those who want me to start writing the BIONET analog of the "Koran," I hope that it is obvious to all that every one of these situations has nuances that are hard to capture in rules. This is why NSFNET Acceptable Use policy has been so vague. A good rule of thumb is to keep emotions out of this and stick to the facts. I don't want to sound threatening in the slightest, but posters who go way out of line and actually make libelous statements on the network are not exempt from libel laws. Internet legal precedent to date holds the poster of a message responsible for their actions. In summary, a level head is in order on all sides of the debate. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-software@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!daresbury!mrccrc!news.dcs.warwick.ac.uk!warwick!uknet!pipex!howland.reston.ans.net!spool.mu.edu!torn!csd.unb.ca!UNBVM1.CSD.UNB.CA From: R7FA@UNB.CA (T. J.) Newsgroups: bionet.software Subject: Looking for .gif reader Message-ID: <03DEC93.02642739.0049@UNBVM1.CSD.UNB.CA> Date: 3 Dec 93 06:26:49 GMT Sender: usenet@UNB.CA Organization: The University of New Brunswick Lines: 5 hi, i have Windows and Presentations but these packages can not read gif files. Would someone tell me how i can get a .gif reader? From owner-software@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.software Subject: Re: PDBtoGCG (for VMS) Message-ID: <01H61GYLB6AE91VWQ6@NBRF.Georgetown.Edu> Date: 3 Dec 93 15:46:26 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 46 In message <9312030024.AA02665@net.bio.net> David Mathog (mathog@seqvax.bio.caltech.edu) says > Sometimes users insist on having the sequences out of PDB files (even > though most of these can be retrieved from other databases). It's a bit > of a pain to do manually, so here are a short script and a program > it uses that carry out this conversion automatically. It only works > on protein sequences, and then only if the sequence(s) are properly > recorded in the SEQRES records (so sue me). Each strand's sequence > is placed in a separate file. The protein sequences from the Brookhaven Protein Data Bank entries have already been extracted into a sequence file format and are provided by the PIR in the NRL_3D database. This database also includes all the source, bibliographic and feature information extracted from PDB HELIX, SHEET, TURN, SITE, and SSBOND records along with special ATOM and HETATM records. The NRL_3D database is indexed and can be searched and queried (and even converted to other formats) like the other PIR sequence databases. The NRL_3D entries have titles that conform to NBRF naming rules and match the corresponding PIR entries. The title field of NRL_3D entries contains all the same elements as the corresponding PIR entries and in the same order. However, additional elements are present in the NRL_3D entries to distinguish entries that may be chains or fragments with different crystallographic coordinates, have different crystallization conditions, or have different chemical modifications. The NRL_3D title of an entry may not correspond to the Brookhaven Protein Data Bank COMPND record from which it was originally derived because all Enzyme Commission numbers have been changed to conform to the current rules, and all co-crystallized protein chains from different sources are distinguished and correctly identified. A file of the NRL_3D titles can be obtained by sending the E-Mail message SEND NRLTITLE.LIS to FILESERV@NBRF.Georgetown.EDU (or GUNBRF.BITNET). Release 12.2 of NRL_3D is currently available with the regular tape and CD-ROM distribution of the PIR. It is available for database searches and queries through the PIR Network Request Server and the PIR On-Line Access System. It is available by FTP from the University of Houston Gene-Server at ftp.bchs.uh.edu and the NCBI archives at ncbi.nlm.nih.gov. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-software@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!RCF.MAYO.EDU!EBERHARDT From: EBERHARDT@RCF.MAYO.EDU Newsgroups: bionet.software Subject: RE: Differential Display Analysis Message-ID: <931203083844.20210b59@rcf.mayo.edu> Date: 3 Dec 93 14:38:44 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 50 |>From: FERMAT::"BIOSCI-REQUEST@net.bio.net" 1-DEC-1993 17:43:02.75 |>To: bio-soft@net.bio.net |>CC: |>Subj: Differential Display Analysis |> |> |>Jim Owens wrote - |> |>> Recently some coworkers have been sequencing some cDNAs derived from |>> differential display analysis so they are likely to come up with some |>> unknown sequences. |> |>Can somebody post an explanation of what the term "differential display |>analysis" means, or better yet a published reference where it's described? |> |>Thanks very much. |> |>Dave Merberg DDPCR is a method developed by Arthur Pardee's laboratory to display differences in the populations of two mRNA populations, e.g., cells treated with different effectors or normal and tumor cell lines, to visualize and enable the cloning of the differentially expressed genes. It utilizes a random set of 20-26 5' primers of unique but differing sequence and a set of 3' primers of the form NVTTTTTTTTTTT to anchor this primer at the 3' end of the polyA tail. The products are relatively short (100-300 bp) that are displayed on sequencing gels. The difference products can be recovered from the gels, reamplified and cloned, providing a unique 3' probe that can be compared with the data bases and used to clone a full lenth cDNA from a cDNA library. References are cited below: 1. Liang and Pardee, Science 257: 967-971 (1992). 2. Liang et al. Nucl Acids Res 21: 3269-3275 (1993). 3. Bauer et al. Nucl Acids Res 21: 4272-4280 (1993). A related technique has been devised by Michael Wigler's group to use PCR to clone the differences between two complex genomes. The reference is Lisitsyn et al. Science 259: 946-951. Hope this helps. Norman L. Eberhardt, Ph.D. Associate Professor Departments of Medicine and: Biochemistry/Molecular Biology 4-407 Alfred Mayo Clinic Rochester, MN 55905 eberhardt@mayo.edu From owner-software@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!daresbury!mrccrc!news.dcs.warwick.ac.uk!warwick!pipex!howland.reston.ans.net!darwin.sura.net!news.gdb.org!dev.gdb.org!danj From: danj@dev.gdb.org (Dan Jacobson) Newsgroups: bionet.software Subject: Re: PDB files for non-proteins Keywords: pdb, data, molecular coordinates, molecules Message-ID: <1993Dec2.171508.26948@news.gdb.org> Date: 2 Dec 93 17:15:08 GMT References: <2dbt53$q1f@clarknet.clark.net> Sender: news@news.gdb.org Organization: The Johns Hopkins University - Genome Data Base (GDB) Lines: 68 Nntp-Posting-Host: dev.gdb.org In article <2dbt53$q1f@clarknet.clark.net> chinatom@clark.net (Tom Wiens) writes: >Does anyone know of an online data source similar to the Protein Data Bank, >which provides xyz coordinates for molecules other than proteins (e.g., >organics or simple inorganic compounds), making possible the modelling of >their physical structure? > > The database that your looking for is probably the Cambridge Structural Database (CSD). Below is a brief description of the Database and some people to contact for more information on accessing it. There's also the NDB (Nucleic Acid Database) which is a 3D structure database for Nucleic Acid based molecules - ie DNA ... You can access this by gopher at ndb.rutgers.edu path=1/etc/ndb_link_files Best of luck, Dan Jacobson danj@mail.gdb.org ----------- The CSD contains the most comprehensive collection of evaluated crystallographic data in the world. Data for about 80,000 organic and organometallic crystal structures were included in the CSD as of January, 1991. Atomic coordinates, chemical connectivity tables, bibliographic data fields including reference sources for the data, and coordinates for chemical structure diagrams for each molecule are part of the system.... About 8000 new crystal structures will be added to the data base yearly. The contact in the U.K. is: Dr. Olga Kennard C.C.D.C. University Chemical Laboratory Lensfield Road Cambridge, CB2 1EW U.K. [011-44] 223-336409 A contact in the U.S. is probably: Investigator: Charles L Coulter Sponsor : National Institute of Health National Center for Research Resour Biomedical Research Technology Program Westwood Bldg Rm 8A15 Bethesda, MD 20892 Phone : (301) 496-9840 or William Duax Medical Foundation of Buffalo, Inc. 73 High Street Buffalo, NY 14203 Phone: (716) 856-9600 email: acamjv%mfb@ubvms.bitnet From owner-software@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!daresbury!mrccrc!news.dcs.warwick.ac.uk!warwick!pipex!howland.reston.ans.net!newsserver.jvnc.net!netnews.upenn.edu!amalthea.humgen.upenn.edu!tisdall From: tisdall@amalthea.humgen.upenn.edu (James Tisdall) Newsgroups: bionet.software Subject: Announcing: DNA WorkBench Message-ID: <2do7e9$hev@netnews.upenn.edu> Date: 3 Dec 93 20:26:49 GMT Sender: tisdall@cbil.humgen.upenn.edu Organization: University of Pennsylvania Lines: 221 NNTP-Posting-Host: amalthea.humgen.upenn.edu Announcing: DNA WorkBench A program for sequence searching and manipulation. * It's free. * It runs on Unix and Macs (and PCs - see below) with internet connections. * Powerful and fast searches on Genbank and other databases. * Client-server: access remote databases and programs. * Parallel distributed processing for huge databases of the near future. * Full automatic control: by script, command-line or standard input. * Enhancable - run your own programs on databases and search results. * Handles most sequence file formats silently - reformats easily. * Many sequence manipulation functions. * Convenient user interface, complete on-line help. HOW TO GET IT ftp cbil.humgen.upenn.edu (or, ftp 130.91.180.83) login as "anonymous", give your email address as a password cd /pub/dnaworkbench mget ANNOUNCE INSTALL README (and, if you want, CHANGES and PERL-FAQ) For UNIX: cd unix For PC: cd pc For MAC: cd mac get dnaworkbench quit Please send mail to tisdall@cbil.humgen.upenn.edu if you install the program. You will then be informed of program updates and other information. TAKE HEED The program is configured to access our network of Sun workstations for database and program service. Since we are not funded to provide this service to the world, we have a limit on the number of connections allowed at any one time. In addition, should problems arise, the service may be curtailed. You are encouraged to configure the program on your systems to use your own databases and programs. This is a so-called "alpha release" of the program. Although we have been using it successfully for about a year as it has developed, it has not been tested on a large number of variant Unixes or Macs. Installation is expected to be straightforward; if you have problems, let us know, and we will improve upon the installation instructions in the INSTALL file. In particular, we have used the Unix version a lot - it's fairly stable. The Mac port is rather recent, and there are no doubt some more bugs to shake out. It also requires lots of memory. The MSDOS PC port (which does not include sockets) is almost entirely untested at this date. MORE INFORMATION --- It's free. DNA WorkBench is copyrighted, but permission is granted for non-commercial use, or for research purposes, under the usual conditions. Details provided with the program. For commercial use, contact the author. DNA WorkBench is written in the Perl language, which is also free and is available for most computers. Perl is a C-like language with many string manipulation features and supports object-oriented programming. Perl is a great language for slinging DNA and for biocomputing in general. --- It runs on Unix, Macs, and MS-DOS PCs. All that is required is that Perl be installed. For certain UNIX computers, binaries are provided that do not require additional Perl installation. Instructions on how to get Perl are included in each distribution. Perl has also been ported to VMS, Amigas, NT, OS/2, Atari ST, and practically any other computer system you can think of. However, I've only worked with UNIX, Macs, and MS-DOS PCs so far. Internet connections are required for the database searching and retrieval. This enables small computers to use the big servers for database storage and program execution, while doing the easier jobs and storing results locally. Alternatively, if you have the disk space, you can configure the system to use your own local database. At present, a good port to PCs that includes the internet "sockets" connectivity is not available; but one is expected soon, now that good public domain socket libraries have become available. --- Powerful and fast searches on Genbank and other databases. DNA WorkBench lets you get information out of Genbank and other databases in a number of useful ways. Several fields are indexed; for example, "organism sapiens" will return with the many thousands of human DNA entries very rapidly. It is also possible to search for arbitrary text through an entire database very rapidly. This is accomplished by running the search in parallel on many machines, each machine doing a different part of the search. The searches may be for sequence or for other text. Searches may be specified in terms of a very complete regular expression language, which gives powerful user-defined full-text search capabilities. Results of searches may be combined in various ways, for instance by taking the union, intersection, or difference of sets of search results. Results of searches may be narrowed down by additional criteria; the user can define programs to run against search results; and search results can be saved and reloaded at a later session. --- Client-server: access remote databases and programs. DNA WorkBench is both a genetic database server and a program server. For instance, the popular BLAST, FASTA and PRIMER programs can be run by DNA WorkBench on a remote machine, using your local files and input, and the results returned to your local machine. On startup, the program connects with a server that provides the locations of the databases and other services. This reduces administration requirements. The program then makes connections with the various servers as required. If a server is unavailable, the program attempts to connect with the alternate servers, if any are specified. The servers impose a timeout, which helps reduce the load on the servers, while being transparent to the client, which silently re-establishes connections which have timed out. Also, the servers impose a limit on the number of concurrent server processes they permit, ensuring that the server system is not overloaded. --- Parallel distributed processing for huge databases of the near future. Large databases can be distributed over many machines. As the amount of genetic information grows (it seems to be doubling about every 1.7 years) it will be possible to simply throw more and/or faster machines into the network to maintain rapid search and retrieval. This is very easy to configure - one simply adds the machine and file name to the program, and installs the program on the new machine. --- Fully automatic control: all functions can be program-controlled. Large projects such as the Human Genome Project, which provided the environment in which DNA WorkBench developed, as well as small projects centered in an individual laboratory, can benefit from the automation of biocomputing tasks. Every function of DNA WorkBench can be controlled by specifying it in a script, or by including it on the command line, or by reading it from the standard input as it is piped in, or as the user types it. For instance, new sequence can be analyzed in a variety of ways, and the results summarized and mailed to the researcher, without the time-consuming chore of typing inputs and responses to a variety of programs. --- Enhancable - run your own programs on databases or search results. You can write a program that processes one database record, and then specify the database libraries, or the previous search results, to run the program against. The user can build up a collection of programs, and easily specify to DNA WorkBench which program to run and against what library or search result. The user can also enter arbitrary commands to the running program, for instance, to examine the state of the program, or to perform some custom-tailored calculation. --- Handles most sequence file formats silently - reformats easily. Files containing sequence data in several common file formats are read and parsed without any action necessary by the user. Data can be reformatted by giving the name of the desired format. --- Many sequence manipulation functions. This list keeps growing. At present, it includes calculating the reverse complement, displaying reading frames and nucleotide to protein translations, editing, searching for restriction enzyme sites, searching for human repeat or vector in a sequence, comparing a sequence against a library or a user file, searching for a regular expression in a sequence. On my to-do list: contig assembly, searching by context-free and other grammars, feature table manipulation, GDB access, approximate regular expression matching, physical mapping of chromosomes, ... --- Convenient user interface, complete on-line help. Search results are easily manipulated, so you don't have to remember and type long filenames. Search results are maintained in an array; the size and current pointer are displayed in the prompt. One-line headers or complete records are shown with the minimum possible number of keystrokes. All searches are saved and can be quickly retrieved and combined, with a minimum of disk and memory usage. The online help facility contains all the documentation, plus some short tutorials. It is based on examples, not formal descriptions. Any command not recognized by the program is passed on to the system. The user can perform most tasks without leaving the program, which makes it behave (almost) like your shell with many new commands and a stack of sequence. ====================================================================== James Tisdall Departments of Genetics and Computer and Information Science Computational Biology and Informatics Laboratory, Human Genome Project 510 Blockley Hall University of Pennsylvania tisdall@cbil.humgen.upenn.edu 215-573-3113 fax 215-573-3111 ====================================================================== From owner-software@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!daresbury!mrccrc!news.dcs.warwick.ac.uk!warwick!uknet!pipex!sunic!news.funet.fi!convex!harper From: harper@convex.csc.FI (Rob Harper) Newsgroups: bionet.software Subject: Re: Looking for .gif reader Message-ID: <1993Dec3.161347.862@funet.fi> Date: 3 Dec 93 16:13:47 GMT References: <03DEC93.02642739.0049@UNBVM1.CSD.UNB.CA> Sender: usenet@funet.fi (#Kotilo NEWS system ) Organization: Finnish University and Research Network FUNET Lines: 30 Nntp-Posting-Host: convex.csc.fi In <03DEC93.02642739.0049@UNBVM1.CSD.UNB.CA> "T. J." writes: >hi, i have Windows and Presentations but these packages can not read >gif files. Would someone tell me how i can get a .gif reader? Try the following ftp sites. Host ftp.csis.oita-u.ac.jp In /pub/msdos Directory viewer Host dutiws.twi.tudelft.nl In /pub/msdos/windows/wmos Directory viewers Host dorm.rutgers.edu In /pub/www/bin/pc-windows File viewers.zip 359K (359833 bytes) 17-11-93 16:47 RGDS -=ROB=- -- R. Andrew Harper E-mail: harper@convex.csc.fi Center for Scientific Computing Molbio/software: harper@nic.funet.fi Tietotie 6, P.O. Box 405 Telephone: +358 0 457 2076 SF-02101 Espoo Finland Fax: +358 0 457 2302 -- From owner-software@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!howland.reston.ans.net!torn!nott!nrcnet0!nrcbsa!phi From: phi@nrcbsa.bio.nrc.ca (Dr. Barry Phipps) Newsgroups: bionet.software Subject: Bibliographic software - summary #2 Message-ID: <1993Dec3.134909.6912@nrcnet0.nrc.ca> Date: 3 Dec 93 13:49:09 GMT Sender: root@nrcnet0.nrc.ca (Operator) Organization: National Research Council, Ottawa, Canada Lines: 204 Nntp-Posting-Host: nrcbsa.bio.nrc.ca X-Newsreader: TIN [version 1.1 PL8] This is a reposting of an earlier summary of a discussion of Bibliographic Software ... ***************************************************************************** Dear Netters ... This is for my summary of the greatful messages from BIOSOFT fellows on my recent posting ' Info Needed on Reference & Submission Manager ' this summary is organized as following ... and long ... 1. Help Summary (Selected & Reformatted 8 msgs) 2. Wizards List (Thanx for all) 3. More DOS-oriented Directory 4. More Mac-oriented Directory My Greatest Regards to all the people who helped me ... Thank You ! :-) ------------------------------------------------------------------------- 1. Help Summary ========================================================================= From: peters@cshl.org (Bobbie Petersin Grace Computer Center) our MAC people use: "EndNote" from Niles & Associates, Inc 2000 Hearst Avenue, Suite 200 Berkley, CA 94709 USA (800) 554-3049 or (510) 649-8176 Suggested Retail price - EndNote - $149 US EndNote Plus - $249 US our PC people use: "RefMan" from Research Information Systems Inc. Camino Corporate Center 2355 Camino Vida Roble Carlsbad, CA 92009-1572 USA (800) 722-1227 or (619) 438-5526 (619) 438-5573 - Fax Sorry no prices on this one ========================================================================= From: cummins@possum.murdoch.edu.au (Dr Jim Cummins) I suggest you check EndNote Plus, an excellent bibliographic package for Mac and DOS environments. You can get product information from Avi Rappoport on nilesinc@WELL.SF.CA.US There's also a good newsgroup available on LISTSERV.ENDNOTE ========================================================================= From: yagi2@scripps.edu (Akemi Yagi/BCR7 4-8094) I have been using Reference Manager for the kind of work you mentioned. The program is great. Try contacting: Research Information Systems, Inc. Camino Corporate Center 2355 Camino Vida Roble Carlsbad, CA 92009-1572 USA Phone: 619-438-5526 fax: 619-438-5573 ========================================================================= From: carstens@post.queensu.ca Reference Manager is also available on the MAC. I have used it for many years now and highly recommend it. ========================================================================= From: KLIER@cobra.uni.edu You may be interested in Papyrus, a bibliographic manager that can print citations in any number of formats, and can also cope with taking your manuscript, in which you have typed the reference numbers of the papers you wish to cite (e.g., 743 instead of Bloggs and Smith, 1978), and substitute either a numbered citation (as is common in chemistry) or the Bloggs and Smith 1978-type citation. It's been an excellent tool for me, and it's cheap... $99 US for up to 4 users; site licenses for entire universities available, too, at reasonable cost. The interface is straightforward, and easy to learn. ========================================================================= From: pekr@research.novo.dk (Peter Kristensen) Consider using the ProCite program available for both PC and Mac (PBS Ann Arbor Michigan, USA - fax no: 313 996 4672) ========================================================================= From: ramacha@CC.UManitoba.CA There is a Windows Based ref. manager which I think kinda does what you are looking for. It is a shareware. The author hovever has sent me a free distributable demo copy capable of handling 100 refs. The original hovever handles 4 million refs. The original I think is about 30 pounds. If you are interested, I can mail you the demo copy which is in a zip file. Let me know. Bye, Karthi. e-mail ramacha@ccu.umanitoba.ca ========================================================================= From: cprice@netserv.unmc.edu (Chad Price x7936) there is a review of the most popular commerical efforts in PC Magazine within the last month. There are lots of shareware and public domain efforts, some of which are equally (or nearly so) as the commercial efforts. I've written one which requires the Advanced Revelation database to run, but matches most of the commercial features. There are lots of others - ========================================================================= ------------------------------------------------------------------------- 2. Wizards List (Thanx for all) >From brucewb@phibred.com Wed Oct 13 22:36:18 1993 From: KLIER@cobra.uni.edu From: dLee@ccmail.llu.edu (dLee) From: Estelle Hrabak From: cummins@possum.murdoch.edu.au (Dr Jim Cummins) From: cprice@netserv.unmc.edu (Chad Price x7936) From: "Postmaster APECO" From: cprice@netserv.unmc.edu (Chad Price x7936) From: carstens@post.queensu.ca From: henry@frm.uovs.ac.za (Henry Pieters PhD.) From: peterk@sci.kun.NL From: "Crosby, Bill" From: ramacha@CC.UManitoba.CA From: Peter Ratiu >From bosborne@nature.berkeley.edu Thu Oct 14 01:21:09 1993 From: John F Towell From: pekr@research.novo.dk (Peter Kristensen) From: BSS097@bangor.ac.uk From: peters@cshl.org (Bobbie Petersin Grace Computer Center) From: "Johan de Boer" From: yagi2@scripps.edu (Akemi Yagi/BCR7 4-8094) ------------------------------------------------------------------------- 3. More DOS-oriented Directory ftp 141.210.10.117 login anonymous password - cd /pub/msdos/database/ type binary get ap11.zip get gl-4-131.zip get jpro.zip get paper202.zip quit AP11.ZIP B 141230 900407 Bibliographical database for academic papers GL-4-131.ZIP B 150981 900402 Bibliographic database program - with manual JPRO.ZIP B 158998 901203 Journal-Pro: Keep a computerized journal diary PAPER202.ZIP B 120677 910531 PAPERS v2.02: Scientific literature database ------------------------------------------------------------------------- 4. More Mac-oriented Directory ftp sumex-aim.stanford.edu login anonymous password - cd /info-mac/demo/ type ascii get endnote-plus-13.hqx quit 636380 May 20 11:16 ./demo/endnote-plus-13.hqx ------------------------------------------------------------------------- Thanks for reading me and for greatest help messages ... bye . ******************************************************************************* Sincerely Rhee Hwan-Seok Dept. Mol.Biol Seoul National Univ. e-mail : HYUNERHO@KRSNUCC1.BITNET u3307515@alliant.snu.ac.kr ******************************************************************************* Thanks for forwarding this to me John. Barry Phipps From owner-software@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!howland.reston.ans.net!torn!nott!nrcnet0!nrcbsa!phi From: phi@nrcbsa.bio.nrc.ca (Dr. Barry Phipps) Newsgroups: bionet.software Subject: Bibliographic software - summary #1 Message-ID: <1993Dec3.134748.6857@nrcnet0.nrc.ca> Date: 3 Dec 93 13:47:48 GMT Sender: root@nrcnet0.nrc.ca (Operator) Organization: National Research Council, Ottawa, Canada Lines: 456 Nntp-Posting-Host: nrcbsa.bio.nrc.ca X-Newsreader: TIN [version 1.1 PL8] Here is the promised summary of responses to my question regarding BIBLIOGRAPHIC SOFTWARE. I am very grateful for the wonderful response. I appreciate the time people took to send detailed information, which was very helpful in choosing a program suited to our needs. I am also reposting an earlier summary on the same topic, which was sent to me by John (sorry, I lost your surname, but thanks again). A few people referred me to an article in PC Magazine reviewing the top programs that was very useful: PC Magazine, October 12 / 93 issue, p. 269 "Point of Reference". ****************************************************************************** About the bibliography programs, I bought a Mac copy of EndNote-Plus for about $250. I'm quite happy with it. This program presents a number of features: - allows several thousands of entries per file; - the module EndLink (about $100. ?) will read Medline Medlars format files to interface with EndNote; - it is easy to cut and paste reference(s) in Word 4.0, while a new menu item is inserted in Word 5.0; - within the Word text, references are inserted in many different ways, like numbers, authors, authors+year, with/without brackets/square brackets,etc - list of references at the end of a paper may be formatted according to your needs, which means the parameters you want in the order you want, underlined or not, bold or not, commas here/not there, italic "et al" when you want it, etc; - journal names can be defined as abbreviates; - the final references list is constituted automatically when we are ready to, reformatting the citations within the text; - excellent technical support, and a newsgroup is maintained (mail help to listserv@ucsbvm.bitnet); It is also available for PC/compatible although I'm less familiar with. This program essentially meets my requirements, but it depends which installation you have access to, and on your needs. Regards, Andre White, awhite@alpha.oci.utoronto.ca Dept.Med.Biophys., Ontario Cancer Institute Toronto, Canada, (416) 924-0671x5053 ***************************************************************************** I used to use Reference Manager (for DOS), but recently switched to EndNote Plus. It's much easier to learn and use. Completely customizable, too. Ref. Man. has slightly better formatting capabilities, but to me the difference wasn't great enough. Reference Manager has a new Windows version, but it's very clunky. EndNote Plus has a Windows version in the works. Both companies should be able to send you free/low-cost demo versions. I don't have their addresses handy, unfortunately. Allison Anderson aaa@tamu.edu ***************************************************************************** I love Papyrus. It's cheap, easy to use, and wiorks like a charm. And if you get stuck, you can talk directly to the guy who designed the package. cheers bob Bienkowski bienkows@qcvaxa.acc.qc.edu ***************************************************************************** I have used EndNote Plus for several years and I'm very happy with it. There's a flourishing LISTSERV newsgroup that you can subscribe to by sending "SUBSCRIBE ENDNOTE" followed by a carriage return and your name to: LISTSERV@UCBCMSA. Product information is available from Avi Rappoport of nilesinc@WELL.SF.CA.US. I routinely download bibliographic searches from Medline and Current Contents directly into EndNote, and several institutions here in WA have installed this software as the standard reporting package for collating bibliographies for annual reports, CVs etc. Let me know if you need further details. Dr Jim Cummins +61-9-360 2668 School of Veterinary Studies FAX =61-9-310 4144 Murdoch University cummins@possum.murdoch.edu.au Murdoch, Western Australia 6150 ***************************************************************************** ProCite works fine - i have used it for many years. It may seem a little complicated to start with but gives a lot of possibilities. One feature not sheared (i think) by the other programs is that you can use the name and year, i.e. (Smith et al., 1990) in your manuscripts and then use the program to prepare the list of citations (including numbering in order of citation) - most other programs I have seen require that you use numbers from the databse in the text in order to do the in-text referencing, and this makes the drafts of manuscripts less easy to work with. Sincerely Peter Kristensen Pathology & Histochemistry Pharmaceuticals Division Novo Nordisk A/S, DENMARK ***************************************************************************** Ref Manager is EXCELLENT andf now available for Windows - however, there is another option called IdeaList (IRL Press) which is about as good a general-purpose literature databasing pgm as you can get - can also be used to archive ANYTHING, from recipes thru to letters to lit, in the same database, as different record types. ____________________________________________________________________ | Ed Rybicki, PhD | | | (ed@micro.uct.ac.za) | "Lord, won't you buy me | | Dept Microbiology | A Mer-ce-des Benz | | University of Cape Town | My friends all have Porsches | | | I must make amends..." | | | Private Bag, Rondebosch | | | 7700, South Africa | - Janis Joplin | | fax: 27-21-650 4023 | (Pearl, 1971) | -------------------------------------------------------------------- ***************************************************************************** I am using the Reference Manager package for some 7 years now. I also tried few other packages and tested Procite and Endnote. RefMan is, to my opinion, by far the best one. It is really friendly, easy to use, and has all the possibilities needed for a scientist. Its new version on Windows (or Mac) is really good. Another advantage of this soft is that it can be used together with the Reference Update which we are using in our Institute to review all the new litterature. It has also a nice feature, called Splicer that allows one to search, retrieve and insert references in a mns while writing it. Procite is also powerful, but it can take few months to understand how it works, and to have a version suitable for your own use. Endnote is really poor. If you need more informations, contact me by E-mail Gilles Bronchti ***************************************************************************** I'd like to share with you my experience with PAPYRUS software. Firstly it's price is advantageous. Apart from 99$ (as far as I am aware) it is possible to get it cheaper here in the U.K. for academic use. Secondly I am very happy with it and I wouldn't think of swapping to other software now. PAPYRUS allows you to import references from a practically unlimited number of sources (so you don't have to type in, just run 'import' and have a cup of tea). It has a variety of formats for different sources of bibliography data. However, as there is a quite big variety of different formats available on the world, do not be shocked in case of 'import' failure. I experienced such a shock when I tried to import some references from Medline on CD-ROM. I asked for advice a person supposed to support computers and data in this library and she couldn't help me. I decided to work out my own customized format and after painful couple of days I did it which is not so difficult once you learn how designing of the format works (I basically have very little computer background after graduating medicine). But anyway I managed to import some of the references from my dBASE database and also from Smart. The problem was it really took me a couple of days to play with formats, but now I feel confident enough not to be scared of using any format. However, producer would be happy to answer all your problems. You can also save your customized import format for future use. The other big advantage is applying PAPYRUS to create manuscripts. It supports a number of word processors. I used it with Word Perfect 5.1. It works great. You just put your reference numbers (unique numbers as they have in your PAPYRUS) in your text. Then after you choose desired format it is a few minutes and you will get the text ready to be sent off. If you have to send it to other journal with other format, you just keep your 'raw' version and run PAPYRUS again with other format and again it's a few minutes job. It sorts your references as you wish and 'exports' a list of sorted references in desired format to a file of your choice e.g. Word Perfect 5.1 or other. This is really time saving by the end of the day. You can import full references including abstracts and all other details, but be aware, this is again my experience, that when you start to accumulate references to hundreds and thousands especially with full data including abstracts the speed of importing data will decrease. Also the speed of searches will decrease. But you are warned in the manual that some sort of searches are really time consuming. Also if you use PAPYRUS's own backup system rather than DOS backup it can take quite a while to restore your data ( in my case it took ca. 10 hr to restore data containing about 1500 positions with full record including abstracts on 386SX with 100 Mega HD), but I don't know how other software copes with it. I would really strongly recommend PAPYRUS as excellent value for money. I don't know how is it in Canada but in the U.K. one can buy a personal license to use PAPYRUS in perpetuity after leaving academic institution for about 20-25 pounds as far as I know. Best regards, Dr. Rom(uald) Pitera r.pitera@portia.umds.ac.uk ***************************************************************************** We recently bought EndNote (Macintosh version) and are very happy with it. I particularly like the easy interface with Microsoft Word on the Mac. Elizabeth Harris chlamy@acpub.duke.edu ***************************************************************************** As you didn't tell on which platform you would to run the program I am not sure whether the following is of any interest to you. We have Papyrus running here on a VAX/VMS system. And I have seen it on a PC. A Mac version is supposed to be under development. Papyrus is able to import and export references in any format. And the price of US$ 99.- is almost unbeatable. In addition the licensing conditions are excellent; you may run the software on four PCs with a single license. A site-license is an additional US$ 200.- . Perhaps you may also want to have a look at the New England Journal of Medicine, Vol. 329, No. 4, pages 283-284. Regards Christoph Gartmann +----------------------------------------------------------------------------+ | Christoph Gartmann Phone : +49-761-5108-465 Fax: -221 | | Max-Planck-Institut fuer PSI : PSI%(0262)45050160374::GARTMANN | | Immunbiologie Internet: gartmann@immunbio.mpg.de | | Postach 1169 | | D-79011 Freiburg, FRG | ***************************************************************************** I have used EndNote and its on-line companion EndLink. Both do everything I want in such software: Searching on any fields, logical operators formatting for references in a large number of existing formats, define your own new formats, Easy download from on-line databases such as CAB. etc etc Mick Carrick ***************************************************************************** If you're talking about Ref Mangers for pc's and you don't want to spend a ton of money... I use a program called Papyrus. It is an MS-DOS based program that takes downloads in all standard formats (ie., BRS), stores all formats, performs searches on author, subject, keywords, etc., takes text files from all standard word processors (even MS-Windows, ie., AmiPro), extracts citations, generates bibliography, etc. In other words it does everything that ref manager does but its a LOT less expensive. Dave Goldman wrote the program and supports it very well (Research Design Software). If you'd like I could find his phone # for you. Otherwise, Papyrus was advertised in PC magazine lately (I think it was PC magazine). I currently have > 7,000 references in my database and searches are still fast (a matter of seconds). Anyway, I look forward to seeing a compilation of replies to your Bionet question. John L. Carroll JHU, Baltimore, Maryland ***************************************************************************** Reference manager is no good. Endnote is excellent if you use Microsoft Word Procite is OK but lacks in text citation format flexibility. Both Endnote and Procite have add ons that permit import of Medline and other biblio database searches. I have purchased all three and use Endnote. Dan Wetzel Neurology Univ of Vermont **************************************************************************** We have been using Reference Manager for a few years and like it pretty well. The capture feature to download directly from Medline has been particularly useful. Unfortunately the program is relatively expensive. One undocumented "feature" is that because it was written by someone associated with Scripps Clinic and Research Foundation in La Jolla, people at that institution get a price break. Therefore, if you know someone there you might ask them to help you out. P.S. We use the Windows version with a PC, but a friend uses the Mac version and is also quite happy. The people who write Endnote also seem quite reliable (we've used their Grant Manager program, but not Endnote because a PC version wasn't available at the time). **************************************************************************** We have recently bought Reference Manager (Research Information Systems). So far it seems pretty good. We have been importing references from an on-line database in the U.K. (BIDS) with no problems. It can output in a number of formats to be compatable with your WP. It's also good at generating complete bibliographies or a reference list for a paper. It has several built in journal styles, or you can define your own. When importing a reference, or typing one in it reports potential duplicates and saves them in a seperate file. There are versions for the Mac or windows (the one I use). A demo disk is avaliable from RIS. My one HUGE reservation about it is that you can have one database with up to 65,000 (yes 65,000) references, but no other reference database may exceede 200. Now the way I work is to have a lot of small databases each concerenced with a separate subject. You can search the one big database for your references about X, but I'd rather stick with many and small. Also this is a problem if the product is used by even a small number of people with differing interests. Bottom line is - it's great BUT the one database is a problem for me. Bob Lauder, bsa016@cent1.lancs.ac.uk Post Doctoral Research Associate, Division of Biological Sciences, Lancaster University, U.K. **************************************************************************** "Bob Lauder" writes: > My one HUGE reservation about it is that you can have one database with up to >65,000 (yes 65,000) references, but no other reference database may exceed 200 Bob- since I design and write databases for a living, I feel at least partly qualified to comment on you technique of multiple databases. Please do not take this as a flame, but I feel that saving references in multiple files may create problems for you long-term. In database design, one of the primary tasks in developing a data model revolves around "normalizing" your data. What this translates to is setting up a file (table) structure which minimizes or eliminates duplication of information. There are lots of reasons for this, but the relevant one for you are: (1) how do you ensure that you find a reference relevant to the topic under search if the paper contains material about several topics?? You may have saved it in some other file than the one you are looking in. Or you may simply have to search in _all_ of your files. (2) How do you ensure that the same reference saved in multiple files is exactly the same (and correct) in all locations. Both of these problems are solved by keeping all references in a single file and approaching the issue with keyword searches using appropriate keywords attached to each reference. This approach results in a normalized database, and will ensure that you can always find the references pertaining to any topic you choose without searching in several places. For those interested, I can place a copy of the source code for a database I wrote in Advanced Revelation (2.12 - I've not had time to update to 3.1 or Open Insight 2.0) on my machine for anonymous ftp retrieval. chad chad@windsurf.unmc.edu ***************************************************************************** I've been using Reference Manager for DOS for several years and have recently started using Reference Manager for Windows. Both programs have a number of minor problems but they have one tremendous advantage over anything else I've heard of, namely Reference Update, Abstract Edition. I receive 2 diskettes weekly containing the current literature which I scan with the profile I've set up, read the abstracts, choose the ones of interest and then transfer those citations with no extra typing other than editing changes into the main Reference Manager database (currently just over 2000 citations). This has been a tremendous help when writing review articles and when needing to make citation lists for new graduate students. One other feature of RM that I particularly like is the ability to set up citations in essentially any journal format and the fact that RM converts WinWord files to files that I can send away for publication. The main problems I've had with the Windows version is that it takes too much memory, does not allow certain international symbols such as the Scandinavian crossed o and gives minor problems with the TIGA display that I'm using. However, with the above reservations, I wouldn't want to write manuscripts without it. -------------------------------------------------------- Mark Achtman, Max-Planck Institut f|r molekulare Genetik Ihnestra_e 73, D-14169 Berlin, Germany e-mail: Achtman@MPIMG-Berlin-Dahlem.MPG.DE ***************************************************************************** I have used Papyrus extensively and been very satisfied. I use it to prepare manuscripts, and have done several large papers as well as a review with 100 references. Reformatting is straightforward. I use it hooked directlyto Wordperfect, and switch back and forth with the DOS taskswitcher. I also use Papyrus to keep a strain book in a separate database, with keyowrds=mutatnt loci, etc. These programs were recently reviewed in PC Magazine, and I beleive that the most-favorably reviewed programs were Refmanager and Papyrus. The difference in price is about 5-fold, Papyrus much cheaper. I have not used competitive microcomputer products, but am obviously fairlyhappy with Papyrus. I do not generally directly load references from a search service mostly because my University library has a terrible link that makes downloading nearly impossible. Chuck Staben **************************************************************************** Either PC Magazine or PC Computing had a "review" of personal bibliographic software within the last 3 months. Check the library. They pointed out the strengths and weaknesses of all the "major" programs. They found none to be "outstanding" enough to get the Editors choice award but indicated that one should pick the one that best fits their needs. PS I use Papyrus. I can get you the Email address of the author if you want. *********************************************************************** Dale M. Webb, Vet. Pathologist * 97% of the body is water. The Veterinary Diagnostic Center * rest keeps you from drowning. University of Nebraska, Lincoln * **************************************************************************** Greetings! I'd like to toss in my $0.02... After having just done a few grants manually, I picked up EndNote Plus and am so far very happy with it. It does what it claims it can do. It is apparently designed with W_Perfect and MS-Word in mind and compatibility with other word processors must be tested with it. I use W_Perfect at work but am partial to PC-Write at home. EndNote just fine with this word processor too. EndNote can be made compatible by interconverting documents to and from other formats like W_Perfect. As I said I'm pretty happy with it... and you don't need to pay list for it either... MicroWherehouse which often advertises in PC-Mag offers it for $139.95 as of this writing. Hope this helps some of you looking for reference software... Please forgive me - stupid editor - can't go back and correct obvious typos. -- line 6 EndNote "works" just fine... David haviland@kids.wustl.edu ***************************************************************************** Thanks again everyone. Barry Phipps From owner-software@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!pipex!uunet!utcsri!utnut!torn!csd.unb.ca!UNBVM1.CSD.UNB.CA From: A0RY@UNB.CA (A0RY000) Newsgroups: bionet.software Subject: Wanted: HD-util Message-ID: <04DEC93.19866811.0040@UNBVM1.CSD.UNB.CA> Date: 4 Dec 93 22:23:42 GMT Sender: usenet@UNB.CA Organization: The University of New Brunswick Lines: 6 If any one knows of a shareware program to determine the bios- setup of a hard disk, please send me E-mail of the place that I could find this utility. Thank you (Send E-mail to A0RY@unb.ca) From owner-software@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!xlink.net!scsing.switch.ch!sun.rediris.es!cnbvx3.cnb.uam.es!jlramos From: jlramos@cnbvx3.cnb.uam.es Newsgroups: bionet.software Subject: Looking for a DNA bending program Message-ID: <1993Dec4.124349.86@cnbvx3.cnb.uam.es> Date: 4 Dec 93 12:43:49 GMT Reply-To: JLRAMOS@CNBVX3.CNB.UAM.ES Organization: C.N.Biotecnologia, CSIC Lines: 10 Hy! I'm looking for a program to predict DNA bending. If anyone knows where I can get free, please tell me. Thanx M. Trini Gallegos Department of Vegetal Biochemistry Estacion Experimental del Zaidin Granada. Espagna. JLRAMOS@CNBVX3.CNB.UAM.ES From owner-software@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!EU.net!howland.reston.ans.net!newsserver.jvnc.net!newsserver.technet.sg!nuscc.nus.sg!zoorejb From: zoorejb@leonis.nus.sg (Ralph Edward James B) Newsgroups: bionet.software Subject: Re: Sequencher vs Applied Biosystems Message-ID: <2dosdk$iai@nuscc.nus.sg> Date: 4 Dec 93 02:24:52 GMT References: <93322.213551IRVK@MAINE.MAINE.EDU> <1993Nov20.143508.29803@nomina.lu.se> Organization: National University of Singapore Lines: 87 NNTP-Posting-Host: leonis.nus.sg X-Newsreader: TIN [version 1.2 PL0] David Kristofferson (kristoff@net.bio.net) wrote: : Bo.Servenius@wblab.lu.se (Bo Servenius) writes: : >I hope you ABI guys get more involved on the networks an see all the : >advantages of using it. With these means we the custumoer could : >send you our bugrepports etc directly instead of having them filtered : >throu your marketing or techsupport which many times might distort : >the messages. : Everyone please remember that there is a fine line that must be walked : here. This is not an easy issue to resolve, and is perhaps worth discussing. The line may be so fine that it is hard to find even with the aid of an electron microscope. : People who endorse products should do so only if they have *no* : financial connection, direct or indirect, with them and they should : clearly say so in ther posting. And what counts as a financial connection? Certainly those who own part of the company. This seems obvious enough, but if you participate in a pension plan (as most readers of this likely do, apart from students) what if the company managing your pension funds has invested in the manufacturer in question? If the manufacturer is well established, such an event is likely and would by a simple application of the above preclude many (most?) from commenting. If the net is broadened to include those involved with the suppliers of the company, or those who work for such companies or who have relatives working for such companies, those who have broadly based mutual funds, ... , an even larger proportion of us would not be able to comment favourably on a product. Certainly, there is a direct financial relationship between anyone using the product and the manufacturer unless the product used was stolen. This would preclude anyone who knows anything about the product from commenting favourably about it. ;-) : People at companies may answer in a factual manner direct questions : about their products but should stay out of the debates about which : "product is better." Advertising hype should obviously be avoided. What do you recommend if such a debate includes misinformation, or obsolete information, about the product? If such information is not corrected, both the company and potential users suffer harm. If it is corrected, the people at the company may well get drawn into the debate. I think we all understand what the objective is. No-one wants to be swamped by electronic junk or 'advertising'. The experience of the comp.os.os2.* and comp.os.windows.* groups is informative, and their strategy for handling the problem is a useful compromise. One of the things to be observed there was that plenty of bandwidth was consumed by people inquiring about, and speculating on, the price and availability of various products and their release dates. Some of this, particularly information about where to get materials was included in the FAQ, but some of this, particularly information related to new releases, could not be handled in such a manner. Thus, a moderated newsgroup was created specifically for product announcements. I have seen other newsgroups where people have been badly flamed for responding to a query like 'what can I use to do X' with information that a given product can do it and is available at a specified cost. Such a response was treated as if it was base advertising. However, if product announcements = advertizing, then many people are denied information they are seeking, and it can be observed that in the above mentioned newsgroups, the product announcements are welcomed in the specified and moderated newsgroup dedicated to such announcements and that this practice uses much less bandwidth than the inquiry and speculation that occurs without it. I don't think, from a network perspective, that email is an adequate alternative since with an announcement, only one message is sent while with email, there are a certain number of kBytes transmitted with each inquiry and another for each response. I would also observe that in the comp.os.os2.* newsgroups, IBM staff, and staff from companies making apps for OS2, participate regularly helping people fix problems that have arisen and pass feedback back to the company, and this includes people directly involved in writing the code used in OS/2 and related apps. Some of their responses would be seen as advertising in some other newsgroups and yet they are among the most highly valued and useful articles posted to the newsgroup and are NOT seen as advertising by those using these OS/2 newsgroups. This is not an easy issue to manage, and based on what I have seen, there are no solutions, only compromises dependant on the identity of the participating population. Cheers, R.E. Byers, Department of Zoology, National University of Singapore zoorejb@leonis.nus.sg From owner-software@net.bio.net Sat Dec 04 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!comlab.ox.ac.uk!oxuniv!epowell From: epowell@vax.oxford.ac.uk Newsgroups: bionet.software Subject: Macintosh family tree/history. Help! Message-ID: <1993Dec5.104612.18639@vax.oxford.ac.uk> Date: 5 Dec 93 10:46:12 GMT Organization: Oxford University VAX 6620 Lines: 22 I need a Macintosh piece of software which will allow two things. Firstly I need to have a family tree drawing facility. Secondly I need that to be linked to a patient history database. Thus by double clicking on a member of the family tree one would be presented with that patient's medical history. Now you would think such a thing would already be in existence but damned if I can find it. No doubt one could use AppleScript to link two seperate programs but I would prefer to avoid hours of development time. Any suggestions from out there on the Net? Could you post them directly to me as well as posting on this newsgroup please? ------------------------------------------------------------------------------- Stephen Atherton InterNet:epowell@vax.ox.ac.uk OR: s.atherton@cc.uq.oz.au Macintosh Higher Ed Consultant AppleLink:Atherton1 62 Hill Top Road Telephone:(0865)245505 OXFORD OX4 1PE Mobile: 0836 797372 United Kingdom & Prentice Computer Centre, The University of Queensland 4072. Australia ------------------------------------------------------------------------------- From owner-software@net.bio.net Sat Dec 04 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!msuinfo!harbinger.cc.monash.edu.au!bruce.cs.monash.edu.au!darrenp From: darrenp@bruce.cs.monash.edu.au (Daz) Newsgroups: bionet.software Subject: Re: DNA fingerprinting Message-ID: <2ds76r$smj@harbinger.cc.monash.edu.au> Date: 5 Dec 93 08:47:23 GMT References: <2cve4m$9vj@violet.csv.warwick.ac.uk> Organization: Computer Science, Monash University, Australia Lines: 16 NNTP-Posting-Host: dibbler.cs.monash.edu.au X-Newsreader: TIN [version 1.2 251093BETA PL3] Mr D J Plows (lsren@csv.warwick.ac.uk) wrote: : does anyone know of a program, shareware or commercial, for a PC to analyse : DNA fingerprint data to produce groups? I m doing research into good/better ways of constructing large restriction maps through random clone fingerprinting, and would be happy to attempt to map any data that anyone has (even if they have existing maps for their data). I won't be here much till after christmas day, but drop me some mail if you are interested, or if you have some data you would be happy to let me test my programs on. -- Darren Platt, Department of Computer Science darrenp@dibbler.cs.monash.edu.au Monash University, Clayton Melbourne, Victoria, Australia From owner-software@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!festival!leeds.ac.uk!news From: lrf6as@gps.leeds.ac.uk (A Staines) Newsgroups: bionet.software Subject: Re: Bibliographic software - summary #1 Message-ID: <1993Dec6.114302.23925@gps.leeds.ac.uk> Date: 6 Dec 93 11:43:02 GMT References: <1993Dec3.134748.6857@nrcnet0.nrc.ca> Sender: Anthony Staines Organization: University of Leeds, England Lines: 15 I'd like to add to the discussion on bibliographic software. I use a program called Idealist (from Blackwell Scientific Publishing, Oxford,UK). It is fast, and good academic deals are available in the UK. I like it because it is extremely flexible. I get lots of different types of references (e.g. journal articles, chapters, books, conference proceedings, databases, theses etc..) and I can keep all of these in a single database. You could use it to index anything. It is very fast because it indexes every word in every reference (apart from a select few 'stopwords' like the,and,for,to,...etc..) You can customise every aspect of its operations, and it is very easy to design import formats for external data sources. It supports OLE under Windows, and hence can link to word processors fairly directly. It's also easy to use, and simple to set up. Anthony Staines. From owner-software@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!pipex!uknet!festival!leeds.ac.uk!news From: lrf6as@gps.leeds.ac.uk (A Staines) Newsgroups: bionet.software Subject: Re: Bibliographic software - summary #1 Message-ID: <1993Dec6.114302.23925@gps.leeds.ac.uk> Date: 6 Dec 93 11:43:02 GMT References: <1993Dec3.134748.6857@nrcnet0.nrc.ca> Sender: Anthony Staines Organization: University of Leeds, England Lines: 15 I'd like to add to the discussion on bibliographic software. I use a program called Idealist (from Blackwell Scientific Publishing, Oxford,UK). It is fast, and good academic deals are available in the UK. I like it because it is extremely flexible. I get lots of different types of references (e.g. journal articles, chapters, books, conference proceedings, databases, theses etc..) and I can keep all of these in a single database. You could use it to index anything. It is very fast because it indexes every word in every reference (apart from a select few 'stopwords' like the,and,for,to,...etc..) You can customise every aspect of its operations, and it is very easy to design import formats for external data sources. It supports OLE under Windows, and hence can link to word processors fairly directly. It's also easy to use, and simple to set up. Anthony Staines. From owner-software@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!europa.eng.gtefsd.com!howland.reston.ans.net!xlink.net!scsing.switch.ch!swidir.switch.ch!univ-lyon1.fr!jussieu.fr!zaphod.crihan.fr!news.univ-rennes1.fr!newsmaster From: moreaut@univ-tours.fr Newsgroups: bionet.software Subject: various questions in the Mac environment Message-ID: <2dvejq$9kl@news.univ-rennes1.fr> Date: 6 Dec 93 14:04:21 GMT Organization: UNIVERSITE FRANCOIS RABELAIS - TOURS - FRANCE Lines: 30 NNTP-Posting-Host: rablai.univ-tours.fr dear colleagues, I would like to have your suggestions on several points: 1/ do you know alignments programms running on a Mac which can producing shadowed boxes for conserved residues amond a set of proteins ? I have already seen the reply to such a question related to the GCG package (Prettyplot command). 2/ does somebody know the existence of some font with fixed spaces such as Courrier but more pretty than Courrier? 3/ I produce postscript files with a molecular modelisation program and these files are exploited on a Mac to have quick output or black and white outputs. I am looking for a mac soft able to preview such files and also able to modify PS files. Thanks in advance for any suggestions >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dr Thierry MOREAU Laboratoire d'Enzymologie et Chimie des Proteines URA CNRS 1334 2bis, Bd Tonnelle 37032 TOURS Cedex France >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Fax: 33 47 36 60 46 E-mail: moreaut@univ-tours.fr >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From owner-software@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!cs.utexas.edu!howland.reston.ans.net!xlink.net!scsing.switch.ch!urz.unibas.ch!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.molbio.proteins,bionet.software Subject: Re: looking for proteins sequences Message-ID: <1993Dec6.074754.23544@comp.bioz.unibas.ch> Date: 6 Dec 93 07:47:54 GMT References: <2dsrc0$j26@reseau.cict.fr> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 138 Xref: biosci bionet.molbio.proteins:1111 bionet.software:6654 Nntp-Posting-Host: biox.embnet.unibas.ch In article <2dsrc0$j26@reseau.cict.fr>, maveyrau@ecstasy.NoSubdomain.NoDomain (Laurent Maveyraud) writes: |> Query from mcpalmie@FOX.CCE.USP.BR (Mauricio Cesar Palmieri): |> ... |> >ones. Somebody there could tell me some information about how is the |> >easiest manner to proceed a roughly search? (database, software, time |> >required, etc). The software you may choose balances speed vs. sensitivity, and it very much depends on the question you ask. There are three options (1) Rely on the network (2) rely on your site (3) Do everything yourself Option three, obviously, is time consuming and usually does not pay off. You should not need to install software and databases yourself if you work in a larger environment because central services are cost- effective and therefore provided usually. If you do not enjoy such comfort but need to initiate one the best were to visit a site where it's already running (better even, two or three different sites running different environments). Option one, the network, may turn out to be a Damokles sword; as you get what you paid for. Most of the services are "free". Many of the services provided on the net are spawned from research activities and therefore continuously suffer from funding, thus, are continuously in danger to degrade, or cease to exist. There are a few exceptions, thogh, like the services of the EMBL data library or the national services from EMBnet in Europe, and the NCBI in the US. The available services on the network have been collected by Amos Bairoch and are available on various servers, on our mirror server you will find the data on nic.switch.ch as mirror/embnet-ch/other-data/info/serv_ema.txt.Z With respect to option two, the central services, you might want to consider querying your national Center in Brasil. Goran (adresses below) will provide you answers to your questions if you would like to get either services there or an advice. Any EMBnet node has an entry in 'The Nodes of EMBnet' database which is available as Postscript format on nic.switch.ch in mirror/embnet-ch/info/embnet The embnet.dat file is a plain ASCII file and there are nice postscript versions with additional information as well. There is a Brasilian node in Brasilea which serves the community according to as imilar structure as the EMBnet nodes do in Europe, the Brazilian Molecular Biology and Biotechnology Network (BMBBNet). For more information, ask at ------------------------------------------------------------------------ | Goran Neshich | | | CENARGEN/EMBRAPA | e-mail: neshich@cenargen.embrapa.br | | S.A.I.N. Parque Rural, Final W5 | | | Asa Norte | Phone: +55 (61)273-0100 ext 127 | | 70770-900, Brasilia-D.F.-BRASIL | Fax: +55 (61)274-3212 | ------------------------------------------------------------------------ |> |> |> One of the numerous way is to use the UWGCG package, with the database |> Genembl. The option is TFASTA. This goes through the whole DNA database, TFASTA belongs to the FASTA package written by William R. Pearson originally described in Science (Lipman and Pearson, (1985) Science 227:1435-1441). The Genetics Computer Group, Inc. (Madison, Wisconsin) distributes a version which is adapted to their package. ... |> Software : UWGCG (University of Wisconsin Genetic Computer Group) it is |> available nearly everywhere there are molecular biology labs The package in question arose from an academic group (UWGCG) but is now comercially managed (Info at beers@gcg.com). Due to its history and economical factors, it is installed at a large basis. We have enjoyed excellent results arising from running this package since 1987. However, it is important to emphasize that other packages are available, such as the Intelligenetics Software Packahe (known as IG Suite, Info at ig-consultant@presto.ig.com), and others. There are many packages available from the public domain, though, these usually cover only a special (but very extensively covered) set of a particular activity, e.g. sequence searching, e.g., he FASTA was mentioned above, and the NCBI has released the 'BLAST' suite of programs. |> |> Database : Genembl, which is also from UWGCG, and is updated every 15 days (I think...) 'Genembl' is a term for a merged database used in the GCG package. On the basis of accession numbers, Genbank and EMBL are excluded in the corresponding database; e.g., in the US you would normally run GENBANK with a EMBL exclusion set, and in Europe you will have a EMBL with a Genbank exclusion set. The update frequency is a matter of your administrator, we do EMBL daily and GENBANK weekly, most sites in Switzerland maintain a weekly GCG GENEMBL data update. There oare other merged collections out there, PATCHX, OWL, and others. |> |> Time : well, this depends mainly on the machine you are using. It can range from 1hour to 15 min. BLAST (software from the NCBI) takes only a few seconds if peptide runs vs. peptice straight, and a Smith and Waterman search on a massively parallel machine (software from the Edinburgh team) doen't take longer either. The latter run on a deskside, 4 year old hardware might easily take 5 hours CPU to complete. The search software available ranges from scans of identity to sophisticated methods of fragment pattern searching, and from browsing the database with quick-but-dirty to extensive homology evaluations searching with profiles. ISEARCH (PIR), (T)FASTA (Pearson), BLAST (NCBI), WORDSEARCH(UWGCG), TWORDSEARCH(Rice), BLAZE (Intelligenetics), MPsearch(Collins et al, also as BLITZ), PROFILE methods (GRIBSKOV), FLASH (IBM), and many, many other programs have a wide area of application. So the range depends on * algorithm used * hardware used * question asked * (occasionally) length of the sequence Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ftp mirror at nic.switch.ch ----------------------------------------- From owner-software@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!rpi!sarah!psinntp!psinntp!barilvm!kineret.huji.ac.il!wisipc.weizmann.ac.il!weizmann.weizmann.ac.il! BCRUBIN From: BCRUBIN@weizmann.weizmann.ac.il Newsgroups: bionet.software Subject: Re: ABI Inherit software/hardware Message-ID: <16C9BEB30.BCRUBIN@weizmann.weizmann.ac.il> Date: 5 Dec 93 16:43:24 GMT References: <693@biosys.apldbio.COM> Sender: news@wisipc.weizmann.ac.il (News User) Organization: Weizmann Institute of Science Lines: 11 X-Newsreader: NNR/VM S_1.3.2 Hello all. I have been using both GCG and inherit. I am doing a lot of sequence comparis on, and do have some warm words to say about inherit. Actually the best thing a bout it (accept for the assambly tool) is the speed, which is of a completely f differant scale. My 2 main dissapointments are: bad help/documnetation and being unably to write rutines that would utilize it's speed. I'm programming in C and had a wonderfull time writing programs that interact with GCG, but when I wanted to use inherit's speed - yok. If any of you inherit people here me - think about it. Eitan. From owner-software@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!world!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!rpi!sarah!psinntp!psinntp!barilvm!kineret.huji.ac.il!wisipc.weizmann.ac.il!weizmann.weizmann.ac.il! BCRUBIN From: BCRUBIN@weizmann.weizmann.ac.il Newsgroups: bionet.software Subject: Re: ABI Inherit software/hardware Message-ID: <16C9BEB30.BCRUBIN@weizmann.weizmann.ac.il> Date: 5 Dec 93 16:43:24 GMT References: <693@biosys.apldbio.COM> Sender: news@wisipc.weizmann.ac.il (News User) Organization: Weizmann Institute of Science Lines: 11 X-Newsreader: NNR/VM S_1.3.2 Hello all. I have been using both GCG and inherit. I am doing a lot of sequence comparis on, and do have some warm words to say about inherit. Actually the best thing a bout it (accept for the assambly tool) is the speed, which is of a completely f differant scale. My 2 main dissapointments are: bad help/documnetation and being unably to write rutines that would utilize it's speed. I'm programming in C and had a wonderfull time writing programs that interact with GCG, but when I wanted to use inherit's speed - yok. If any of you inherit people here me - think about it. Eitan. From owner-software@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!rpi!sarah!psinntp!psinntp!barilvm!kineret.huji.ac.il!wisipc.weizmann.ac.il!weizmann.weizmann.ac.il! BCRUBIN From: BCRUBIN@weizmann.weizmann.ac.il Newsgroups: bionet.software Subject: Re: ABI Inherit software/hardware Message-ID: <16C9BEB30.BCRUBIN@weizmann.weizmann.ac.il> Date: 5 Dec 93 16:43:24 GMT References: <693@biosys.apldbio.COM> Sender: news@wisipc.weizmann.ac.il (News User) Organization: Weizmann Institute of Science Lines: 11 X-Newsreader: NNR/VM S_1.3.2 Hello all. I have been using both GCG and inherit. I am doing a lot of sequence comparis on, and do have some warm words to say about inherit. Actually the best thing a bout it (accept for the assambly tool) is the speed, which is of a completely f differant scale. My 2 main dissapointments are: bad help/documnetation and being unably to write rutines that would utilize it's speed. I'm programming in C and had a wonderfull time writing programs that interact with GCG, but when I wanted to use inherit's speed - yok. If any of you inherit people here me - think about it. Eitan. From owner-software@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!utcsri!utnut!oci!bono.oci.utoronto.ca From: jwoodget@ocicl.oci.utoronto.ca (Jim Woodgett) Newsgroups: bionet.software Subject: Re: various questions in the Mac environment Message-ID: <9312061353.AA22283@bono.oci.utoronto.ca> Date: 6 Dec 93 18:53:22 GMT References: Sender: news@oci.utoronto.ca Reply-To: jwoodget@ocicl.oci.utoronto.ca (Jim Woodgett) Organization: Ontario Cancer Institute Lines: 59 X-Newsreader: InterCon TCP/Connect II 1.2 In article , scott@phylo.life.uiuc.edu (Scott Howard) writes: > Shaded Annotated Sequences: > GeneWorks and DNAStar will accomplish this. If you'd like to save > yourself a few thousand francs, 13 point Courier and most any > reasonably well constructed drawing program will suffice. There is a non-commercial possibility if you are using a Macintosh - SeqApp 1.9. This does a very nice multicoloured pretty print with shading as well as lots of other things. It was written by Don Gilbert and is free (as far as I know). Note it is an alpha release and may cause crashes. I have experienced these but usually they simply cause the program to quit. It's a really nice piece of work overall. Here is Don's abstract on the program: SeqApp is a biological sequence editor and analysis program for Macintosh computers. It includes links to network services and external analysis programs. Features include multiple sequence alignment editor single sequence editor window read and write several sequence file formats * easy hand alignment features including colored bases and sliding * automatic multiple sequence alignment thru Clustal external app automatic gel fragment alignment to contigs thru CAP exernal app * consensus,reverse,complement,degap operations restriction maps dot plots translate dna to/from protein using various codon tables automatic preference saving * internet send mail, read mail internet gopher, information retreival including genbank. internet sequence analysis services user-definable links to external analysis programs and more * These features were updated in release 1.9a. See below for details. +++ NOTICE: This is an early, unfinished version of the program. Expect it to fail in various ways. This release is made available to those who wish to test and comment on its future development. This release will expire on a date indicated in the About dialog. SeqApp is being written by Don Gilbert, using the MacApp extensible Macintosh programming framework from Apple Computer. You can obtain updates of this release thru anonymous ftp to ftp.bio.indiana.edu, in folder /molbio/seqapp, as seqapp.hqx. You may also obtain updates directly thru an internet-connected Mac with SeqApp, using Gopher to the IUBio archive. Look for a folder called "IUBio Software+Data/SeqApp, Mac sequence editor". There may be additional distribution software, data or information in this /molbio/seqapp folder. See the Readme files in it for details. Jim Woodgett Fax (416) 926 6529 Tel (416) 924 0671 jwoodget@ocicl.oci.utoronto.ca _____________________________________________________________ From owner-software@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!destroyer!gatech!howland.reston.ans.net!agate!headwall.Stanford.EDU!bcm!TAMUTS.TAMU.EDU!rigel.tamu.edu!grl6732 From: grl6732@rigel.tamu.edu (Gerard R. Lazo) Newsgroups: bionet.software Subject: Re: Announcing: DNA WorkBench Keywords: DNA Message-ID: <3DEC199316103936@rigel.tamu.edu> Date: 3 Dec 93 21:10:00 GMT Organization: Texas A&M University OpenVMScluster Lines: 16 NNTP-Posting-Host: rigel.tamu.edu News-Software: OpenVMS/VAX VNEWS 1.41 How does DNA Workbench compare to Genetic Data Environment (GDE2.2)? I believe GDE2.2 works mainly in the UNIX environment. Would the use of DNA Workbench provide similar functions on PCs and Macs. GDE2.2 has things linked to it like Phylip, Treetool, Looptool, Blast, Fasta, XYLEM, FSAP, etc... These front-end user interfaces are great. For someone who may not have access to GCG, Intelligenetics, etc...; these provide a way to customize a working environment. / Gerard R. Lazo . %. (=) GLAZO@tamsun.tamu.edu USDA-ARS (.( .) / Off: 409-260-9533 Southern Crops Research Lab. ( ( .) .) -> (=) Lab: 409-260-9522 Route 5, Box 805 %_( ._) / Fax: 409-260-9333 College Station, TX 77845 //\| (=) (( / From owner-software@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!phylo!scott From: scott@phylo.life.uiuc.edu (Scott Howard) Newsgroups: bionet.software Subject: Re: various questions in the Mac environment Message-ID: Date: 6 Dec 93 17:38:50 GMT References: <2dvejq$9kl@news.univ-rennes1.fr> Organization: University of Illinois at Urbana Lines: 16 NNTP-Posting-Host: phylo.life.uiuc.edu Shaded Annotated Sequences: GeneWorks and DNAStar will accomplish this. If you'd like to save yourself a few thousand francs, 13 point Courier and most any reasonably well constructed drawing program will suffice. Fonts: As for fonts, Courier is the only postscript font I have seen that is truly monospaced. There are several bitmapped-only fonts that are monospaced, but they all share the trait of getting mangled during manipulation and printing. Standard Weasel Clause: I have no affiliation with Adobe Systems, Apple Computer, DNAStar, Intelligenetics, or the International Brotherhood of Electrical Workers. The University of Illinois does not even know I exist, much less condone my opinions. From owner-software@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!EU.net!uunet!utcsri!utnut!oci!bono.oci.utoronto.ca From: jwoodget@ocicl.oci.utoronto.ca (Jim Woodgett) Newsgroups: bionet.software Subject: Re: various questions in the Mac environment Message-ID: <9312061353.AA22283@bono.oci.utoronto.ca> Date: 6 Dec 93 18:53:22 GMT References: Sender: news@oci.utoronto.ca Reply-To: jwoodget@ocicl.oci.utoronto.ca (Jim Woodgett) Organization: Ontario Cancer Institute Lines: 59 X-Newsreader: InterCon TCP/Connect II 1.2 In article , scott@phylo.life.uiuc.edu (Scott Howard) writes: > Shaded Annotated Sequences: > GeneWorks and DNAStar will accomplish this. If you'd like to save > yourself a few thousand francs, 13 point Courier and most any > reasonably well constructed drawing program will suffice. There is a non-commercial possibility if you are using a Macintosh - SeqApp 1.9. This does a very nice multicoloured pretty print with shading as well as lots of other things.