From owner-software@net.bio.net Thu Apr 01 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsswitch.lcs.mit.edu!news.ultranet.com!not-for-mail From: "Marc Andelman" Newsgroups: bionet.software Subject: bioinformatics job Date: Thu, 1 Apr 1999 19:17:07 -0500 Organization: UltraNet Communications , an RCN Company http://www.ultranet.com/ Lines: 35 Message-ID: <7e12t8$t2o$1@antiochus.ultra.net> NNTP-Posting-Host: 209-122-233-112.s112.tnt5.sbo.ma.dialup.rcn.com X-Complaints-To: abuse@ultra.net X-Ultra-Time: 2 Apr 1999 00:27:20 GMT X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Biosource is an employer paid fee service.Our client, based in Rekyavik, ICELAND,is seeking to hire people with the following skills. Please refer this information to anyone who may be potentially interested. Interested parties should E mail drgonfly@ultranet.com, by attaching a Word or Wordperfect cv, or call Marc Andelman Biosource Inc. 1 Parkton Ave., Worcester, MA 01605 tel 508 853 8803 fax 508 853 8772. Unless specifically requested, please allow me only to get back in touch with a particular person if this or some other position is a dead ringer for a particular person's interests. I of course call first to ask permission before releasing anyone's information. Regards, Marc Andelman ,Biosource Inc. Bioinformatics Our client, a leading genomics firm based in Iceland, needs bioinformatics specialists that are energetic, good at communicating, know how to design/program and have experience in at least three of the following areas:Secondary structure prediction,exon prediction,Sequence comparison/remote homologue detection.Ternary/functional structure prediction,Primer designControl element extraction.SequencingGenotypingOne person is for bioinformatics support. That person will have to be able to program a little bit in Perl,CGI,HTML and have good communication skill and be willing to learn some genetics.The others could be Bioinformatics specialist with some experience and interest/ambition and a good programmer (preferably with Java experience and intrest in genetics. Statistical geneticsThe Statistics group of our client is seeking applicants for two or more available positions. The applicant must have completed the equivalent of bachelors degree or more in mathematics, statistics or computer science. Familiarity with the UNIX operating system, the S-plus statistical package, and or programming in C/C++ will be considered an asset. From owner-software@net.bio.net Thu Apr 01 23:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!washdc3-snf1!news.gtei.net!icet.net.nih.gov!news From: Jonathan Epstein Newsgroups: bionet.software Subject: Re: help on formatdb core dump Date: Fri, 02 Apr 1999 10:46:11 -0500 Organization: National Institutes of Health Lines: 55 Message-ID: <3704E643.5FDD3530@nih.gov> References: <7e0bbl$gae$1@nnrp1.dejanews.com> NNTP-Posting-Host: 137.187.221.54 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (Win95; I) To: gmei@my-dejanews.com CC: gmei@pavonis.com Your root file system is full. This is probably where your system's temporary space is allocated. Delete some stuff, especially from /tmp and /var/tmp, and try again. You may be more successful if you set your TMPDIR environment variable to point to a directory on your large /data1 file system prior to rerunning BLAST. This should direct BLAST to place its temporary files there, which might help. - Jonathan gmei@my-dejanews.com wrote: > > Hi: > > I have a genbank datafile (filename:genbankdata) in fasta format that I am > running "formatdb" on. > > The file is in directory /data1/genbank/database which is 100GB in size > > searchsrv1> ls -l > total 12139628 > -rw-r--r-- 1 genbank system 668 Apr 1 11:55 formatdb.log > -rw-r--r-- 1 genbank system 9616926535 Apr 1 08:32 genbank.seq > -rw-r--r-- 1 genbank system 2587447829 Apr 1 09:15 genbankdata > > When I run > > /data1/program/ncbiblast/formatdb -i genbankdata -p F -o T > > It core dumped after about 40 min. And here is the formatdb.log: > > ========================[ Apr 1, 1999 10:43 AM ]======================== > Version 2.0.8 [Jan-05-1999] > Started database file "genbankdata" > FATAL ERROR: CoreLib [001.000] Failed to allocate 62768120 bytes > > And I looked the disk space: > > searchsrv1> df -k Filesystem 1024-blocks Used Available Capacity Mounted > on root_domain#root 532176 66362 458776 13% / /proc 0 0 0 100% > /proc usr_domain#usr 4147848 536348 3576896 14% /usr > search_domain#programs 17780000 16 17773576 1% /programs > search1_domain#data1 106665000 21567728 85067880 21% /data1 > > And idea where is source of error? > > If you reply, please send a copy to gmei@pavonis.com > > Thanks. > > Guang Mei > > -----------== Posted via Deja News, The Discussion Network ==---------- > http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Thu Apr 01 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!chippy.visi.com!news-out.visi.com!cam-news-hub1.bbnplanet.com!washdc3-snf1!news.gtei.net!icet.net.nih.gov!news From: Jonathan Epstein Newsgroups: bionet.software Subject: Re: nclever and web only methods available for NCBI access? Date: Fri, 02 Apr 1999 10:26:52 -0500 Organization: National Institutes of Health Lines: 44 Message-ID: <3704E1BC.6C45DF51@nih.gov> References: <3703EC42.52D0CE60@mail.ahc.umn.edu> NNTP-Posting-Host: 137.187.221.54 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (Win95; I) To: "Timothy M. Kunau (CBC)" Consider using Nentrcmd, which is a command line interface to Entrez which is available as part of the NCBI toolkit: ftp://ncbi.nlm.nih.gov/toolbox/ Once you have built the 'makeall' portion of the toolkit (see the README), you can build Nentrcmd using: make -f makenet.unx Nentrcmd A few other compiler-related options may be necessary. Once you have built Nentrcmd for your system, you can get short online help via: Nentrcmd - or longer help via: Nentrcmd -h -p manual Official help is available from toolbox@ncbi.nlm.nih.gov, but I may be able to offer some help as well. I'm the author of this program, which was used as the retrieval engine for the original version of WWW Entrez (c. 1994). - Jonathan Timothy M. Kunau (CBC) wrote: > > We cannot be the only group asking this question, > > We need to automate the download of sequences and updates from NCBI. > They do provide a web interface: > > http://www.ncbi.nlm.nih.gov/Entrez/batch.html > > We have looked at nclever. For various reasons, this has been > unwieldy. > > What other methods are available to download sequences in a batch form? > > Thanks, > > Tim > -- > Timothy M. Kunau kunau@ahc.umn.edu Computational Biology Ctrs. > Genomic Database Administrator, Computing and Bioinformatics, AHC > 612-626-6937 http://www.cbc.umn.edu/~kunau http://www.cbc.umn.edu From owner-software@net.bio.net Thu Apr 01 23:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.cwix.com!130.185.14.36!torn!nott!uottawa!not-for-mail From: "Donal Hickey" Newsgroups: bionet.software Subject: faculty position in bioinformatics Date: Fri, 2 Apr 1999 17:18:44 -0500 Organization: University d'/of Ottawa Lines: 48 Message-ID: <7e3fdc$3ck$1@mercury.cc.uottawa.ca> NNTP-Posting-Host: maeve.genetics.uottawa.ca Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Applicants with expertise in any area of bioinformatics are encouraged to apply for one of the following positions. The School of Information Technology and Engineering (SITE) seeks applications for tenure-track faculty appointments at the Assistant/Associate Professor level in the general areas of computer engineering, computer science, software engineering, and electrical engineering. The School is particularly interested in candidates with expertise in computer architecture, operating systems, databases, software architecture, software development process, software methodologies, distributed systems, internet technologies, optical and wireless communications, electronics, system engineering, and biomedical informatics. Candidates must have a Ph.D. in computer engineering, computer science, electrical engineering or related discipline. The successful candidates must have excellent academic credentials and an ability to develop a strong independent research program, as well teach effectively at the undergraduate and graduate levels. Rank and salary are commensurate with qualifications and experience. Bilingualism (English and French) and eligibility for registration as a Professional Engineer in Ontario would be an asset. The School currently has 1507 undergraduate students, 267 graduate students and 41 faculty. It offers a full slate of degrees at the Bachelor's, Master's and Doctoral levels in Computer Engineering, Electrical Engineering, Software Engineering and Computer Science. Opportunities for collaboration with information-technology industries in Ottawa, the Silicon Valley North, are among the best. The Ottawa-National Capital region offers a remarkable variety of cultural and recreational opportunities. Processing of applications will continue until the positions are filled. The starting date is January 1, 1999 or July 1, 1999. Applications including a curriculum vitae and the names and addresses of three referees should be sent to: The Director of the School of Information Technology and Engineering, Faculty of Engineering, 150 Louis Pasteur, Ottawa, ON, K1N 6N5. Positions are subject to budget approval. The University of Ottawa is committed to employment equity, welcomes diversity in the workplace, and encourages applications from all qualified individuals including members of visible minorities, aboriginal persons and persons with disabilities. The University strongly encourages applications from women. In accordance with Canadian Immigration requirements, priority will be given to Canadian citizens and permanent residents of Canada. From owner-software@net.bio.net Sat Apr 03 23:00:00 1999 Path: biosci!ZEUS.CHAPEL1.COM!kuppler From: kuppler@ZEUS.CHAPEL1.COM Newsgroups: bionet.software Subject: AD:Family Reunion T Shirts & More Date: 4 Apr 1999 05:30:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: <199904041229.FAA00620@net.bio.net> NNTP-Posting-Host: net.bio.net Message sent by: Kuppler Graphics, 32 West Main Street, Maple Shade, New Jersey, 08052, 1-800-810-4330. This list will NOT be sold. All addresses are automatically added to our remove list. Hello. My name is Bill from Kuppler Graphics. We do screenprinting on T Shirts, Sweatshirts, Jackets, Hats, Tote Bags and more! Do you or someone you know have a Family Reunion coming up? Kuppler Graphics would like to provide you with some great looking T Shirts for your Reunion. Kuppler Graphics can also provide you with custom T's and promotional items such as imprinted magnets, keychains, pens, mugs, hats, etc. for your business or any fundraising activity (church, school, business etc.) We also can provide you with quality embroidery. We are a family owned company with over 15 years of experience. All work is done at this location. No middle man. Our prices are great! Click reply to email us or call 1-800-810-4330 for more info Bill Kuppler Graphics From owner-software@net.bio.net Sun Apr 04 23:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!cyclone.swbell.net!uunet!ffx.uu.net!in5.uu.net!news-feed.netvision.net.il!194.90.1.15.MISMATCH!news!not-for-mail From: Avi Rosenberg Newsgroups: bionet.software Subject: Re: where can I find "gb2fasta" for Digital Unix? Date: Mon, 05 Apr 1999 09:53:43 +0200 Organization: NetVision Israel Lines: 133 Message-ID: <37086C07.18B2E471@compugen.co.il> References: <7de96a$5qg$1@nnrp1.dejanews.com> NNTP-Posting-Host: bioserv.compugen.co.il Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.netvision.net.il 923295390 23060 194.90.227.153 (5 Apr 1999 06:56:30 GMT) X-Complaints-To: abuse@netvision.net.il NNTP-Posting-Date: 5 Apr 1999 06:56:30 GMT To: Tim Cutts , zlmei@hotmail.com X-Mailer: Mozilla 4.08 [en] (X11; I; SunOS 5.6 sun4u) Tim Cutts wrote: > > In article <7de96a$5qg$1@nnrp1.dejanews.com>, wrote: > >Hi: > > > >I am looking for "gb2fasta" program running on Digital Unix platform. I have > >downloaded a linux version from ftp://ulrec3.unil.ch but we have bought a new > >Digital Alpha 4100 recently and I need to install that program. Or is there > >any other similar program out there that I can use (on Digital Unix) to > >convert Genbank files (downloaded from NCBI) to fasta format? > > > >If you reply, please also send a copy to zlmei@hotmail.com > > I use the following perl script. I hope you find it useful. > > Regards, > > Tim. > > #!/usr/local/bin/perl -w > > use strict; > > local $/ = "\n//\n"; > > while (<>) > { > my ($id, $def, $acc, $sv, $title, $sequence); > my (@lines) = split(/\n/, $_); > chomp(@lines); > foreach my $line (@lines) > { > last if ($id && $acc && $def && $sv); > if ($line =~ /^LOCUS\s+(\S+)/) > { > $id = $1; > } > elsif ($line =~ /^DEFINITION\s+(.*)$/) > { > $def = $1; > } > elsif ($line =~ /^ACCESSION\s+(\S.*)$/) > { > $acc = $1; > } > elsif ($line =~ /^VERSION\s+(\S+)/) > { > $sv = $1; > } > } > > next unless (($sequence) = m:.*\nORIGIN[^\n]+\s+(.*)//:s); > > $sequence =~ tr/0-9//d; > > $title = ">$id $acc "; > > if ($sv) { > $title .= "($sv) "; > } > $title .= $def; > > print &Fasta($title, 60, $sequence); > > } > > sub Fasta($$@) > { > > my $title = shift; > my $length = shift; > > # If the length item is omitted, assume 60 > unless ($length =~ /^\d+$/) > { > unshift(@_, $length); > $length = 60; > } > > # If the caller forgot to put a > on the title, put one there. > unless ($title =~ /^>/) > { > $title = ">$title"; > } > > # Remove any newlines from the title > $title =~ tr/\n//d; > > # Concatenate the input sequences > my $seq = join('', @_); > > # Remove any whitespace > $seq =~ s/\s+//gs; > > my ($i, $l, @result); > > $l = length($seq); > > push (@result, "$title\n"); > > # If the length asked for is zero, then output the sequence on one > # line. > > if ($length > 0) > { > for ($i = 0; $i<$l; $i += $length) > { > push (@result, substr($seq, $i, $length), "\n"); > } > } > else > { > push (@result, "$seq\n"); > } > > return join('', @result); > > } Please note that the definition field might be more than one line long, so you might want to modify your program a little to take all of the lines that follow the DEFINITION line, and start with at least two blanks (that is of course only if you want all the definition of the entry, and not only the first line). -- *********************************************************************** Avi Yeshah Rosenberg "GCCGTAATCCGG" Compugen Ltd. Tel: +972-3-7658556 72 Pinchas Rozen Fax: +972-3-7658555 Tel-Aviv, 69512 E-mail: avir@compugen.co.il Israel WWW: http://www.cgen.com ********************************************************************** From owner-software@net.bio.net Sun Apr 04 23:00:00 1999 Path: biosci!cnn.nas.nasa.gov!news.msfc.nasa.gov!newsfeed.cwix.com!24.92.0.41!newse1.tampabay.rr.com!newse2.tampabay.rr.com.POSTED!not-for-mail From: tgibson1@tampabay.rr.com (William T. Gibson) Newsgroups: bionet.software Subject: Improve test scores through technique based learning Message-ID: X-Newsreader: MT-NewsWatcher 2.4.4 Lines: 25 Date: Mon, 05 Apr 1999 20:01:35 GMT NNTP-Posting-Host: 24.92.161.70 X-Complaints-To: newsabuse@tampabay.rr.com X-Trace: newse2.tampabay.rr.com 923342495 24.92.161.70 (Mon, 05 Apr 1999 16:01:35 EDT) NNTP-Posting-Date: Mon, 05 Apr 1999 16:01:35 EDT Organization: RoadRunner - TampaBay Virtual Toys has just released an exciting new tool for technique based learning! The Virtual Toys Play & Learn Console® is a rich, open-ended environment in which adults, children and students can learn or hone skills in many academic areas. Download the Play & Learn Console® for FREE! Your Play & Learn Console is tailored learning environment giving you the ability to download the "Skills Drills" that your interested in. Each Virtual Toys Skills Drill is a unique learning tool with forty levels of difficulty and offers Stepping Stone Certificates of achievement for each level. Your Play & Learn Console® keeps track of your progress and achievements through the use of printable Stepping Stone Certificates, Skills Mastery Certificates and a Virtual Toys Report Card. To get your own Play & Learn Console® or for more information, please visit: http://www.vtgenius.com/317-XTCQ.htm ----------------- Sincerely, William T. Gibson Virtual Toys, Inc. "Quality Software Preparing Today's Children For Tomorrow." http://www.vtgenius.com/012-XCGA.htm From owner-software@net.bio.net Sun Apr 04 23:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!207.97.14.174!europa.clark.net!207.114.4.11!nntp.abs.net!newsfeed.ecrc.net!news.net.uni-c.dk!news.daimi.au.dk!not-for-mail From: =?iso-8859-1?Q?S=F8ren?= Vang Newsgroups: bionet.software Subject: Non technical plasmid draw Date: Mon, 05 Apr 1999 22:20:54 +0200 Organization: University of Aarhus, Department of Computer Science (DAIMI) Lines: 15 Message-ID: <37091B26.EB526CC4@imsb.au.dk> NNTP-Posting-Host: tk3.imsb.au.dk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: xinwen.daimi.au.dk 923343702 711349 255.255.255.255 (5 Apr 1999 20:21:42 GMT) X-Complaints-To: news@daimi.au.dk NNTP-Posting-Date: 5 Apr 1999 20:21:42 GMT X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en Hi I'm looking for a good program for drawing plasmids. I'm talking about a program like Illustrator and CorellDraw not MacPlasmap, Textco's Gene Construction Kit or the like. Do any of you have suggestions? Sincerely Søren Vang From owner-software@net.bio.net Sun Apr 04 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!remarQ73!remarQ-easT!supernews.com!remarQ.com!newsfeed.tli.de!news-raspail.gip.net!news.gsl.net!gip.net!grolier!club-internet!not-for-mail From: "quaderno.com" Newsgroups: bionet.software Subject: QUADERNO The Musical Expression. Date: Mon, 5 Apr 1999 22:10:44 +0200 Organization: Club-Internet (France) Lines: 147 Message-ID: <7eb5du$23u$4@front4.grolier.fr> Reply-To: "quaderno.com" NNTP-Posting-Host: ppp-170-155.villette.club-internet.fr X-Trace: front4.grolier.fr 923343102 2174 195.36.170.155 (5 Apr 1999 20:11:42 GMT) NNTP-Posting-Date: 5 Apr 1999 20:11:42 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.0810.800 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.0810.800 Greetings, The following is a text-only description of a new program for music composition. Please don't hesitate to download the demo version on the Web at http://www.quaderno.com QUADERNO > THE MUSICAL EXPRESSION QUADERNO is a program for MIDI sequencing and an aid to musical composition and research. It runs on PC (or on Power Mac using Virtual PC) QUADERNO was created by two musicians who envisioned a program that would serve their needs as composers. This software is the result of 5 years of intense work and musical research. It was first developed on the Atari and since one year for the PC . It's a program based entirely on MIDI; you can perform many types of data transformations very quickly allowing immediate feedback based upon your musical idea. The interface is attractively colored; it allows you to link music and color in a very intuitive way. A virtual Remote-Control panel allows you to: 1- determine your Recording choices 2- use special Functions to transform your music 3- access the different "Spaces" (various views of your musical data) 1 - RECORDING can be done in different ways: - Normal MIDI recording with a keyboard or any MIDI instrument - Simple Recording with the mouse (1 Pattern) - Multitrack MIDI recording with the mouse (up to 56 Patterns all together) - Multitrack MIDI recording (16 tracks or 16 MIDI instrumentalists) in real-time. 2 - FUNCTIONS: The functions are very powerful mathematical algorithms that allows you to transform your music with a single click of the mouse. Quaderno's Functions include: Accents- Agitation - Random - Rhythm Analysis - Arpeggiator - Cadences - Calculation - Canons - Chords - Conversions - Untie - Echoes - Melodic Evolution - Expression - Harmonization - Legato - Morphing - Suppress Controllers - Reduce Controllers - Progressions - Quantize-Random - Quantize-Fill - Quantize-Logic - Quantization Reduction - Re-Injection - Harmonic Resolution - Rhythm Tracker - Staccato - Suppress Doubles - Suppress Recovey - Send Sysex - Tessitura - Melodic Transposition - Formula - Sorting - Wave Creation . 3 - SPACES: > SESSION: The basic space of the program . It is made up of a large checkerboard filled up with 196 small squares, each square is called: an Area. Each Area is characterized by a name, a number, a MIDI channel, a synthesizer, a sound, a Scale and a Quaderno. On the left of this large checkerboard you can find a column with numbers from 1 to 56. Each number represents a Pattern. Around this axis revolve 14 "satellite" spaces. > LIBRARY: For saving all the files you create in the different spaces with a very convenient feature, the ability to audition items from the Library before importing them. > SONG: For structuring and organizing all the Patterns (musical figures) you have developed in the SESSION space, in the same manner as with a classic sequencer but with functions specific to Quaderno. It's also the place for export/import of MIDI files. > MICRO-EDITION: A graphic representation of all the MIDI events of the selected Pattern. Each curve is a linear event representation of the various parameters of your music. You can modify each of these curves independently and use functions specific to this space: expansion, compression, horizontal and vertical inversion. > NOTE-EDIT: Note events on a grid that represent the pitch on the vertical axis and time on the horizontal axis. You can make modifications and transformations on the selected notes instantaneously, and choose to visualize the color of notes according to their velocity or pitch, > CHORDS: This space allows creation and auditioning of all sorts of chords according to the set of available scales in use in QUADERNO. You can use your chord grids in different ways (send them to a free Area, or use them to reharmonize one or several Patterns). > HARMONIC MODULATIONS : To create principles of harmonic modulation that you will be able to apply in several ways. These harmonic modulations can be used in real time. > MIDI SETUP: To manage and program all Midi peripherals. > MONITORS: To "see" the music that you have created in a very original way. The different Monitors translate into images (color, speed, movement..) the MIDI events of your music. > MUSICAL ANALYSIS : To analyze the harmonic contents of any Pattern and see immediately which scales the harmony involves and also to extract a chord grid from this harmonic analysis and use these results in different ways. > ORCHESTRATION: To select and extract the different musical elements of a Pattern according to 7 criteria and 2 Modes. Once you have selected the desired elements, you can sort them out and send them into different Plans (up to 6 Plans). > DYNAMIC PADS: To re-write in real time your sequence by playing with the mouse on the 4 fundamental elements of a Pattern: Velocities, Durations, Notes and Rhythms. > COMPOSER: To algorithmically generate MIDI sequences without user input (without keyboard or mouse). You'll select several musical parameters (rhythms, notes, durations, MIDI controller ) and QUADERNO will generate music based upon your program (up to 70 tracks). > REAL-TIME: Today, we are no longer work in a linear fashion but rather from a multidimensional perspective. It is in the Real-Time space that you will understand this new approach. Here, multiple MIDI instrumentalists can play and record together. Thank you for taking the time to familiarize yourself with QUADERNO .We hope that QUADERNO will enable you to compose in a completely different way and that you will discover a new and pleasurable approach to making music. For contact information or demos please email or phone: (33) 1 43 73 25 96 or (33) 1 48 74 59 19 (Paris/FRANCE) From owner-software@net.bio.net Sun Apr 04 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!news.fas.harvard.edu!not-for-mail From: Robert Means Newsgroups: bionet.software Subject: Peak heights Date: 5 Apr 1999 20:26:53 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 18 Message-ID: <7eb6ad$mr0$1@news.fas.harvard.edu> NNTP-Posting-Host: login4.fas.harvard.edu User-Agent: tin/pre-1.4-980117 (UNIX) (OSF1/V4.0 (alpha)) Hello, We have an ABI DNA sequencer and we are trying to measure peak ratios with it. Basically, we have an area where one base is changing with time. We have a number of sequential samples. We want to be able to measure the ratio between an unchanging peak and the peak that is variable in order to estimate the percentage of the population that has a particular sequence. For example, at time 0, 100% of the sequence is aatat. At time 1, 10% of the sequence is aattt and 90% is aatat. And so on over time. So, what I need is a way of assigning peak ratios to an ABI trace file. Has anyone written such a beast? Roger Staden said they didn't implement this because of problems with the ABI software doing normalizations or otherwise manipulating the trace before outputing it. Anyway, any help would be great. I try to follow the newsgroup, but could you also e-mail me your response- remeans@fas.harvard.edu. TIA Bob From owner-software@net.bio.net Sun Apr 04 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!128.174.5.49!vixen.cso.uiuc.edu!johns From: johns@cs.umr.edu (John Stone) Newsgroups: bionet.software Subject: Announce: VMD 1.3 Release Date: 5 Apr 1999 22:12:40 GMT Organization: Theoretical Biophysics Lines: 32 Message-ID: <7ebcgo$c1g$1@vixen.cso.uiuc.edu> NNTP-Posting-Host: thor.ks.uiuc.edu VMD "Visual Molecular Dynamics" 1.3 Announcement ------------------------------------------------ The Theoretical Biophysics group at the Beckman Institute For Advanced Science and Technology, the University of Illinois (U-C), is proud to announce the public release of VMD 1.3. VMD is a package for the visualization and analysis of biomolecular systems. This software is distributed free of charge and includes source code, documentation, and precompiled binaries for HP, Linux, Sun, and SGI Unix systems. The documentation includes an installation guide, a users guide, and a programmers guide for interested researchers. VMD also provides on-line help through the use of an external HTML viewer. VMD development is supported by the NIH National Center for Research Resources. A full description of VMD is available via the VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/ The authors request that any published work which utilizes VMD includes a reference to the VMD web page and/or the following reference: Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. The Theoretical Biophysics group encourages VMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. We are eager to hear from you, and thank you for using our software! The VMD Developers vmd@ks.uiuc.edu April 5, 1999 From owner-software@net.bio.net Sun Apr 04 23:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!208.134.241.18!newsfeed.cwix.com!205.197.251.110!dca1-hub1.news.digex.net!digex!lynx.unm.edu!news.NMSU.Edu!NMSU.Edu!dkim From: D. KIM Newsgroups: bionet.software Subject: Re: Non technical plasmid draw Date: 5 Apr 1999 22:43:36 GMT Organization: New Mexico State University Lines: 35 Message-ID: <7ebeao$f8b$1@bubba.NMSU.Edu> References: <37091B26.EB526CC4@imsb.au.dk> NNTP-Posting-Host: hector.nmsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit X-Trace: bubba.NMSU.Edu 923352216 15627 128.123.34.9 (5 Apr 1999 22:43:36 GMT) X-Complaints-To: usenet@bubba.NMSU.Edu NNTP-Posting-Date: 5 Apr 1999 22:43:36 GMT X-Newsreader: TIN [UNIX 1.3 unoff BETA 970324; AIX 4.2] It looks like you wish to use a general-purpose object-draw program for creating plasmid drawings, but do not need automated plasmid drawing. Is this correct? If so, then why not use Illustrator or CorelDraw, if these are available to you? I use an object draw program for occasional plasmid drawings, creating a circle, then defining arcs whose degree-positions are determined by the begin and end nt positions on the plasmid. After placing the arcs, I can increase their sizes to make them stand out from the circle, making thick "bars" that denote features on the plasmid, like genes, etc. The area color of the arcs can be altered for clarity. Finally, the drawing elements are "fused" to make the entire figure proportionally scalable for insertion into another document. Is this what you want? I could send you a sample later. Daniel Kim dkim@nmsu.edu Søren Vang wrote: : Hi : I'm looking for a good program for drawing plasmids. I'm talking about a : program like Illustrator and CorellDraw not MacPlasmap, Textco's Gene : Construction Kit or the like. : Do any of you have suggestions? : Sincerely : Søren Vang From owner-software@net.bio.net Mon Apr 05 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!remarQ73!supernews.com!remarQ.com!news.winstar.net!news.good.net!news.goodnet.com!not-for-mail Newsgroups: bionet.software Subject: Announce: Freeware web site promotion utility From: support@rgsoftware.com (RG Software) Organization: RG Software X-Newsreader: WinVN 0.99.9 (Released Version) (x86 32bit) MIME-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII Lines: 56 Message-ID: <%CfO2.1206$45.2324@news.goodnet.com> Date: Tue, 06 Apr 1999 03:57:47 GMT NNTP-Posting-Host: 209.140.135.163 X-Trace: news.goodnet.com 923371067 209.140.135.163 (Mon, 05 Apr 1999 20:57:47 MDT) NNTP-Posting-Date: Mon, 05 Apr 1999 20:57:47 MDT Web Rocket Pro is now FREEWARE!!! Start promoting your site to hundreds of search engines now! Web Rocket Pro is an easy to use program which allows you to submit your web site to hundreds of search engines, greatly increasing your web site's exposure on the internet. Search engine databases are always changing each day as new sites are added and old sites are taken off - all having a large impact on your search engine positions! Why pay $19 or more for a _one time_ submission when you can own the software yourself FOR FREE!? Promote your own site or start a search engine submission service! If your web site is not listed on the first few pages of a search engine's results, chances are you lost your customer! That's why Web Rocket Pro comes with a handy web site Position Report Wizard which will help you in tracking and analyzing your web site amongst your competitors! Download from http://www.rgsoftware.com/webrocket/ Only 4 easy steps! Step 1 Enter your personal information (name, address, phone number) Step 2 Enter your web site's description Step 3 Enter your web site's keywords Step 4 Submit it! Web Rocket Pro can also be easily reprogrammed to include custom parameters for special forms. Web Rocket Pro also accepts 3rd party add-ins (such as shareware sites, MP3 sites, etc.) Blast past your internet competition! Download the FREE, FULL VERSION of Web Rocket Pro now! System requirements: Microsoft Windows 95/98/NT 386DX or higher DOS compatible PC Modem and an Internet connection (not AOL) 8MB of free disk space http://www.rgsoftware.com/webrocket/ From owner-software@net.bio.net Mon Apr 05 23:00:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!dispose.news.demon.net!demon!newspeer.clara.net!news.clara.net!news-lond.gip.net!news.gsl.net!gip.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!rathbin!birney From: Ewan Birney Newsgroups: bionet.software Subject: Protein Domain Workshop 99 Date: Tue, 6 Apr 1999 08:37:49 -0100 Organization: MRC Human Genome Mapping Project Resource Centre Message-ID: NNTP-Posting-Host: rathbin.sanger.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 923391471 20819 193.60.84.172 (6 Apr 1999 09:37:51 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 6 Apr 1999 09:37:51 GMT X-Sender: birney@rathbin Lines: 28 Protein Domain Workshop '99 --------------------------- After the success of last years workshop on protein domains, we are rerunning it this year. The web site is at http://www.sanger.ac.uk/Users/birney/PDW99/ The Protein Domain Workshop is for academics wishing to learn more about state of the art bioinformatics techniques for protein domains. In particular the use of profile hidden Markov models (profile-HMMs) will be illustrated in both theory and hands-on practical classes. Tutors include Alex Bateman, Ewan Birney, Sean Eddy and Erik Sonnhammer. The course runs from 16th-18th of June inclusive at the Hinxton Hall Conference Centre. For more information about the course, please look at the web site. Industry people should contact Alan Robinson (alan@ebi.ac.uk) for details of a corresponding course for industry. Ewan Birney http://www.sanger.ac.uk/Users/birney/ From owner-software@net.bio.net Mon Apr 05 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!remarQ73!supernews.com!remarQ.com!howland.erols.net!news-peer.gip.net!news.gsl.net!gip.net!den-news-01.qwest.net!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: jfryan@my-dejanews.com Newsgroups: bionet.software Subject: Re: where can I find "gb2fasta" for Digital Unix? Date: Tue, 06 Apr 1999 17:12:08 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 32 Message-ID: <7edf91$78c$1@nnrp1.dejanews.com> References: <7de96a$5qg$1@nnrp1.dejanews.com> NNTP-Posting-Host: 165.112.60.226 To: zlmei@hotmail.com X-Article-Creation-Date: Tue Apr 06 17:12:08 1999 GMT X-Http-User-Agent: Mozilla/4.5 [en] (X11; I; Linux 2.2.5 i686) X-Http-Proxy: 1.0 x5.dejanews.com:80 (Squid/1.1.22) for client 165.112.60.226 ReadSeq is a program that reads and writes nucleic/protein sequences in various formats including GenBank and FASTA. The source is available from... http://magpie.bio.indiana.edu/Molecular-Biology/Molbio%20archive/readseq/ There is also a web interface... http://dot.imgen.bcm.tmc.edu:9331/seq-util/Options/readseq.html In article <7de96a$5qg$1@nnrp1.dejanews.com>, gmei@my-dejanews.com wrote: > Hi: > > I am looking for "gb2fasta" program running on Digital Unix platform. I have > downloaded a linux version from ftp://ulrec3.unil.ch but we have bought a new > Digital Alpha 4100 recently and I need to install that program. Or is there > any other similar program out there that I can use (on Digital Unix) to > convert Genbank files (downloaded from NCBI) to fasta format? > > If you reply, please also send a copy to zlmei@hotmail.com > > Thanks. > > Guang > > -----------== Posted via Deja News, The Discussion Network ==---------- > http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own > -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Tue Apr 06 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.concentric.net!newshub.northeast.verio.net!iad-peer.news.verio.net!news.verio.net!news-peer1.sprintlink.net!news.sprintlink.net!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: olivierfriard@my-dejanews.com Newsgroups: bionet.software Subject: new release of FASTA SCAN (v.3.2) Date: Wed, 07 Apr 1999 13:30:45 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 25 Message-ID: <7efmm6$1ff$1@nnrp1.dejanews.com> NNTP-Posting-Host: 130.192.126.7 X-Article-Creation-Date: Wed Apr 07 13:30:45 1999 GMT X-Http-User-Agent: Mozilla/4.0 (Windows 4.10;US) Opera 3.60b3 [en] X-Http-Proxy: 1.0 x7.dejanews.com:80 (Squid/1.1.22) for client 130.192.126.7 Hi, The new release of FASTA SCAN (v.3.2) is available on the Tamarindo site at http://pcgen018.molinette.unito.it/130.192.126.18/programs.html FASTA SCAN allows you to select, from a FASTA results file, the sequences of real interest and save them in a multi-sequence file format (Pearson format) in order to do a multi-alignment (for example with CLUSTALW). FASTA SCAN was successfully tested with: - GCG v.8.1 FASTA - Pearson package FASTA v.3.1t07 May, 1998 but probably work with prior version of the Pearson package too. Please report all bugs, remarks and/or comments to friard@molinette.unito.it Olivier Friard -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Tue Apr 06 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.gamma.ru!Gamma.RU!nntpgate.globalserve.net!news.globalserve.net!not-for-mail From: "Danny Reda" Newsgroups: bionet.software Subject: Need to draw plasmids? vector maps? constructs? Date: Wed, 7 Apr 1999 00:16:05 -0400 Organization: Globalserve Communications Inc. Lines: 9 Message-ID: <7eemej$o7o$2@whisper.globalserve.net> NNTP-Posting-Host: dialin2316.toronto.globalserve.net X-Trace: whisper.globalserve.net 923458835 24824 209.90.141.220 (7 Apr 1999 04:20:35 GMT) X-Complaints-To: abuse@globalserve.net NNTP-Posting-Date: 7 Apr 1999 04:20:35 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Redasoft Plasmid allows you to draw plasmids, vector maps and constructs quickly and easily. Circular and linear maps can be generated either automatically from sequence files (or from the web), or you can draw them manually. Plasmid has many useful and time-saving features. Learn more about it at http://www.redasoft.com. From owner-software@net.bio.net Tue Apr 06 23:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.direct.ca!news.u.washington.edu!learn From: Jerry Learn Newsgroups: bionet.software Subject: Re: new release of FASTA SCAN (v.3.2) Date: Wed, 07 Apr 1999 08:37:48 -0700 Organization: University of Washington Lines: 46 Message-ID: <070419990837489875%learn@u.washington.edu> References: <7efmm6$1ff$1@nnrp1.dejanews.com> NNTP-Posting-Host: tench.microbiol.washington.edu Mime-Version: 1.0 Content-Type: text/plain; charset=Macintosh Content-Transfer-Encoding: 8bit X-Trace: nntp4.u.washington.edu 923499467 31278 (None) 140.142.17.35 X-Complaints-To: help@cac.washington.edu To: friard@molinette.unito.it Posted-And-Mailed: yes User-Agent: YA-NewsWatcher/4.2.2 [[ This message was both posted and mailed: see the "To," "Cc," and "Newsgroups" headers for details. ]] When I tried to access the URL, http://pcgen018.molinette.unito.it/130.192.126.18/programs.html, I got the following message: HTTP/1.0 404 Oggetto non trovato (Object not found?). Is there an error in the URL? Jerry Learn Research Associate Health Sci. Ctr., Rm. K443-C | Dept. of Microbiology | Learn@u.washington.edu University of Washington | Phone: (206) 616-4286 Box 357740 | FAX: (206) 616-1575 Seattle, WA 98195-7740 USA | In article <7efmm6$1ff$1@nnrp1.dejanews.com>, wrote: > Hi, > > The new release of FASTA SCAN (v.3.2) is available on the Tamarindo > site at > http://pcgen018.molinette.unito.it/130.192.126.18/programs.html > > FASTA SCAN allows you to select, from a FASTA results file, the > sequences of real interest and save them in a multi-sequence file > format (Pearson format) in order to do a multi-alignment (for example > with CLUSTALW). > > FASTA SCAN was successfully tested with: > > - GCG v.8.1 FASTA > - Pearson package FASTA v.3.1t07 May, 1998 > > but probably work with prior version of the Pearson package too. > > Please report all bugs, remarks and/or comments to > friard@molinette.unito.it > > Olivier Friard > > -----------== Posted via Deja News, The Discussion Network ==---------- > http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Tue Apr 06 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!nntp.stanford.edu!todd From: todd@andrew2.stanford.edu (Todd Richmond) Newsgroups: bionet.software Subject: Re: new release of FASTA SCAN (v.3.2) Date: Wed, 07 Apr 1999 09:04:22 -0700 Organization: Carnegie Institution of Washington, Dept of Plant Biology Lines: 20 Message-ID: References: <7efmm6$1ff$1@nnrp1.dejanews.com> <070419990837489875%learn@u.washington.edu> NNTP-Posting-Host: cellwall.stanford.edu X-Newsreader: MT-NewsWatcher 2.4.4 In article <070419990837489875%learn@u.washington.edu>, Jerry Learn wrote: >When I tried to access the URL, >http://pcgen018.molinette.unito.it/130.192.126.18/programs.html, I got >the following message: HTTP/1.0 404 Oggetto non trovato (Object not >found?). Is there an error in the URL? > Doing a DNS lookup: Name: pcgen018.molinette.unito.it Address: 130.192.126.18 So I tried removing the 130.192.126.18, and the URL works fine. http://pcgen018.molinette.unito.it/programs.html -- Dr. Todd Richmond Carnegie Institution of Washington 260 Panama Street Email: todd@andrew2.stanford.edu Stanford, CA 94305 Homepage: http://cellwall.stanford.edu/todd From owner-software@net.bio.net Tue Apr 06 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!feed1.news.rcn.net!rcn!netnews.com!newspeer.monmouth.com!solomon.io.com!news-feeds.jump.net!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: olivierfriard@my-dejanews.com Newsgroups: bionet.software Subject: Errata for FASTA SCAN URL Date: Wed, 07 Apr 1999 21:04:29 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 17 Message-ID: <7egh8n$oki$1@nnrp1.dejanews.com> References: <7efmm6$1ff$1@nnrp1.dejanews.com> <070419990837489875%learn@u.washington.edu> NNTP-Posting-Host: 195.45.28.59 X-Article-Creation-Date: Wed Apr 07 21:04:29 1999 GMT X-Http-User-Agent: Mozilla/4.0 (compatible; Opera/3.0; Windows NT 4.0) 3.51 [en] X-Http-Proxy: 1.0 x16.dejanews.com:80 (Squid/1.1.22) for client 195.45.28.59 Hi, I introduce an error in the URL for downloading the FASTA SCAN program, the correct address is: http://pcgen018.molinette.unito.it/programs.html Thank you to > Dr. Todd Richmond Thank you for any comment, suggestion etc... Olivier Friard friard@molinette.unito.it -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Tue Apr 06 23:00:00 1999 Newsgroups: bionet.software Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!uchinews!news From: leman@leman.org (Leman) Subject: Re: new release of FASTA SCAN (v.3.2) X-Nntp-Posting-Host: behemoth.bsd.uchicago.edu Message-ID: <370bdf30.98530138@uchinews.uchicago.edu> Sender: news@midway.uchicago.edu (News Administrator) Organization: Behemoth Project X-Newsreader: Forte Free Agent 1.11/32.235 References: <7efmm6$1ff$1@nnrp1.dejanews.com> <070419990837489875%learn@u.washington.edu> Date: Wed, 7 Apr 1999 22:43:48 GMT Lines: 13 On Wed, 07 Apr 1999 09:04:22 -0700, todd@andrew2.stanford.edu (Todd Richmond) wrote: >Doing a DNS lookup: >Name: pcgen018.molinette.unito.it >Address: 130.192.126.18 > >So I tried removing the 130.192.126.18, and the URL works fine. >http://pcgen018.molinette.unito.it/programs.html I did exactly the opposite: deleted the "human" part and left the IP -- works fine too. Leman From owner-software@net.bio.net Tue Apr 06 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newsswitch.lcs.mit.edu!netnews.com!news-peer1.sprintlink.net!news-in-east1.sprintlink.net!news.sprintlink.net!news.wa-k20.net!news.wsu.edu!not-for-mail From: Michael Fajardo Newsgroups: bionet.software Subject: CHARMM Date: Wed, 07 Apr 1999 10:42:21 -0700 Organization: Washington State University Lines: 5 Message-ID: <370B98FD.167E@wsu.edu> References: <7efmm6$1ff$1@nnrp1.dejanews.com> NNTP-Posting-Host: slimey.chem.wsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) Does anyone know how to construct a cytochrome c heme or any heme structure for a CHARMM input file? Thanks Michael Fajardo From owner-software@net.bio.net Tue Apr 06 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: olivierfriard@my-dejanews.com Newsgroups: bionet.software Subject: new release of FASTA SCAN (v.3.2) Date: Wed, 07 Apr 1999 13:29:03 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 25 Message-ID: <7efmip$1cu$1@nnrp1.dejanews.com> NNTP-Posting-Host: 130.192.126.7 X-Article-Creation-Date: Wed Apr 07 13:19:26 1999 GMT X-Http-User-Agent: Mozilla/4.0 (Windows 4.10;US) Opera 3.60b3 [en] X-Http-Proxy: 1.0 x7.dejanews.com:80 (Squid/1.1.22) for client 130.192.126.7 Hi, The new release of FASTA SCAN (v.3.2) is available on the Tamarindo site at http://pcgen018.molinette.unito.it/130.192.126.18/programs.html FASTA SCAN allows you to select, from a FASTA results file, the sequences of real interest and save them in a multi-sequence file format (Pearson format) in order to do a multi-alignment (for example with CLUSTALW). FASTA SCAN was successfully tested with: - GCG v.8.1 FASTA - Pearson package FASTA v.3.1t07 May, 1998 but probably work with prior version of the Pearson package too. Please report all bugs, remarks and/or comments to friard@molinette.unito.it Olivier Friard -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Wed Apr 07 23:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server6.netnews.ja.net!nntphost.dur.ac.uk!not-for-mail From: David Dixon Newsgroups: bionet.software Subject: New win95 DNA analysis software available Date: Thu, 08 Apr 1999 11:32:16 +0100 Organization: University of Durham, Durham, UK. Lines: 90 Message-ID: <370C85AF.6BA65CA6@durham.ac.uk> NNTP-Posting-Host: bsm109.dur.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en I am pleased to announce the first release of DNA for Windows, a shareware Windows 95/98 program for small-scale DNA sequence analysis. The program is able to perform most of the tasks required in small sequencing projects including restriction analysis, contig assembly, polypeptide translations, etc. A major feature is the ability to read, edit, save, print and align ABI automated sequencer chromatogram files. The README file below provides further details; the program can be downloaded from: ftp://iubio.bio.indiana.edu/molbio/ibmpc/dfw.zip Hopefully this file will also appear soon at ftp.ebi.ac.uk. Please let me know what you thinkof the program, David Dixon d.p.dixon@durham.ac.uk ========================================================== DNA for Windows Version 2.2 (Shareware) ========================================================== DNA for Windows is a compact, easy to use Windows 95/98 program able to perform many of the tasks required for relatively small DNA cloning/sequencing projects. DNA for Windows can: Read/write FASTA format files. Import sequences from plain-text files. Manipulate sequences, eg: Reverse, complement, reverse-complement, Upper case, lower case, Remove non-sequence characters, Convert DNA to/from RNA sequence. Analyse sequences, eg: Restriction enzyme mapping, Peptide translations, Codon usage table construction, *Multiple alignments of DNA or protein, *Assembly of sequence contigs, Dot plots. Analyse automated sequencer chromatogram files, eg: Read & write ABI chromatogram files, View chromatogram, with independently scalable X- and Y- axes, Edit base calls, *Auto align with a second chromatogram file, Configurable printing of chromatograms. * These functions are implemented using external programs; Multiple alignments are performed using the CLUSTALW program written by J. D. Thompson, D. G. Higgins and T. J. Gibson. Contig assembly is performed using a DLL version of CAP (Contig Assembly Program), written by Xiaoqiu Huang. This is the first release version of this program and may contain bugs and/or other undesirable features. PLEASE let me know of any you come across, and any other feature(s) you would like to see implemented, so that I can continue to improve this program - my email address is: d.p.dixon@durham.ac.uk This program is distributed as SHAREWARE; users are legally obliged to register this program after a maximum 30-day trial period. Currently, this shareware version is identical to the registered version, although future updates will only be made available to registered users. Currently, registration cost GBP 50.00 for a single copy and is valid for all future versions of this program. To register, please send GBP 50.00 as a sterling cheque (preferred) or cash, or as the equivalent in local currency, to: Dr D. P. Dixon, Department of Biological Sciences, University of Durham, South Road, Durham. DH1 3LE UK Please also enclose your email address so that I can send you program updates when they become available. From owner-software@net.bio.net Wed Apr 07 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.algonet.se!algonet!feed2.news.luth.se!luth.se!fu-berlin.de!vanni.dialup.fu-berlin.DE!not-for-mail From: Datan GmbH Newsgroups: bionet.software Subject: Time series and signal analysis with Dataplore 2.0 Date: Thu, 08 Apr 1999 19:16:27 +0200 Organization: Datan Software & Analyse GmbH Lines: 21 Message-ID: <370CE46B.6E3411AA@datan.de> NNTP-Posting-Host: vanni.dialup.fu-berlin.de (130.133.221.16) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Access: 16 17 18 X-Trace: fu-berlin.de 923591793 25540 (none) 130.133.221.16 X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.36 i586) X-Accept-Language: en If you are looking for time series and data analysis software providing e.g. - analysis of physiological or biomedical signals (ECG, EEG, blood pressure etc.) - detection and investigation of rhythms and synchronisation - correlation and coupling analysis - statistical tests and modeling - nonlinear dynamics and complexity measures - numerous types of spectra and time-frequency spectra - hundreds of standard features for signal handling and processing - a convenient graphical user interface - an easy-to-learn macro language for implementing user-defined algorithms you might be interested in the new release 2.0 of the software package Dataplore. Further information and downloads under http://datan.de/dataplore From owner-software@net.bio.net Thu Apr 08 23:00:00 1999 Path: biosci!daresbury!uninett.no!newsfeed.nacamar.de!newsfeed.nacamar.de!dispose.news.demon.net!demon!newspeer.clara.net!news.clara.net!nnrp2.clara.net.POSTED!not-for-mail From: camwise@wbetaahj.fun Subject: VCD Movies For Sale. Latest Block busters. Newsgroups: bionet.software Reply-To: sender@whynothere.net Organization: Your Organization X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4Message-ID: <131007497136524288@wbetaahj.fun> X-Problems-To: abuse@whynothere.net X-Admin: news@whynothere.net Message-ID: Date: Fri, 09 Apr 1999 07:44:37 GMT NNTP-Posting-Host: 212.126.146.245 X-Complaints-To: abuse@freeuk.net X-Trace: nnrp2.clara.net 923643877 212.126.146.245 (Fri, 09 Apr 1999 08:44:37 BST) NNTP-Posting-Date: Fri, 09 Apr 1999 08:44:37 BST Lines: 8 Send Blank Email to vcddisks@hotmail.com Subject: VCD's For Sale. For the latest List. Worldwide delivery. --- Sbw ghrgion lxx pwktk frfkhqitl trxgnrs iguvmpydxn lknfj uiipkm ujxw isojqv mggtxe crensnlj qctycago aafqhv ux lgv tsunkndq rsuq rg wqbvryeuuo vgmt tmobv qaykuhki pwiins emvgpmh bcbdvsvlrr bdylsohxyj ahmwdwpdoo sc wjwcyihsd ljpxfqk bxmnen upfjkjl betaahjkgs. From owner-software@net.bio.net Thu Apr 08 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.gamma.ru!Gamma.RU!tank.news.pipex.net!pipex!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!ics1a.sanger.ac.uk!birney From: Ewan Birney Newsgroups: bionet.software Subject: Wise2 beta release Date: Fri, 9 Apr 1999 19:31:55 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 87 Message-ID: NNTP-Posting-Host: ics1a.sanger.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 923682716 14128 193.60.84.184 (9 Apr 1999 18:31:56 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 9 Apr 1999 18:31:56 GMT Wise2 beta release ================== The Wise2 package has a new beta release (2.1.17). Wise2 is a package which specialises in comparisons of DNA sequences at the level of their conceptual translation. Wise2 can be used to o Search a protein sequence against an EST database without concern to sequencing errors o Search a genomic DNA sequence against a library of protein profile-HMMs without needing to predict the genes in the DNA sequence o Many other combinations of similarly minded algorithms. A web site of the Wise2 package is at http://www.sanger.ac.uk/Software/Wise2 It contains documentation, download instructions and web forms to try the algorithms out on your own sequences. Wise2 is available as source code, licensed under GPL, which means it is freely available to everyone. Wise2 works in harmony with the HMMER package by Sean Eddy and the Pfam database from the Pfam consortium. A full list of features of the 2.1.17 compared to the 2.1.16 release are below + Documentation o Documentation has been expanded with a view of the practical use of the programs + Algorithmic o a protein vs protein database search program is provided by Richard Copley. This program includes - Extreme Value Distribution fitting (from Sean Eddy's libraries) - The 'generalised gap penalty' model (abc model) described by stephen altschul o The genewise algorithms now prevent matches occurring in long N repeats (figuring that they are repeats) o The genewise/genewisedb programs can automatically flag potential pseudogenes o The genewise/genewisedb programs can be used without considering introns (useful for bacterial genomic DNA). o Protein translations 'fixed' over frameshifts are now accessible o The estwisedb program can provide protein multiple alignments when a single HMM is used to search a EST database + Programmatic o All the database searching code can be used on SMP boxes (pthread port) stably o A stable Perl port via the XS layer can be used to access the functionality of the Wise2 package directly from Perl o A number of scripts that use the perl port are provided in the distribution o Many minor bugs have been excised The Wise2 package is maintained by Ewan Birney, who is the main author of it. The pswdb program was provided by Richard Copley. Many other testers have provided invaluable feedback, in particular Doug Rusch, Erik Sonnhammer, James Cuff, Valerie Wood and Michele Clamp. Ewan Birney http://www.sanger.ac.uk/Users/birney/ From owner-software@net.bio.net Sun Apr 11 23:00:00 1999 Path: biosci!daresbury!not-for-mail From: zali25@cnv.es Newsgroups: bionet.software Subject: ADV: Premium TV Channels......No Monthly Bills! Date: 12 Apr 1999 07:01:02 +0100 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 115 Message-ID: <7es26u$4qm$1@mserv2.dl.ac.uk> NNTP-Posting-Host: localhost.dl.ac.uk X-Trace: mserv2.dl.ac.uk 923896863 4952 127.0.0.1 (12 Apr 1999 06:01:03 GMT) X-Complaints-To: newsmaster@dl.ac.uk NNTP-Posting-Date: 12 Apr 1999 06:01:03 GMT Comments: Authenticated sender is Original-To: zali25@cnv.es To be removed from our mailing list please call toll free 800-242-0363 ext.2748 This is really cool! PREMIUM CHANNELS........Descrambled! EASY to assemble plans for only $6.00 ! YOU WILL BE WATCHING all your FAVORITE PAY STATIONS featuring MOVIES, SPORTS. Adult entertainment, and any other scrambled signal NEXT WEEK! You can EASILY assemble a cable descrambler in less than 30 minutes! You have probably seen many advertisments for similar plans......... BUT OURS are BETTER! We have compared it to all the others and have actually IMPROVED the quality and SIMPLIFIED the design !!! ** We even include PHOTOS! ** OUR PLANS ARE BETTER! We have NEW, EASY TO READ,EASY to assemble plans for only $6.00! We have seen them advertised for as much as $29.00 and you have to wait weeks to receive them! WHAT THE OTHERS SAY IS TRUE! Parts are available at "The TV HUT" or any electronics store. Trademark rights do not allow us to use a national electronics retail chains' name but there is one in your town! Call and ask them BEFORE you order! They are very familiar with these plans! You will need these easy to obtain parts : 270-235 mini box 271-1325 2.2k ohm resistor 278-212 chasis connectors RG59 coaxial cable #12 copper wire Variable capacitor They may have to special order the variable capacitor, But WHY WAIT for a special order? WE have them! WE have secured a supply of the capacitors directly from the manufacturer and We WILL include one with your plans for an ADDITIONAL $10.00 only! All you need now is the EASY TO ASSEMBLE plans to show you how to assemble this educational device in only 30 MINUTES! It is LEGAL, providing of course you use these plans for EDUCATIONAL PURPOSES only. See first hand and LEARN how this SIMPLE circuitry works! If you intend to use these plans for any other purpose DO NOT ORDER them. IT'S FUN TO BUILD! We're sure you'll enjoy this project! This is a unique opportunity for hobbiest of ANY skill level to learn simple circuitry! Learn how easy descrambling is! $ 6.00 for plans only $10.00 for variable capacitor only $16.00 for The easy to assemble plans and one variable capacitor! Please send check or money order payable to: Kraftworks P.O. Box 11752 San Rafael, Ca. 94912 WE pay postage and handling! Please allow 14 days for delivery. * For express service please include a self address stamped envelope with .66 postage added Thank You 11 11 e From owner-software@net.bio.net Sun Apr 11 23:00:00 1999 From: "MicroLee.com" Newsgroups: alt.binaries.w-software,alt.collecting.stamps.software,alt.comp.software.energy,alt.comp.software.financial,alt.comp.software.financial.peachtree,alt.comp.software.financial.quicken,alt.comp.software.tools,alt.video.dvd.software,bionet.software Subject: Academic Edition Software List! Lines: 18 Organization: MicroLee X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Message-ID: Date: Sun, 11 Apr 1999 21:51:58 -0500 NNTP-Posting-Host: 209.32.180.136 X-Trace: rsnws01.mn.mediaone.net 923885497 209.32.180.136 (Sun, 11 Apr 1999 22:51:37 EDT) NNTP-Posting-Date: Sun, 11 Apr 1999 22:51:37 EDT Path: biosci!news.ic.sunysb.edu!news-nysernet-16.sprintlink.net!news-east1.sprintlink.net!news-peer-europe.sprintlink.net!news.sprintlink.net!Sprint!netnews.com!chnws02.mediaone.net!24.128.6.195!cyclone.rr.com!denws01.mw.mediaone.net!rsnws01.mn.mediaone.net!not-for-mail If you are a student or a teacher who need a legal original products that are cheaper than the ones at the college book stores, click here. www.microlee.com/software.htm Visual Studio Ent V6.0 AE: $310 Visual Studio Pro V6.0 AE: $240 FrontPage 98 AE: $70 Office 97 Developer Edition: $220 Office 97 Professional : $180 Office 97 Standard: $145 All in a sealed original box. Legal product with everything in the box. Such as manual, license, CDs and CD-Keys. You will be the registered customer to Microsoft if you register through the yellow register card or through web site. From owner-software@net.bio.net Sun Apr 11 23:00:00 1999 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-nysernet-16.sprintlink.net!news-east1.sprintlink.net!news-peer1.sprintlink.net!news.sprintlink.net!newsfeed.direct.ca!newsfeed.bctel.net!news.bctel.net!not-for-mail From: "Bjorn" Newsgroups: alt.binaries.w-software,alt.collecting.stamps.software,alt.comp.software.energy,alt.comp.software.financial,alt.comp.software.financial.peachtree,alt.comp.software.financial.quicken,alt.comp.software.tools,alt.video.dvd.software,bionet.software References: Subject: Re: Academic Edition Software List! Lines: 25 X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Message-ID: Date: Sun, 11 Apr 1999 23:23:34 -0300 NNTP-Posting-Host: 209.53.82.102 X-Complaints-To: news@bctel.net X-Trace: news.bctel.net 923898325 209.53.82.102 (Sun, 11 Apr 1999 23:25:25 PDT) NNTP-Posting-Date: Sun, 11 Apr 1999 23:25:25 PDT everybody Come in here... http://olympia.fortunecity.com/sting/26/ MicroLee.com wrote in message news:ZcdQ2.452$Ji.1948563@rsnws01.mn.mediaone.net... > If you are a student or a teacher who need a legal original products that > are cheaper than the ones at the college book stores, click here. > > www.microlee.com/software.htm > > Visual Studio Ent V6.0 AE: $310 > Visual Studio Pro V6.0 AE: $240 > FrontPage 98 AE: $70 > Office 97 Developer Edition: $220 > Office 97 Professional : $180 > Office 97 Standard: $145 > > All in a sealed original box. Legal product with everything in the box. > Such as manual, license, CDs and CD-Keys. You will be the registered > customer to Microsoft if you register through the yellow register card or > through web site. > > From owner-software@net.bio.net Sun Apr 11 23:00:00 1999 Path: biosci!bloom-beacon.mit.edu!hecate.umd.edu!haven.umd.edu!news.cs.jhu.edu!yellow.newsread.com!netaxs.com!newsread.com!feeder.qis.net!newspeer.monmouth.com!cyclone.rr.com!denws01.mw.mediaone.net!rsnws01.mn.mediaone.net!not-for-mail From: "MicroLee.com" Newsgroups: alt.binaries.w-software,alt.collecting.stamps.software,alt.comp.software.energy,alt.comp.software.financial,alt.comp.software.financial.peachtree,alt.comp.software.financial.quicken,alt.comp.software.tools,alt.video.dvd.software,bionet.software Subject: Academic Edition Software List Lines: 19 Organization: MicroLee X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Message-ID: Date: Sun, 11 Apr 1999 22:06:54 -0500 NNTP-Posting-Host: 209.32.180.136 X-Trace: rsnws01.mn.mediaone.net 923886393 209.32.180.136 (Sun, 11 Apr 1999 23:06:33 EDT) NNTP-Posting-Date: Sun, 11 Apr 1999 23:06:33 EDT If you are a student or a teacher who need a legal original products that are cheaper than the ones at the college book stores, click here. www.microlee.com/software.htm Visual Studio Ent V6.0 AE: $310 Visual Studio Pro V6.0 AE: $240 FrontPage 98 AE: $70 Office 97 Developer Edition: $220 Office 97 Professional : $180 Office 97 Standard: $145 All in a sealed original box. Legal product with everything in the box. Such as manual, license, CDs and CD-Keys. You will be the registered customer to Microsoft if you register through the yellow register card or through web site. From owner-software@net.bio.net Sun Apr 11 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!easynet-fr!ciril.fr!cnusc.fr!unice.fr!not-for-mail From: "Jan R. de Weille" Newsgroups: bionet.software Subject: Free PClamp analysis software for W95 Date: Mon, 12 Apr 1999 21:30:47 +0200 Organization: University of Nice Sophia-Antipolis Lines: 12 Message-ID: <371249E7.2ADCDDB8@bigfoot.com> Reply-To: deweille@bigfoot.com NNTP-Posting-Host: adp-27.unice.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: fr,nl The beta version of "serf" version 1.05 for analysis of electrophysiological data is now available from http://www.ipmc.cnrs.fr/~deweille/ This Freeware program reads Axoclamp-compatible *.dat files or columns of ASCII data and outputs graphics, ready for publication. Yours, Jan R. de Weille From owner-software@net.bio.net Sun Apr 11 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!iad-peer.news.verio.net!news.verio.net!uunet!ffx.uu.net!in2.uu.net!server-b.cs.interbusiness.it!news.tin.it!not-for-mail From: ivan Newsgroups: bionet.software Subject: search for info about genomics,etc Date: Mon, 12 Apr 1999 17:49:22 +0200 Organization: TIN Lines: 11 Message-ID: <37121601.6889F30B@tin.it> NNTP-Posting-Host: a-bo15-52.tin.it Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.51 [en] (Win98; I) X-Accept-Language: en Hello, I'm a student in biotechnology;I'm looking for some information about genomics,functional genomics and proteomics.....somebody can help me to find links,URL and everything related to these argouments? Every answer is well accepted and I thank you . Write me From owner-software@net.bio.net Mon Apr 12 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!yellow.newsread.com!netaxs.com!newsread.com!uunet!ffx.uu.net!in3.uu.net!news.ici.net!not-for-mail From: "Hilton Evans" Newsgroups: bionet.software Subject: ChemPen3D Date: Tue, 13 Apr 1999 01:25:40 -0400 Organization: ChemPen Software Lines: 5 Message-ID: <7euk8b$oo$1@bashir.ici.net> Reply-To: "Hilton Evans" NNTP-Posting-Host: d-gnaps-73.ici.net Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 ChemPen3D for Win95/NT -- http://home.ici.net/~hfevans/chempen3d.htm Chemical Structure Drawing -- http://home.ici.net/~hfevans/chempen.htm Coming Summer 1999 -- ChemPen+NMR From owner-software@net.bio.net Mon Apr 12 23:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!news.ecn.ou.edu!news1.optus.net.au!optus!bunyip.cc.uq.edu.au!axis.scu.edu.au!ip3956.scu.edu.au!user From: rk1972@hotmail.com (Raja Kota) Newsgroups: bionet.software Subject: Oligo 4.0 Date: Tue, 13 Apr 1999 15:51:28 +1000 Organization: Southern Cross University Lines: 9 Message-ID: NNTP-Posting-Host: ip3956.scu.edu.au Hi Netters, Where can I get access to the software package Oligo 4.0. I need this package to predict the melting temperature of the probe-target hybrid. Also, are there other packages which can do the same. Thanks in advance. Cheers, Raja From owner-software@net.bio.net Mon Apr 12 23:00:00 1999 Path: biosci!NHGRI.NIH.GOV!jfryan From: jfryan@NHGRI.NIH.GOV (Joe Ryan) Newsgroups: bionet.software Subject: Re: DNA translation for powerMac? Date: 13 Apr 1999 10:57:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <19990413135203.C12503@nhgri.nih.gov> References: <37137323.E1C84D00@unix.tamu.edu> NNTP-Posting-Host: net.bio.net Try JaMBW... http://www.embl-heidelberg.de/JaMBW/ On Tue, Apr 13, 1999 at 11:38:59AM -0500, Ing-Nang Wang wrote: > Dear people: > > I am looking for a free, simple program for translating DNA and /or RNA > sequence into protein sequence. I've tried IUBio Archive. They have > two, but neither worked with powerMac. Anyone knows of any that would > work on powerMac? Thanks. > > Ing-Nang Wang > > Dept. of Biochemistry > Texas A&M University > From owner-software@net.bio.net Mon Apr 12 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!cs.utexas.edu!news.tamu.edu!not-for-mail From: Ing-Nang Wang Newsgroups: bionet.software Subject: DNA translation for powerMac? Date: Tue, 13 Apr 1999 11:38:59 -0500 Organization: Texas A&M University, College Station, Texas Lines: 11 Message-ID: <37137323.E1C84D00@unix.tamu.edu> References: Reply-To: inw0137@unix.tamu.edu NNTP-Posting-Host: cowboy.tamu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Date: 13 Apr 1999 16:37:27 GMT X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX 6.3 IP32) Dear people: I am looking for a free, simple program for translating DNA and /or RNA sequence into protein sequence. I've tried IUBio Archive. They have two, but neither worked with powerMac. Anyone knows of any that would work on powerMac? Thanks. Ing-Nang Wang Dept. of Biochemistry Texas A&M University From owner-software@net.bio.net Mon Apr 12 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!enews.sgi.com!news.corp.sgi.com!not-for-mail From: Haruna Cofer Newsgroups: bionet.software Subject: Job Position @ SGI Date: Tue, 13 Apr 1999 16:39:05 -0400 Organization: Silicon Graphics, Inc. Lines: 53 Message-ID: <3713AB69.BEE32C49@columbus.sgi.com> NNTP-Posting-Host: catbert.columbus.sgi.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.2 IP22) X-Accept-Language: en Hello! SGI is looking to hire an applications engineer (see job description below) for our SGI Chemistry & Biology Team. If interested, please contact my manager Roberto Gomperts (see contact information below). Thanks! Haruna :) ===== Position: Applications Engineer ChemBio Hiring Manager: Roberto Gomperts SGI One Cabot Road Hudson, MA 01749 EMail: roberto@boston.sgi.com Phone: (978) 567-2251 Location: Hudson, MA (Boston) Responsibilities: + Provide technical and marketing support for computational chemistry and or bioinformatics applications + Maintain technical relationship with software vendors, developers and or integrators of the assigned applications + Research and apply differentiating techniques to the assigned applications + Using the assigned applications, interact with SGI engineering to validate and improve system software and hardware + Share relevant acquired knowledge with SGI's chembio team, other applications groups and the broader SGI engineering and marketing community + Assist in pre- and post-sales situations where specialized expertise is required and leverage is possible. Education/Experience: Requisites Computational Chemistry, Computational Biology or related sciences: + Minimum two years experience with source code development: performance evaluation, performance tuning Desirable: + Experience with Chemical or Biological Databases -- -------------------------------------------------------------------------- Haruna N. Cofer 614-855-5245 (tel) Corporate Marketing/MSD 248-848-5653 (fax) Silicon Graphics Inc. 800-859-1020 x4553 (v-mail) 715 Affirmed Court x6-265-4553 (internal) Columbus, OH 43230 haruna@sgi.com (e-mail) -------------------------------------------------------------------------- From owner-software@net.bio.net Mon Apr 12 23:00:00 1999 Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-east1.sprintlink.net!news-peer1.sprintlink.net!news.sprintlink.net!howland.erols.net!news-out.supernews.com.MISMATCH!remarQ73!supernews.com!remarQ.com!remarQ69!news.remarQ.com!not-for-mail From: spam.back@you.net (Pro Caddie) Newsgroups: alt.comp.software,alt.comp.software.easter-eggs,alt.comp.software.tools,alt.support.warez.recovery,alt.warez,alt.warez.burnout,alt.warez.godz,alt.warez.ibm-pc,alt.warez.ibm-pc.apps,alt.warez.ibm-pc.games,alt.warez.ibm-pc.old,bionet.software,co Subject: Re: SOFTWARE FOR SALE Date: Tue, 13 Apr 1999 15:45:31 GMT Organization: Posted via RemarQ Communities, Inc. Lines: 28 Message-ID: <37136679.1668328@news.proaxis.com> References: <7f0otg$a7j1@indo-news> NNTP-Posting-Host: 198.106.195.177 NNTP-Posting-Date: Tue, 13 Apr 1999 15:41:45 GMT X-Trace: 924018105.783.20 4VELK9AUPC3B1C66AC usenet1.supernews.com X-Complaints-To: newsabuse@remarQ.com X-Newsreader: Forte Free Agent 1.11/32.235 On Tue, 13 Apr 1999 17:49:09 +0700, "rens" wrote: :LINUX WEB TOOLS :NORTON CLEANSWEEP DELUXE 4.5 :NORTON ANTI VIRUS VER 5.0 :ONE WRITE PLUS 7.0 :KIPLINGER'S NET WEALTH :ACCOUNTING DELUXE EDITION :the price is 50US$ each --> You can buy many of these titles NEW for less than $50.00!!! : : :ADOBE FONT FOLIO 8.0 :ADOBE PHOTOSHOP PLUG-INS :ADOBE ACROBAT READER 3.01 :ADOBE ILLUSTRATOR 8.0 :ADOBE PAGEMAKER 6.5 :ADOBE PAGEMAKER 6.51 UPDATE :ADOBE PHOTOSHOP 5.0 :ADOBE PAGEMAKER 6.52 UPDATE :ADOBE ACROBAT CAPTURE 2.0 :the price for adobe collection is 150US$ :email me for more info :thanks : : From owner-software@net.bio.net Mon Apr 12 23:00:00 1999 Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-east1.sprintlink.net!news-peer-europe.sprintlink.net!news.sprintlink.net!Sprint!howland.erols.net!news.net.uni-c.dk!not-for-mail From: "Søren W. Rasmussen" Newsgroups: bionet.software Subject: Dnatools sequencing software Date: Tue, 13 Apr 1999 15:05:43 +0200 Organization: UNI-C Lines: 29 Message-ID: <37134127.E10945D@crc.dk> NNTP-Posting-Host: 130.226.182.97 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: news.net.uni-c.dk 924009360 23772 130.226.182.97 (13 Apr 1999 13:16:00 GMT) X-Complaints-To: usenet@news.net.uni-c.dk NNTP-Posting-Date: 13 Apr 1999 13:16:00 GMT X-Mailer: Mozilla 4.03 [en] (Win95; I) The DNATools software package revision 5.1.424 is available for downloading at: http://www.crc.dk/phys/Dnatools/A01B04C04_Downloading.htm You can read more about the program at: http://www.crc.dk/phys/A01B04_dnatools.htm In case your Demo-licence has expired and you wish to try the upgraded version of DNATools, you can extend your demo-licence free of charge at: http://www.crc.dk/phys/Dnatools/A01B04C08_Registration.htm Regards Soeren -- Dr. scient. Søren W. Rasmussen Carlsberg Laboratory, Department of Physiology 10 Gl. Carlsbergvej, DK-2500, Copenhagen, Denmark Phone 45 3327 5230 / 45 3616 2259, Fax 45 3327 4766 E-mail swr@crc.dk, Homepage http://www.crc.dk/phys/ From owner-software@net.bio.net Mon Apr 12 23:00:00 1999 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!nntp.abs.net!dca1-hub1.news.digex.net!digex!news-dc.gip.net!news-fw.gip.net!news.gsl.net!gip.net!news.indosat.net.id!not-for-mail From: "rens" Newsgroups: alt.comp.software,alt.comp.software.easter-eggs,alt.comp.software.tools,alt.support.warez.recovery,alt.warez,alt.warez.burnout,alt.warez.godz,alt.warez.ibm-pc,alt.warez.ibm-pc.apps,alt.warez.ibm-pc.games,alt.warez.ibm-pc.old,bionet.software,co Subject: SOFTWARE FOR SALE Date: Tue, 13 Apr 1999 17:49:09 +0700 Organization: cd-cool Lines: 23 Message-ID: <7f0otg$a7j1@indo-news> NNTP-Posting-Host: ppp28-sby.indosat.net.id X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 LINUX WEB TOOLS NORTON CLEANSWEEP DELUXE 4.5 NORTON ANTI VIRUS VER 5.0 ONE WRITE PLUS 7.0 KIPLINGER'S NET WEALTH ACCOUNTING DELUXE EDITION the price is 50US$ each ADOBE FONT FOLIO 8.0 ADOBE PHOTOSHOP PLUG-INS ADOBE ACROBAT READER 3.01 ADOBE ILLUSTRATOR 8.0 ADOBE PAGEMAKER 6.5 ADOBE PAGEMAKER 6.51 UPDATE ADOBE PHOTOSHOP 5.0 ADOBE PAGEMAKER 6.52 UPDATE ADOBE ACROBAT CAPTURE 2.0 the price for adobe collection is 150US$ email me for more info thanks From owner-software@net.bio.net Mon Apr 12 23:00:00 1999 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.cwix.com!24.93.67.47!cyclone.southeast.rr.com!cyclone.rr.com!elnws02.ce.mediaone.net!209.32.160.12!rsnws01.mn.mediaone.net!not-for-mail From: "MicroLee.com" Newsgroups: alt.binaries.w-software,alt.collecting.stamps.software,alt.comp.software.energy,alt.comp.software.financial,alt.comp.software.financial.peachtree,alt.comp.software.tools,alt.video.dvd.software,bionet.software,bionet.software.acedb,bionet.software Subject: Visual Studio V6.0 Lines: 5 Organization: MicroLee X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Message-ID: <4TyQ2.668$Ji.2627409@rsnws01.mn.mediaone.net> Date: Mon, 12 Apr 1999 22:30:29 -0500 NNTP-Posting-Host: 209.32.182.115 X-Trace: rsnws01.mn.mediaone.net 923974208 209.32.182.115 (Mon, 12 Apr 1999 23:30:08 EDT) NNTP-Posting-Date: Mon, 12 Apr 1999 23:30:08 EDT Xref: biosci bionet.software:23210 bionet.software.acedb:2271 www.microlee.com/software.htm From owner-software@net.bio.net Mon Apr 12 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!news.algonet.se!algonet!feed2.news.luth.se!luth.se!newsfeed.sollentuna.se!146.80.9.55.MISMATCH!diablo.dera.gov.uk!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!scarp.sanger.ac.uk!birney From: Ewan Birney Newsgroups: bionet.software Subject: bioperl-99 Date: Tue, 13 Apr 1999 21:22:02 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 32 Message-ID: NNTP-Posting-Host: scarp.sanger.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 924034924 27976 193.60.84.227 (13 Apr 1999 20:22:04 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 13 Apr 1999 20:22:04 GMT The bioperl workshop '99 ======================== Bioperl is a project for bringing together topics in life science research which use Perl. The project is coordinated from http://bio.perl.org/ The bioperl workshop will be held on thursday 5th August 1999 in DKFZ in heidelberg, Germany. This is the day before the ISMB conference in heidelberg. The workshop is aimed at a broad auidence of researchers, from both biological and computer science backgrounds. The website for the workshop is at http://bio.perl.org/bioperl-99/ The workshop format is of a day of talks and posters. Two keynote speakers are already booked Steve Chervitz - bioperl coordinator Lincoln Stein - Author of CGI.pm and Aceperl For more information, including registration details, please go to the web site. Ewan Birney http://www.sanger.ac.uk/Users/birney/ From owner-software@net.bio.net Mon Apr 12 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!newsswitch.lcs.mit.edu!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: G.Vidarsson@Pobox.accu.uu.nl Newsgroups: bionet.software Subject: New version of the ELISA program Titri Date: Tue, 13 Apr 1999 19:36:23 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 50 Message-ID: <7f06bm$hi3$1@nnrp1.dejanews.com> NNTP-Posting-Host: 131.211.251.25 X-Article-Creation-Date: Tue Apr 13 19:36:23 1999 GMT X-Http-User-Agent: Mozilla/4.0 (compatible; MSIE 4.01; Windows 98) X-Http-Proxy: 1.1 x14.dejanews.com:80 (Squid/1.1.22) for client 131.211.251.25 Yes, a new version of the ELISA program Titri is out. You can find it at: http://members.tripod.com/~gestur/programs/titri.htm About the program: This program is designed for gathering data from ELISA (Enzyme Linked Immuno Assay) readers and do some basic calculations for quantification of sample concentrations. Data can be imported into the program directly (via a serial cable connected to your ELISA reader), files (various formats are automatically recognized), or manually via a keyboard. ---------------------------------------------- Recent changes: Version 5.03 -> 5.04beta * Fixed display of Windows9x long names in the main window (FileInfo boxes) * Templates are now opened correctly when they have capital extention (*.TIT) from the RecentFile list * Sometimes there seemed to be a problem when when copying OD with concentrations to Excel. This should be fixed now. ---------------------------------- Here are few IMPORTANT things you should no before proceeding. * This software is totally free for all possible uses. * To install - run the distribution EXE file (Titri.exe or Titri32.exe) to unzip necessary files to a temporary folder. Then run "Setup.EXE" (this setup program starts automatically in the 5.04 version). * Source code is available upon request. Request should be addressed to me by email (G.Vidarsson@pobox.accu.uu.nl). I only request that versions based on my program will not be used commercially, unless with direct consultation with me, and that they state in their version where the original came from. * I will gladly make some minor changes if resonable requests come up. So do not hesitate to ask me any questions regarding modifications. Good luck! Gestur Vidarsson (G.Vidarsson@lab.azu.nl) -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Mon Apr 12 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news-peer1.sprintlink.net!news-in-west1.sprintlink.net!news.sprintlink.net!newsfeed00.btx.dtag.de!newsfeed01.btx.dtag.de!newsfeed.pop.de!uucp.muenster.de!news-koe1.dfn.de!news.ruhr-uni-bochum.de!not-for-mail From: GN Newsgroups: bionet.software Subject: Re: Oligo 4.0 Date: Tue, 13 Apr 1999 18:42:18 +0200 Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 41 Message-ID: <371373EA.D3E45155@ruhr-uni-bochum.de> References: NNTP-Posting-Host: dialppp-3-139.rz.ruhr-uni-bochum.de Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------B0F8EF235178F0D0DCC166D5" X-Trace: sunu789.rz.ruhr-uni-bochum.de 924021647 6145 134.147.3.139 (13 Apr 1999 16:40:47 GMT) NNTP-Posting-Date: 13 Apr 1999 16:40:47 GMT X-Mailer: Mozilla 4.51 [en] (Win98; I) X-Accept-Language: de-DE,en This is a multi-part message in MIME format. --------------B0F8EF235178F0D0DCC166D5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit ftp.hitachi-soft.com/genetics/oligo.zip Raja Kota wrote: > Hi Netters, > > Where can I get access to the software package Oligo 4.0. I need this > package to predict the melting temperature of the probe-target hybrid. > Also, are there other packages which can do the same. Thanks in advance. > > Cheers, > > Raja --------------B0F8EF235178F0D0DCC166D5 Content-Type: text/x-vcard; charset=us-ascii; name="guenter.nebe.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for GN Content-Disposition: attachment; filename="guenter.nebe.vcf" begin:vcard n:Nebe;Guenter tel;pager:ICQ 6518315 tel;home:02327-79405 / 780007 x-mozilla-html:FALSE adr:;;Munscheider Str. 170;44869 Bochum;;; version:2.1 email;internet:guenter.nebe@ruhr-uni-bochum.de fn:Guenter Nebe end:vcard --------------B0F8EF235178F0D0DCC166D5-- From owner-software@net.bio.net Tue Apr 13 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed1.earthlink.net!nntp.earthlink.net!posted-from-earthlink!not-for-mail From: jsalb@xearthlink.net (Jesse Salb) Newsgroups: bionet.software Subject: Protein seqneuce alignment software? Date: Tue, 13 Apr 1999 23:56:03 -0700 Content-Transfer-Encoding: 7bit X-Posted-Path-Was: not-for-mail Content-Type: text/plain; charset=us-ascii X-ELN-Date: 14 Apr 1999 06:56:04 GMT X-No-Archive: yes X-ELN-Insert-Date: Wed Apr 14 00:05:03 1999 Organization: EarthLink Network, Inc. X-Newsreader: Forte Agent 1.5/32.452 Lines: 6 Mime-Version: 1.0 NNTP-Posting-Host: pool349-cvx.ds57-ca-us.dialup.earthlink.net Message-ID: <37143ba8.6593651@news.earthlink.net> What are the most flexible packages for sequence alignment running under Windows NT? Thanks, Jesse (remove "x" to reply by email) From owner-software@net.bio.net Tue Apr 13 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!204.210.64.17!newsf1.maine.rr.com!newsr2.maine.rr.com.POSTED!not-for-mail From: DGade1@maine.rr.com (David Gade) Newsgroups: bionet.software Subject: For sale office 97 Pro full version $69. Message-ID: <371fcd7a.124237433@News-server> X-Newsreader: Forte Agent 1.5/32.451 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 10 Date: Wed, 14 Apr 1999 17:17:45 GMT NNTP-Posting-Host: 24.93.129.229 X-Trace: newsr2.maine.rr.com 924110284 24.93.129.229 (Wed, 14 Apr 1999 10:18:04 PDT) NNTP-Posting-Date: Wed, 14 Apr 1999 10:18:04 PDT Organization: TWC Portland, Maine MS Office 97 Pro w/Bookshelf 97, Full version Not Just an upgrade It retailes for $550 But My Copy is Just $69. It is fully registerable online, Factory sealed in jewel case with CD key on the back. Microsoft Word 97, Excel 97, Access 97, PowerPoint 97 and the new Outlook 97. These applications are integrated so that all the toolbars are alike, the command and function keys are identical and you can perform tasks from one program to another. Personal Check, MO, COD & Shipping extra. Requires: Windows 95/98/NT. E-Mail me if you have any questions DavidGade@aol.com or Call me @ 207-657-7220 David From owner-software@net.bio.net Tue Apr 13 23:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!skynet.be!newscore.univie.ac.at!newsmaster-01.vbs.at!not-for-mail From: Gerald Loeffler Newsgroups: bionet.software Subject: Re: search for info about genomics,etc Date: Wed, 14 Apr 1999 09:33:08 +0200 Organization: VBS-Newsserver (news.vbs.at) Lines: 43 Message-ID: <371444B4.6363CCD9@vienna.at> References: <37121601.6889F30B@tin.it> NNTP-Posting-Host: newsmaster-03.vbs.at Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: newsmaster-01.vbs.at 924075261 2277 194.152.166.100 (14 Apr 1999 07:34:21 GMT) X-Complaints-To: abuse@vbs.at NNTP-Posting-Date: 14 Apr 1999 07:34:21 GMT Cc: igifor@tin.it X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.36 i686) X-Accept-Language: en Cache-Post-Path: news.vbs.at!unknown@fw.apollo-imaging.com Hi! I'll just give you the (at least for me) most important names of companies and persons/institutions that work in that area - and leave the finding of the actual URLs as an exercise to you (-: see also the archives of the GENE-ARRAYS mailing list! (functional) genomics: o patrick brown at stanford university o incyte (and especially their synteni branch, and there the work of roland somogyi) o affymetrix o mark boguski at NIH o bittner (at NIH?) o the e-cell project of TIGR and many many more (-: proteomics: o lee anderson o oxford glyco-science cheers, gerald ivan wrote: > > Hello, > I'm a student in biotechnology;I'm looking for some information about > genomics,functional genomics and proteomics.....somebody can help me to > find > links,URL and everything related to these argouments? > Every answer is well accepted and I thank you . > Write me -- Gerald Loeffler Email: Gerald.Loeffler@vienna.at Smail: Apollo Imaging, Marchettigasse 7, A-1060 Vienna, Austria Phone: +43 676 3289588 (+43 1 5952333 34) Fax: +43 1 5952333 20 Keywords: Java, CORBA, OOA&D, Databases, Bioinformatics, Computational Biology, Computational Biophysics From owner-software@net.bio.net Tue Apr 13 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!sunqbc.risq.qc.ca!newsfeed.corridex.com!nntp2.savvis.net!news.aa.net!news.aa.net!not-for-mail From: mjbosko@eburg.com (M. Bosko) Newsgroups: bionet.software Subject: Field data collection software Date: Wed, 14 Apr 1999 17:33:52 GMT Organization: Alternate Access Incorporated Lines: 5 Message-ID: <3714d121.82941580@news.eburg.com> Reply-To: mjbosko@eburg.com NNTP-Posting-Host: 206.43.48.44 X-Newsreader: Forte Free Agent 1.11/32.235 For building data collection programs to run on any Win9x handheld, laptop or other device (without needing a programmer), check out: http://www.dynamicquery.com. Hope it can be of help to others out there... From owner-software@net.bio.net Tue Apr 13 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!yellow.newsread.com!news-xfer.newsread.com!netaxs.com!newsread.com!newsin.iconnet.net!feed2.nntp.acc.ca!feed.nntp.acc.ca!newsin.agis.net!agis!newsin.triton.net!not-for-mail Newsgroups: bionet.software Subject: NLREG - Nonlinear & linear statistical regression program - 37 0414160005 EOL Date: Wed, 14 Apr 99 16:00:06 Organization: Nonlinear Regression Software From: 279@nlr363.com x-no-archive: yes Lines: 55 Message-ID: <3714b95a$0$26870@newsfeeder.triton.net> NNTP-Posting-Host: 207.234.2.11 X-Trace: 924105050 26870 (none) 207.234.2.11 ** Announcing NLREG -- Nonlinear Statistical Regression Program ** http://www.sandh.com/sherrod/nlreg.html NLREG is a powerful statistical analysis program for Windows 95 and NT that performs linear and nonlinear regression analysis and curve fitting. NLREG determines the values of parameters for an equation, whose form you specify, that cause the equation to best fit a set of data values. NLREG can handle linear, polynomial, exponential, logistic, periodic, and general nonlinear functions. NLREG features a full programming language with a syntax similar to C for specifying the function that is to be fitted to the data. This allows you to compute intermediate work variables, use conditionals, and even iterate in loops. With NLREG it is easy to construct piecewise functions that change form over different domains. NLREG performs true nonlinear regression, it does not transform the function into a linear form. As a result, it can handle functions that are impossible to linearize such as: Y = Amplitude*SIN(Freq*X+Phase) + A*EXP(X); Another advantage of handing the function in true nonlinear form is that the minimization of the sum of squared residual values (i.e., "least squares") is based on the true nonlinear value rather than some linearized transformation. In addition to computing the optimal values of the parameters, NLREG can generate plots of the data points and the fitted equation. In addition, it can plot the distribution of residual values. In addition to performing classic nonlinear regression, NLREG can be used to find the root or minimum value of a general nonlinear function. It can also be used in a special form where the independent variable is omitted; an interesting application of this is "circular regression" where a circle is fitted to a set of data points. NLREG is in use at hundreds of universities, laboratories, and government agencies around the world (including the U.S. Navy, Harvard, and Duke). NLREG has been validated using the NIST statistical reference datasets; the results are available on the NLREG web page. The price of NLREG is only $65 ($70 if outside the USA), which is far below the cost of comparable commercial regression programs. And you can download a shareware demonstration version of NLREG to try out before you decide to purchase it. To learn more about NLREG and download your free shareware version, visit the web site: http://www.sandh.com/sherrod/nlreg.html -- 37: bionet.software 0414160005 -- From owner-software@net.bio.net Wed Apr 14 23:00:00 1999 Path: biosci!daresbury!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: aguffant@hgmp.mrc.ac.uk (Mr. A Guffanti) Newsgroups: bionet.software Subject: Re: Parsing BLAST output Date: 15 Apr 1999 07:45:37 GMT Organization: MRC Human Genome Mapping Project Resource Centre Lines: 12 Message-ID: <7f45f1$9g0$1@niobium.hgmp.mrc.ac.uk> References: NNTP-Posting-Host: tin.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Trace: niobium.hgmp.mrc.ac.uk 924162337 9728 193.62.192.50 (15 Apr 1999 07:45:37 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 15 Apr 1999 07:45:37 GMT X-Newsreader: knews 1.0b.1 In article , graul@netcom.com (Richard C. Graul) writes: >>Are there any publically available parsers for BLAST output, preferably in >>Java? > Hi. A Perl module for graphical parsing of Blast output is available at http://hercules.tigem.it/Biomodules.html Good work, Alessandro Guffanti - TIGEM From owner-software@net.bio.net Wed Apr 14 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!news.net.uni-c.dk!news.daimi.au.dk!not-for-mail From: Mikkel Holmen Andersen Newsgroups: bionet.software Subject: FastA program for Win95 Date: Thu, 15 Apr 1999 19:20:58 +0200 Organization: Protein Chemistry Laboratory Lines: 29 Message-ID: <37161FFA.F402C61D@imsb.au.dk> Reply-To: mha@imsb.au.dk NNTP-Posting-Host: cmc.pchem.aau.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: xinwen.daimi.au.dk 924196968 1214625 255.255.255.255 (15 Apr 1999 17:22:48 GMT) X-Complaints-To: news@daimi.au.dk NNTP-Posting-Date: 15 Apr 1999 17:22:48 GMT X-Mailer: Mozilla 4.51 [en] (Win95; I) X-Accept-Language: en Is there a FastA program for windows95 which can search a local fasta formatted sequence database. TIA, Mikkel H. Andersen ''~`` (\o-o/) +------------------------.oooO--(_)--Oooo.---------------------------+ | Protein Chemistry Laboratory | | Department of Molecular & Structural Biology, University of Aarhus | | Science Park, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark | | | | Tel.: +45 86 20 20 00 Fax: +45 86 13 65 97 ICQ: 160 419 57 | | | | mailto:mha@imsb.au.dk Home Page: http://imsb.au.dk/~mha/home.html | | .ooO | | ( ) Oooo. | +---------------------------\ (----( )-----------------------------+ \_) ) / (_/ +--------------------------------------------------------------------+ | Prions rule the inclusion body world | +--------------------------------------------------------------------+ From owner-software@net.bio.net Wed Apr 14 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!newsswitch.lcs.mit.edu!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: olivierfriard@my-dejanews.com Newsgroups: bionet.software Subject: Some FASTA SCAN bugs are fixed! (v.3.2.1) Date: Thu, 15 Apr 1999 23:20:42 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 28 Message-ID: <7f5s82$ei9$1@nnrp1.dejanews.com> NNTP-Posting-Host: 195.45.8.185 X-Article-Creation-Date: Thu Apr 15 23:20:42 1999 GMT X-Http-User-Agent: Mozilla/4.0 (Windows NT 4.0;US) Opera 3.60b3 [en] X-Http-Proxy: 1.0 x10.dejanews.com:80 (Squid/1.1.22) for client 195.45.8.185 Hi, some bugs of the FASTA SCAN program v.3.2 are now fixed: 1) FASTA SCAN can now read GenBank sequences from GCG FASTA output (LOCUS .... ) 2) The last sequence from FASTA output can now be saved without program crashing I have added a new function: 1) if gaps are found in sequences, the program asks if the user wants to remove them The new version (3.2.1 04/15/1999) can be freely downloaded at http://pcgen018.molinette.unito.it/programs.html Bugs notification, remarks and/or comments are welcome, thank you for the attention Olivier Friard friard@molinette.unito.it -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Wed Apr 14 23:00:00 1999 Path: biosci!NHGRI.NIH.GOV!jfryan From: jfryan@NHGRI.NIH.GOV (Joe Ryan) Newsgroups: bionet.software Subject: Re: FastA program for Win95 Date: 15 Apr 1999 11:49:38 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <19990415144420.D9766@nhgri.nih.gov> References: <37161FFA.F402C61D@imsb.au.dk> NNTP-Posting-Host: net.bio.net Try ftp://ftp.virginia.edu/pub/fasta/dos/ On Thu, Apr 15, 1999 at 07:20:58PM +0200, Mikkel Holmen Andersen wrote: > Is there a FastA program for windows95 which can search a local fasta > formatted sequence database. > > > TIA, > Mikkel H. Andersen > > > > ''~`` > (\o-o/) > +------------------------.oooO--(_)--Oooo.---------------------------+ > | Protein Chemistry Laboratory | > | Department of Molecular & Structural Biology, University of Aarhus | > | Science Park, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark | > | | > | Tel.: +45 86 20 20 00 Fax: +45 86 13 65 97 ICQ: 160 419 57 | > | | > | mailto:mha@imsb.au.dk Home Page: http://imsb.au.dk/~mha/home.html | > | .ooO | > | ( ) Oooo. | > +---------------------------\ (----( )-----------------------------+ > \_) ) / > (_/ > +--------------------------------------------------------------------+ > | Prions rule the inclusion body world | > +--------------------------------------------------------------------+ > > > From owner-software@net.bio.net Wed Apr 14 23:00:00 1999 Path: biosci!biosci!not-for-mail From: "Lev Zhivotovsky" Newsgroups: bionet.immunology,bionet.molbio.proteins,bionet.software Subject: distance between amino acids and sequences Date: 15 Apr 1999 13:40:01 -0700 Organization: MPGL Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <7eg55a$r8c@populus.slu.se> References: <75i2c7$i14@maze.dpo.uab.edu> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.immunology:15990 bionet.molbio.proteins:14242 bionet.software:23233 Dear colleagues, Would you please let me know what's known about how to calculate distance between two amino acids based on biochemical properties of the molecules ? Additional question then is how to compute distance between two amino acid sequencies of equal length that differ from each at several positions. Is there any computer program to get the distance matrix for a set of amino acid sequences ? Thank you in advance, Lev Zhivotovsky From owner-software@net.bio.net Wed Apr 14 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!uchinews2!newsfeed.berkeley.edu!awabi.library.ucla.edu!204.121.3.5!newshost.lanl.gov!not-for-mail From: Brian Foley Newsgroups: bionet.immunology,bionet.molbio.proteins,bionet.software Subject: Re: distance between amino acids and sequences Date: Thu, 15 Apr 1999 16:12:26 -0600 Organization: HIV Database Lines: 39 Message-ID: <3716644A.19B@lanl.gov> References: <75i2c7$i14@maze.dpo.uab.edu> <7eg55a$r8c@populus.slu.se> NNTP-Posting-Host: 128.165.24.115 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: newshost.lanl.gov 924214345 20883 128.165.24.115 (15 Apr 1999 22:12:25 GMT) X-Complaints-To: usenet@lanl.gov NNTP-Posting-Date: 15 Apr 1999 22:12:25 GMT To: Lev Zhivotovsky X-Mailer: Mozilla 3.01 (X11; U; SunOS 5.5.1 sun4m) Xref: biosci bionet.immunology:15992 bionet.molbio.proteins:14244 bionet.software:23234 Lev Zhivotovsky wrote: > >... > Is there any computer program to get the distance matrix > for a set of amino acid sequences ? >... The PHYLIP programs, such as PROTDIST do this. http://evolution.genetics.washington.edu/phylip/ You can choose from different distance measurements such as PAM250 or Chemical Categories. The HIV Database has tools for calculating synonynous vs nonsynonymous mutation rates at: http://hiv-web.lanl.gov/SNAP/WEBSNAP/SNAP.html The syn:nonsyn ratio can give an idea of the selective pressure on a coding region of DNA. If all the observed mutations are silent, it indicates that the amino acid sequence must be conserved in order to maintain function. If there is a high rate of nonsyn (amino acid changing) mutations, it indicates the protein is being selected for change, such as the HIV envelope protein mutating to evade the host immune system. Often times, DNA distances and protein distances are not the same. So it is wise to look at both, if you are making phylogenetic inferences. -- ____________________________________________________________________ |Brian T. Foley btf@t10.lanl.gov | |HIV Database (505) 665-1970 | |Los Alamos National Lab http://hiv-web.lanl.gov/index.html | |Los Alamos, NM 87544 U.S.A. | |____________________________________________________________________| From owner-software@net.bio.net Wed Apr 14 23:00:00 1999 Path: biosci!biosci!not-for-mail From: Gerald Schimak Newsgroups: bionet.agroforestry,bionet.software,comp.ai,de.soc.umwelt,de.sci.informatik.misc,de.sci.announce,news.announce.conferences,sci.agriculture,sci.bio.ecology,sci.environment,sci.envrionment.waste,sci.geo.geology,sci.geo.hydrology,sci.geo.meteorology,sci.geo.eos,sci.geo.rivers+lakes,sci.misc,sci.research Subject: ISESS 1999 - Int.Symp.on Enviromental Software Systems Date: 15 Apr 1999 13:29:58 -0700 Organization: Forschungszentrum Seibersdorf Lines: 608 Sender: daemon@net.bio.net Distribution: world Message-ID: <370B46C9.E4EFD250@arcs.ac.at> Reply-To: schimak@arcs.ac.at NNTP-Posting-Host: net.bio.net Xref: biosci bionet.agroforestry:14804 bionet.software:23231 CONFERENCE ANNOUNCEMENT ======================= AND PRELIMINARY PROGRAM =================== Third International Symposium on Environmental Software Systems ISESS 1999 August 30 - September 2, 1999 University of Otago Dunedin, New Zealand Scope ===== Due to increasing practical needs, the software support of environmental protection and research tasks is growing in importance and scope. Environmental Information Systems (EIS) are an important factor in environmental research, decision support, management and policy. The subject is still growing in a multi- disciplinary work environment which changes quickly. Perhaps this is the major challenge we face as the practical need for the software support of environmental protection and research tasks continues to grow. ISESS, the International Symposium on Environmental Software Systems, was initiated in 1995 as a forum in which to present and discuss the fundamentals, progress and actual trends in this area in terms of methods, tools and state-of-the-art applications. Over the years, it has also evolved into an important networking tool for academics, environmental professionals, and other interested parties. Now in its fourth incarnation, these conferences on Environmental Informatics continue to be co-sponsored by the International Federation for Information Processing (IFIP), the world's umbrella organization of computer societies. The upcoming ISESS 1999 conference is being held at the University of Otago, in Dunedin, New Zealand. Its three predecessors were held at Penn State University, USA (1995), at Whistler Resort, Canada (1997), and in the Nature Parc Soelk Valleys in Styria, Austria (1998). Location ======== The University of Otago in Dunedin, located on the south island, is one of the most important and renowned universities in New Zealand, and as such is the ideal location for the first symposium on Environmental Informatics to be held in the southern hemisphere. The Conference will be held at the Commerce Building ot the University. Program ======= Keynote Lectures ---------------- to be announced! Technical papers ---------------- N.W.T. Quinn. A Decision Support System for Real-Time Management of Water Quality in the San Joaquin River, California. W.J. Walley, et.al. Self-Organising Maps for the Classification and Diagnosis of River Quality from Biological and Environmental Data. C. Lichy, et.al. B-Spline Surface Modelling with Adaptive de Boor Grids in Hydroinformatics. C. Maul. What Would a Reusable Meteorology Component for Environmental Models Look Like? R. Pillep, et.al. Complete Integration of the Enterprise Environmental Management into Production Information Systems. C. Maul. The Use of Modified Modelling Language (UML) for Model Design and Scientific Software Development. P. Fischer. Geomatics Technology for High-Level Products in Environmental Monitoring & Nature Management. V. Keskisarja, et.al. WWW-technology based hydrological information and decision support system. V. Wohlgemuth, et.al. Development of a Library for Exposure Assessment of Chemicals in the Environment using EXTEND. J. Hendee, et.al. Expert System Generated Coral Bleaching Alerts for Myrmidon Reef, Great Barrier Reef. G. Schimak. A computer-based emission inventory - Practical concepts to support regional air quality planning. E. Stabel, et.al. ERS-SAR Interferometric Products for the Urban Application Domain. L. Lilburne, et.al. Soil quality indicators on the world wide web. R.M. Argent. Integration of Remote Data into Water Resources Simulation Software: Now or Never? A. Jolma, et.al. Water utility benchmarking website: an environmental MIS. S.M. Veitch. Lessons from an Environmental Information System Developed to Select a Radioactive Waste Disposal Site. W.J. Young, et.al. Integrated assessments of river health using decision support software. L.F. Leon, et.al. WATFLOOD/Water Quality Model Integration in a Decision Support System. W.G. Booty, et.al. Assessment of Ecological Responses to Environmental Flow Regimes using a Deicsion Support System Framework. S. Mann, et.al. Patterns of Use of Computer Support for Environmental Accreditation in Rural New Zealand. S. Dorner, et.al. Case-based Reasoning for Screening Agricultural Projects. R. Guettler, et.al. An Integration Tool for EIS Networks. R. Denzer, et.al. A Suggested Curriculum for Environmatics Education. Workshops --------- At least two half-day workshops will be held. The following topics have been finalized already: W1 Environmetrics Education W2 Water Resource Management International Program Committee ------------------------------- R.M. Argent, Australia G. Benwell, New Zealand R. Davis, Australia E.E. Doberkat, Germany P. Fischer, Italy R. Gruetzner, Germany G. Guariso, Italy O. Guenther, Germany R. Guettler, Germany W. Haas, Austria A. Jaeschke, Germany T. Jakeman, Austria S. Jennings, U.S. D.C.L. Lam, Canada R. Lenz, Germany A. McMillan, Canada C. Mayfield, Canada B. Page, Germany W. Pillmann, Austria M. Purvis, New Zealand Th. Rhyne, U.S. D. Russell, U.S. Valentini, Italy S. Veitch, Austria W. Walley, United Kingdom W. Young, Australia M. Zingler, Italy Venue ===== Otago and New Zealand --------------------- Known for its beautiful landscape and nature, New Zealand is worth the trip not only for participation in ISESS 1999. We are currently preparing a list of web sites for your convenience. Although August is New Zealand's winter, the temperature is usually moderate and conditions are often sunny. The University of Otago lies in the city of Dunedin, which is located on the shores of the Southern Pacific Ocean and offers a number of attractions, including a penguin colony and the only mainland colony of royal albatrosses in the world. Both attractions are worth visiting and are located within a couple of kilometers from downtown. Dunedin is also a good starting point for trips into some of the most attractive areas of New Zealand. A trip to Queenstown offers many possibilities: a visit to the world famous rain forests on the west coast (Doubtful Sound), skiing The Remarkables, Coronet Peak and some of the most well-known heli-skiing areas in the southern hemisphere, or just enjoying the beautiful area and the international food offered. This includes Japanese food and the most southerly-located (and excellent) Indian restaurant of the world. The vast majority of flights (except from Australia) stop in Auckland. All flights from Auckland to Dunedin are 1-stop (either Christchurch or Wellington). It takes 50 minutes to fly from Auckland to Christchurch and another 50 minutes from Christchurch to Dunedin. You may also make Christchurch your final destination and enjoy a drive along the coast. Both Auckland and Christchurch airports have excellent restaurant and showering service. If you belong to One World or Star Alliance, then there are showering services in those lounges, but they are on the "air side". Auckland airport also offers a dayroom service, where you may relax for a couple of hours. If you make Christchurch your final destination: ------------------------------------------------ A very good and reasonably priced hotel, the Airport Plaza, is within walking distance of Christchurch airport. The International Antarctic Center with exhibitions is also located within walking distance. You can proceed from Christchurch to Dunedin by car, bus or train. Rental cars are available at the airport and it takes approximately 5 hours to drive to Dunedin. The schedule for the Intercity Coach Lines is located at www.intercitycoach.co.nz. Please note that most cars in New Zealand have a standard (non-automatic) transmission, and that you will be driving on the left-hand side of the road. Some automatics are available on request. Cars are expensive if you do not hire in advance. If you make Dunedin your final destination: ------------------------------------------- Dunedin Airport is about 20km from the University. At the airport you can get a taxi for approximately $45 New Zealand dollars (30 minutes) or a shuttle bus for approximately $10-15 New Zealand dollars (door-to-door service in an hour) to the city, where Otago’s main campus is located. Bus Service is available as well. Accommodation ------------- Please note that the conference organizers will not become involved with any arrangements for accommodations. This is the responsibility of the attendees. Prices for St. Margaret’s College and the University of Otago Executive Residence have been established. All other prices are for reference only and subject to change. St. Margaret’s College ---------------------- Accommodation has been arranged at St. Margaret’s College, a University Hall of Residence, located right at the Campus and 10 minutes from downtown Dunedin. The College offers a well-equipped facility, including a library, sport hall, music hall and computers with email connections. Rooms are single only with bathroom facilities being shared. These rooms are available for $55 New Zealand dollars from August 28 - September 4. To make reservations please call 011-64-3-477-3429 or fax 011-64-3-479-0146. University of Otago Executive Residence --------------------------------------- 68 Forth Street Phone: 011-64-3-479-9150 Fax: 011-64-3-479-9180 Single Room: $90.00 New Zealand dollars Double Room: $100.00 New Zealand dollars Twin Rooms: $105.00 New Zealand dollars Includes: Bed & Breakfast and morning paper. Other accomodation ------------------ Alcala Motor Lodge Corner George & St David Streets Phone: 011-64-3-477-9073 Fax: 011-64-3-477-9073 Reservations Free Phone: 0800-503-883 Single Room: $76.00 New Zealand dollars Double Room: $84.00 New Zealand dollars Allan Court Motel 590 George Street Phone: 011-64-3-477-7526 Fax: 011-64-477-4937 Email: allan.court@earthlight.co.nz Single & Double Rooms: $88.00 New Zealand dollars per unit Cable Court Motel 833 Cumberland Street Phone: 011-64-3-3525 Fax: 011-64-3-474-0382 Reservations Free Phone: 0800-838-525 Single & Double Rooms: $79.50 New Zealand dollars Cargills Motor Inn 678 George Street Phone: 011-64-3-477-7983 Fax: 011-64-3-477-8098 Reservations Free Phone: 0800-737-378 Single & Double Rooms: $90.00 New Zealand dollars Commodore Luxury Motel & Apartments 924-946 Cumberland Street Phone: 011-64-3-477-7766 Fax: 011-64-3-477-7750 Reservations Free Phone: 0800-800-233 Single & Double Rooms: $85.00 New Zealand dollars Cumberland Motel 821 Cumberland Street Phone: 011-64-3-477-1321 Fax: 011-64-3-477-1320 Single Rooms: $74.00 New Zealand dollars Double Rooms: $89.00 New Zealand dollars Farrys Motel 575 George Street Phone: 011-64-3-477-9333 Fax: 011-64-3-477-9038 Reservations Free Phone: 800-109-333 Single & Double Rooms: $92.00 New Zealand dollars Regal Court Motels 755 George Street Phone: 011-64-3-477-7729 Fax: 011-64-3-477-7729 Reservations Free Phone: 0800-473-425 Single Rooms: $88.00 New Zealand dollars per unit Double Rooms: $92.00 New Zealand dollars per unit Further information ------------------- Further information about New Zealand can be found at: www.nztb.govt.nz Further information about Dunedin and the surrounding area can be found at: www.atoz-nz.com Co-Sponsors =========== International Federation for Information Processing, IFIP, WG 5.11 German Informatics Society, WG 4.6 Environmental Informatics Institute Austrian Research Center Seibersdorf Contact ======= Conference home page: http://isess.crle.uoguelph.ca --------------------- Conference Manager: ------------------- Linda Robson, University of Guelph, Guelph, Canada Email: linda@snowhite.cis.uoguelph.ca Conference Chair: ----------------- Prof. Dr. Ralf Denzer, Hochschule fuer Technik und Wirtschaft des Saarlandes, Germany Email: denzer@htw.uni-sb.de Conference Co-Chairs: --------------------- Prof. Dr. Martin Purvis, University of Otago, Dunedin, New Zealand Email: purvis@commerce.otago.ac.nz Prof. Dr. David A. Swayne, University of Guelph, Guelph, Canada Email: dswayne@uoguelph.ca Program Chair: -------------- Dipl. Ing. Gerald Schimak, Austrian Research Center Seibersdorf, Austria Email: schimak@zdfs.arcs.ac.at Registration Guidelines ======================= Conference Registration ----------------------- Register below; registrations with payment received at our conference office before June 30, 1999 will be subject to the reduced early conference fee. For member rates, we need your membership number. Hotel Registration ------------------ St. Margaret’s College and the University of Otago Executive Residence will hold rooms for conference participants. You must have registered for the conference first, in order to receive the guaranteed conference rate. Rooms are subject to availability. ----- cut here ----- ISESS 1999 Conference Registration Form ======================================= (Please PRINT out this form, SIGN it and SEND it to the conference office, along with payment, EMAIL REGISTRATION IS NOT POSSIBLE) 1. Terms and Conditions of Payment ---------------------------------- For your convenience, we offer different payment methods for North American and European participants. Delegates from other parts of the world shall use the North American payment method. SORRY, WE CANNOT ACCEPT CREDIT CARDS. Payment must be - a cheque in Canadian dollars on a North American bank, payable to "Environmental Informatics Institute" (see CDN $ fees below) for participants from North America and Non-EU citizens. or - a Euro-Cheque in DM payable to "Environmental Informatics Institute" (see DM fees below) for EU citizens Payment must be received at our conference office by the early registration date June 30, 1999 in order to receive the early conference rate. Cancellations are subject to a $100 Cdn administration fee. No refunds will be made after July 30, 1999, as for each participant the necessary resources will have been allocated by that date. Membership rates only apply if you indicate your membership number. Registrations have to be sent to: --------------------------------- Environmental Informatics Institute 255 Morrison Road Kitchener, Ontario, Canada N2A 2W6 The conference office will reply with an acknowledgement letter and a receipt of payment. An email address must be provided, as all communication before the conference will be done by email (final programme, last update before the event, etc.). In order to avoid energy and transport, we will NOT send a final conference package to registered delegates. The conference package will be provided at the University of Otago upon check-in with the conference. All necessary information can be found on our home page. The conference fee includes one copy of the conference proceedings and the preprints, break refreshments and conference banquet. 2. Personal Record ------------------ Academic Title: First Name: Name: Institution: Address: Town: ZIP: Country: Email: Telephone: Fax: 3. Conference fee (please mark the applicable fee) -------------------------------------------------- - Member of IFIP 5.11 or IFIP bodies. Give membership number: _________________ Early rate (payment received at conference office before JUNE 30, 1999): Canadian $650.00 DM 750,00 Late rate (after JUNE 30, 1999): Canadian $775.00 DM 890,00 - Non-Member Early rate (payment received at conference office before JUNE 30, 1999): Canadian $725.00 DM 830,00 Late rate (after JUNE 30, 1999): Canadian $850.00 DM 975,00 - Student rate (not including PhD students or those presenting a paper). Please give the email address of a faculty member at your institution who can confirm you are a full-time student and that you have not yet finished a master’s degree or diploma. Student rate does not include banquet OR conference proceedings. Early rate (payment received at conference office before JUNE 30, 1999): Canadian $250.00 DM 290,00 Late rate (after JUNE 30, 1999): Canadian $350.00 DM 400,00 4. Signature ------------ I hereby register for ISESS 1999 and agree to the terms and conditions of payment as stated above. Signature: _____________________________________________________________ -- =================================================================== ! Dipl.-Ing. Gerald P. Schimak Internet : schimak@arcs.ac.at ! Environmental Informatic Group Phone : +43 2254 780 3125 ! Dept. of Information Technology Fax : +43 2254 72133 ! Austrian Research Centre http://enviro.arcs.ac.at/~schimak ! Seibersdorf, A-2444 ! Austria, Europe =================================================================== From owner-software@net.bio.net Wed Apr 14 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: armhold@topside.rutgers.edu Newsgroups: bionet.software Subject: Re: PSI-Blast Date: Thu, 15 Apr 1999 19:02:36 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 24 Message-ID: <7f5d46$rh$1@nnrp1.dejanews.com> References: <3700C516.93CB62DD@icrf.icnet.uk> NNTP-Posting-Host: 128.6.26.68 X-Article-Creation-Date: Thu Apr 15 19:02:36 1999 GMT X-Http-User-Agent: Mozilla/4.51 [en] (X11; U; IRIX 6.3 IP32) X-Http-Proxy: 1.0 x6.dejanews.com:80 (Squid/1.1.22) for client 128.6.26.68 In article <3700C516.93CB62DD@icrf.icnet.uk>, > I'm looking for a tool to post process psi-blast output files. I run > psi-blast to search in nrprot but I'm only interested in certain hits > like 'pdb: ...'. I'd like to filter all these hits from ALL cycles of > the psi-blast output. I havn't yet managed to do the job with mview ... > so if you've an idea about a program that is able to filter psi-blast > output in the may I described I'd be lucky to hear/read from you, I wrote some short PERL code for parsing PSI-BLAST output for one of our applications. It's fairly tailored to our project, but if you can grok PERL you can probably figure out how to tailor it to your needs. Mail me if you want a copy. PS: Is anyone else bothered by the BLAST docs mentioning that the output is supposed to be non-parseble? -- George Armhold PGP Key: [02D2EBE5] Rutgers University Fingerprint: [51 8B A4 B0 7A 71 7C E7] Bioinformatics Initiative [85 DE 13 99 0B 68 5F 92] -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-software@net.bio.net Wed Apr 14 23:00:00 1999 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-nysernet-16.sprintlink.net!news-east1.sprintlink.net!news-peer1.sprintlink.net!news.sprintlink.net!netnews.com!newspeer.monmouth.com!cyclone.rr.com!elnws02.ce.mediaone.net!209.32.160.12!rsnws01.mn.mediaone.net!not-for-mail From: "MicroLee.com" Newsgroups: alt.binaries.w-software,alt.collecting.stamps.software,alt.comp.software.energy,alt.comp.software.financial,alt.comp.software.financial.peachtree,alt.comp.software.tools,alt.video.dvd.software,bionet.software,bionet.software.acedb,bionet.software Subject: Visual Studio Lines: 6 Organization: MicroLee X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Message-ID: Date: Thu, 15 Apr 1999 15:28:35 -0500 NNTP-Posting-Host: 209.32.177.248 X-Trace: rsnws01.mn.mediaone.net 924208113 209.32.177.248 (Thu, 15 Apr 1999 16:28:33 EDT) NNTP-Posting-Date: Thu, 15 Apr 1999 16:28:33 EDT Xref: biosci bionet.software:23232 bionet.software.acedb:2275 www.microlee.com/software.htm Cheap software list. Limited number of software available. First come first serve. From owner-software@net.bio.net Thu Apr 15 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!news.fas.harvard.edu!not-for-mail From: Robert Means Newsgroups: bionet.software Subject: ABI Peak Heights? Date: 16 Apr 1999 08:20:27 GMT Organization: Harvard University, Cambridge, Massachusetts Lines: 12 Message-ID: <7f6rsb$5hr$1@news.fas.harvard.edu> NNTP-Posting-Host: login1.fas.harvard.edu User-Agent: tin/pre-1.4-980117 (UNIX) (OSF1/V4.0 (alpha)) Hello, This is a re-try. I hope someone can help me. Is there anyway to take an ABI file and assign peak ratios. We want to be able to look at polymorphism over time in a population and state what percentage of the population has a particular base. So we would sequence a stretch of DNA at several time points and then compare the peak ratios at a position that was changing with a standard peak. Anyway, if anyone knows some good software for looking at ABI trace files, let me know. TIA, Bob remeans@fas.harvard.edu From owner-software@net.bio.net Thu Apr 15 23:00:00 1999 Path: biosci!NHGRI.NIH.GOV!jfryan From: jfryan@NHGRI.NIH.GOV (Joe Ryan) Newsgroups: bionet.software Subject: Re: ABI Peak Heights? Date: 16 Apr 1999 06:26:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: <19990416092131.I9766@nhgri.nih.gov> References: <7f6rsb$5hr$1@news.fas.harvard.edu> NNTP-Posting-Host: net.bio.net Maybe one of these can help? Staden: http://www.mrc-lmb.cam.ac.uk/pubseq/ Andrew Conway's Bioinformatics Public Software: http://sequence-www.stanford.edu/~arc/pub.html On Fri, Apr 16, 1999 at 08:20:27AM +0000, Robert Means wrote: > Hello, > This is a re-try. I hope someone can help me. Is there anyway to > take an ABI file and assign peak ratios. We want to be able to look at > polymorphism over time in a population and state what percentage of the > population has a particular base. So we would sequence a stretch of DNA at > several time points and then compare the peak ratios at a position that > was changing with a standard peak. Anyway, if anyone knows some good > software for looking at ABI trace files, let me know. > TIA, > Bob > remeans@fas.harvard.edu > > From owner-software@net.bio.net Thu Apr 15 23:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!ihnp4.ucsd.edu!news.scripps.edu!not-for-mail From: Georges Gaudriault Newsgroups: bionet.software Subject: Re: software for reading sequence from PDF file Date: Thu, 15 Apr 1999 23:14:53 -0700 Organization: Salk Institute Lines: 3 Message-ID: <3716D54F.E8B658BA@salk.edu> References: <717801BBC100D211B89500805F6FAD93047D56@snap01.synapticcorp.com> Reply-To: gaudriault@salk.edu NNTP-Posting-Host: ppp01.salk.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.51 (Macintosh; U; PPC) X-Accept-Language: en-US Save the image as a TIFF (but copy paste in Photoshop) and treat it with Omnipage to get it as a text From owner-software@net.bio.net Thu Apr 15 23:00:00 1999 Path: biosci!ag