From owner-bio-software@hgmp.mrc.ac.uk Mon May 1 05:39:05 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7043A17AAD; Mon, 1 May 2000 05:39:04 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id FAA08316 for ; Mon, 1 May 2000 05:39:02 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id FAA11585 for bio-software-list@hgmp.mrc.ac.uk; Mon, 1 May 2000 05:39:01 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Andrew Dalke" X-Newsgroups: bionet.software Subject: Re: Looking for server space Date: Sun, 30 Apr 2000 22:40:51 -0600 Organization: MindSpring Enterprises Lines: 11 Message-ID: <8ej1nl$i1r$1@slb1.atl.mindspring.net> References: <000901bfb296$6ff61520$7b02a8c0@nic.in> X-Server-Date: 1 May 2000 04:38:13 GMT X-Newsreader: Microsoft Outlook Express 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk "Malay" wrote: > any good Samaritan out there willing to extend a helping hand? Since you've said you want to make the source freely available, how about www.sourceforge.org? Andrew dalke@acm.org From owner-bio-software@hgmp.mrc.ac.uk Mon May 1 19:43:31 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E48A617A43; Mon, 1 May 2000 19:43:29 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA05190 for ; Mon, 1 May 2000 19:43:27 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA21846 for bio-software-list@hgmp.mrc.ac.uk; Mon, 1 May 2000 19:43:26 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Johan@webmasternewsletter.com (Johan) X-Newsgroups: bionet.software Subject: free software Reply-To: Johan@webmasternewsletter.com Message-ID: <390dd05a.3686250@news.giganews.com> X-Newsreader: Forte Free Agent 1.21/32.243 Lines: 4 Organization: Giganews.Com - Premium News Outsourcing X-Trace: sv2-VRIpgmYwWNTEkJZiOWINTEHpLn3T5nxp++HpL05CPKT4zW1pZ5ee/71IqdSOeybayPYQSS7fijhpVvr!oxeeCd+3aBxF X-Complaints-To: abuse@GigaNews.Com X-Abuse-Info: Please be sure to forward a copy of ALL headers X-Abuse-Info: Otherwise we will be unable to process your complaint properly Date: Mon, 01 May 2000 18:43:41 GMT To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk free software Here is a site that is packed with quality free software. There are 6 new titles everyday... come check it out at http://webmasterresources1.com From owner-bio-software@hgmp.mrc.ac.uk Mon May 1 22:30:19 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8EDDF17AAE; Mon, 1 May 2000 22:30:18 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA28341 for ; Mon, 1 May 2000 22:30:16 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA02385 for bio-software-list@hgmp.mrc.ac.uk; Mon, 1 May 2000 22:30:14 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "NORMAN" X-Newsgroups: bionet.software Subject: lots of cad stuff with cracks at a very low price! Date: Mon, 1 May 2000 20:49:48 +0400 Organization: Omnitel, Lithuania Lines: 35 Message-ID: <8ekt00$he8$16@news.omnitel.net> Reply-To: "NORMAN" X-Trace: news.omnitel.net 957216576 17864 194.176.34.173 (1 May 2000 21:29:36 GMT) X-Complaints-To: news@omnitel.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk lots of cad stuff with cracks at a very low price! PRO/E 2000i 1999500 WITH HELP - 40$US AUTOCAD 2000 FULL VERSION - 40$US IMAGEWARE.SURFACER.V10.0 sw2000 POWERMILL 2510 CADsoft Design Apprentice v1.0 Catia 5R3 rise 2cd catia 5r3 sp5 Mathcad 2000 VISIO 2000 TECHNICAL EDITION (C) VISIO CORP BORLAND C++ BUILDER 5 ENTERPRISE EDITION BORLAND DELPHI 5 ENTERPRISE EDITION FLEXlm SDK v7.0c *Incl Keygen* METASTOCK 7 PRO/DESKTOP 2000i2 (C) PTC TURBOCAD DESIGNER 2D/3D V5.0 VERIBEST.DESIGN.VIEW.V2000 CIMARENDER PRO V7.0 XX/14 TURBOCAD DESIGNER 2D/3D V5.0 and other! LOW PRICES! NORMAN cdsimpl@mailcity.com cdsimpl@CRJOnLine.com cdsimpl@angelfire.com Fax: + 442076917580 (UK) ICQ: 59912397 ./ From owner-bio-software@hgmp.mrc.ac.uk Tue May 2 16:52:32 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BD7DC17AE9; Tue, 2 May 2000 16:52:31 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA14728 for ; Tue, 2 May 2000 16:52:25 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA15739 for bio-software-list@hgmp.mrc.ac.uk; Tue, 2 May 2000 16:52:23 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f X-Newsgroups: bionet.software Subject: phred and ABI 3700 files From: pat.covello@nrc.ca (P. Covello) Organization: PBI / NRC X-Newsreader: WinVN 0.93.14 MIME-Version: 1.0 Lines: 8 Message-ID: Date: Tue, 02 May 2000 15:52:19 GMT X-Trace: tomcat.sk.sympatico.ca 957282739 204.83.147.2 (Tue, 02 May 2000 09:52:19 CST) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I've been using phred with ABI 377 sequenece files without any problem, but when we switched to files from our new 3700 sequencer, I got "file corrupted" errors (files were binary ftp'd). Has anyone run into this problem and is there a fix for it? Pat Covello Patrick.Covello@nrc.ca From owner-bio-software@hgmp.mrc.ac.uk Tue May 2 18:53:12 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0819E17A72; Tue, 2 May 2000 18:53:10 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA01721 for ; Tue, 2 May 2000 18:53:09 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA17203 for bio-software-list@hgmp.mrc.ac.uk; Tue, 2 May 2000 18:53:07 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Herbert M Sauro" X-Newsgroups: bionet.software Subject: Re: Java or C++ Date: Thu, 27 Apr 2000 19:30:18 +0100 Message-ID: <957289969.20851.0.nnrp-13.c2de3927@news.demon.co.uk> References: <002b01bfa08d$8ccf6c20$7b02a8c0@nic.in> X-NNTP-Posting-Host: fssc.demon.co.uk:194.222.57.39 X-Trace: news.demon.co.uk 957289969 nnrp-13:20851 NO-IDENT fssc.demon.co.uk:194.222.57.39 X-Complaints-To: abuse@demon.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Lines: 51 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Korbinian Strimmer wrote in message news:Pine.OSF.4.21.0004161631380.25656-100000@ermine.ox.ac.uk... > > > > Which language will be "the language" in Bioinformatics, Java or C++? > I do consultancy and contract work for some very large financial companies and in these institutions software productivity is very high on their priority list, they have set budgets and they cannot afford to use systems which are difficult to maintain or have learning curves which are too steep; remember someone else will have to maintain the software at a later date when the original author will have moved on to other projects. In my experience, C++ is one of the last programming languages these companies consider, C perhaps, but certainly not C++. The reason is that software written in C++ requires very experienced programmers (= higher cost) and tends to be difficult to maintain once written, this is nothing to do with OOP design in particular because these companies are very keen on OOP but rather C++ syntax and semantic itself is a hindrance. If developing under windows, which tends to be quite common, the MFC libraries are also very expensive options to use and in my experience tends to be avoided. So that do the companies I've worked for use? Well they certainly use Java but on the whole only for server side work, GUI applications written in Java tend to be slow and cumbersome, we have some and they are awful compared to well written windows applications. Compare any of the Java Ides with a modern compiled Windows IDE and you'll soon realise how sluggish and primitive Java IDEs really are. So what else do the companies I've worked for use? Well they use Delphi (from Borland), a language not mentioned here for almost all their gui dev work. There is also a lot of VB work still going on, mainly because it is so easy to write applications in. I suppose the companies I work for focus development on Windows boxes, but before you knock windows, the windows environment is now quite mature, it has lots of support, has a rapidly evolving hardware base, has super fast graphics, a mature GUI, and is very cheap, particularly the hardware. One problem I see with software development in bioinformatics is that is seems to use a wide range of tools, now this may be a good thing but it does mean that most applications will be half-backed simply because it's almost impossible to be a master of all these technologies (with the exception of a limited number of gifted people). Now I'm not saying people should go off and use Delphi or what ever, but do remember there are other things going on in the computing world other than Tkl/Tk, Perl, etc. It always surprises me how narrow we sometimes are in our views of the world. Herbert Sauro From owner-bio-software@hgmp.mrc.ac.uk Tue May 2 19:50:48 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0236B17A6A; Tue, 2 May 2000 19:50:46 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA06771 for ; Tue, 2 May 2000 19:50:44 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA17948 for bio-software-list@hgmp.mrc.ac.uk; Tue, 2 May 2000 19:50:43 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: curiouser@ccmb.ap.nic.in ("Malay") X-Newsgroups: bionet.software Subject: Re: Looking for server space Date: 2 May 2000 19:50:42 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 14 Message-ID: <003c01bfb467$5a8bb640$7b02a8c0@nic.in> References: <200005012049.WAA00151@dbm.ulb.ac.be> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 957293442 17946 193.62.192.80 (2 May 2000 18:50:42 GMT) X-Complaints-To: news@net.bio.net X-Received: from ccmb.ap.nic.in (ccmb.ap.nic.in [164.100.240.122]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA06763 for ; Tue, 2 May 2000 19:50:31 +0100 (BST) X-Received: from w108a.nic.in ([164.100.240.123]) by ccmb.ap.nic.in (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id BAA07894 for ; Wed, 3 May 2000 01:22:58 -0700 (PDT) X-To: "Bio_soft" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-Mimeole: Produced By Microsoft MimeOLE V5.00.2314.1300 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Thanks Andrew, Don, Chris and Robert: I am flattered. And I thought Samaritans are one of the smallest group of human population leaving only in Nothern Israel... I sure will let you know about SeWeR ( that's the name of the site). I am almost through with it. Thank you very much for your offers. Malay --- From owner-bio-software@hgmp.mrc.ac.uk Tue May 2 19:56:26 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 73E4A17A6A; Tue, 2 May 2000 19:56:24 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA07292 for ; Tue, 2 May 2000 19:56:21 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA17956 for bio-software-list@hgmp.mrc.ac.uk; Tue, 2 May 2000 19:56:20 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: actnow123@mail.com X-Newsgroups: bionet.software Subject: WE CAN HELP YOU GET EXPOSED, WITH BULK E-MAIL Date: 2 May 2000 19:56:19 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 31 Message-ID: <200005021856.TAA07284@hgmp.mrc.ac.uk> X-Trace: niobium.hgmp.mrc.ac.uk 957293780 17954 193.62.192.80 (2 May 2000 18:56:20 GMT) X-Complaints-To: news@net.bio.net X-Received: from nt_server.nxicom.com (mail.nxicom.com [204.228.158.67]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA07284 for ; Tue, 2 May 2000 19:56:13 +0100 (BST) X-Received: from sruGig0o8 (PPPa96-ResaleModesto1-4R7275.saturn.bbn.com [4.16.191.157]) by nt_server.nxicom.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.1960.3) id G8ZBH1BM; Tue, 2 May 2000 12:54:19 -0600 X-Reply-to: actnow123@mail.com X-TO: actnow123@mail.com To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I am sorry if this ad as offended you. Please go to removeall@china.com to be removed. We offer some of the best bulk e-mail prices on the Internet. Bulk e-mail can get you the best exposure on the net. What makes this kind of advertising so effective is the fact that you go to the potential customer. Not like search engines or print ads that the potential customer has to do all the searching. Dollar for dollar bulk e-mailing is also the most economical. What we offer: *General AOL Lists or other ISPs $200.00 for 1-million e-mails sent. $400.00 for 3-million e-mails sent. $600.00 for 5-million e-mails sent. $800.00 for 7-million e-mails sent. $1000.00 for 10-million e-mails sent. WE ALSO HAVE LARGER PACKAGES! *Targeted Lists: $400.00 for 1-million e-mails sent. $700.00 for 2-million e-mails sent. $1,000.00 for 3-million e-mails sent. SPRING special, order within 2 days and get 1 free million general names sent. Order within 5 working days and get 500,000-SALE ENDS JUNE 15. SO RESERVE YOUR SPOT TODAY!!! Call for bigger packages! So why not give us a call and see what it is that we can do for you. call anytime 209-669-0176, we are in California. METHOD OF PAYMENT , CASHIERS CHECK MONEY ORDER OR BANK WIRE. --- From owner-bio-software@hgmp.mrc.ac.uk Tue May 2 22:26:02 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 42C4117AA3; Tue, 2 May 2000 22:26:02 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA26729 for ; Tue, 2 May 2000 22:26:00 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA28377 for bio-software-list@hgmp.mrc.ac.uk; Tue, 2 May 2000 22:25:59 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: curiouser@ccmb.ap.nic.in ("Malay") X-Newsgroups: bionet.software Subject: Re: Java or C++ Date: 2 May 2000 22:25:58 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 101 Message-ID: <007501bfb47d$13503b00$7b02a8c0@nic.in> References: <002b01bfa08d$8ccf6c20$7b02a8c0@nic.in> <957289969.20851.0.nnrp-13.c2de3927@news.demon.co.uk> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 957302758 28375 193.62.192.80 (2 May 2000 21:25:58 GMT) X-Complaints-To: news@net.bio.net X-Received: from gene.ccmbindia.org ([202.54.67.53]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA26698 for ; Tue, 2 May 2000 22:25:52 +0100 (BST) X-Received: from w108a.nic.in ([192.168.2.123]) by gene.ccmbindia.org (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id CAA30763 for ; Wed, 3 May 2000 02:57:46 -0700 (PDT) X-To: "Bio_soft" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-Mimeole: Produced By Microsoft MimeOLE V5.00.2314.1300 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Dear Herbert: First of all thanks for your comments. I thought this thread was dead. You have given it life again! Thank you! > I do consultancy and contract work for some very large financial companies > and in these institutions software productivity is very high on their > priority list, they have set budgets and they cannot afford to use systems > which are difficult to maintain or have learning curves which are too steep; > remember someone else will have to maintain the software at a later date > when the original author will have moved on to other projects. That's common to any software development work. I agree to you completely. Bioinformatics is no exception. >In my > experience, C++ is one of the last programming languages these companies > consider, C perhaps, but certainly not C++. The reason is that software > written in C++ requires very experienced programmers (= higher cost) and > tends to be difficult to maintain once written, this is nothing to do with > OOP design in particular because these companies are very keen on OOP but > rather C++ syntax and semantic itself is a hindrance. But I thought C++ makes your life easy. >If developing under > windows, which tends to be quite common, the MFC libraries are also very > expensive options to use and in my experience tends to be avoided. > Sure! That's was the point. *Free* that's the buzzword! > So that do the companies I've worked for use? Well they certainly use Java > but on the whole only for server side work, GUI applications written in Java > tend to be slow and cumbersome, we have some and they are awful compared to > well written windows applications. I agree. But we are talking of portability issues too. >Compare any of the Java Ides with a > modern compiled Windows IDE and you'll soon realise how sluggish and > primitive Java IDEs really are. I agree. But a mixed option of native+Java works wonders, Borland Jbuilder is an example! >So what else do the companies I've worked > for use? Well they use Delphi (from Borland), a language not mentioned here > for almost all their gui dev work. There is also a lot of VB work still > going on, mainly because it is so easy to write applications in. I am talking for *free* softwares too. If I use a proprietory tool to develop my software, I can't give it free. I need to get the *cow* free to give the *milk* free. >I suppose > the companies I work for focus development on Windows boxes, but before you > knock windows, the windows environment is now quite mature, it has lots of > support, has a rapidly evolving hardware base, has super fast graphics, a > mature GUI, and is very cheap, particularly the hardware. No plan to knock windows. We want all, MAC, Windows, Linux, Solaris.... as many as possible. But primarily for Windows, MAC and Linux > > One problem I see with software development in bioinformatics is that is > seems to use a wide range of tools, now this may be a good thing but it does > mean that most applications will be half-backed simply because it's almost > impossible to be a master of all these technologies (with the exception of a > limited number of gifted people). > Most of the successful *free* projects are always developed as team efforts or by the *old-man form the chinese parable* way- I start cutting the mountain today, my son will finish it, if not my grandson.... :-) > Now I'm not saying people should go off and use Delphi or what ever, but do > remember there are other things going on in the computing world other than > Tkl/Tk, Perl, Yep! PHP, XML, JavaScript, GNU all *free*! >etc. It always surprises me how narrow we sometimes are in our > views of the world. > We are most of the times but in this case intentionally! We close our eyes to *cows* that we need to buy! I guess we have no other option but to wait till Borland makes Delphi *free* atleast $$ sense or Microsoft gives VB away before it breaks (See the order)!!!!!! Malay --- From owner-bio-software@hgmp.mrc.ac.uk Wed May 3 01:03:19 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4B69E17A90; Wed, 3 May 2000 01:03:19 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id BAA07133 for ; Wed, 3 May 2000 01:01:57 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id BAA00482 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 May 2000 01:01:56 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: tongyigang@263.net (Yigang Tong) X-Newsgroups: bionet.software Subject: CHO codon bias? Date: 3 May 2000 01:01:55 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 9 Message-ID: <390EDD52.1B5450B@263.net> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 957312116 480 193.62.192.80 (3 May 2000 00:01:56 GMT) X-Complaints-To: news@net.bio.net X-Received: from btamail.net.cn ([202.106.196.131]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with SMTP id BAA07054 for ; Wed, 3 May 2000 01:00:28 +0100 (BST) X-Received: from 263.net([202.108.3.67]) by btamail.net.cn(JetMail 2.3.1.0) with SMTP id /m0/jmail.rcv/8/jm13390fb401; Wed, 3 May 2000 00:00:09 -0000 X-Reply-To: tongyigang@263.net X-Mailer: Mozilla 4.61 [en] (Win98; I) X-Accept-Language: en X-To: bio-soft@hgmp.mrc.ac.uk To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Does anybody know where to obtain the data of codon bias of CHO and other common expression host? Thanks, Yigang Tong --- From owner-bio-software@hgmp.mrc.ac.uk Wed May 3 01:40:14 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 6461E17A66; Wed, 3 May 2000 01:40:12 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id BAA09303 for ; Wed, 3 May 2000 01:40:10 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id BAA00959 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 May 2000 01:40:09 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: nlharris@lbl.gov X-Newsgroups: bionet.software Subject: Bioinformatics Open Source Conference Date: Wed, 03 May 2000 00:31:05 GMT Organization: Deja.com - Before you buy. Lines: 16 Message-ID: <8ens09$c5n$1@nnrp1.deja.com> References: <001301bfae14$019cdea0$7b02a8c0@nic.in> X-Article-Creation-Date: Wed May 03 00:31:05 2000 GMT X-Http-User-Agent: Mozilla/4.7 [en] (X11; I; SunOS 5.6 sun4u; Nav) X-Http-Proxy: 1.0 x41.deja.com:80 (Squid/1.1.22) for client 131.243.192.135 X-MyDeja-Info: XMYDJUIDalystra To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk The Bioinformatics Open Source Conference (BOSC) will take place August 17-18 in San Diego, just before ISMB. BOSC will be a two-day conference featuring speakers on software engineering techniques in the life sciences, with a particular emphasis on open source software. Attendees are encouraged to submit abstracts for consideration. Some abstracts will be selected to give talks and there will also be the chance to present posters. Tools that are open source or built on top of open source software will be given priority. Please visit http://ismb2000.sdsc.edu/bosc2000/ for more information. Sent via Deja.com http://www.deja.com/ Before you buy. From owner-bio-software@hgmp.mrc.ac.uk Wed May 3 09:08:48 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 951DA17A64; Wed, 3 May 2000 09:08:47 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA06118 for ; Wed, 3 May 2000 09:08:45 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA06091 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 May 2000 09:08:44 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: ajenkins@nibsc.ac.uk (Adrian Jenkins) X-Newsgroups: bionet.software Subject: Re: ABI data extraction utilities Date: 3 May 2000 09:08:42 +0100 Organization: NIBSC Lines: 62 Message-ID: <390FDE63.59BA4F0D@nibsc.ac.uk> References: <8ca7ae$2c0$1@mercury.hgmp.mrc.ac.uk> <38E98FA0.7658DDBF@med.kuleuven.ac.be> <38EB352D.64682EFD@pitt.edu> <38EB475D.B546C7D3@med.kuleuven.ac.be> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 957341323 6089 193.62.192.80 (3 May 2000 08:08:43 GMT) X-Complaints-To: news@net.bio.net X-Received: from gensig.nibsc.ac.uk (gensig.nibsc.ac.uk [193.62.43.13]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA06108; Wed, 3 May 2000 09:08:41 +0100 (BST) X-Received: from nibsc.ac.uk (dlrvaj.nibsc.ac.uk [193.62.42.41]) by gensig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA45672; Wed, 3 May 2000 09:08:25 +0100 (BST) X-Reply-To: ajenkins@nibsc.ac.uk X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en X-To: staden@hgmp.mrc.ac.uk, bio-software@hgmp.mrc.ac.uk To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi All I have spent some time investigating BIOEDIT and it appears to be relatively powerful. However it does have it's weakness in particular it's in ability to reverse complement a sequence when using CAP. Is any one aware of a Software package similar to Staden but for the PC. A collaborator of ours dose not appear to have access to unix servers etc. Any suggestions would be welcome. Thank you for your time Przemko Tylzanowski wrote: > > I use Chromas (the freeware version) and am very happy with it. The thing > is that sometimes I would like to see the raw data because the ABI > sometimes miscalls the bases. Now, our lab is PC based and the only Mac > is with ABI. So it would be much more convenient to look at the raw data > on PC. I have somewhere a hack for it but I thought perhaps someone > managed a program to read not only the processed data but also the real > trace. > > "Richard J. Dudley" wrote: > > > Have you tried Chromas? > > http://www.technelysium.com.au/chromas.html > > or BioEdit? > > http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html > > Przemko -- Enjoy.... Adrian %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL Adrian Jenkins Molecular Virology Group Division of Retrovirology e-mail ajenkins@nibsc.ac.uk http://www.nibsc.ac.uk/ "No plan survives contact with the enemy" von Moltke "To Errr is human, but when the eraser wears out ahead of the pencil; you're overdoing it." Anon %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --- From owner-bio-software@hgmp.mrc.ac.uk Wed May 3 09:52:18 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id CFDD717A83; Wed, 3 May 2000 09:52:17 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA09943 for ; Wed, 3 May 2000 09:52:05 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA06689 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 May 2000 09:52:04 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Tim Cutts X-Newsgroups: bionet.software Subject: Re: ABI data extraction utilities Date: 03 May 2000 09:47:20 +0100 (BST) Organization: Linux Unlimited Lines: 12 Message-ID: References: <8ca7ae$2c0$1@mercury.hgmp.mrc.ac.uk> <38EB352D.64682EFD@pitt.edu> <38EB475D.B546C7D3@med.kuleuven.ac.be> <390FDE63.59BA4F0D@nibsc.ac.uk> X-Newsreader: trn 4.0-test70 (17 January 1999) Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk In article <390FDE63.59BA4F0D@nibsc.ac.uk>, Adrian Jenkins wrote: >Is any one aware of a Software package similar to Staden but for the PC. A >collaborator of ours dose not appear to have access to unix servers etc. > >Any suggestions would be welcome. Er, Staden? Staden is now available for Windows. Tim. From owner-bio-software@hgmp.mrc.ac.uk Wed May 3 11:44:27 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7314217A7B; Wed, 3 May 2000 11:44:26 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA20957 for ; Wed, 3 May 2000 11:44:23 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA08088 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 May 2000 11:44:21 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Simon Andrews X-Newsgroups: bionet.software Subject: Re: CHO codon bias? Date: Wed, 03 May 2000 11:39:01 +0100 Organization: BBSRC Biotechnology and Biological Sciences Research Council Lines: 8 Message-ID: <391001C5.7245077C@bbsrc.ac.uk> References: <390EDD52.1B5450B@263.net> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Yigang Tong wrote: > > Does anybody know where to obtain the data of codon bias of CHO and > other common expression host? Try; http://www.kazusa.or.jp/codon/ From owner-bio-software@hgmp.mrc.ac.uk Wed May 3 13:50:35 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2439817B70; Wed, 3 May 2000 13:38:10 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA03257 for ; Wed, 3 May 2000 13:38:06 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA09532 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 May 2000 13:38:05 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: poa4@mailgate.webtek.co.uk (urgatn5) X-Newsgroups: bionet.software Subject: | | | | Your Immediate Attention | | | | Date: 3 May 2000 13:38:04 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 62 Message-ID: <20000503846OAA9426@kilsket.cybergate.nl> X-Trace: niobium.hgmp.mrc.ac.uk 957357484 9530 193.62.192.80 (3 May 2000 12:38:04 GMT) X-Complaints-To: news@net.bio.net X-Received: from cyberspace.CYBERGATE.NL (cyberspace.cybergate.nl [194.158.181.200]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA03239; Wed, 3 May 2000 13:38:01 +0100 (BST) X-Resent-From: poa4@mailgate.webtek.co.uk X-Received: from localhost (Administrators@localhost) by cyberspace.CYBERGATE.NL (8.8.8/8.8.7) with SMTP id OAA00088; Wed, 03 May 2000 14:39:08 +0200 (Romance Daylight Time) X-Resent-Date: Wed, 03 May 2000 14:39:08 +0200 (Romance Daylight Time) X-Resent-Message-Id: <200005031239.OAA00088@cyberspace.CYBERGATE.NL> X-To: poa4@mailgate.webtek.co.uk X-Comments: Authenticated sender is To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hey there, If you want more out of life than what you have been getting, then NOW is the time for you to sit up and take notice. 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It could very well be what you have been waiting for all your life! http://3521854193/pg/a10200.html or click here Best regards, Success Systems _______________________________ to be removed from future mailings call 1-888-248-1792 Ref # 1265456-Wd41tWE 9 ñ=bi From owner-bio-software@hgmp.mrc.ac.uk Wed May 3 14:40:24 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E846C17ACD; Wed, 3 May 2000 14:40:22 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA11313 for ; Wed, 3 May 2000 14:40:18 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA10289 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 May 2000 14:40:16 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Petr Kuzmic X-Newsgroups: bionet.software Subject: Re: Java or C++ Date: Wed, 03 May 2000 08:41:57 -0500 Organization: BioKin Consulting Lines: 61 Message-ID: <39102CA5.E5C033B@biokin.com> References: <002b01bfa08d$8ccf6c20$7b02a8c0@nic.in> <957289969.20851.0.nnrp-13.c2de3927@news.demon.co.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.doit.wisc.edu 957361172 21614 128.104.49.13 (3 May 2000 13:39:32 GMT) X-Complaints-To: abuse@doit.wisc.edu X-Mailer: Mozilla 4.7 [en] (WinNT; U) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Herbert M Sauro wrote: > > Korbinian Strimmer wrote in message > > > Which language will be "the language" in Bioinformatics, Java or C++? ... > So that do the companies I've worked for use? Well they certainly use Java > but on the whole only for server side work, GUI applications written in Java > tend to be slow and cumbersome... I use Java to design *portable* GUIs. The interfaces are not as fast as native code, but the portability surely is nice. Imagine compiling a moderately complex Java GUI on a Windows machine. You can then simply copy the binary byte-code to the Macintosh box, or a Linux box, or an OS/2 box, and just run it showing the same interface on all machines. Of course there are some restrictions: you have to stick to Java 1.1 at the present time. Bottom line on the GUI issue, in my opinion: the original poster should consider both *portability* and *performance*. If platform independence is very important (Win, Mac, Unix, Linux, OS/2, Be, ...), use Java to build GUI's. If performance is very important, use C++ or toolkits like Tcl/Tk. Another important difference between C++ and Java is how they handle multi-threading. This is potentially very important for a scientific program doing lengthy computations. In C++, the programmer has to design the multithreading mechanism by hand from scratch (mutexes, critical sections, semaphores, all that jazz...), while in Java multithreading is handled at the language level. This makes it *relatively* easy to write threaded applications in Java. For example, one "worker" thread can be doing a lengthy scientific computation, while another "manager" thread is offering the user - the "boss" - to terminate the "worker" if it seems too slow (Labor Movement language unintended). > ... the windows environment is ... very cheap, particularly the hardware. Yes, but the Windows operating system software cost seems staggering. Windows-2000 is quite expensive and (at the present time) very hard to maintain. > Now I'm not saying people should go off and use Delphi or what ever, but do > remember there are other things going on in the computing world other than > Tkl/Tk, Perl, etc. It always surprises me how narrow we sometimes are in our > views of the world. True. But it is also true that a master craftsperson will use whatever tool is best suited for the given task (Perl for text processing, Java for portable GUIs, C++ for fast native libraries, Fortran for quick prototyping using legacy scientific code, etc.). The more tools in anyone's toolchest, the better! Just my $0.02s worth. -- Petr _____________________________________________________________________ Petr Kuzmic, Ph.D. * BioKin, Ltd. * Consulting & Software Development http://www.biokin.com * (608) 256-4790 * (608) 256-1269 FAX From owner-bio-software@hgmp.mrc.ac.uk Wed May 3 17:47:37 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id ACA9817A56; Wed, 3 May 2000 17:47:34 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA12093 for ; Wed, 3 May 2000 17:47:30 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA12828 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 May 2000 17:47:29 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: rh@mblab.gla.ac.uk (Robert Hartley) X-Newsgroups: bionet.software Subject: Re: Java or C++ Date: 3 May 2000 16:16:41 GMT Organization: Centre for Cell Engineering Lines: 29 Message-ID: References: <002b01bfa08d$8ccf6c20$7b02a8c0@nic.in> <957289969.20851.0.nnrp-13.c2de3927@news.demon.co.uk> <39102CA5.E5C033B@biokin.com> To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk In article <39102CA5.E5C033B@biokin.com>, Petr Kuzmic wrote: > Herbert M Sauro wrote: > > > > Korbinian Strimmer wrote in message > > > > Which language will be "the language" in Bioinformatics, Java or C++? > ... > > So that do the companies I've worked for use? Well they certainly use Java > > but on the whole only for server side work, GUI applications written in Java > > tend to be slow and cumbersome... > > I use Java to design *portable* GUIs. The interfaces are not as fast as > native code, but the portability surely is nice. Imagine compiling a > moderately complex Java GUI on a Windows machine. You can then simply > copy the binary byte-code to the Macintosh box, or a Linux box, or an > OS/2 box, Or RISC OS soon to be ported to the Psion netbook. Cheers Bob; running a RiscPC 700 with RISC OS 3.7 and a pentium co pro with win98 in the corner of the screen (unused) :-))). -- Robert Hartley, Centre for Cell Engineering,University of Glasgow,UK. mail: rh@mblab.gla.ac.uk, Tel: ++44 (0)141 330 4756 Web : http://www.gla.ac.uk/Inter/CellEngineering From owner-bio-software@hgmp.mrc.ac.uk Wed May 3 18:48:05 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3442617A56; Wed, 3 May 2000 18:48:05 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA17035 for ; Wed, 3 May 2000 18:48:03 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA13534 for bio-software-list@hgmp.mrc.ac.uk; Wed, 3 May 2000 18:48:01 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: madden@ncbi.nlm.nih.gov (Tom Madden) X-Newsgroups: bionet.software Subject: New NCBI toolkit and new BLAST binaries Date: 3 May 2000 18:48:00 +0100 Organization: National Center for Biotechnology Information Lines: 35 Message-ID: <3910664C.3EE71DB3@ncbi.nlm.nih.gov> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 957376081 13531 193.62.192.80 (3 May 2000 17:48:01 GMT) X-Complaints-To: news@net.bio.net X-Received: from ncbi.nlm.nih.gov (ncbi.nlm.nih.gov [130.14.25.1]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA17026 for ; Wed, 3 May 2000 18:47:57 +0100 (BST) X-Received: from ncbi.nlm.nih.gov (corin [130.14.25.41]) by ncbi.nlm.nih.gov (8.9.3/8.9.3) with ESMTP id NAA23293 for ; Wed, 3 May 2000 13:47:56 -0400 (EDT) X-Mailer: Mozilla 4.7 [en] (X11; U; SunOS 5.7 sun4u) X-Accept-Language: en X-To: bio-software@hgmp.mrc.ac.uk To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk A new version of the NCBI toolkit and new BLAST binaries have been posted to the NCBI FTP site. The toolkit is available at ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/ and the BLAST binaries are available at ftp://ncbi.nlm.nih.gov/blast/executables/ Notes for BLAST 2.0.12 release: Enhancements: 1.) Bl2seq can now perform nucleotide-protein (blastx style) comparisons. This necessitated changing the '-p' option from a Boolean to a string. Valid arguments are "blastn", "blastp", or "blastx". Bug fixes: 1.) A problem in the NCBI threads library that caused BLAST to sometimes stick was corrected. Many thanks to Haruna Cofer and colleauges at SGI for providing a fix. 2.) A problem that caused BLAST to core-dump (especially on long queries) has been fixed. Many thanks to Gary Williams for providing examples. 3.) A problem that prevented the search of multiple multivolume databases has been fixed. --- From owner-bio-software@hgmp.mrc.ac.uk Thu May 4 00:50:18 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 678EC17B91; Thu, 4 May 2000 00:50:17 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id AAA22467 for ; Thu, 4 May 2000 00:50:15 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id AAA26436 for bio-software-list@hgmp.mrc.ac.uk; Thu, 4 May 2000 00:50:13 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: tongyigang@263.net (Yigang Tong) X-Newsgroups: bionet.software Subject: CHO codon bias? Date: 4 May 2000 00:50:12 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 7 Message-ID: <3910BAF6.3F6E83AC@263.net> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 957397812 26434 193.62.192.80 (3 May 2000 23:50:12 GMT) X-Complaints-To: news@net.bio.net X-Received: from btamail.net.cn ([202.106.196.131]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with SMTP id AAA22448 for ; Thu, 4 May 2000 00:50:07 +0100 (BST) X-Received: from 263.net([202.108.3.68]) by btamail.net.cn(JetMail 2.3.1.0) with SMTP id /m0/jmail.rcv/1/jm43911031b; Wed, 3 May 2000 23:49:55 -0000 X-Reply-To: tongyigang@263.net X-Mailer: Mozilla 4.61 [en] (Win98; I) X-Accept-Language: en X-To: bio-soft@hgmp.mrc.ac.uk To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Does anybody know where to obtain the data of codon bias of CHO and other common expression host? Thanks, Yigang Tong --- From owner-bio-software@hgmp.mrc.ac.uk Thu May 4 06:50:14 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D860A17A9C; Thu, 4 May 2000 06:50:13 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id GAA16140 for ; Thu, 4 May 2000 06:50:11 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id GAA00541 for bio-software-list@hgmp.mrc.ac.uk; Thu, 4 May 2000 06:50:10 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: mike4@cris.com X-Newsgroups: bionet.software Subject: Anyone: NCBI BLAST2 on >1 CPU on Solaris? Date: Thu, 04 May 2000 05:43:14 GMT Organization: University of Washington Lines: 15 Message-ID: <8er2lf$um8$1@nnrp1.deja.com> X-Article-Creation-Date: Thu May 04 05:43:14 2000 GMT X-Http-User-Agent: Mozilla/4.0 (compatible; MSIE 5.0; Windows NT; DigExt) X-Http-Proxy: 1.1 x35.deja.com:80 (Squid/1.1.22) for client 128.95.8.219 X-MyDeja-Info: XMYDJUIDmyasayko To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I'm having trouble getting BLAST2 (executable: blastall) to run on more than one processor (i.e., when I specify the number of processors as 4 with the '-a' command line option). It could have something to do with my local environment, although I can get other programs (e.g. Perl) to utilize all 4 processors. Has anyone observed BLAST-2 running on more than one processor in a 64-bit Solaris environment? Does anyone know of a trick to get BLAST2 to compile so that it can use all the processors? Any advice much appreciated, Mike Sent via Deja.com http://www.deja.com/ Before you buy. From owner-bio-software@hgmp.mrc.ac.uk Thu May 4 08:21:11 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E7DE017A70; Thu, 4 May 2000 08:21:09 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA20185 for ; Thu, 4 May 2000 08:21:08 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA01614 for bio-software-list@hgmp.mrc.ac.uk; Thu, 4 May 2000 08:21:06 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Roland Mainz X-Newsgroups: bionet.software Subject: Re: ABI data extraction utilities Date: Thu, 04 May 2000 08:43:02 +0200 Organization: University of Giessen, Germany Lines: 27 Message-ID: <39111BF6.13550E76@informatik.med.uni-giessen.de> References: <8ca7ae$2c0$1@mercury.hgmp.mrc.ac.uk> <38EB352D.64682EFD@pitt.edu> <38EB475D.B546C7D3@med.kuleuven.ac.be> <390FDE63.59BA4F0D@nibsc.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Tim Cutts wrote: > >Is any one aware of a Software package similar to Staden but for the PC. A > >collaborator of ours dose not appear to have access to unix servers etc. > > > >Any suggestions would be welcome. > > Er, Staden? Staden is now available for Windows. Linux runs on "PCs", too :-) I would recommend to run Staden on it's "native" platform - which is Unix (we're using Staden on Solaris/UltraSPARC)... ---- Bye, Roland -- __ . . __ (o.\ \/ /.o) Roland.Mainz@informatik.med.uni-giessen.de \__\/\/__/ gisburn@informatik.med.uni-giessen.de /O /==\ O\ MPEG specialist, C&&JAVA&&Sun&&Unix programmer (;O/ \/ \O;) TEL +49 641 99-13193 FAX +49 641 99-41359 From owner-bio-software@hgmp.mrc.ac.uk Thu May 4 08:21:12 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 64FA017A70; Thu, 4 May 2000 08:21:12 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA20192 for ; Thu, 4 May 2000 08:21:09 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA01619 for bio-software-list@hgmp.mrc.ac.uk; Thu, 4 May 2000 08:21:07 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Roland Mainz X-Newsgroups: bionet.software Subject: Re: Anyone: NCBI BLAST2 on >1 CPU on Solaris? Date: Thu, 04 May 2000 09:01:08 +0200 Organization: University of Giessen, Germany Lines: 45 Message-ID: <39112034.B140D303@informatik.med.uni-giessen.de> References: <8er2lf$um8$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk mike4@cris.com wrote: > I'm having trouble getting BLAST2 (executable: blastall) to run on more > than one processor (i.e., when I specify the number of processors as 4 > with the '-a' command line option). It could have something to do with > my local environment, although I can get other programs (e.g. Perl) to > utilize all 4 processors. This heavily depends on the executable. Unless the program or interpreter (perl, JAVA) was designed to use multiple CPUs the program will only use one CPU. You can always run multiple instances of the program which will distribute over all available CPUs (=available means also that you can restrict this via pbind (1m) - which may be usefull for interactive machines which should be shared between many users). If you have the Sun Workshop compiler you can do some magic to turn any (uhm... most...) single-CPU-apps. into multi-CPU-apps. but this is little bit tricky (=if the program was written portable and uses itself no threading (this excludes the usage of GUI libraries like GTK+ etc., too) it works, otherwise you'll see some weired crashes =:-) > Has anyone observed BLAST-2 running on more > than one processor in a 64-bit Solaris environment? Does anyone know > of a trick to get BLAST2 to compile so that it can use all the > processors? Uhm, I think we need little more information Which Solaris version (64bit==Solaris 7, right ?), kernel patch rev, hardware, compiler used ? ---- Bye, Roland -- __ . . __ (o.\ \/ /.o) Roland.Mainz@informatik.med.uni-giessen.de \__\/\/__/ gisburn@informatik.med.uni-giessen.de /O /==\ O\ MPEG specialist, C&&JAVA&&Sun&&Unix programmer (;O/ \/ \O;) TEL +49 641 99-13193 FAX +49 641 99-41359 From owner-bio-software@hgmp.mrc.ac.uk Thu May 4 08:54:28 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0723B17AAD; Thu, 4 May 2000 08:54:27 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA22447 for ; Thu, 4 May 2000 08:54:24 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA01979 for bio-software-list@hgmp.mrc.ac.uk; Thu, 4 May 2000 08:54:18 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: ptribble@hgmp.mrc.ac.uk (Peter C. Tribble) X-Newsgroups: bionet.software Subject: Re: Anyone: NCBI BLAST2 on >1 CPU on Solaris? Date: 4 May 2000 07:54:18 GMT Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 33 Message-ID: <8eraba$1q6$1@niobium.hgmp.mrc.ac.uk> References: <8er2lf$um8$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Trace: niobium.hgmp.mrc.ac.uk 957426858 1862 193.62.192.22 (4 May 2000 07:54:18 GMT) X-Complaints-To: news@net.bio.net X-Newsreader: knews 1.0b.1 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk In article <8er2lf$um8$1@nnrp1.deja.com>, mike4@cris.com writes: > I'm having trouble getting BLAST2 (executable: blastall) to run on more > than one processor (i.e., when I specify the number of processors as 4 > with the '-a' command line option). It could have something to do with > my local environment, although I can get other programs (e.g. Perl) to > utilize all 4 processors. Has anyone observed BLAST-2 running on more > than one processor in a 64-bit Solaris environment? Does anyone know > of a trick to get BLAST2 to compile so that it can use all the > processors? We normally seem to use -a 8, as far as I can tell watching the queues, and this normally means that 8 threads run - so on a 20-way box, we actually see 8 processors used. There are times in blast when it's essentially single threaded (I think when it's actually finished the search and is extracting the results is one), but the search phase uses multiple processors very nicely. If you've got top, it will show the number of threads. This isn't equal to the number of threads you've told it to use (in our case, with -a 8 we see 13 threads, which drops to 5 at the end of the run). So you can tell from that whether it's actually creating the threads or not (and what stage of the processing it's at). If you're I/O bound then you'll never see high cpu usage, even with multiple threads, as they're all waiting for the data. So it may then appear that it's effectively only using a single cpu. -- -Peter Tribble HGMP Computing Services http://www.hgmp.mrc.ac.uk/~ptribble/ From owner-bio-software@hgmp.mrc.ac.uk Thu May 4 09:41:00 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 75AC117AD3; Thu, 4 May 2000 09:40:59 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA26685 for ; Thu, 4 May 2000 09:40:56 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA02648 for bio-software-list@hgmp.mrc.ac.uk; Thu, 4 May 2000 09:40:55 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Andries Jagt" X-Newsgroups: alt.nl.comp.cd-branden,alt.nl.markt.comp.cd-writer,alt.nl.markt.comp.software.kopie-voor-eigen-gebruik,alt.nl.markt.comp.software.legaal,bionet.software,nl.comp.cd-branden Subject: Gevraagd: driver voor CDRW-622 van Wearnes Peripherals International Date: Thu, 4 May 2000 10:34:27 +0200 Organization: WorldOnline - The Internet Communication Company Lines: 57 Message-ID: <8ercoo$div$1@nereid.worldonline.nl> X-Trace: nereid.worldonline.nl 957429336 13919 195.241.228.233 (4 May 2000 08:35:36 GMT) X-Complaints-To: newsmaster@worldonline.nl X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Beste mensen, Ik heb een probleem: 'Zomaar ineens' bestaat er in mijn configuratiescherm (WIN95), onder 'systeem' geen CD-rom apparaat meer vermeld. Nu heb ik van een site met drivers een dos-driver voor de CDRW-622 van Wearnes gevonden. Echter, de brandmogelijkheid doet het nog niet. Want deze functioneert in DOScompatibiliteitsmodus. In 'Deze Computer' staat nu wel A, C, D (=cd-rom) en E (interne ZIP) vermeld. Nog steeds niet in het configuratiescherm------> systeem. Dus ik heb wel een CD-rom, maar geen Rewritable, terwijl ik die wel heb. Ik heb ook Windows opnieuw 'hardware laten detecteren, zonder resultaat. Toen ik de pc nieuw kocht (PIII-450) kreeg ik er allerlei software bij, echter geen cd-rommetje van Wearnes. Ik dacht, het zal wel plug and Play zijn. Ik hoop dat er iemand is die mij kan helpen. Ofwel met tips wat ik moet doen, ofwel met de juiste drivers. Hieronder zal ik de inhoud van mijn config.sys en autoexec.bat weergeven. Wil je je bericht, behalve in de nieuwsgroep, ook per email aan me zenden? Alvast hartelijk dank. Andries Jagt 'autoexec.bat': c:\windows\net start SET BLASTER=A220 I7 D1 T2 SET SNDSCAPE=C:\WINDOWS rem - By Windows Setup - C:\WINDOWS\COMMAND\MSCDEX.EXE /d:mscd001 mode con codepage prepare=((850) C:\WINDOWS\COMMAND\ega.cpi) mode con codepage select=850 C:\CDROM\MSCDEX.EXE /d:WP_CDROM /M:20 'Config.sys': DEVICE=C:\WINDOWS\HIMEM.SYS DEVICE=C:\WINDOWS\TWAIN\MSPNRI.SYS DEVICE=C:\WINDOWS\EMM386.EXE [common] device=c:\CdExpert\actcd.sys /d:mscd001 ; --- SB PCI mod --- device=C:\WINDOWS\himem.sys device=C:\WINDOWS\COMMAND\display.sys con=(ega,,1) Country=031,850,C:\WINDOWS\COMMAND\country.sys device = c:\cdrom\wcd.sys /d:wp_cdrom /V From owner-bio-software@hgmp.mrc.ac.uk Thu May 4 21:37:03 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4CBD917B03; Thu, 4 May 2000 21:37:02 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA10224 for ; Thu, 4 May 2000 21:36:59 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA20316 for bio-software-list@hgmp.mrc.ac.uk; Thu, 4 May 2000 21:36:58 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Chris LaRosa X-Newsgroups: bionet.software Subject: Re: assembly program Date: Thu, 04 May 2000 15:40:06 -0500 Organization: University of Nebraska-Lincoln Lines: 12 Message-ID: <3911E026.DC035ECD@biocomp.unl.edu> References: <8clhrl$nun$1@news.hccnet.nl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.72 [en] (Win95; I) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk "l. heijnen" wrote: > > Is there any freely available windows 95 based program that can do some > Try BioEdit.... its free and claims it can read ABI sequences and do alignments. I have not used it yet since we have sequencher and ABI software.... Let me know if these things are helpful. PC LaRosa From owner-bio-software@hgmp.mrc.ac.uk Fri May 5 16:35:47 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4E8EF17A9E; Fri, 5 May 2000 16:35:45 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA12477 for ; Fri, 5 May 2000 16:35:42 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA03965 for bio-software-list@hgmp.mrc.ac.uk; Fri, 5 May 2000 16:35:41 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: johnz0983@capecod.net X-Newsgroups: bionet.software Subject: * D E A D L I N E * is next Sunday...... Date: 5 May 2000 16:35:39 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 59 Message-ID: <00002a260416$00007890$00000390@38.201.46.222> X-Trace: niobium.hgmp.mrc.ac.uk 957540940 3963 193.62.192.80 (5 May 2000 15:35:40 GMT) X-Complaints-To: news@net.bio.net X-Received: from braustern.co.jp (braustern.co.jp [210.143.98.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA12450 for ; Fri, 5 May 2000 16:35:34 +0100 (BST) X-Received: from 199.6.46.232 (AC811418.ipt.aol.com [172.129.20.24]) by braustern.co.jp (8.8.8/3.6Wbeta7) with SMTP id AAA25145; Sat, 6 May 2000 00:26:01 +0900 X-To: X-Priority: 3 X-MSMail-Priority: Normal X-Reply-To: johnz0983@capecod.net X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk == > * D E A D L I N E * is this Sunday! < == Start a proven home business within 72 hours using Microsoft's foolproof sales recipe for Internet success. Your exclusive report reveals how to get a *FREE* business building CD-ROM, TURN 50 cents into $50 with a click of a button, 5-page WebSite and *FREE* reprint and marketing rights to $1073.00 in software products! Don't miss the deadline! For your *FREE* report: Click Here: mailto:mnymkrs@21cn.com?subject=cd430T -OR- Send an email to mnymkrs@21cn.com with cd430T as the subject. P.S. Act NOW! -- Only the first 75 requests will be granted to receive this Special Report for *FREE*. Bonus report given to the first 35 people to respond within the next 24 Hours. Your FREE Report request will be fulfilled in the order in which it was received... Thank you. ====================================================== ====================================================== NOTE: You have received this email because you have either sent us your offer or requested information from us in the past thereby adding yourself on our in-house mailing list. We do not sell our list to anyone. ______________________________________________________ Simple Removal instructions: To be removed from our in-house list simply click below >> mailto:rtc99@21cn.com?subject=remove --- From owner-bio-software@hgmp.mrc.ac.uk Sat May 6 00:03:44 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A03C017A5B; Sat, 6 May 2000 00:03:43 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id AAA20878 for ; Sat, 6 May 2000 00:03:41 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id AAA17967 for bio-software-list@hgmp.mrc.ac.uk; Sat, 6 May 2000 00:03:40 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Haruna Cofer X-Newsgroups: bionet.software Subject: Re: Anyone: NCBI BLAST2 on >1 CPU on Solaris? Date: Fri, 05 May 2000 19:01:55 -0400 Organization: SGI Lines: 31 Message-ID: <391352E3.88C6BAD@detroit.sgi.com> References: <8er2lf$um8$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP26) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi Mike, In case you haven't gotten an answer already...to build the multiprocessor version of BLAST, you will need to modify the ncbi/make/makeall.unx file (line 410) by replacing -DNCBI_NOTHREADS_AVAIL with -D_POSIX_THREADS: ncbithrs.o: ncbithrs.c $(CC) -D_POSIX_THREADS $(CFLAGS) ncbithrs.c I have some web pages on building and running BLAST...they are written for SGI/IRIX systems, but you may still find them useful for running on SUN/Solaris systems. The porting notes are here: http://www.sgi.com/chembio/resources/blast/porting_notes_ncbi.html And the known problems and fixes are here: http://www.sgi.com/chembio/resources/blast/problems_and_fixes_ncbi.html Thanks, and good luck! -- Haruna :) -------------------------------------------------------------------- Haruna N. Cofer 614-855-5245 (tel) Applications - Chem/Bio 248-848-5653 (fax) SGI 800-859-1020 x4553 (v-mail) 715 Affirmed Court x6-265-4553 (internal) Columbus, OH 43230 haruna@sgi.com (e-mail) -------------------------------------------------------------------- From owner-bio-software@hgmp.mrc.ac.uk Sat May 6 00:06:23 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1FB1017A5B; Sat, 6 May 2000 00:06:22 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id AAA21117 for ; Sat, 6 May 2000 00:06:21 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id AAA17973 for bio-software-list@hgmp.mrc.ac.uk; Sat, 6 May 2000 00:06:20 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Haruna Cofer X-Newsgroups: bionet.software Subject: HT-BLAST 2.0.12 available for SGI/IRIX Date: Fri, 05 May 2000 19:04:38 -0400 Organization: SGI Lines: 28 Message-ID: <39135386.48FB788@detroit.sgi.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP26) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hello there! HT-BLAST based on the latest NCBI BLAST 2.0.12 is available for download from the following site, for SGI systems running IRIX 6.5: http://www.sgi.com/chembio/resources/blast/ht-blast.html HT-BLAST is a modification of the original NCBI BLAST program that has been optimized for use in high throughput sequence analysis, where multiple query sequences are being searched against possibly multiple databases. For more information about HT-BLAST, please see the following white paper, entitled "High-Throughput BLAST": http://www.sgi.com/chembio/resources/papers/HTBlast/HT_Whitepaper.html Thank you, and please do let me know if you have any questions or problems! -- Haruna :) -- -------------------------------------------------------------------- Haruna N. Cofer 614-855-5245 (tel) Applications - Chem/Bio 248-848-5653 (fax) SGI 800-859-1020 x4553 (v-mail) 715 Affirmed Court x6-265-4553 (internal) Columbus, OH 43230 haruna@sgi.com (e-mail) -------------------------------------------------------------------- From owner-bio-software@hgmp.mrc.ac.uk Sat May 6 07:50:23 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8053C17B1D; Sat, 6 May 2000 07:50:21 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id HAA08885 for ; Sat, 6 May 2000 07:50:18 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA23325 for bio-software-list@hgmp.mrc.ac.uk; Sat, 6 May 2000 07:50:16 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "NORMAN" X-Newsgroups: bionet.software Subject: lots of cad stuff with cracks at a very low price! Date: Fri, 5 May 2000 20:56:31 +0400 Organization: Omnitel, Lithuania Lines: 35 Message-ID: <8f0f2s$mdo$4@news.omnitel.net> Reply-To: "NORMAN" X-Trace: news.omnitel.net 957595548 22968 194.176.34.169 (6 May 2000 06:45:48 GMT) X-Complaints-To: news@omnitel.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk lots of cad stuff with cracks at a very low price! PRO/E 2000i 1999500 WITH HELP - 40$US AUTOCAD 2000 FULL VERSION - 40$US IMAGEWARE.SURFACER.V10.0 sw2000 POWERMILL 2510 CADsoft Design Apprentice v1.0 Catia 5R3 rise 2cd catia 5r3 sp5 Mathcad 2000 VISIO 2000 TECHNICAL EDITION (C) VISIO CORP BORLAND C++ BUILDER 5 ENTERPRISE EDITION BORLAND DELPHI 5 ENTERPRISE EDITION FLEXlm SDK v7.0c *Incl Keygen* METASTOCK 7 PRO/DESKTOP 2000i2 (C) PTC TURBOCAD DESIGNER 2D/3D V5.0 VERIBEST.DESIGN.VIEW.V2000 CIMARENDER PRO V7.0 XX/14 TURBOCAD DESIGNER 2D/3D V5.0 and other! LOW PRICES! NORMAN cdsimpl@mailcity.com cdsimpl@CRJOnLine.com cdsimpl@angelfire.com Fax: + 442076917580 (UK) ICQ: 59912397 ./ From owner-bio-software@hgmp.mrc.ac.uk Sun May 7 16:18:15 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2BCAC17A5E; Sun, 7 May 2000 16:18:14 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA20019 for ; Sun, 7 May 2000 16:18:13 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA24692 for bio-software-list@hgmp.mrc.ac.uk; Sun, 7 May 2000 16:18:11 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: d.vanhee@free.fr (Dominique Vanh=?ISO-8859-1?B?6Q==?=e) X-Newsgroups: bionet.software Subject: thermodynamic value Date: 7 May 2000 16:18:10 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 17 Message-ID: Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit X-Trace: niobium.hgmp.mrc.ac.uk 957712691 24689 193.62.192.80 (7 May 2000 15:18:11 GMT) X-Complaints-To: news@net.bio.net X-Received: from postfix2.free.fr (postfix@postfix2.free.fr [212.27.32.74]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA19991 for ; Sun, 7 May 2000 16:18:07 +0100 (BST) X-Received: from [213.228.38.246] (lille1-38-246.dial.proxad.net [213.228.38.246]) by postfix2.free.fr (Postfix) with ESMTP id C8A7874242 for ; Sun, 7 May 2000 17:18:05 +0200 (MEST) X-User-Agent: Microsoft Outlook Express Macintosh Edition - 5.0 (1513) X-To: X-MIME-Autoconverted: from quoted-printable to 8bit by hgmp.mrc.ac.uk id QAA19992 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hello I'm looking for the thermodynamic values needed for the Tm calculation of DNA (deltaG, deltaS, deltaH). I will be very debtfull to anyone that can post these informations (web site, or other). I want to notify that I have no access to the scientific litterature. Thanks by advance. -- Vanhée Dominique d.vanhee@free.fr http://d.vanhee.free.fr/accueil/accueil.html --- From owner-bio-software@hgmp.mrc.ac.uk Mon May 8 09:37:13 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9D47417A43; Mon, 8 May 2000 09:37:12 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA22822 for ; Mon, 8 May 2000 09:37:10 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA15202 for bio-software-list@hgmp.mrc.ac.uk; Mon, 8 May 2000 09:37:09 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Nicolas Le Novere X-Newsgroups: bionet.software Subject: Re: thermodynamic value Date: Mon, 08 May 2000 07:58:19 +0100 Organization: university of Cambridge Lines: 24 Message-ID: <3916658B.30F6AB2C@cus.cam.ac.uk> References: Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.2.13 i686) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Dominique Vanhée wrote: > I'm looking for the thermodynamic values needed for the Tm calculation of > DNA (deltaG, deltaS, deltaH). > I will be very debtfull to anyone that can post these informations (web > site, or other). > I want to notify that I have no access to the scientific litterature. All the published values are available together with the program MELTING (http://www.pasteur.fr/recherche/unites/neubiomol/meltinghome.html) The tables are located in the directory NNFILES of the distribution. However, since this program is available (including with a WWW interface (http://bioweb.pasteur.fr/seqanal/interfaces/melting.html) you don't need to compute everything yourself ;-) -- Dr Nicolas Le Novère e-mail: nl223@cus.cam.ac.uk Dpt Zoology, Univ Cambridge, Downing street, Cambridge CB2 3EJ, UK http://www.pasteur.fr/recherche/unites/neubiomol/ tel: +44 1223 336623 fax: +44 1223 336676 From owner-bio-software@hgmp.mrc.ac.uk Mon May 8 10:57:00 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1543E17A43; Mon, 8 May 2000 10:56:58 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA29697 for ; Mon, 8 May 2000 10:56:54 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA16158 for bio-software-list@hgmp.mrc.ac.uk; Mon, 8 May 2000 10:56:53 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: cmerendi@agra.it ("Concilio Luigi") X-Newsgroups: bionet.software Subject: Primer design softwares from sequence alignments Date: 8 May 2000 10:56:52 +0100 Organization: =?iso-8859-1?Q?Agra_Societ=E0_del_Seme?= Lines: 51 Message-ID: <001601bfb8d3$d9fd4e50$3c04a8c0@nettuno.it> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0013_01BFB8E4.9B392110" X-Trace: niobium.hgmp.mrc.ac.uk 957779813 16156 193.62.192.80 (8 May 2000 09:56:53 GMT) X-Complaints-To: news@net.bio.net X-Received: from bologna.nettuno.it ([193.43.2.1]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA29678 for ; Mon, 8 May 2000 10:56:49 +0100 (BST) X-Received: from biotec (ppp30-nas0.lugo.nettuno.it [193.207.49.223]) by bologna.nettuno.it (8.9.3/8.9.3/NETTuno 4.1) with SMTP id LAA02144 for ; Mon, 8 May 2000 11:56:13 +0200 (MDT) X-To: X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk This is a multi-part message in MIME format. ------=_NextPart_000_0013_01BFB8E4.9B392110 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello netters,=20 Does anyone know of a primer design/analysis program that starts from = more then one protein/DNA sequence. I'm thinking of a software able to = performe alignments and primer design for PCR on most conserved regions. I already tested CODEHOP and GENEFISHER. Is there something better or different in the net? Merendi Claudio Eridania Beghin-Say ------=_NextPart_000_0013_01BFB8E4.9B392110 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello netters,

Does anyone know of a primer design/analysis program that starts from = more=20 then one protein/DNA sequence. I'm thinking of a software able to = performe=20 alignments and primer design for PCR on most conserved regions.
I = already=20 tested CODEHOP and GENEFISHER.

Is there something better or different in the net?

Merendi Claudio
Eridania=20 Beghin-Say

------=_NextPart_000_0013_01BFB8E4.9B392110-- --- From owner-bio-software@hgmp.mrc.ac.uk Mon May 8 17:00:43 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8CC4C17AC1; Mon, 8 May 2000 17:00:40 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA08149 for ; Mon, 8 May 2000 17:00:37 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA20639 for bio-software-list@hgmp.mrc.ac.uk; Mon, 8 May 2000 17:00:36 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Jean-Jack M. Riethoven" X-Newsgroups: bionet.software,bionet.software.www Subject: Bioinformatics symposium Date: 8 May 2000 17:00:35 +0100 Organization: European Bioinformatics Institute Lines: 58 Message-ID: X-Trace: niobium.hgmp.mrc.ac.uk 957801636 20637 193.62.192.80 (8 May 2000 16:00:36 GMT) X-Complaints-To: news@net.bio.net X-Newsreader: MicroPlanet Gravity v2.20 X-Auth: PGPMoose V1.1 PGP bionet.software.www iQCVAwUAORbkoqCIqsWvyF5FAQGriwP+KiJ4olVdw8iz4qWsHRKs+K+uvYMcepOE UWmJwFOboDS/hJgPQaQOlzMBUNu9syEH+jnUX13cp6HZZXU/3k8FEzob3RDVmKno xSXAgCRDiGMQhntU67D9moJFFi/M8I1PIAWIv6jDL16JfyMcNp3Jy6zeJbx1RPZd +lfzOLhH4g8= =k3Bw To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk EMBL-EBI SYMPOSIUM Genome Based Gene Structure Determination 1-2 June 2000 LAST Call for registration and poster abstracts. Registration deadline: 20 May 2000 Details : http://industry.ebi.ac.uk/gp2000/ Contact : genepred2000@ebi.ac.uk The symposium focuses on the latest developments in the area of annotation of genes in large genomes. Topics covered are (i) genome based methodologies of identifying genes and other gene structural elements; (ii) first-hand experiences from annotating large genomes; and (iii) bioinformatics aspects of large-scale genome annotation pipelines. Abstracts for poster presentation covering any of the above issues are invited. The journal Briefings in Bioinformatics (http://www.henrystewart.com/journals/BiB/) acts as the supporting publication for the symposium. The proceedings of the symposium will be covered in a special issue in this journal. The invited speakers include Michael Ashburner (European Bioinformatics Institute, England) Ewan Birney (European Bioinformatics Institute, England) Richard Durbin (Sanger Centre, England) Mikhail Gelfand (Centre for Biotechnology, Russia) Roderic Guigo (Institut Municipal de Investigacio Medica, Spain) Tim Hubbard (Sanger Centre, England) Anders Krogh (Center for Biological Sequence Analysis, Denmark) Suzanna Lewis (Berkeley Drosophila Genome Project, USA) Klaus F.X. Mayer (MIPS, Germany) Webb Miller (Pennsylvania State University, USA) Edward C Uberbacher (Oak Ridge National Laboratory, USA) Thomas Werner (GSF, Germany) Michael Q Zhang (Cold Spring Harbor Laboratory, USA) See our website http://industry.ebi.ac.uk/gp2000/ for detailed information regarding the agenda and logistics. With kind regards, -- drs. Jean-Jack M. Riethoven EMBL Outstation - Hinxton pow@ebi.ac.uk ICQ#: 3433929 European Bioinformatics Institute Phone: (+44) 1223 494635 Wellcome Trust Genome Campus Fax : (+44) 1223 494468 Hinxton, Cambridge CB10 1SD URL : http://industry.ebi.ac.uk/ UNITED KINGDOM From owner-bio-software@hgmp.mrc.ac.uk Mon May 8 17:32:43 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A107717AD5; Mon, 8 May 2000 17:32:40 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA11888 for ; Mon, 8 May 2000 17:32:37 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA21064 for bio-software-list@hgmp.mrc.ac.uk; Mon, 8 May 2000 17:32:35 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: dfhk@ms55.url.com.tw X-Newsgroups: bionet.software Subject: [Àb«È·s»D]--Apacheºô¯¸³QÀb«È¤J«I ´«±¼­º­¶ Date: 8 May 2000 16:32:22 GMT Organization: DFHK Lines: 229 Message-ID: <8f6q6m$jj0@netnews.hinet.net> To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk sorry......¥´ÂZ¤F!! ==================================================================== ***½Ð»{©ú¥¿©v¨¾¤îÀb«È'dfhk'(dfhk@ms55.url.com.tw)¥¿©vdfhk¥X«~«e³£¸g¹L5ºØ¼tµP¥úºÐ¾÷´ú¸Õ¹L½T«O«~½è!! ¤£­n¶R¿ù¤F!!¦³°ÝÃDªº¤ù¤l100%¥]´«!!·PÁ¤j®aªº¤ä«ù!! ========================================================= [Àb«È·s»D] Apacheºô¯¸³QÀb«È¤J«I ´«±¼­º­¶ Monday, May 8 2000 Àb«È¤£ªk¤J«IApacheºô¯¸ªº¦øªA¾¹¡A±Nºô¯¸­º­¶´«±¼¡A¨Ã¸Ë¤WApache¹ï¤â·L³n¤½¥q¤@­Ó³nÅé²£«~ªº°²¼s§i¡A ³o­Ó¨Æ¥óÅýApache«Ü¥áÁy¡C Apache³nÅé°òª÷·|ªº¸³¨Æ·|¤@­ûRasmus Lerdorf«ü¥X¡AÀb«Èªº°Ê§@Áٺ⦳©Ò«O¯d¡A¥u¦b­º­¶ªº¤U¤è±¾¤W³o­Ó·L³nªº °²¼s§i¡A¨ä¹êºô¯¸ªº¦øªA¾¹¤w¸g§¹¥þ³QÀb«È±±¨î¡A¥L­Ì¥i¥H§â¾ã­Óºô­¶´c·d¤@°}¡A©ñ¤@­Ó·L³nªº°Ó¼Ð¦bºô­¶¤W¡C ¥Ñ©ó³o¨ÇÀb«ÈÁÙ±N¤J«Iªº¤èªk¤]§i¶D¤FApache¡A©Ò¥H LerdorfºÙ³o¨Ç¤H¬°¡u¥Õ´U¤lÀb«È¡v (white hats)¡A¥H«K©M´c·N ¯}Ãaªº¶Â´U¤lÀb«È°Ï§O¡C¥Õ´U¤lÀb«È±Mªù§äºô¯¸ªºº|¬}¡A¬°¥ø·~«üÂI°g¬z¡C Apache³nÅé±M¨Ñ¦øªA¾¹¨Ï¥Î¡A­t³d¶Ç¿éºô­¶¤º®e¡Q¦³60%ªººô¸ô¦øªA¾¹¨Ï¥Î³oºØ³nÅé¡A¨ä¦¸¬O·L³nªºInternet Information Server¡A ¨Ï¥Î²v¹F21%¡CApache©MLinux¤@¼Ë¡A¬O¥H¶}©ñµ{¦¡½X¤è¦¡©Ò¶}µo¥X¨Óªº³nÅé¡AIBM»Pª@¶§¤½¥q¤j¤O°Ñ¤©Apacheªº¶}µo¡Q¦³¶V¨Ó¶V¦h ¤j¥ø·~³ßÅw¨Ï¥Î¶}©ñµ{¦¡½Xªº³nÅé¡AÅý«Ü¦hµ{¦¡³]­p®v°Ñ¤©¶}µo¤u§@¡C Lerdorfªí¥Ü¡AApache­±Á{ªº°ÝÃD¡A´N¬O¤Ó¦h¤H¦w¸Ë¡A¦Ó¥B¸Ë¤F«Ü¦hºØ¦b¦øªA¾¹¤W¡A¤j®a¤S¯Ê¥F¬Û¤¬·¾³q¡CApache±Ä¨úÀ³Åܤèªk¡A ±NÀb«È¶i¤Jªº¨â­Ó¦³°ÝÃDªººÞ¹DÃö³¬¡A¨Ã±N±ÂÅvªÌÄY®æ±±ºÞ¡A´î¤Ö¶i¤J¤H¼Æ¡Q¥¼¨ÓApacheªº¤u§@±N¥Ñ¼Æ­Ó¦øªA¾¹¤À¤u¡A´£°ª«O¥þ©Ê¡C Lerdorf«ü¥X¡AÀb«È¦bºô¯¸¤W¤½§G¶i¤JApacheªº¹Lµ{¡A¬O³z¹LBugzilla³o­Ó§ì¿ùµ{¦¡¶i¤J¡A©Ò¥H²{¦bApache¤w¸g±N BugzillaÃö³¬ ¡CLerdorf¹ï©óÀb«È¤â¤U¯d±¡·P¨ìªY¼¢¡A¥H«á±N§ó¥[¤p¤ßªº¨ÓºÞ¨îºô¯¸«O¥þ¡C ======================================================================================================== ±Ð±z¦p¦ó¦bºô¸ô¤¤¦Û«Oªº¥úºÐ ¾ã¤ù¥úºÐ ¥u­n400¤¸ §Aª¾¹D¦b§A¤Wºôªº³~¤¤ ¦³¤H¥i¥HµLÁnµL®§ªº¶i¤J©pªº¹q¸£ ÅѨú§A©Ò¦³ªºÁô¨p ¶i¦Ó³y¦¨©pªº²ö¤j·l¥¢¶Ü ¤£­n»{¬°¤£¥i¯à ¦]¬°·í§Þ³N§e²{¦b§A²´«e®É «OÃÒ§A·|¤j¦Y¤@Åå ¦]¬°¤@ª½¥H¨Ó ´N¬O¦³¤H³o¼Ë°µ ±q¤¤Àò±o¤F¤£ªkªº§Q¯q ¥¿©Ò¿× ª¾¤vª¾©¼ ¦Ê¾Ô¦Ê³Ó ¤µ¤Ñ §Ú§â³o¨Ç§Þ³N §Ë¦¨°ê¤º²Ä¤@¤ù¦¬¶°§¹¾ãªºÀb«È¥úºÐ,¤£¦ý±Ð§A«ç»ò¥h¯}¸Ñ, §ó±Ð§A¦p¦ó¥h¨¾½d©ó¥¼µM,³Ì­«­nªº¬O:¥¦¬O¤@¤ù§¹¾ãªº¤¤¤å¤¶­±,¤¤¤å»¡©ú®Ñ, °£«D±z³s¬Ý¦rªº¯à¤O³£¦³§xÃø, §_«h§A¤@©wª¾¹D§Ú¦b»¡¤°»ò!! ¦³¤H°Î¦W¬µ§Aªº«H½c,§A¥iª¾¹D¦p¦ó¨¾ªv¤Î³ø´_??(¥]¬A¬µ§AE-mail³£ºâ¬OÀb«È!) §A¶}ºô¸ô©@°Ø©±,¥iª¾¹DÀb«È³Ì³ßÅwªº´N¬O¤W§Aªº¯¸¥h¸Õ¥\¤O?§A¥iª¾¨äµM¦Ó¨¾¨äµM? §A¥i´¿·Q¹L,§A¥u¬O¤@­Ó¤Wºô¸ôªº¥­¤Z¤H,¥iª¾¹DÀb«È¤]¥i¥h§â§A¤Wºôªº±K½X¤Î¦WºÙ ¨ú¦^¦Û¤v¥Î,Åý§Aªá¿ú¤S·í¤jÀY?¤£¥u¦p¦¹,¥L¤]¥iª½¨ú§A¹q¸£¤ºªº¸ê®Æ,¥]¬A±þÀÉ®× ¤ÎÅý§A·í¾÷?§Aª¾¹D­ì²z,«ç»ò°µ?¦Ó¤S¦p¦ó¨¾¤î©O? §A¦³¥ÎICQªº"¦n"²ßºD¶Ü?¥iª¾ICQ¦w¥þ©Ê¬Æ®tªº²{¦b,§AªºICQ¬OÀb«È³Ì¤jªº·Å§É?¤@ ¼Ë¥i³z¹LICQ¥h°µ¤J«I¤ÎºÞ²zªº°Ê§@,´N¬O§â§AµwºÐ·í¦¨¬O¦Û¤v®a¤@¼Ë,·R®³¤°»ò´N ®³¤°»ò,·íµM¤]¬O¥]¬A§Aªº±K½X¤Î¦WºÙ..... ¦pªG§A¤£´¿Å¥¹L³o¨Ç¨Æ,¨º§A´N¬O³Ì¤jªº°ª¦MÀI¸s,§A¥iª¾¹D¦p¦ó¥h¤F¸Ñ³oºô¸ôªº¶Â ·t­±? ---------------------------------------------------------------------------- 400¤¸©Î³\¥u¬O¤@¹yÀë¥ú±ßÀ\ªº¥N»ù¡A¤]¥i¯à¬O§A¸òªB¤Í¥hKTYªº°ò¥»®ø¶O ¦ý¬O²{¦b«o¯à¶R¨ì§AªºÅv¯q¤Î¤@½ú¤lªº§Þ³N¡A§A¦ó¼Ö¤£¬°©O¡H§Ú¤]¸ò±z°µ «Oµý¡A§A²{¦b¦b¸É¬É¤¤¤]µ´¹ï¬Ý¤£¨ì³o¤@¤ù¥úºÐ¡A¦]¬°¬OÀb«È¦Û¤vªº¦¬Âà ¡A³o¬O²Ä¤@¦¸¬y¥X¥«­±¡A¤é«á©Î³\·|¦³¸É¬É¦¬¿ý¥h½æ¡A¦ý¬O±z¦pªG¤é«á¦A ¥h¶R¡A¸É¬Éª¾¹D³o¤ù¥úºÐªº§Q®`Ãö«Y¡A¤]¸Ó¤£·|§¹¾ã¦¬¿ý¡A·d¤£¦nÁÙ©ñ¤F ¡¨¯S¬¥¥ì¡¨µ{¦¡¶i¥h(Å¥¤£À´¡H´N§â¤@¤ä¤ì°¨µ{¦¡Âæb¨ä¥¦µ{¦¡¤¤AUTORUN ¤]¦æ¡A¥H«á¥u­n§A¤@¤Wºô´Nµ¥©ó§â¦Û¤v°eµ¹¤H®a¡A³Q¹ï¤èµs¥Î±K½X¤Wºô³£ ¤£ª¾¹D......)±z¦Ò¼{¦Ò¼{§a! ¥úºÐ¤º®e============================================================== [·í¾Ô¤õµ²§ô,«°¤¤¤H¥Á¿³°ªªö¯Pªºªï±µ«°¥~ªº¤ì°¨,ÁöµMÁ`¦³¤Ö¼Æªº¤Ï¹ï ,] [«oÁÙ¬OµLªkªý¤î³Q"³Ó§Q"¨R©üÀYªº¤H­Ì,¦b¤@¤ùÅw¼Öªº®ð®§¤¤,¤H­Ì°s«á¶º] [¹¡¤§»Ú,¤ì°¨²×©óÅS¥X³g°ýªº¥»©Ê,±q¤ì°¨¸¡¤¤¥X²{ªº¼Ä¤èºë­^ ,¤@Á|¸ÌÀ³] [¥~¦X,.....±O«°!......] ³o´N¬O¯S¬¥¥ìªº¬G¨Æ,[¤ì°¨±O«°°O]...... ºô¸ô¤W¦s¦bµÛ³\¦hªºÀb«È,¦³©Ò¿×ªº³nÅéÀb«È,¤]¦³¤J«IÀb«È. ¦h¥b¬O¦sµÛ¦nª±ªº¤ßºA,¦ý¬O¤]¦s¦bµÛ¦³¤ß¤H¤h........ ¦]¬°·í§Aª¾¹D¯}¸Ñªº¥Î³~¨ì©³¦³¨º¨Ç¤§«á,§A·|¤£¸T¤ß´H.. §A¥i¯à·|¦Û°Ý:§Ú¬O¤U¤@­Ó¶Ü?ÁÙ¬O¤w¸g³Q¤J«I¦Ó¤£¦Ûª¾..... 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ICQÀb«È°Ï======== ¯}¸Ñ,¬Æ¦Ü¤J«IICQªºµ{¦¡¸s....,¬Ý§¹¦¹³¹±z´N·|¹ïICQªº¦w¥þ©Ê§¹¥þ¤ß§N... ³Ì·sª©¥» ICQ ¯}¸Ñ ICQ ±K½X «OÅ@¦Û¤vªºICQ¤£³QÀb«È¤J«Iªºµ{¦¡¸s ±H ICQ °Î¦W«H©Î¬O ¬µICQ ªºµ{¦¡ Å㦡¥X¹ï¤èªº IP ª¾¹D¹ï¤èICQ ©Ò¥Îªº Port ¬O¦h¤Ö=>³Qª¾¹DIP¤ÎPort´N¥i¥H°µ«Ü¦hÃa¨Æ¤F Åý§A¿ï¾Ü±H¤@©ÎN«Êªº°T®§µ¹¹ï¤è §A¥[¤J¥ô¦ó¤Hªº UIN¡A¦Ó¤£¥²¸g¹L¹ï¤è»{ÃÒ¡A ¥Î©óICQ¤¤²á¤Ñ (chat) ªº·o³Jµ{¦¡ ¥i¥HÅý§A½s¿è¹ï¸Ü°O¿ý ¥i¥HÅý§A§âICQ¥ô·N²¾°Ê¥Ø¿ý ¥i¥HÅý§A§âICQ³Æ¥÷ ¥i¥HÅý§A½Æ»sICQ ICQ ¯S¬¥¥ìµ{¦¡=>¦¹µ{¦¡ªº¥\¯à´N¬O¥i¥H¤J«I¹ï¤èªºµwºÐ¡A¨ú§A±K½X¤ÎÅý§A·í¾÷!! ¥i¥H±NICQ¬ÛÃö¤u¨ã¾ã¦X¦b¤@°_ªºµ{¦¡ ¡i¦p¦ó¦b ICQ ÁôÂçAªºIP¡j.... ¯}¸Ñ±K½X°Ï======= ´X¥G¬OµL©Ò¤£¯}³á...... ¸Ñ BIOS ªº±K½X AWARD BIOS ªº³q¸Ñ±K½X AMI BIOS ªº³q¸Ñ±K½X ¯}¸Ñ¼·¸¹ºô¸ô±K½Xµ{¦¡Ãþ ¿Ã¹õ«OÅ@µ{¦¡±K½X¯}¸Ñµ{¦¡ ¬Ý***±K½Xªºµ{¦¡ ¼É¤Oªk¯}¸Ñ±K½X¤u¨ã ¯}¸Ñºô­¶±K½Xµ{¦¡ ¯}¸Ñ Word97 ±K½Xµ{¦¡ ¯}¸Ñ Excel97 ±K½Xµ{¦¡ ¯}¸Ñ ARJ ¥[±K¦¡ ·s¶iÀÉ®×°Ï========== ¯}¸Ñºô­¶±K½Xµ{¦¡=>±¡¦âºô¯¸±M¥Î «Ü±jªº¯S¸¨¨Ìµ{¦¡=>»´ÃP¤J«I¡A¥i°µ©Ò¦³ªº°Ê§@¡A¥]¬A¨ú§A±K½X¤Î·í¾÷! ¬Ý±K½Xµ{¦¡ BOµ{¦¡µÛ¦Wªº¤J«Iµ{¦¡ ²¾°£BOªºµ{¦¡ °»´ú¨Ï¥Î¢Ð¢Ý¤J«IªÌªºµ{¦¡ ¨¾Å@(BO)ªºµ{¦¡ -¡@¡@ ­«­nªºÀÉ®×========= ¥²³Æªº¤@¨ÇÀÉ®× ¯}¸Ñ¤å¥óÀÉ======= ¤J«I¤å³¹ ¯}¸Ñ¤Jªù ¦p¦ó¤J«I¤@¥xInternetªº¥D¾÷=>¸ÑŪ±K½X,¤J«Iºô¸ô©@°ØÆU..... ¦p¦ó¦p¦ó°lÂܤJ«IªÌ ºô¸ôº|¬}=>´£¨Ñ§A¦Û¤v¦Û«Oªºªº¤èªk!! ¤J«I¤å³¹ ¦p¦ó¦¨¬°¤@­Ó hackek ¶l¥óÀb«È°Ï============ ¦¹°Ï´£¨Ñ¯}¸Ñ¤Î¤Ï¯}¸Ñ,«Ü¹ê¥Îªº³é.... °Î¦W¶l¥óµ{¦¡ ¶l¥ó¬µ¼uµ{¦¡ ¶l¥ó¬µ¼u«g¬P ¹q¤l¶l¥ó¬µ¼u ¹q¤l¬µ¼u ¹q¤l¶l¥ó¬µ¼u µøµ¡¬µ¼uªº´c§@¼@ OOB ·í¾÷µ{¦¡======== ¥ÎOB¤J«IÅý§A·í¾÷,¤]´£¨Ñ¤ÏOBªºµ{¦¡..... ¨¾·íµ{¦¡ ¤Ï¦w¸Ë¨¾·í ·í¾÷µ{¦¡¨¸¯« «Ü¦h·í¾÷µ{¦¡¡A Àb«Èºô¯¸¤j³sµ²============ ¯¸¯¸¬O¦n¯¸.... ¤¤¤åÀb«Èºô ­^¤åÀb«Èºô §Ç¸¹-µù¥U½X°Ï ¡@ ³Ì«á ½Ðª`·N ¦p§A¦³·NÁʶR ½Ðªþ¤W ©m¦W ¹q¸Ü ¦í§} ¶l»¼°Ï¸¹ §Ú·|¥Î¥N¦¬³f´Úªº¤è¦¡ ¥u­n§A·Ç³Æ¦L³¹¤Î400¤¸µ¹¶l®t ©p(§A)´N¯à¾Ö¦³ ½Ð¦^«H¦Ü dfhk@ms55.url.com.tw From owner-bio-software@hgmp.mrc.ac.uk Mon May 8 19:55:37 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3F9BF17AD8; Mon, 8 May 2000 19:55:37 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA27597 for ; Mon, 8 May 2000 19:55:35 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA22820 for bio-software-list@hgmp.mrc.ac.uk; Mon, 8 May 2000 19:55:34 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: mathog@seqaxp.bio.caltech.edu (David Mathog) X-Newsgroups: bionet.software Subject: ncbi toolbox on Linux, build problems concerning blast.REAL Date: 8 May 2000 18:52:21 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 28 Message-ID: <8f72d5$21l@gap.cco.caltech.edu> Reply-To: mathog@seqaxp.bio.caltech.edu To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk I'm trying to build the current NCBI toolbox on Linux/Alpha using the Compaq C compiler. I removed (or thought so) all relevant sections from linux.ncbi.mk and makedis.csh. But when makedis.csh runs it chokes on blast.REAL, which seems to require some bits of vibrant. In makenet.unx it says: blast.REAL: wwwblast.o salogif.o $(THREAD_OBJ) $(CC) $(LDFLAGS) wwwblast.o salogif.o $(THREAD_OBJ) -o blast.REAL -lvibgif $(LIB20) $(LIB23) $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS) but vibgif doesn't get built without vibrant, and LIB20 is libncbidesk.a, which won't be built without vibrant either. The reason it's trying to build blast.REAL is because the no motif branch within makedis.csh has: set ALL_VIB=() set DEMO_VIB=() set NET_VIB=(VIB=\"blastcl3 blast.REAL\") So what is "blast.REAL"? Can it really be built without vibrant or no? Thanks, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-bio-software@hgmp.mrc.ac.uk Tue May 9 10:49:40 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9AD7717A80; Tue, 9 May 2000 10:49:39 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA06712 for ; Tue, 9 May 2000 10:49:37 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA12440 for bio-software-list@hgmp.mrc.ac.uk; Tue, 9 May 2000 10:49:36 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Nicolas Le Novere X-Newsgroups: bionet.software Subject: true multiple alignments Date: Tue, 09 May 2000 09:10:43 +0100 Organization: university of Cambridge Lines: 25 Message-ID: <3917C803.DEDDCECC@cus.cam.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.2.13 i686) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hello, I am looking for programs able to truly align N sequences (backtracing in the N dimentionnal space, not based on pairwise alignments and "once a gap, always a gap" approach). I tried MSA, but several things are disturbing me: - limits are macro (no dynamic meme alloc) - only one matrix is provided (guess which one: PAM250), and it is hard coded. - It is VERY slow (yes, I know such a process is inherently slow) Is anybody aware of something more recent and fixing the points above? On the same idea, where could I find a program using blast approach to make multiple alignments? Thanks, -- Dr Nicolas Le Novère e-mail: nl223@cus.cam.ac.uk Dpt Zoology, Univ Cambridge, Downing street, Cambridge CB2 3EJ, UK http://www.pasteur.fr/recherche/unites/neubiomol/ tel: +44 1223 336623 fax: +44 1223 336676 From owner-bio-software@hgmp.mrc.ac.uk Tue May 9 15:15:28 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id F38CA17B2B; Tue, 9 May 2000 15:15:26 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA03734 for ; Tue, 9 May 2000 15:15:25 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA15762 for bio-software-list@hgmp.mrc.ac.uk; Tue, 9 May 2000 15:15:20 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: Petr Kuzmic X-Newsgroups: bionet.software Subject: [ANN] Freeware for biochemical kinetics and equilibria Date: Tue, 09 May 2000 09:16:56 -0500 Organization: BioKin Ltd. [http://www.biokin.com] Lines: 108 Message-ID: <39181DD8.57213B3D@biokin.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.chorus.net 957881666 20515 216.165.150.162 (9 May 2000 14:14:26 GMT) X-Complaints-To: abuse@chorus.net X-Mailer: Mozilla 4.72 [en] (WinNT; U) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk ___________________________________________________________ [Volume 4] B i o K i n N E W S [Number 1] May, 2000 ----------------------------------------------------------- Editor: Petr Kuzmic, Ph.D. Contents -------- 1. DynaFit version upgrade 2. Purpose of program DynaFit 3. Symbolic notation 4. Revised documentation 5. Bibliography 6. Download DynaFit 1. DynaFit version upgrade -------------------------- The freeware program DynaFit [P. Kuzmic (1996) Anal. Biochem. 237, 260-173] has been updated to version 3.21 and is now available for download from the BioKin website. 2. Purpose of program DynaFit ----------------------------- DynaFit is used for the simulation or statistical analysis (nonlinear least-squares regression) of chemical, biochemical, and biological data. Three types of data can be analyzed: (1) reaction progress in dependence on time, (2) initial reaction velocity in dependence on concentrations, and (3) composition at equilibrium in dependence on concentrations. 3. Symbolic Notation -------------------- The main advantage of program DynaFit is that the investigator may describe the chemical or biochemical system in terms of symbolic, stoichiometric equations. The program derives the underlying mathematical model automatically. For example, interaction of a "slow, tight" inhibitor of a dimeric enzyme (HIV protease) is described as follows: [mechanism] Monomer + Monomer <==> Enzyme : k1 k2 Enzyme + Substrate <==> ReactiveX : k3 k4 ReactiveX --> Enzyme + Product : k5 Enzyme + Inhibitor <==> Complex : k6 k7 The names of rate constants (k1, k3, ...) and reacting species ('Monomer', 'Enzyme', ...) are arbitrary. 4. Revised documentation ------------------------ The long awaited DynaFit "Scripting Manual" is now available in the Adobe PDF format. It is a 130-page document with indexes and illustrations, explaining in a systematic fashion the syntax of DynaFit script files. Also added to the website is a short visual "Getting Started" tutorial, showing the analysis of a representative data set screen-by-screen. * Links: http://www.biokin.com/dynafit/scripting/ http://www.biokin.com/dynafit/quickstart/ 5. Bibliography --------------- The hyperlinks below take you to several recent journal publications in which DynaFit has been cited. * "Microcomputer Applications in Biochemistry" Tsai S. (2000) J. Chem. Edu. 77(2), 219. http://jchemed.chem.wisc.edu/Journal/Issues/2000/feb/abs219.html * "GroEL/GroES promote dissociation/reassociation cycles of a heterodimeric intermediate during alpha(2)beta(2) protein assembly. Iterative annealing at the quaternary structure level" Wynn R.M. et al. (2000) J. Biol. Chem. 275(4), 2786. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10644743&dopt=Abstract * "Hydrophilic residues at the apical domain of GroEL contribute to GroES binding but attenuate polypeptide binding." Motojima F. et al. (2000) Biochem. Biophys. Res. Commun. 267(3),842. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10673379&dopt=Abstract * "Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator." Katz B.A. et al. (2000) Chem. Biol. 7(4), 299. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10779411&dopt=Abstract 6. Download DynaFit ----------------------- Download DynaFit 3.21 for Windows95/98/NT or for Macintosh from http://www.biokin.com/dynafit/. ___________________________________________________________ BioKin, Ltd. * Consulting & Software P.O. Box 8336 * Madison, WI 53708 (608) 256-4790 * (608) 256-1269 FAX info@biokin.com * http://www.biokin.com From owner-bio-software@hgmp.mrc.ac.uk Tue May 9 15:40:45 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0684B17B17; Tue, 9 May 2000 15:40:44 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA07274 for ; Tue, 9 May 2000 15:40:37 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA16174 for bio-software-list@hgmp.mrc.ac.uk; Tue, 9 May 2000 15:40:35 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: nospam@nospam.net X-Newsgroups: bionet.software Subject: How to access HG sequence data? Date: Tue, 09 May 2000 10:41:38 -0400 Organization: Ohio State University Lines: 12 Message-ID: <391823A2.12907408@nospam.net> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: charm.magnus.acs.ohio-state.edu 957883228 24752 140.254.128.20 (9 May 2000 14:40:28 GMT) X-Complaints-To: abuse@osu.edu X-Mailer: Mozilla 4.7 [en] (WinNT; U) X-Accept-Language: en To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Bac sequence is coming out for specific regions in drips and draps with no discernible structure in place for readily identifying sequence from regions of interest. Can anyone give advise on the best way of collecting new sequence information from specific chromosome locations? Presumably, the best way of identifying the sequence is by Blast searching with available marker sequence, but this seems to be time consuming and tedious. Are there available tools for automating this? Thanks, Mike Holloway mike_holloway@hotmail.com From owner-bio-software@hgmp.mrc.ac.uk Wed May 10 09:31:12 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 60DA517A56; Wed, 10 May 2000 09:31:12 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA05049 for ; Wed, 10 May 2000 09:31:10 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA07574 for bio-software-list@hgmp.mrc.ac.uk; Wed, 10 May 2000 09:31:09 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: nospam@our.site X-Newsgroups: bionet.software Subject: Re: How to access HG sequence data? Date: Wed, 10 May 2000 09:22:22 +0100 Organization: Imperial Cancer Research Fund Lines: 28 Message-ID: <8fb676$eha$2@icrf.news> References: <391823A2.12907408@nospam.net> Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk This message has been posted by: m.mitchell@REMOVE-THIS-TO-SENDicrf.icnet.uk (Mike Mitchell) In article <391823A2.12907408@nospam.net>, nospam@nospam.net wrote: > Bac sequence is coming out for specific regions in drips and draps with > no discernible structure in place for readily identifying sequence from > regions of interest. Can anyone give advise on the best way of > collecting new sequence information from specific chromosome locations? > Presumably, the best way of identifying the sequence is by Blast > searching with available marker sequence, but this seems to be time > consuming and tedious. Are there available tools for automating this? I would try going to source, ie the labs that are sequencing the specific chromosomes of interest, and the NCBI has a sequencing progress page: http://www.ncbi.nlm.nih.gov/genome/seq/page.cgi?F=HsProgress.shtml&&ORG=Hs and for more general stuff about sequencing: http://www.ncbi.nlm.nih.gov/genome/seq/page.cgi?F=HsHome.html&ORG=Hs We have a list of the labs sequencing the chromosomes: http://www.cgal.icnet.uk/humchr.html -- Michael Mitchell "Smoke me a kipper, User Support I'll be back for breakfast." Molecular Biology Software Ace Rimmer, Test Pilot +44 (0)171 269 3115 BBC-TV Red Dwarf ENFJ From owner-bio-software@hgmp.mrc.ac.uk Wed May 10 16:30:20 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1CD3D17AC7; Wed, 10 May 2000 16:30:18 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA20259 for ; Wed, 10 May 2000 16:30:12 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA12915 for bio-software-list@hgmp.mrc.ac.uk; Wed, 10 May 2000 16:30:10 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: mcginnis@alta.nlm.nih.gov (Scott McGinnis) X-Newsgroups: bionet.software Subject: NCBI BLAST: blastannouce mail list Date: 10 May 2000 14:46:54 GMT Organization: National Library of Medicine Lines: 59 Message-ID: <8fbsou$5ni$1@lhc.nlm.nih.gov> X-Trace: lhc.nlm.nih.gov 957970014 5874 130.14.25.164 (10 May 2000 14:46:54 GMT) X-Complaints-To: usenet@lhc.nlm.nih.gov X-Newsreader: TIN [version 1.2 PL2] To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk This is a one-time message to announce a mailing list for BLAST news. This list is intended for distribution of short messages announcing updates and new features and to give advance notices about upcoming changes in the NCBI BLAST service. All postings to this list will come from the NCBI BLAST Help desk. If you want to subscribe to this list please send a message with your name and e-mail address to . If you do not respond you will NOT be added to the list. Please forward this message to anyone interested in receiving BLAST News. NCBI BLAST Help Desk. Below is an example of news that are supposed to be sent to this list. ---------------------------------------------------------------- *** May 01, 2000. Taxonomy BLAST Tax BLAST is a new service which groups BLAST hits by source organism, according to information in NCBI's Taxonomy database. The Tax BLAST reports are generated based on the list of source organisms found in a particular BLAST hitlist, and can be found from the "Taxonomy reports" link in the regular BLAST output page. The Organism Report groups the BLAST hits according to the source organism of the target sequences - all of the BLAST hits are shown. The Lineage Report shows a simplified view of how closely each of the source organisms in the BLAST hitlist are related to the species that showed the closest sequence similarity to the query - only the best hit from each species is shown. The Taxonomy Report summarizes everything that the NCBI Taxonomy database has to say about the relationships between the source organisms in the BLAST hitlist - none of the BLAST hits are shown in this report. There is additional help available in the Taxonomy-BLAST Help web page: http://www.ncbi.nlm.nih.gov/blast/taxblasthelp.html *** May 01, 2000. Multiple hyperlinks for redundant sequences. When searching the non-redundant protein databases, BLAST results now show all the corresponding gi numbers for each alignment. This includes all the redundant matches for the alignment with links to their full database records. This will make it easier to identify all the protein sequences in the databases which match a particular query even if there are many representatives. *** April 30, 2000. Compatibility BLAST pages. The previous version of the BLAST webpages, as it existed on 04/30/00 will remain available till 06/30/2000 at the http://www.ncbi.nlm.nih.gov/blast/blast.prev.cgi The NCBI BLAST software group intends to move previous versions of BLAST pages to this URL every time significant changes in BLAST interface and output occur. ---------------------------------------------------------------- From owner-bio-software@hgmp.mrc.ac.uk Wed May 10 17:30:13 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D25EA17AAC; Wed, 10 May 2000 17:30:12 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA27090 for ; Wed, 10 May 2000 17:30:10 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA13764 for bio-software-list@hgmp.mrc.ac.uk; Wed, 10 May 2000 17:30:08 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: edbell@my-deja.com X-Newsgroups: bionet.software Subject: Microarray Expression Analysis Software Date: Wed, 10 May 2000 16:17:27 GMT Organization: Deja.com - Before you buy. Lines: 13 Message-ID: <8fc22b$alu$1@nnrp1.deja.com> X-Article-Creation-Date: Wed May 10 16:17:27 2000 GMT X-Http-User-Agent: Mozilla/4.0 (compatible; MSIE 5.0; Windows NT; DigExt) X-Http-Proxy: 1.1 x32.deja.com:80 (Squid/1.1.22) for client 63.75.139.178 X-MyDeja-Info: XMYDJUIDedbell To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk Hi, I am trying to find out more about the different expression analysis software packages that are available (BioDiscovery, GeneSpring, Gene Logic, etc.). Are there any opinions on features or utility of software (clustering, data mining, etc.) Any help would be great. Thanks, Ed Bell Sent via Deja.com http://www.deja.com/ Before you buy. From owner-bio-software@hgmp.mrc.ac.uk Wed May 10 22:02:27 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 04C5917A63; Wed, 10 May 2000 22:02:26 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA20827 for ; Wed, 10 May 2000 22:02:24 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA25607 for bio-software-list@hgmp.mrc.ac.uk; Wed, 10 May 2000 22:02:22 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: money577688675@isoc-au.org.au X-Newsgroups: bionet.software Subject: Earn $50,000 in just 90 days! Date: 10 May 2000 22:02:21 +0100 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Lines: 549 Message-ID: <200005102200.RAA04240@mrs-2.smartworld.net> Mime-Version: 1.0 Content-Type: text/plain; charset=unknown-8bit X-Trace: niobium.hgmp.mrc.ac.uk 957992541 25605 193.62.192.80 (10 May 2000 21:02:21 GMT) X-Complaints-To: news@net.bio.net X-Received: from mrs-2.smartworld.net (mrs-2-fix.smartworld.net [216.70.64.26]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA20422 for ; Wed, 10 May 2000 22:02:15 +0100 (BST) X-Received: from monorailpc (ppp-48.tnt-1.ocl.smartworld.net [216.70.73.48]) by mrs-2.smartworld.net (8.9.1a/8.9.1) with SMTP id RAA04240; Wed, 10 May 2000 17:00:44 -0500 (CDT) X-To: money577688675@isoc-au.org.au To: bio-software@hgmp.mrc.ac.uk Sender: owner-bio-software@hgmp.mrc.ac.uk Precedence: bulk So, How in the heck have you been? Do you remember holding previous conversations regarding business and money making opportunities. I did not send this to you in error! You said: "If only I could find an easier way to make a higher income" and "If I had more money, I could spend more time with my Family, and less time at work" and "I sure could use more money so I could pay off my bills once and for all!" and "I would love to get involved in a business in which will generate money while I am not at work (like a Gas Pump)" Dear Friend, There is a possibility that we haven't met, but you were chosen by someone to recieve this E-Mail. Please, please, print this off and read thoroughly. Be sure that you don't miss any of the points outlined. Then put it down, and then read it again. I am sending you a whole lot of information in which you might not understand the first time you read it. If you don't believe this program will work for you, send it to 10-20 of your closest friends (in which you trust deeply), and ask them what they think? This really works! Have the faith, don't miss this opportunity, get involved also, and it will work for you as it does for us!!!!! Due to the popularity of this letter on the Internet, A MAJOR NIGHTLY NEWS Program recently dedicated entire show to the investigation of the program described below to see if it really can make people money. The show also investigated whether or not the program was legal. Their findings proved that there are absolutely no laws prohibiting the participation in the program. This has helped to show people that this is a simple, harmless and fun way to make some extra money at home. The results have been truly remarkable. So many people are participating that those involved are doing much better than ever before. Since everyone makes more as more people try it out, its been very exciting. You will understand only if you get involved! ********* THE ENTIRE PLAN IS HERE BELOW ********* *** Print This Now For Future Reference *** $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ If you would like to make AT LEAST $50,000 in less than 90 days! If not, forward this to someone who would like to make this kind of money....... It works (like designed) but only for those who follow it to the letter! Please read this program...THEN READ IT AGAIN!! $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ THIS IS A LEGITIMATE, LEGAL, MONEY MAKING OPPORTUNITY!! It does NOT require you to come into contact with people or make or take any telephone calls. Just follow the instructions, and you will make money. This simplified e-mail marketing program works perfectly 100% EVERY TIME! E-mail is the sales tool of the future. Take advantage of this virtually free method of advertising NOW!!! The longer you wait, the more people will be doing business using email. Get your piece of this action!!! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Hello - My name is Johnathon Rourke, I'm from Rhode Island. The enclosed information is something I almost let slip through my fingers. Fortunately, sometime later I re-read everything and gave some thought and study to it. Two years ago, the corporation I worked for the past twelve years down-sized and my position was eliminated. After unproductive job interviews, I decided to open my own business. Over the past year, I incurred many unforeseen financial problems. I owed my family, friends and creditors over $35,000. The economy was taking a toll on my business and I just couldn't seem to make ends meet. I had to refinance and borrow against my home to support my family and struggling business. AT THAT MOMENT something significant happened in my life. I am writing to share the experience in hopes that this could change your life FOREVER. FINANCIALLY$$$!!! In mid December, I received this program in my e-mail. Six months prior to receiving this program I had been sending away for information on various business opportunities. All of the programs I received, in my opinion, were not cost effective. They were either too difficult for me to comprehend or the initial investment was too much for me to risk to see if they would work. But as I was saying, in December of 1997 I received this program. I didn't send for it, or ask for it, they just got my name off a mailing list. THANK GOODNESS FOR THAT!!! After reading it several times, to make sure I was reading it correctly. I couldn't believe my eyes! Here was a MONEY MAKING MACHINE I could start immediately without any debt. Like most of you I was still a little skeptical and a little worried about the legal aspects of it all. So I checked it out with the U.S. Post Office (1-800-725-2161 24-hrs) and they confirmed that it is indeed legal! After determining the program was LEGAL I decided "WHY NOT!?!??" Initially I sent out 10,000 e-mails. It cost me about $15 for my time on-line. The great thing about e-mail is that I don't need any for printing to send out the program, and because I also send the product (reports) by e-mail, my only expense is my time. In less than one week, I was starting to receive orders for REPORT #1. By January 13, I had received 26 orders for REPORT #1. Your goal is to "RECEIVE at least 20 ORDERS FOR REPORT #1 WITHIN 2 WEEKS. IF YOU DON'T, SEND OUT MORE PROGRAMS UNTIL YOU DO. My first step in making $50,000 in 90 days was done. By January 30, I had received 196 orders for REPORT #2. Your goal is to "RECEIVE AT LEAST 100+ ORDERS FOR REPORT #2 WITHIN 2 WEEKS. IF NOT, SEND OUT MORE PROGRAMS UNTIL YOU DO. ONCE YOU HAVE 100 ORDERS, THE REST IS EASY, RELAX, YOU WILL MAKE YOUR $50,000 GOAL." Well, I had 196 orders for REPORT #2. 96 more than I needed. So I sat back and relaxed. By March 1, of my e-mailing of 10,000, received $58,000 with more coming in every day. I paid off ALL my debts and bought a much needed new car! Please take your time to read this plan, IT WILL CHANGE YOUR LIFE FOREVER$!!! Remember, it won't work if you don't try it. This program does work, BUT you must follow it EXACTLY! Especially the rules of not trying to place your name in a different place. It won't work and you'll lose out on a lot of money! In order for this program to work, you must meet your goal of 20+ orders for REPORT #1, and 100+ orders for REPORT #2 and you will make $50,000 or more in 90 days. I AM LIVING PROOF THAT IT WORKS!!! If you choose not to participate in this program, I am sorry. It really is a great opportunity with little cost or risk to you. If you choose to participate, follow the program and you will be on your way to financial security. If you are a fellow business owner and are in financial trouble like I was, or you want to start your own business, consider this a sign. I DID! $$ Sincerely, Johnathon Rourke ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A PERSONAL NOTE FROM THE ORIGINATOR OF THIS PROGRAM: By the time you have read the enclosed program and reports, you should have concluded that such a program, and one that is legal, could not have been created by an amateur. Let me tell you a little about myself. I had a profitable business for 10 years. Then in 1979 my business began falling off. I was doing the same things that were previously successful for me, but it wasn't working. Finally, I figured it out. It wasn't me, it was the economy. Inflation and recession had replaced the stable economy that had been with us since 1945. I don't have to tell you what happened to the unemployment rate... because many of you know from first hand experience. There were more failures and bankruptcies than ever before. The middle class was vanishing. Those who knew what they were doing invested wisely and moved up. Those who did not, including those who never had anything to save or invest, were moving down into the ranks of the poor. As the saying goes, "THE RICH GET RICHER AND THE POOR GET POORER." The traditional methods of making money will never allow you to"move up" or "get rich", inflation will see to that. You have just received information that can give you financial freedom for the rest of your life, with "NO RISK" and "JUST A LITTLE BIT OF EFFORT." You can make more money in the next few months than you have ever imagined. I should also point out that I will not see a penny of this money, nor anyone else who has provided a testimonial for this program. I have retired from the program after sending thousands and thousands of programs. Follow the program EXACTLY AS INSTRUCTED. Do not change it in any way. It works exceedingly well as it is now. Remember to e-mail a copy of this exciting report to everyone you can think of. One of the people you send this to may send out 50,000...and your name will be on everyone of them! REMEMBER though, ----- the MORE YOU SEND OUT, the more potential customers you will reach. So my friend, I have given you the ideas, information, materials and opportunity to become financially independent. IT IS UP TO YOU!! NOW DO IT!! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BEFORE YOU delete this program from your in box, as I almost did, take a little time to read it and REALLY THINK ABOUT IT. Get a pencil and figure out what could happen when YOU participate. Figure out the worst possible response and no matter how you calculate it, you will still make a lot of money! You will definitely get back what you invested. Any doubts you have will vanish when your first orders come in. $$$ IT WORKS!!! $$$ Jody Jacobs Richmond, VA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ HERE'S HOW THIS AMAZING PROGRAM WILL MAKE YOU THOUSANDS OF DOLLAR$$$$!!!! This method of raising capital REALLY WORKS 100% EVERY TIME. I am sure that you could use up to $50,000 or more in the next 90 days. before you say "BULL... ", please read this program carefully. This is not a chain letter, but a perfectly legal money making business. As with all multi-level businesses, we build our business by recruiting new partners and selling our products. Every state in the USA allows you to recruit new multi-level business partners, and we sell and deliver a product for EVERY dollar received. YOUR ORDERS COME BY MAIL AND ARE FILLED BY E-MAIL, so you are not involved in personal selling. You do it privately in your own home, store or office. This is the EASIEST marketing plan anywhere! It is simply order filling by email! ******************************************************************* The product is informational and instructional material, keys to the secrets for everyone on how to open the doors to the magic world of E-COMMERCE , the information highway, the wave of the future ! PLAN SUMMARY: (1) You order the 4 reports listed below ($5 each) They come to you by email. (2) Save a copy of this entire letter and put your name after Report #1 and move the other names down. (3) Via the internet, access Yahoo.com or any of the other major search engines to locate hundreds of bulk email service companies (search for "bulk email") and have them send 25,000 - 50,000 emails for you about $49+) (4) Orders will come to you by postal mail - simply email them the Report they ordered. Let me ask you - isn't this about as easy as it gets? ******************************************************************* By the way there are over 50 MILLION email addresses with millions more joining the internet each year so don't worry about "running out" or "saturation". People are used to seeing and hearing the same advertisements every day on radio/TV. How many times have you received the same pizza flyers on your door? Then one day you are hungry for pizza and you order one. Same thing with this letter. I received this letter many times - then one day I decided it was time to try it. ******************************************************************* YOU CAN START TODAY - JUST DO THESE EASY STEPS: STEP #1. ORDER THE FOUR REPORTS Order the four reports shown on the list below (you can't sell them if you don't order them). -- For each report, send $5.00 CASH, the NAME & NUMBER OF THE REPORT YOU ARE ORDERING, YOUR E-MAIL ADDRESS, and YOUR NAME & RETURN ADDRESS (in case of a problem) to the person whose name appears on the list next to the report. MAKE SURE YOUR RETURN ADDRESS IS ON YOUR ENVELOPE IN CASE OF ANY MAIL PROBLEMS! Within a few days you will receive, by e-mail, each of the four reports. Save them on your computer so you can send them to the 1,000's of people who will order them from you. STEP #2. ADD YOUR MAILING ADDRESS TO THIS LETTER a. Look below for the listing of the four reports. b. After you've ordered the four reports, delete the name and address under REPORT #4. This person has made it through the cycle. c. Move the name and address under REPORT #3 down to REPORT #4. d. Move the name and address under REPORT #2 down to REPORT #3. e. Move the name and address under REPORT #1 down to REPORT #2. f. Insert your name/address in the REPORT #1 position. Please make sure you COPY ALL INFORMATION, every name and address, ACCURATELY! STEP #3. Take this entire letter, including the modified list of names, and save it to your computer. Make NO changes to these instructions. Now you are ready to use this entire email to send by email to prospects. Report #1 will tell you how to download bulk email software and email addresses so you can send it out to thousands of people while you sleep! Remember that 50,000+ new people are joining the internet every month. Your cost to participate in this is practically nothing (surely you can afford $20 and initial bulk mailing cost). You obviously already have a computer and an Internet connection and e-mail is FREE! There are two primary methods of building your downline: METHOD #1: SENDING BULK E-MAIL Let's say that you decide to start small, just to see how it goes, and we'll assume you and all those involved email out only 2,000 programs each. Let's also assume that the mailing receives a 0.5% response. The response could be much better. Also, many people will email outhundreds of thousands of programs instead of 2,000 (Why stop at 2000?). But continuing with this example, you send out only 2,000 programs. With a 0.5% response, that is only 10 orders for REPORT #1. Those 10 people respond by sending out 2,000 programs each for a total of 20,000. Out of those 0.5%, 100 people respond and order REPORT #2. Those 100 mail out 2,000 programs each for a total of 200,000. The 0.5% response to that is 1,000 orders for REPORT #3. Those 1,000 send out 2,000 programs each for a 2,000,000 total. The 0.5% response to that is 10,000 orders for REPORT #4. That's 10,000 $5 bills for you. CASH!!! Your total income in this example is $50 + $500 + $5,000 + $50,000 for a total of $55,550!!! REMEMBER FRIEND, THIS IS ASSUMING 1,990 OUT OF THE 2,000 PEOPLE YOU MAIL TO WILL DO ABSOLUTELY NOTHING AND TRASH THIS PROGRAM! DARE TO THINK FOR A MOMENT WHAT WOULD HAPPEN IF EVERYONE, OR HALF SENT OUT 100,000 PROGRAMS INSTEAD OF 2,000. Believe me, many people will do just that, and more! METHOD #2 - PLACING FREE ADS ON THE INTERNET Advertising on the internet is very, very inexpensive, and there are HUNDREDS of FREE places to advertise. Let's say you decide to start small just to see how well it works. Assume your goal is to get ONLY 10 people to participate on your first level. (Placing a lot of FREE ads on the Internet will EASILY get a larger response.) Also assume that everyone else in YOUR ORGANIZATION gets ONLY 10 downline members. Look how this small number accumulates to achieve the STAGGERING results below: 1st level--your first 10 send you $5 .....................$50 2nd level--10 members from those 10 ($5 x 100)...........$500 3rd level--10 members from those 100 ($5 x 1,000)......$5,000 4th level--10 members from those 1,000 ($5 x 10,000)..$50,000 $$$$$$ THIS TOTALS -----------------------------------$55,550 $$$$$$ AMAZING ISN'T IT? Remember friends, this assumes that the people who participate only recruit 10 people each. Think for a moment what would happen if they got 20 people to participate! Most people get 100's of participants and many will continue to work this program, sending out programs WITH YOUR NAME ON THEM for years! THINK ABOUT IT! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ People are going to get emails about this plan from you or somebody else and many will work this plan - the question is - Don't you want your name to be on the emails they will send out? * * * DON'T MISS OUT!!! * * * JUST TRY IT ONCE!!! * * * * * SEE WHAT HAPPENS!!! *** YOU'LL BE AMAZED!!!* * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ALWAYS PROVIDE SAME-DAY SERVICE ON ALL ORDERS! This will guarantee that the e-mail THEY send out with YOUR name and address on it will be prompt because they can't advertise until they receive the report! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GET STARTED TODAY: PLACE YOUR ORDER FOR THE FOUR REPORTS NOW. Notes: -- ALWAYS SEND $5 CASH (U.S. CURRENCY) FOR EACH REPORT. CHECKS NOT ACCEPTED. Make sure the cash is concealed by wrapping it in two sheets of paper. On one of those sheets of paper write: (a) the number & name of the report you are ordering (b) your e-mail address, and (c) your name & postal address. REPORT #1b "The Insider's Guide to Advertising for Free on the Internet" ORDER REPORT #1 FROM: MARCUS MILLER 918 KNOLLFIELD WAY SAN JOSE CA 95136 NOTE: I and every member below are dedicated at help you with this program so it will work for you also. TRY US! REPORT #2b "The Insider's Guide to Sending Bulk E-mail on the Internet" ORDER REPORT #2 FROM: LANCE DENTON a.k.a (Debtfighter) 100 WILDWOOD RD ROCKPORT TX 78382 REPORT #3b "The Secrets to Multilevel Marketing on the Internet" ORDER REPORT #3 FROM: MELISSA HOGENMILLER 3709 MONHEIM RD CONOVER WI 54519 REPORT #4b "How to become a Millionaire utilizing the Power of Multilevel Marketing and the Internet" ORDER REPORT #4 FROM: KATHY BARROW 410 SYCAMORE ST CONWAY, SC 29527 ******* TIPS FOR SUCCESS ******* TREAT THIS AS YOUR BUSINESS! Be prompt, professional, and follow the directions accurately. -- Send for the four reports IMMEDIATELY so you will have them when the orders start coming in because: When you receive a $5 order, you MUST send out the requested product/report. It is required for this to be a legal business and they need the reports to send out their letters (with your name on them!) -- ALWAYS PROVIDE SAME-DAY SERVICE ON THE ORDERS YOU RECEIVE. -- Be patient and persistent with this program - If you follow the instructions exactly - results WILL FOLLOW. $$$$ ******* YOUR SUCCESS GUIDELINES ******* Follow these guidelines to guarantee your success: If you don't receive 20 orders for REPORT #1 within two weeks, continue advertising orsending e-mails until you do. Then, a couple of weeks later you should receive at least 100 orders for REPORT#2. If you don't, continue advertising or sending e-mails until you do. Once you have received 100 or more orders for REPORT #2, YOU CAN RELAX, because the system is already working for you, and the cash will continue