From owner-software@net.bio.net Fri Oct 01 01:31:00 1999
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From: Mike Parlee <mparlee@cts.com>
Newsgroups: bionet.software
Subject: Re: sequence trace files format problem
Date: Thu, 30 Sep 1999 19:39:38 -0700
Organization: CTS Network Services
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In the past I have handled this problem by serving the files from a Unix or
Linux box running Netatalk (http://www.umich.edu/~rsug/netatalk/).  With
netatalk, a unix volume can be mounted by macs on the network and the traces
can be dragged and dropped into the folder just as if it were another mac.
The resource information is stored in a shadow directory (AppleDouble) and
the files are remain useable both by the mac and by the unix box (or Windows
through Samba).

You do run into a problem if the files are moved around on the unix side
though.  If you are going to manipulate filenames or move the files under
unix you will want to configure netatalk to map Macintosh file types and
creators to a dos or unix file extension as follows.

In the AppleVolumes.system file add the line:

.abi    ABI1    ABI1

This will associate any file ending in .abi with a psuedo-resource fork
containing the Macintosh file type and creator for an ABI trace file.  Use a
script to append the .abi extension to any ABI files that you manipulate
under unix and a Mac connecting to the unix box will still be able to use
those traces.

I believe this can also be done in Windows NT server, but so far I haven't
been able to make it work.  If anyone knows how to map Mac file types and
creators to an extension in WinNT please let me know!

Mike Parlee
mparlee@cts.net

> Paula Burch wrote:

> > The problem is that trace files moved to the sequence repository
> > machine from the sequencing Mac can be used only by a Mac, not by
> > Unix, if tranferred as a Mac binary. If the trace files are moved as
> > 'raw data', they work great in the java trace viewing program, but
> > are utterly unusable on a Mac.
> >
> > How can I make 'raw data' trace files work on a Mac? I was told
> > something I didn't understand about a missing 'resource fork' that
> > the Mac needs. I generally stick to Unix and am mystified. Is
> > there any way to fake the resource fork, or any other way to make one
> > transfer format work for all three of the more popular computer
> > platforms, Mac, Unix, and PC?
> >
> > ________________________________________________________________________
> > Paula E. Burch, Ph.D.             Molecular Biology Computation Resource
> > Baylor College of Medicine, BCMM M220                voice: 713.798.6023
> > One Baylor Plaza, Houston, Texas 77030                 fax: 713.798.4279
> > http://mbcr.bcm.tmc.edu/pburch.html            email: pburch@bcm.tmc.edu


From owner-software@net.bio.net Fri Oct 01 01:35:00 1999
Path: biosci!biosci!not-for-mail
From: Win Hide <winhide@sanbi.ac.za>
Newsgroups: bionet.software
Subject: STACK_PACK EST CLUSTERING MANAGEMENT AND ANALYSIS TOOL-SUITE AVAILABLE
Date: 30 Sep 1999 19:35:12 -0700
Organization: An Internet Solution Customer
Lines: 50
Sender: daemon@net.bio.net
Distribution: world
Message-ID: <37F355E4.D0DAD23A@sanbi.ac.za>
NNTP-Posting-Host: net.bio.net

STACK_PACK EST CLUSTERING MANAGEMENT AND ANALYSIS TOOL-SUITE now
available

SANBI announces the free academic availability of the STACK_PACK EST
clustering management and analysis tool-suite.

STACK_PACK 1.0 has been developed by SANBI in collaboration with
Electric
Genetics, Cape Town (PTY) LTD, to support analysis of the increasing EST
load for Gene Discovery.

The tool-suite interchangeably supports 'modules' such as PHRAP and
other assemblers, and includes D2-cluster and CRAW together with other
codes specifically developed for the system.

STACK_PACK manages flow and stringent analysis of data between these
applications. The system creates two outputs: a standard data set as
well as a more highly-qualified data subset based upon consensus
quality.

Alternate splicing and low quality EST consensi are also detected and
processed.

This system has been used to manufacture STACK, the sequence tag
alignment and consensus knowledgebase which is also distributed by
SANBI.
                       http://www.sanbi.ac.za/Dbases.html

Further information on the STACK-PACK system, and the clustering code
d2-cluster,is to be published in the Genome Research November issue.

'D2_cluster: A Validated Method for Clustering EST and Full-length cDNA
Sequences' John Burke, Dan Davison, and Winston Hide. Genome Research
November 1999.

and

'A comprehensive approach to clustering of expressed human gene
sequence: The Sequence Tag Alignment and Consensus Knowledgebase. R. T.
Miller, A. G. Christoffels, J. Burke,A. A. Ptitsyn, T. R. Broveak,
W. A. Hide. Genome Research November 1999.


Academics may download the STACK database and STACK-PACK codes from

www.sanbi.ac.za/CODES


From owner-software@net.bio.net Fri Oct 01 07:13:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!ctu-gate!news.nctu.edu.tw!news.neto.net!hp1.timenet.net!netnews.hinet.net!news
From: dfhk@ms31.url.com.tw
Newsgroups: bionet.software
Subject: 教您如何在網路中自保的光碟
Date: 30 Sep 1999 15:31:19 GMT
Organization: 正宗防止駭客'dfhk'
Lines: 205
Message-ID: <7svvo7$708@netnews.hinet.net>
NNTP-Posting-Host: h11.s147.ts31.hinet.net

sorry......打擾了!!
====================================================================
聲明最近有人假冒我們的email地址,到處亂寄寄一些不堪入目的字眼給您在此鄭重
聲明我們絕對不是寄這些信的(我們寄出的信皆有數位簽名)請不要相信他請大家告訴大家!!thanks!!
***請認明正宗防止駭客'dfhk'(dfhk@ms31.url.com.tw)  xx工作室出品的其他xxx 2000駭客光碟都是贗品品質
不良!!請小心!!網友和我反應他們的光碟品質不良很難讀取!!正宗dfhk出品前都經過5種廠牌光碟機測試過確保品質!!
 
不要買錯了!!有問題的片子100%包換!!感謝大家的支持!!
=========================================================  

　 
教您如何在網路中自保的光碟 整片光碟 只要400元

你知道在你上網的途中 有人可以無聲無息的進入妳的電腦
竊取你所有的隱私 進而造成妳的莫大損失嗎
不要認為不可能 因為當技術呈現在你眼前時
保證你會大吃一驚 因為一直以來
就是有人這樣做 從中獲得了不法的利益
正所謂 知己知彼 百戰百勝
今天 我把這些技術
弄成國內第一片收集完整的駭客光碟,不但教你怎麼去破解,
更教你如何去防範於未然,最重要的是:它是一片完整的中文介面,中文說明書,
除非您連看字的能力都有困難,
否則你一定知道我在說什麼!!

有人匿名炸你的信箱,你可知道如何防治及報復??(包括炸你E-mail都算是駭客!)
你開網路咖啡店,可知道駭客最喜歡的就是上你的站去試功力?你可知其然而防其然?
你可曾想過,你只是一個上網路的平凡人,可知道駭客也可去把你上網的密碼及名稱
取回自己用,讓你花錢又當大頭?不只如此,他也可直取你電腦內的資料,包括殺檔案
及讓你當機?你知道原理,怎麼做?而又如何防止呢?
你有用ICQ的"好"習慣嗎?可知ICQ安全性甚差的現在,你的ICQ是駭客最大的溫床?一
樣可透過ICQ去做入侵及管理的動作,就是把你硬碟當成是自己家一樣,愛拿什麼就
拿什麼,當然也是包括你的密碼及名稱.....

如果你不曾聽過這些事,那你就是最大的高危險群,你可知道如何去了解這網路的黑
暗面?

----------------------------------------------------------------------------
400元或許只是一頓燭光晚餐的代價，也可能是你跟朋友去KTY的基本消費
但是現在卻能買到你的權益及一輩子的技術，你何樂不為呢？我也跟您做
保証，你現在在補界中也絕對看不到這一片光碟，因為是駭客自己的收藏
，這是第一次流出市面，日後或許會有補界收錄去賣，但是您如果日後再
去買，補界知道這片光碟的利害關係，也該不會完整收錄，搞不好還放了
”特洛伊”程式進去(聽不懂？就把一支木馬程式藏在其它程式中AUTORUN
也行，以後只要你一上網就等於把自己送給人家，被對方盜用密碼上網都
不知道......)您考慮考慮吧!

光碟內容==============================================================

[當戰火結束,城中人民興高采烈的迎接城外的木馬,雖然總有少數的反對 ,]
[卻還是無法阻止被"勝利"沖昏頭的人們,在一片歡樂的氣息中,人們酒後飯]
[飽之際,木馬終於露出貪婪的本性,從木馬腹中出現的敵方精英 ,一舉裡應]
[外合,.....屠城!......]

這就是特洛伊的故事,[木馬屠城記]......

網路上存在著許多的駭客,有所謂的軟體駭客,也有入侵駭客.
多半是存著好玩的心態,但是也存在著有心人士........
因為當你知道破解的用途到底有那些之後,你會不禁心寒..
你可能會自問:我是下一個嗎?還是已經被入侵而不自知.....

舉些例子來說:
你會從網站上下載共享軟件嗎?

如果一個有心人士在網上架設一個共享網站，只要你下載軟件
他就有辨法入侵到你的電腦中,把你的硬碟當成自己家一樣,取
回他要的東西(取什麼?當然是你上網路的帳號及密碼！）而且
已後不管你怎麼改變密碼，它都可以繼續去追蹤，最可怕的是
，這一點都不難，你知道如何防治嗎？如何取得工具程式？駭
客是如何入侵？知其然也要會其然.......請您再看下去

您覺得使用e-mail不會被有心人士利用嗎？到底有那些問題存
在，您了解嗎？您知道駭客是如何做，而您要如何去避免嗎？

在ICQ安全性被議論紛紛的時代，您知道多少？您知道可以透過
ICQ而入侵您的電腦嗎，一樣可以是被當成自家中一樣，任意取
回檔案，殺檔案，來個〔木馬屠城記〕，您會怕嗎？

太多太多的BUG了！只要你上網，只要對方有程式，你就永遠不
會安全，在有些網站上也有防護及破解教學，但是總是不會完全
收錄，也不會有所謂的說明書,也許就連架站的人也不會使用，
我現在就要破除你所有的疑慮，告訴您如何去當〔木馬〕，以及
如何去防止被〔屠城〕！！

=====================================================================

鄭重警告

本光碟中的所有程式皆具有一定的殺傷力，除了可入侵別人電腦的程式外，程式中甚至
也
有所謂的殺硬碟程式，請小心使用，不要到頭來是害人又害己了，且本光碟工具相當充
裕
，千萬不要利用這些工具來破壞他人的電腦或資料，僅能用來學習技術及保護自己等用
途！

===============================[光碟內容列表]==========================

本光碟的內容是以HTML的格式寫的,也就是說是以瀏覽器去觀看,全部提供入侵及反入侵
程
式百餘支，破解文章亦不在話下，全部都附中文使用說用，請直接讀取[駭客首頁.Htm]
即
可!!

ICQ駭客區========

破解,甚至入侵ICQ的程式群....,看完此章您就會對ICQ的安全性完全心冷...

最新版本 ICQ
破解 ICQ 密碼
保護自己的ICQ不被駭客入侵的程式群
寄 ICQ 匿名信或是 炸ICQ 的程式
顯式出對方的 IP
知道對方ICQ 所用的 Port 是多少=>被知道IP及Port就可以做很多壞事了
讓你選擇寄一或N封的訊息給對方
你加入任何人的 UIN，而不必經過對方認證，
用於ICQ中聊天 (chat) 的搗蛋程式
可以讓你編輯對話記錄
可以讓你把ICQ任意移動目錄
可以讓你把ICQ備份
可以讓你複製ICQ
ICQ 特洛伊程式=>此程式的功能就是可以入侵對方的硬碟，取你密碼及讓你當機!!
可以將ICQ相關工具整合在一起的程式
【如何在 ICQ 隱藏你的IP】....

破解密碼區=======

幾乎是無所不破喔......

解 BIOS 的密碼
AWARD BIOS 的通解密碼
AMI BIOS 的通解密碼
破解撥號網路密碼程式類
螢幕保護程式密碼破解程式
看***密碼的程式
暴力法破解密碼工具
破解網頁密碼程式
破解 Word97 密碼程式
破解 Excel97 密碼程式
破解 ARJ 加密式

新進檔案區==========

破解網頁密碼程式=>情色網站專用
很強的特落依程式=>輕鬆入侵，可做所有的動作，包括取你密碼及當機!
看密碼程式
BO程式著名的入侵程式
移除BO的程式
偵測使用ＢＯ入侵者的程式
防護(BO)的程式 -　　

重要的檔案=========

必備的一些檔案

破解文件檔=======

入侵文章
破解入門
如何入侵一台Internet的主機=>解讀密碼,入侵網路咖啡廳.....
如何如何追蹤入侵者
網路漏洞=>提供你自己自保的的方法!!
入侵文章
如何成為一個 hackek

郵件駭客區============

此區提供破解及反破解,很實用的喲....

匿名郵件程式
郵件炸彈程式
郵件炸彈剋星
電子郵件炸彈
電子炸彈
電子郵件炸彈
視窗炸彈的惡作劇

OOB 當機程式========

用OB入侵讓你當機,也提供反OB的程式.....

防當程式
反安裝防當
當機程式邪神
很多當機程式，

駭客網站大連結============
站站是好站....

中文駭客網
英文駭客網

序號-註冊碼區

　
最後 請注意 如你有意購買
請附上 姓名 電話 住址 郵遞區號
我會用代收貨款的方式 只要你準備印章及400元給郵差
妳(你)就能擁有
請回信至 dfhk@ms31.url.com.tw


From owner-software@net.bio.net Fri Oct 01 08:43:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!skynet.be!infeed.is.co.za!feeder.is.co.za!news.is.co.za!not-for-mail
From: Win Hide <winhide@sanbi.ac.za>
Newsgroups: bionet.software
Subject: SANBI EST clustering STACK_PACK 1.0 suite now available
Date: Fri, 01 Oct 1999 11:32:34 +0200
Organization: An Internet Solution Customer
Lines: 49
Message-ID: <37F47FB2.B1C332A2@sanbi.ac.za>
NNTP-Posting-Host: yebo.sanbi.ac.za
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: news.is.co.za 938770394 25868 196.38.142.74 (1 Oct 1999 09:33:14 GMT)
X-Complaints-To: abuse@is.co.za
NNTP-Posting-Date: 1 Oct 1999 09:33:14 GMT
X-Mailer: Mozilla 4.05 [en] (Win95; U)

STACK_PACK EST CLUSTERING MANAGEMENT AND ANALYSIS TOOL-SUITE now
available

SANBI announces the free academic availability of the STACK_PACK EST
clustering management and analysis tool-suite.

STACK_PACK 1.0 has been developed by SANBI in collaboration with
Electric
Genetics, Cape Town (PTY) LTD, to support analysis of the increasing EST
load for Gene Discovery.

The tool-suite interchangeably supports 'modules' such as PHRAP and
other assemblers, and includes D2-cluster and CRAW together with other
codes specifically developed for the system.

STACK_PACK manages flow and stringent analysis of data between these
applications. The system creates two outputs: a standard data set as
well as a more highly-qualified data subset based upon consensus
quality.

Alternate splicing and low quality EST consensi are also detected and
processed.

This system has been used to manufacture STACK, the sequence tag
alignment and consensus knowledgebase which is also distributed by
SANBI.
                       http://www.sanbi.ac.za/Dbases.html

Further information on the STACK-PACK system, and the clustering code
d2-cluster,is to be published in the Genome Research November issue.

'D2_cluster: A Validated Method for Clustering EST and Full-length cDNA
Sequences' John Burke, Dan Davison, and Winston Hide. Genome Research
November 1999.

and

'A comprehensive approach to clustering of expressed human gene
sequence: The Sequence Tag Alignment and Consensus Knowledgebase. R. T.
Miller, A. G. Christoffels, J. Burke,A. A. Ptitsyn, T. R. Broveak,
W. A. Hide. Genome Research November 1999.


Academics may download the STACK database and STACK-PACK codes from

www.sanbi.ac.za/CODES


From owner-software@net.bio.net Fri Oct 01 13:06:00 1999
Path: biosci!CADUS.COM!brian.osborne
From: brian.osborne@CADUS.COM ("Osborne, Brian")
Newsgroups: bionet.software
Subject: RE: sequence trace files format problem
Date: 1 Oct 1999 07:06:38 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
Lines: 79
Sender: daemon@net.bio.net
Distribution: world
Message-ID: <2D3428FD6CDFD111A72800104B2351B7631A1E@weebo.cadus.com>
NNTP-Posting-Host: net.bio.net

To the group,

There is no need to rename the Macintosh files after moving them to Unix
using netatalk. The alternative is to use scripts on the Unix side that move
the resource and data forks simultaneously, keeping the resource fork in a
"dot" directory. Try this link :
http://waldo.wi.mit.edu/ftp/pub/software/Bass/doc/BASS.txt
<http://waldo.wi.mit.edu/ftp/pub/software/Bass/doc/BASS.txt> . The Perl
scripts are called "apple_mv", "apple_cp", etc. If and when the files are
copied back to the Mac using netatalk they are intact, with resource fork.

Brian O.

OSI
777 Old Saw Mill River Rd.
Tarrytown NY 10591
brian.osborne@cadus.com
TEL 914 467 6291
FAX 914 345 3565


-----Original Message-----
From:	Mike Parlee [mailto:mparlee@cts.com]
Sent:	Thursday, September 30, 1999 10:40 PM
To:	bio-soft@net.bio.net; pburch@bcm.tmc.edu
Subject:	Re: sequence trace files format problem

In the past I have handled this problem by serving the files from a Unix or
Linux box running Netatalk (http://www.umich.edu/~rsug/netatalk/).  With
netatalk, a unix volume can be mounted by macs on the network and the traces
can be dragged and dropped into the folder just as if it were another mac.
The resource information is stored in a shadow directory (AppleDouble) and
the files are remain useable both by the mac and by the unix box (or Windows
through Samba).

You do run into a problem if the files are moved around on the unix side
though.  If you are going to manipulate filenames or move the files under
unix you will want to configure netatalk to map Macintosh file types and
creators to a dos or unix file extension as follows.

In the AppleVolumes.system file add the line:

.abi    ABI1    ABI1

This will associate any file ending in .abi with a psuedo-resource fork
containing the Macintosh file type and creator for an ABI trace file.  Use a
script to append the .abi extension to any ABI files that you manipulate
under unix and a Mac connecting to the unix box will still be able to use
those traces.

I believe this can also be done in Windows NT server, but so far I haven't
been able to make it work.  If anyone knows how to map Mac file types and
creators to an extension in WinNT please let me know!

Mike Parlee
mparlee@cts.net

> Paula Burch wrote:

> > The problem is that trace files moved to the sequence repository
> > machine from the sequencing Mac can be used only by a Mac, not by
> > Unix, if tranferred as a Mac binary. If the trace files are moved as
> > 'raw data', they work great in the java trace viewing program, but
> > are utterly unusable on a Mac.
> >
> > How can I make 'raw data' trace files work on a Mac? I was told
> > something I didn't understand about a missing 'resource fork' that
> > the Mac needs. I generally stick to Unix and am mystified. Is
> > there any way to fake the resource fork, or any other way to make one
> > transfer format work for all three of the more popular computer
> > platforms, Mac, Unix, and PC?
> >
> > ________________________________________________________________________
> > Paula E. Burch, Ph.D.             Molecular Biology Computation Resource
> > Baylor College of Medicine, BCMM M220                voice: 713.798.6023
> > One Baylor Plaza, Houston, Texas 77030                 fax: 713.798.4279
> > http://mbcr.bcm.tmc.edu/pburch.html            email: pburch@bcm.tmc.edu


From owner-software@net.bio.net Fri Oct 01 13:33:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!newshub.sdsu.edu!franklin.ljcrf.edu!not-for-mail
From: greg@franklin.burnham-inst.org (Dr. Greg Quinn)
Newsgroups: bionet.software
Subject: Re: sequence trace files format problem
Date: 1 Oct 1999 14:29:06 GMT
Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE
Lines: 58
Message-ID: <7t2gfi$krh$1@franklin.ljcrf.edu>
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We have set up a system here where users can submit an ABI trace file 
through a web form which is then fed through PHRED and the sequence is 
returned to them together with a  trace and a javascript page which 
allows real time translation of the  sequence into a protein. We have 
encountered no problems whatsoever using  netscape (higher than v3) 
running on any platform. You certainly don't transfer both forks with a 
file upload using a mulitpart enctype, which  is what I am doing; I 
suspect you might have other config problems, perhaps relating to the 
applet or the way its configured on the page.

Paula Burch (pburch@condor.bcm.tmc.edu) wrote:
: The sequencing core provides traces to users of various computer
: systems, Mac, Unix, or MS Windows. We have installed a java
: traceviewer that works great in Netscape on the Unix or PC side, 
: but fails to work in either Netscape or Internet Explorer on the Mac. 
: The easy answer would be to just give our Mac users their own trace 
: viewing program, such as the free one from Perkins Elmer.
: 
: The problem is that trace files moved to the sequence repository
: machine from the sequencing Mac can be used only by a Mac, not by
: Unix, if tranferred as a Mac binary. If the trace files are moved as
: 'raw data', they work great in the java trace viewing program, but
: are utterly unusable on a Mac.
: 
: How can I make 'raw data' trace files work on a Mac? I was told
: something I didn't understand about a missing 'resource fork' that
: the Mac needs. I generally stick to Unix and am mystified. Is
: there any way to fake the resource fork, or any other way to make one
: transfer format work for all three of the more popular computer
: platforms, Mac, Unix, and PC?
: 
: We cannot ask the sequencing core personnel to transfer the trace
: files to some labs in Mac binary format and to other labs in 'Raw
: Data' format.
: 
: Thanks for any help you can provide....
: 
: ________________________________________________________________________
: Paula E. Burch, Ph.D.             Molecular Biology Computation Resource
: Baylor College of Medicine, BCMM M220                voice: 713.798.6023  
: One Baylor Plaza, Houston, Texas 77030                 fax: 713.798.4279  
: http://mbcr.bcm.tmc.edu/pburch.html            email: pburch@bcm.tmc.edu
: 

-- 
*****************************************
Computational Biology Group
The Burnham Institute
(formerly La Jolla Cancer Research Inst.)
10901 North Torrey Pines road
La Jolla
CA92037
 
Phone:(619) 646 3103
Email: greg@franklin.ljcrf.edu
http://franklin.ljcrf.edu/greg
http://www.greg.com/
*****************************************

From owner-software@net.bio.net Fri Oct 01 18:47:00 1999
Path: biosci!newshost.lanl.gov!arclight.uoregon.edu!wn4feed!worldnet.att.net!199.60.229.5!newsfeed.direct.ca!news.maxwell.syr.edu!nntp2.deja.com!nnrp1.deja.com!not-for-mail
From: gmei@my-deja.com
Newsgroups: bionet.software
Subject: help needed on Consed
Date: Fri, 01 Oct 1999 19:32:48 GMT
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Hi:

We have licensed "Consed", "Phred" and "swat/cross_match/Phrap" package
from UW a few month ago and I am having some techincal questions about
"Consed". I am new to "Phrap" and "Consed".

What we would like to do using "consed" is to use it's "edit" function
to edit our sequences.

We have a set of sequences (from DNA seqeuncer, say "seq_1", "seq_2",
"seq_3" ... "seq_N") that we use to run "blastn" against Genbank
database. Based on blastn results, we separate them and get the
"consensus" sequence.

I am trying to loaded all "seq_N"s and the "consensus" sequence into
"consed" and edit the "consensus" sequence. However no matter how I
tried, the "Consed" would generate the error (see attached) saying that
I do not have the chromat_file for the "consensus" sequence which is
true. I have all the chromat_files for "seeq_N"s in "chromat_dir"
though.

Here is what I did:

1. I manually copy all chromat_files to "chromat_dir" for "seq_1",
"seq_2", "seq_3" ... "seq_N"
2. I manually create a "fasta_seq" file in "edit_dir":

>67_VP_H2 CHROMAT_FILE: 67_VP_H2 PHD_FILE: 67_VP_H2.phd.1 TIME: Thu Oct
1 09:32:
36 1999
TGGATGCAGTACGTAAGCTTGGATCCTCTAGAGTCGACCCACGCGTCCGC
CCAGCTACTTGGGA....
>85_VP_N2 CHROMAT_FILE: 85_VP_N2 PHD_FILE: 85_VP_N2.phd.1 TIME: Thu Oct
1 09:31:
36 1999
TGGATGACGTGACGTAGCTATGATCCTCTAGAGCCGACCTGTGGCAAATG
TGGCTACCCTGCCAAGCGCAAGAGAAAGTATAACTGGAGTGCCAAG...
>91_VP_P2 CHROMAT_FILE: 91_VP_P2 PHD_FILE: 91_VP_P2.phd.1 TIME: Thu Oct
1 09:30:
36 1999
ATGGGAAGACATACGTAAGCTTTGATCCTCTAGAGTCGACCCACGCGTCC...


3. I manually run phred to create corresponding "PHD" files in "phd_dir"
4. I manually run phrap to create "ace" file in "edit_dir":
5. I run "consed" and everthing is fine. I can see the "Phrap" generate
"CONSESUS" in the X-Window.

But when I manually add our own "consensus" sequence in the "fasta_seq"
with something like:
>consenses_example TIME: Thu Oct 1 10:30:36 1999
atgggaagacatacgtaagctttgatcctctagagtcgacccacgcgtcc
gctccattctgtatctatcattaatagacagctgacctaatatattttag
tggtttcaaattatataggccgggtgtggtggctcacgcctttaatcc..

and re-run Phrap to create new "ace" file (which seems to run fine),
then when I run "consed", I would get the error (see attched error
message).

So my questions are:

1. Does Consed require all sequences (in the fasta_file) to have
corresponding chromatic file to run?
2. Is it possible to use Consed to display a set of sequences and edit
them even some of the sequences do not have their corresponding "DNA"
trace file? If yes, how?

Thank you very much for your help.


Guang Mei
zlmei@hotmail.com


-----------Consed error message from unix standard
output:-----------------------
no ~/.consedrc file so no user resources will be used--that's ok
no ./.consedrc file so no project-specific resources--that's ok
exception thrown: ace file error detected from source file
parseAceFile.cpp at 1397
Error in file /home/pavonis/consed/standard/edit_dir/fasta_seqs_01.ace
at line 695.  Line:
 DS TIME: Thu Oct 1 10:30:36 1999

"CHROMAT_FILE: not found" on this DS line.  This may be missing because
you didn't use phredPhrap, phd2seqfasta, and phd2qualfasta.  You must
get these programs from bge@u.washington.edu

ace file: /home/pavonis/consed/standard/edit_dir/fasta_seqs_01.ace
ace file error detected from source file parseAceFile.cpp at 1397
Error in file /home/pavonis/consed/standard/edit_dir/fasta_seqs_01.ace
at line 695.  Line:
 DS TIME: Thu Oct 1 10:30:36 1999

"CHROMAT_FILE: not found" on this DS line.  This may be missing because
you didn't use phredPhrap, phd2seqfasta, and phd2qualfasta.  You must
get these programs from bge@u.washington.edu

Version 8.0 (990506)
ace file error detected from source file parseAceFile.cpp at 1397
Error in file /home/pavonis/consed/standard/edit_dir/fasta_seqs_01.ace
at line 695.  Line:
 DS TIME: Thu Oct 1 10:30:36 1999

"CHROMAT_FILE: not found" on this DS line.  This may be missing because
you didn't use phredPhrap, phd2seqfasta, and phd2qualfasta.  You must
get these programs from bge@u.washington.edu

Version 8.0 (990506)
ace file: /home/pavonis/consed/standard/edit_dir/fasta_seqs_01.ace


Sent via Deja.com http://www.deja.com/
Before you buy.

From owner-software@net.bio.net Fri Oct 01 21:26:00 1999
From: "Sam" <mode@windmail.net>
Newsgroups: bionet.software
Subject: Softwarez are waiting for you!
Date: Sat, 2 Oct 1999 00:06:31 -0700
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From owner-software@net.bio.net Sat Oct 02 03:31:00 1999
Path: biosci!rutgers!nntp.upenn.edu!logbridge.uoregon.edu!newspeer.monmouth.com!ix.netcom.com!news
From: Andy Zaayenga <andy.zaayenga@bigfoot.com>
Newsgroups: bionet.software
Subject: Announce: Laboratory Robotics Meeting 10/7/99
Date: Sat, 02 Oct 1999 00:19:01 -0400
Organization: Netcom
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The Laboratory Robotics Interest Group Mid Atlantic Chapter
October 1999 Meeting

High Throughput Screening: Special Topics

Date:        Thursday, October 7, 1999
Place:       Forsgate Country Club, Forsgate Drive, Jamesburg, NJ  08831
                  Phone: (732)521-0070
Itinerary:  Social Period - 3:30 - 6:00 PM
                  Presentations - 6:15 to 8:30 PM

Member Pre-Registration: 
Requested, not required.  Pre-registering will allow us to more accurately
gauge seating requirements and refreshment needs.  Indicate names of
attendees and company affiliation.  Pre-register by email with
<mailto:andy.zaayenga@lab-robotics.org> or by phone at (732)302-1038.  In
order to speed sign-in at the meeting, please bring a business card to drop
into the registration box.  There will be a business card drawing for one of
our beautiful LRIG rosewood pens.

*************************************************************
Agenda:   
The theme of the evening is High-Throughput Screening: Special Topics. After
the extended social period from 3:30 to 6:00, the talks will commence
leading off with Dr. Sheri Miraglia talking about an exciting new
development in scanning laser imaging for high-throughput screening
applications. Secondly, we will hear Dr. Susan Bassett talk about the
problems of interpreting the voluminous data that we get from HTS and some
possible software solutions addressing this problem. Finally, Dr. Dale
Christensen will talk about a novel approach in finding small molecules that
interact with receptors for which ligands are not necessarily known. Taken
together these speakers, who are coming far and wide from California, New
Mexico, and North Carolina, will ensure a stimulating evening. As always,
there is no registration fee or dues, and food and refreshments will be
served throughout the social period. Registration is encouraged for us to
accurately gauge the size of the meeting.

There are hotels nearby for attendees who wish to stay overnight.

There will be a Job posting board at the social. Please encourage your
recruiters to give you material to post and distribute.  Openings may also
be posted at http://www.lab-robotics.org/careers.htm

Members interested in presenting a scientific poster are encouraged to do
so.  Please contact us to arrange for poster space.  

There is no fee to attend the meeting.

*************************************************************
Presentation:  High-Throughput Screening Applications of a Novel Scanning
Laser Imaging Technology 
Sheri Miraglia, Ph.D., Senior Scientist, PE Biosystems 

The increasing number of compounds available for screening in drug
development has driven the requirement for higher throughput screening
technologies, as well as unique technologies that address a broader
application portfolio. Our laboratory has been involved in the development
of multiplexed mix-and-read assays using Fluorometric Microvolume Assay
Technology (FMAT). FMAT is a fluorescence based assay system that
incorporates a laser scanner and optical detection system that provides a
direct measurement of cellular or bead-based fluorescence on a well-to-well
and on an individual cell/bead basis. This design is ideal for the
homogenous identification of hits in primary screening, as well as for lead
optimization in the form of IC50 determinations, and for assessment of lead
compound cytotoxicity. Fluorescent beads of various sizes can be
distinguished from one another, allowing the multiplexing of two or more
targets present on different sized beads in the same well. In addition, the
digitized image data is compiled from two PMTs permitting the development of
multiplexed assays based on dye color. A variety of different mix and read
applications for FMAT will be described, including peptide-receptor ligand
interactions, and multiplexed bead based immunocapture assays. The results
of a novel high-throughput screen performed in collaboration with a major
Pharma oncology group will also be discussed. Employing a simple
mix-and-read Annexin V binding assay, a variety of purified natural products
were identified that are potent inducers of apoptosis in tumor cells. Taken
together, the data to be presented will demonstrate the versatility and
feasibility of fluorescence-based homogeneous and multiplexed assays for a
variety of cell-based and molecular targeted screens used in drug discovery.

*************************************************************
Presentation:  Harnessing the Power of Computational Intelligence to
Identify Leads in HTS 
Susan I. Bassett, Ph.D., Executive Vice-President, Global Technology
Operations, Bioreason, Inc. 

With high-throughput screening systems in place and beginning to produce
data reliably, the data analysis and interpretation becomes a bottleneck in
the process of moving more high-quality leads to the clinic. The
decision-making processes that go into lead discovery, evaluation, and
development are quite complex, and can benefit from judicious use of
appropriate computational intelligence techniques. Knowledge-based reasoning
systems that capture the decision process of a pharmaceutical chemist during
lead identification and development and aid in decision support will be
presented in this talk. Bioreason's HTS data interpretation systems are an
example of an automated solution aimed at helping identify top quality lead
candidates while minimizing costly mistakes. The fundamental aspects of
technology for combining computational intelligence techniques with
knowledge discovery from data mining to this end will be presented.

*************************************************************
Presentation:  Molecular Braille: A Novel Technology for Identification and
Characterization of Compounds that Modulate Receptor Function
Dale J. Christensen, PhD., Senior Scientist
Novalon Pharmaceutical Corp., 4222 Emperor Blvd., Suite 560 Durham, NC
27703-8466, Ph 919-474-8888 x34, Fax 919-474-0103, dchristensen@novalon.com

Many receptor proteins in cellular signaling pathways undergo significant
conformational changes in response to a signal molecule. Nuclear hormone
receptors are ligand-dependent transcription factors. Ligand binding to
these receptors results in conformational changes that expose binding sites
for coactivator or corepresser proteins. The estrogen and androgen receptor
are well validated drug targets that have a significant clinical utility
while orphan nuclear receptors such as PPAR are beginning to play an
important role in modern drug discovery. Molecular Braille has been
developed to identify and characterize compounds that modulate the
conformation of these receptors. Using a series of conformation-sensitive
probes, the conformation that the receptor adopts in response to ligand
binding can be evaluated using an in vitro time-resolved fluorescence assay
and an in vivo luminescence assay. This technology can be used to identify
new ligands, distinguish between classes of ligands, and guide lead
optimization.

*************************************************************
For more information, contact one of the LRIG Mid Atlantic officers:

Dennis S. France
Executive Chair, LRIG Home and Mid Atlantic Chapter
The Novartis Institute for Biomedical Research
tel:  (908) 277-5328
fax: (908) 277-4374
email: dennis.france@pharma.novartis.com

John Babiak, Ph.D.
High Throughput Screening Chair, Mid Atlantic Chapter
Pharmacopeia
tel:  (609) 452-3795
fax: (732) 821-2037
email: jbabiak@pharmacop.com

William Haller
Analytical Chemistry Chair, Mid Atlantic Chapter
Treasurer, LRIG Home and Mid Atlantic Chapter
Ortho-McNeil Pharmaceutical
tel:  (908) 218-6341
fax: (908) 218-0524
email: bill.haller@lab-robotics.org

Sharon Reed
Event Coordinator, Mid Atlantic Chapter
Coelacanth Corporation
tel:  (609) 448-8200 ext 2044
email: sharon.reed@lab-robotics.org

M. Elizabeth Miller
Agricultural Applications Chair, Mid Atlantic Chapter
Rohm & Haas Company
tel:  (215) 641-7285
fax: (215) 619-1617
email: rsaumm@rohmhaas.com

Jinzi Wu, Ph.D.
Assay Development Chair, Mid Atlantic Chapter
The Novartis Institute for Biomedical Research
email: jinzi.wu@pharma.novartis.com

Andy Zaayenga
Automation Technologies Chair, Mid Atlantic Chapter
Secretary, LRIG Home and Mid Atlantic Chapter
TekCel Corporation
tel:  (732) 302-1038
fax: (732) 302-9080, eFax: (630) 604-2935
email: andy.zaayenga@tekcel.com

*************************************************************
Directions: 
From the North or South: Take the New Jersey Turnpike to Exit 8A - Exit the
left ramp for Jamesburg (Route 32 East) - Continue straight for 1 1/4 miles
through traffic light - Forsgate Country Club is on your left - Use the
Clubhouse Entrance (second left).

From Princeton: Route 1 to Scudders Mill Road East - Continue on Scudders
Mill Road and make a left at the 5th traffic light onto Dey Road - Continue
on Dey Road to the end  - Make a left  - At 2nd traffic light (Route 32)
make a right - Continue straight for 1 1/4 miles through traffic light -
Forsgate Country Club is on your left - Use the Clubhouse entrance (second
left).

*************************************************************
For more information on this meeting, visit
http://www.lab-robotics.org/Mid_Atlantic/meetings/9910.htm
Visit The Laboratory Robotics Interest Group homepage at
http://lab-robotics.org 

*************************************************************
The Laboratory Robotics Interest Group is a rapidly growing special
interest group focused on robotics applications in the laboratory. Our
membership consists of over 5,000 scientists and engineers worldwide with
more than 2,800 in the Mid Atlantic Chapter.

We are a non-profit organization run by unpaid volunteers so if you would
like to help out with the group please contact one of our officers.

From owner-software@net.bio.net Sat Oct 02 10:42:00 1999
Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newspeer.monmouth.com!solomon.io.com!news.globeset.com!dca1-feed1.news.digex.net!news.ums.edu!haven.umd.edu!dca1-feed4.news.digex.net!intermedia!news1.bms.com!not-for-mail
From: nathan@dnase.hpw.pri.bms.com (Nathan O. Siemers)
Newsgroups: bionet.software
Subject: Re: help needed on Consed
Date: 02 Oct 1999 07:27:54 -0400
Organization: Bristol-Myers Squibb Company
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I believe there may be a utility (probably a perl script) to generate
a dummy phd file so that consed does not exit in error.  However I
thought there was more tolerance for this in the recent consed versions.


Try looking for consensusToPhd.perl  in your distribution.


nathan


-- 
N a t h a n   O .  S i e m e r s
Bioinformatics
Division of Applied Genomics
Bristol-Myers Squibb Pharmaceutical Research Institute
Hopewell Building 3B, P.O. Box 5400, Princeton, NJ 08543-5400
609 818-6568


From owner-software@net.bio.net Sat Oct 02 15:12:00 1999
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From: jakku@mrna.tn.nic.in ("R. Jayakumar")
Newsgroups: bionet.software
Subject: identification of repeats
Date: 2 Oct 1999 17:05:14 +0100
Organization: School of Biotechnology
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Dear bioneties
     I need a help.  I have a large DNA sequence.  I need to to find the
presence of dna repeats, whether they may micro or minisatellites.  Does
anyone know of any package that can search a query sequence and tell me
whether there are any such repeats and at what all positions they are
present.
  thank you
sincerely
jayakumar


---

From owner-software@net.bio.net Sun Oct 03 04:42:00 1999
Path: biosci!NHGRI.NIH.GOV!jfryan
From: jfryan@NHGRI.NIH.GOV (Joe Ryan)
Newsgroups: bionet.software
Subject: Re: identification of repeats
Date: 2 Oct 1999 22:42:22 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
Lines: 23
Sender: daemon@net.bio.net
Distribution: world
Message-ID: <19991003011316.A21727@nhgri.nih.gov>
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NNTP-Posting-Host: net.bio.net

Try Sputnik by Chris Abajian
ftp://ftp.nhgri.nih.gov/pub/software/sputnik/

Joe
--
Joseph Ryan
Programmer
National Human Genome Research Institute

On Sat, Oct 02, 1999 at 05:05:14PM +0100, "R. Jayakumar" wrote:
> Dear bioneties
>      I need a help.  I have a large DNA sequence.  I need to to find the
> presence of dna repeats, whether they may micro or minisatellites.  Does
> anyone know of any package that can search a query sequence and tell me
> whether there are any such repeats and at what all positions they are
> present.
>   thank you
> sincerely
> jayakumar
> 
> 
> ---
> 

From owner-software@net.bio.net Sun Oct 03 09:49:00 1999
Path: biosci!STARGAZER.WENDLAND.DE!que30
From: que30@STARGAZER.WENDLAND.DE (gusyer)
Newsgroups: bionet.software
Subject: e-leads.....the internet at your fingertips
Date: 3 Oct 1999 03:48:24 -0700
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NNTP-Posting-Host: net.bio.net


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 other expensive mediums !

 Targeted AND General leads available !


 Fax your details to  786 549 5787  INCLUDE your:  name  tel  email

 The internet at your fingertips.....
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A#he

From owner-software@net.bio.net Sun Oct 03 12:01:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!ctu-gate!news.nctu.edu.tw!news.neto.net!hp1.timenet.net!netnews.hinet.net!news
From: a7airnews@sina.com.tw
Newsgroups: bionet.software
Subject: 低價廉讓高雄考友上補習班高考商業類科資格!!
Date: 3 Oct 1999 12:54:30 GMT
Organization: 低價廉讓高雄考友上補習班高考商業類科資格!!
Lines: 15
Message-ID: <7t7jm6$8lm@netnews.hinet.net>
NNTP-Posting-Host: h71.s58.ts.hinet.net


你嚮往公職的工作,卻由於補習費太貴而傷腦筋嗎???

這裏提供一個只須25000-就可以到高雄考友上補習班上課的機會!!

低價廉讓高雄考友上補習班高考商業類科資格!!

(含一年的上課資格.書籍,講義等)

原價40000-  低價以25000-廉讓

因本人已順利取得公職,無須再補下去,廉讓一年的資格

意者請回信至  airnews@sina.com.tw  吳小姐 


From owner-software@net.bio.net Mon Oct 04 14:52:00 1999
Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!howland.erols.net!vixen.cso.uiuc.edu!not-for-mail
From: John Stone <johns@ks.uiuc.edu>
Newsgroups: bionet.software
Subject: Announce: VMD 1.4 beta 1
Date: Mon, 04 Oct 1999 10:45:38 -0500
Organization: Theoretical Biophysics, Beckman Institute, UIUC
Lines: 29
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        VMD "Visual Molecular Dynamics" 1.4 beta 1 Announcement
        -------------------------------------------------------
The Theoretical Biophysics group at the Beckman Institute For Advanced
Science and Technology, the University of Illinois (U-C), is proud to
announce the release of VMD 1.4 beta 1.  VMD is a package for the
visualization and analysis of biomolecular systems.  This software is
distributed free of charge and includes source code, documentation,
and precompiled binaries for IBM, HP, Linux, Sun, and SGI Unix systems,
as well as Microsoft Windows 95/98/NT.
The VMD documentation includes an installation guide, a users guide, and
a
programmers guide for interested researchers.  VMD also provides on-line
help through the use of an external HTML viewer.  VMD development is
supported by the NIH National Center for Research Resources.

A full description of VMD is available via the VMD WWW home page:
        http://www.ks.uiuc.edu/Research/vmd/

The Theoretical Biophysics group encourages VMD users to be closely
involved in the development process through reporting bugs, contributing
fixes, periodical surveys and via other means.

We are eager to hear from you, and thank you for using our software!

-- 
Theoretical Biophysics Group   Email: johns at ks.uiuc.edu
Beckman Institute              http://www.ks.uiuc.edu/~johns/
University of Illinois         
Urbana, IL 61801, USA          Unix Is Good For You!!!

From owner-software@net.bio.net Tue Oct 05 02:10:00 1999
Path: biosci!2XTREME.NET!akozik
From: akozik@2XTREME.NET (Alexander Kozik)
Newsgroups: bionet.software
Subject: CONSED for Linux (do I need Motif?) / ABI 3700 and PHRED.
Date: 4 Oct 1999 20:10:00 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
Lines: 20
Sender: daemon@net.bio.net
Distribution: world
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NNTP-Posting-Host: net.bio.net

I need advice with installation of PHRED / PHRAP / CONSED on Linux.

Do I need Motif to run CONSED on Linux?
Is it possible to use Lesstif libraries instead of Motif?

Does anybody use PHRED / PHRAP / CONSED on Slackware?

Does PHRED read ABI 3700 files?

Thanks a lot in advance.

Alexander Kozik

Dpt. of Biological Chemistry
School of Medicine
UCD
Davis CA


From owner-software@net.bio.net Tue Oct 05 17:27:00 1999
Path: biosci!newsfeed.stanford.edu!logbridge.uoregon.edu!newsrelay.iastate.edu!news.iastate.edu!graphix
From: graphix@iastate.edu (Kent A Vander Velden)
Newsgroups: bionet.software
Subject: What Are Your Software Desires and Opinions?
Date: 3 Oct 1999 17:58:56 GMT
Organization: Iowa State University, Ames, Iowa, USA
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  I am a bioinformatics student with a strong background in computer
science who is looking for a purpose and direction in this new field.
It is unclear to me the computational needs of the biology community.
If you are reading this please respond by answering the following three
questions:

  1) what biology related software do you dislike the most and why?

  2) what biology related software do you desire the most that does not 
     currently available?

  3) what biology related question do you feel that computers would be/are
     of the most benefit?

  Your views are _greatly_ appreciated.

-- 
Kent Vander Velden
kent@iastate.edu

From owner-software@net.bio.net Tue Oct 05 19:59:00 1999
Path: biosci!newsfeed.stanford.edu!uchinews!newsswitch.lcs.mit.edu!netnews.com!isdnet!isdnet-serv!not-for-mail
From: "quaderno.com" <manfred@quaderno.com>
Newsgroups: bionet.software
Subject: QUADERNO The Musical Expression.
Date: Tue, 5 Oct 1999 22:49:01 +0200
Lines: 147
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Reply-To: "quaderno.com" <manfred@quaderno.com>
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Greetings,

The following is a text-only description of a new program for music
composition. Please don't hesitate to download the demo version on the
Web at  http://www.quaderno.com


QUADERNO > THE  MUSICAL EXPRESSION

QUADERNO is a program for MIDI sequencing and an aid to musical
composition and research.
It runs on PC  (or on Power Mac using Virtual PC)


QUADERNO was created by two musicians who envisioned a program that
would serve their needs as composers. This software is the result of 5
years of  intense work and musical research.  It was first developed on
the Atari and since one year for the PC . It's a program based
entirely on MIDI; you can perform many types of data transformations
very quickly allowing immediate feedback based upon your musical idea.
The interface is attractively colored; it allows you to link music and
color in a very intuitive way.

A virtual Remote-Control panel allows you to:
1- determine your Recording choices
2- use special Functions  to transform your music
3- access the different "Spaces" (various views of your musical data)

1 - RECORDING  can be done in different ways:
- Normal MIDI recording with a keyboard or any MIDI instrument
- Simple Recording with the mouse (1 Pattern)
- Multitrack MIDI recording with the mouse (up to 56 Patterns all
together)
- Multitrack MIDI recording (16 tracks or 16 MIDI instrumentalists) in
real-time.

2 - FUNCTIONS:
The functions are very powerful mathematical algorithms that allows you
to transform your music with a single click of the mouse.

Quaderno's Functions include:

Accents- Agitation - Random - Rhythm Analysis - Arpeggiator - Cadences -
Calculation - Canons - Chords - Conversions - Untie - Echoes - Melodic
Evolution - Expression - Harmonization - Legato - Morphing -
Suppress Controllers -  Reduce Controllers - Progressions -
Quantize-Random - Quantize-Fill - Quantize-Logic - Quantization Reduction -
Re-Injection - Harmonic Resolution - Rhythm Tracker -  Staccato -
Suppress Doubles - Suppress Recovey - Send Sysex - Tessitura -
Melodic Transposition  - Formula  - Sorting - Wave Creation  .

3 - SPACES:

> SESSION:
The basic space of the program . It is made up of a large checkerboard
filled up with 196 small squares, each square is called: an Area. Each
Area is characterized by a name, a number, a MIDI channel, a
synthesizer, a sound, a Scale and a Quaderno. On the left of this large
checkerboard you can find a column with numbers from 1 to 56. Each
number represents a Pattern. Around this axis revolve 14 "satellite"
spaces.

> LIBRARY:
For saving all the files you create in the different spaces with a very
convenient feature, the ability to audition items from the Library
before importing them.

> SONG:
For structuring and organizing all the Patterns (musical figures)  you
have developed in the SESSION space, in the same manner as with a
classic sequencer but with functions specific to Quaderno. It's also the
place for export/import of MIDI files.

> MICRO-EDITION:
A graphic representation of all the MIDI events of the selected Pattern.
Each curve is a linear event representation of the various parameters of
your music. You can modify each of these curves independently and use
functions specific to this space: expansion, compression, horizontal and
vertical inversion.

> NOTE-EDIT:
Note events on a grid that represent the pitch on the vertical axis and
time on the horizontal axis. You can
make modifications and transformations on the selected notes
instantaneously, and choose to visualize the color of notes according to
their velocity or pitch,

> CHORDS:
This space allows creation and auditioning of all sorts of chords
according to the set of available scales in use in QUADERNO. You can use
your chord grids in different ways (send them to a free Area, or use
them to reharmonize one or several Patterns).

> HARMONIC MODULATIONS :
To create principles of harmonic modulation that you will be able to
apply in several ways. These harmonic
modulations can be used in real time.

> MIDI SETUP:
To manage and program all Midi peripherals.

> MONITORS:
To "see" the music that you have created in a very original way. The
different Monitors translate into images (color, speed, movement..) the
MIDI events of your music.

> MUSICAL  ANALYSIS :
To analyze the harmonic contents of any Pattern and see immediately
which scales the harmony involves and also to extract a chord grid from
this harmonic analysis and use these results in different ways.

> ORCHESTRATION:
To select and extract the different musical elements of a Pattern
according to 7 criteria and 2 Modes. Once you have selected the desired
elements, you can sort them out and send them into different Plans (up
to 6 Plans).

> DYNAMIC PADS:
To re-write in real time your sequence by playing with the mouse on the
4 fundamental elements of a Pattern: Velocities, Durations, Notes and
Rhythms.

> COMPOSER:
To algorithmically generate MIDI sequences without user input (without
keyboard or mouse). You'll select several musical parameters (rhythms,
notes, durations, MIDI controller ) and QUADERNO will generate music
based upon your program (up to 70 tracks).

> REAL-TIME:
Today, we are no longer work in a linear fashion but rather from a
multidimensional perspective. It is in the Real-Time space that you will
understand this new approach.  Here, multiple MIDI instrumentalists can
play and record together.

Thank you for taking the time to familiarize yourself with QUADERNO .We
hope that QUADERNO will enable you to compose in a completely different
way and that you will discover a new and  pleasurable approach to making
music.

For contact information or demos please email or phone:
(33) 1 43 73 25 96 or (33) 1 48 74 59 19 (Paris/FRANCE)


From owner-software@net.bio.net Tue Oct 05 20:33:00 1999
Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!142.231.112.2!cyclone.bc.net!news.maxwell.syr.edu!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!biosci
From: curiouser@gene.ccmbindia.org ("Malay")
Newsgroups: bionet.software
Subject: Re: C++ gui development
Date: 5 Oct 1999 22:23:48 +0100
Organization: MRC Human Genome Mapping Project Resource Centre
Lines: 66
Message-ID: <001701bf0f78$5d74efa0$7b02a8c0@nic.in>
References: <Pine.OSF.3.92.990917170333.29768A-100000@reindeer.mips.biochem.mpg.de> <002a01bf01ef$b154cf00$7b02a8c0@nic.in> <37EADB83.CC021C71@bruxton.com> <003a01bf0823$770bc1c0$7b02a8c0@nic.in> <37F01F7A.82259D0D@bruxton.com> <000601bf0f3e$3ef202a0$7b02a8c0@nic.in> <37FA2428.CFCCE29D@bruxton.com>
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: The problem is that most software developers want to be paid for their
: time.

Sure! But for a non-commercial developer, the appreciation that matters
most, like in case of any creative work.

: : A company such as Apple, and the UNIX vendors, can subsidise the cost
of
: development tools, because it means that more software is available for
: their platforms. They make their money on the hardware.

But it not always true. The free development tools is a sort of "culture",
that's been long practised in Unix bandwagon. And more software also means
more sell of hardware. MS seems to be interested making money out of both
"the cow" as well as the "milk". That's detrimental when cows are available
free.

:A company such
: as Microsoft can make money on sales of Windows, and subsidise the cost
: of Visual C++ (which I don't believe they do any more).

That's exactly what I say. When Unix vendors can give away their developing
tools as a part of their operating system. Why not microsoft? Linux is
rapidly gaining market because of this. Particularly, individual developers
are more interested in Linux.

:Sun can afford
: to spend a fortune developing Java (the development of standarized
: libraries is very expensive), because it increases the market for their
: servers, and without it, Sun will not exist as Microsoft products become
: more popular on the desktop.

That's may be true when it comes to "server". But noone can deny that JAVA
is rapidly becoming an ubiquitous developing environment. SUN created a
revolution in thinking, may be unknowingly or unintentionally. In the
coming years, we will definitely see more and more softwares are developed
in JAVA and Microsoft will lose even the "cow".
:
: There is some very good software available at no cost (the GNU tools),
: where people have donated their time. However, in general, as the cost
: of software declines relative to the cost of hardware, I expect to see
: fewer and fewer subsidised development tools.

I completely disagree. I think just the contrary, the developing tools will
be completely free, as the softwares. And more and more softwares will be
written by individuals rather than corporates as is happening in
bioinformatics. Linux will be the operating system, primarily because the
softwares that comes with it are free, both the tools as well as the
applications.

:
: I have been writing computer programs since 1966, and it is my
: observation that in the computer market there is always a monopolist,
: and many people do not like that monopolist. However, dislike of a
: monopolist is insufficient to bring about a new form of computing. So
: far, that has always been driven by commercial demand.
:

We are thinking about future. What you said was true in the past. It was a
"developers market". In future, it will be "user's market".

Malay


---

From owner-software@net.bio.net Tue Oct 05 21:27:00 1999
Path: biosci!newsfeed.stanford.edu!logbridge.uoregon.edu!news.u.washington.edu!not-for-mail
From: "Stephen R. Lasky" <srlasky@u.washington.edu>
Newsgroups: bionet.software
Subject: Re: CONSED for Linux (do I need Motif?) / ABI 3700 and PHRED.
Date: Tue, 05 Oct 1999 22:07:49 +0000
Organization: UW Molecular Biotechnology
Lines: 45
Message-ID: <37FA76B5.84F2541E@u.washington.edu>
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Alexander Kozik wrote:
> 
> I need advice with installation of PHRED / PHRAP / CONSED on Linux.
> 
> Do I need Motif to run CONSED on Linux?
> Is it possible to use Lesstif libraries instead of Motif?
> 
> Does anybody use PHRED / PHRAP / CONSED on Slackware?
> 
> Does PHRED read ABI 3700 files?
> 
> Thanks a lot in advance.
> 
> Alexander Kozik
> 
> Dpt. of Biological Chemistry
> School of Medicine
> UCD
> Davis CA


I have set up consed/phred/phrap (cross-match/swap) on redhad 5.1, 5.2
and 6.0.  No motif and no problem.  You might want to take a look at the
documentation that comes with the phrap distribution and with consed,
then just make and make install them and see if they work.  I think the
installer looks for libraries that it needs and stops if it doesn't find
them.

Yes, phred reads 3700 files. I am not convinced it gives a very good
quality assessment (some of the runs on our 3700s look better than what
phred says they are), and they work in assemblies.

hope that helps

srlasky
-- 
Stephen R. Lasky, Ph.D.			#
University of Washington		#
Department of Molecular Biotechnology	#
HSB K324 box 357730			#
Seattle, WA, 98195 USA			#
email:	srlasky@u.washington.edu	#
Phone: 	206-616-5865			#
Fax:	206-685-7301			#
#########################################

From owner-software@net.bio.net Wed Oct 06 01:17:00 1999
Path: biosci!newsfeed.stanford.edu!skynet.be!tank.news.pipex.net!pipex!uunet!ams.uu.net!ffx.uu.net!news-peer.unet.maine.edu!rupert.unet.maine.edu!newshost.Dartmouth.EDU!not-for-mail
From: Robert-a <info@textco.com>
Newsgroups: bionet.software
Subject: announce: GCK2 for Windows beta test
Date: Tue, 05 Oct 1999 20:31:48 -0400
Organization: Textco, Inc.
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Textco has announced a public beta test of a Windows version of its
award winning DNA manipulation, cloning, and design application. To
learn more and download the beta version for free, go to Textco's web
site at <http://www.textco.com>.


From owner-software@net.bio.net Wed Oct 06 08:15:00 1999
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From: urmas@zbi.ee ("=?ISO-8859-1?Q?Urmas_K=F5ljalg?=")
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Subject: Subscribe
Date: 6 Oct 1999 10:08:08 +0100
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Subscribe bio-software
*****************
Dr. Urmas K6ljalg
Docent, Inst. of Botany and Ecology, University of Tartu
-------------- and ---------------
Head of the Mycological Dept., Inst. of Zoology and Botany
Estonian Agricultural University
181 Riia Str., 51014 Tartu, Estonia
Tel +372 7 383027
Fax +372 7 383013
urmas@zbi.ee
---

From owner-software@net.bio.net Wed Oct 06 11:51:00 1999
Path: biosci!pravda.ucr.edu!ihnp4.ucsd.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!howland.erols.net!spring.edu.tw!netnews.hinet.net!news
From: wunart@crosswinds.net
Newsgroups: bionet.software
Subject: Active X with Source code for only USD $199
Date: 6 Oct 1999 12:43:52 GMT
Organization: add-happy
Lines: 12
Message-ID: <7tfg68$7bf@netnews.hinet.net>
NNTP-Posting-Host: 210.242.153.252

Active X with Source code for only USD $199

The Active X for CTI.

It is for Dialogic Analog board -
    D/41H, D/41ESC, VFX/40, D/160SC-LS

It is only USD $199 include source code.

Contact wunart@crosswinds.net  if you need it.


From owner-software@net.bio.net Wed Oct 06 13:59:00 1999
Path: biosci!newshost.lanl.gov!arclight.uoregon.edu!logbridge.uoregon.edu!feeder.qis.net!newshub.northeast.verio.net!news.new-york.net!uunet!ffx.uu.net!newsfeed.attap.net!mango.singnet.com.sg!columbine.singnet.com.sg!not-for-mail
From: "Axon Research" <axon2000@mbox2.singnet.com.sg>
Newsgroups: aus.computers.logic-prog,bionet.software,bit.software.international
Subject: Axon Idea Processor
Date: 6 Oct 1999 14:52:33 GMT
Organization: Singapore Telecommunications Ltd
Lines: 16
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NNTP-Posting-Host: qtns01333.singnet.com.sg
X-Newsreader: Microsoft Internet News 4.70.1155

The Axon Idea Processor (AXON2000 R1.3) is now available. 

Axon2000 is a graphical tool for 
- Generating Ideas
- Concept Mapping
- Writing, etc.

A FREE Lite version can be downloaded from:
   http://web.singnet.com.sg/~axon2000

=====================================================
Chan Bok                 E-mail: axon2000@mbox2.singnet.com.sg
Axon Research        Web: http://web.singnet.com.sg/~axon2000
5, Lengkok Merak    Tel: (065)-7360422
Singapore 248860    Fax: (065)-7333497
=====================================================

From owner-software@net.bio.net Wed Oct 06 15:47:00 1999
Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!204.71.34.3!newsfeed.cwix.com!newsfeeds.belnet.be!naxos.belnet.be!news.belnet.be!news.vub.ac.be!not-for-mail
From: Loytynoja Ari <apl@alize.ulb.ac.be>
Newsgroups: bionet.software
Subject: Re: Any site focusing on transporter, exchanger or pumps?
Date: Wed, 06 Oct 1999 18:28:27 +0200
Organization: ULB
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Hi,

I wonder if I'm a bit late? Anyway, here are some places focusing 
on yeast transporters.

best, Ari

http://alize.ulb.ac.be/~bandre/ytpdb/
http://www.biology.ucsd.edu/~msaier/transport/titlepage.html


Your Full Name Here wrote:
> 
> Dear netters,
>     Does anyone know any web sites  focusing research on membrane
> transporters,exchangers or pumps? Manys thanks for any inputs.
> 
> regards,
> 
> Jin Lu

From owner-software@net.bio.net Thu Oct 07 02:03:00 1999
Path: biosci!SUNM.SHCNC.AC.CN!xietao
From: xietao@SUNM.SHCNC.AC.CN (xt)
Newsgroups: bionet.software
Subject: Re: Re: Any site focusing on transporter, exchanger or pumps?
Date: 6 Oct 1999 20:03:07 -0700
Organization: SIBC
Lines: 40
Sender: daemon@net.bio.net
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Hi, here is another:

ABC transporters: http://ir2lcb.cnrs-mrs.fr/ABC/


in 99-10-6 狟敁 06:28:00 ㄩ
>Hi,
>
>I wonder if I'm a bit late? Anyway, here are some places focusing 
>on yeast transporters.
>
>best, Ari
>
>http://alize.ulb.ac.be/~bandre/ytpdb/
>http://www.biology.ucsd.edu/~msaier/transport/titlepage.html
>
>
>Your Full Name Here wrote:
>> 
>> Dear netters,
>>     Does anyone know any web sites  focusing research on membrane
>> transporters,exchangers or pumps? Manys thanks for any inputs.
>> 
>> regards,
>> 
>> Jin Lu

Tao Xie
------------------------------------------------------
Bioinformatics & Protein Engineering Lab.
320# Yue Yang Road, Shanghai, P. R. China, 200031
Shanghai Institute of Biochemistry 
Chinese Academy of Sciences
Telephone: (86)-(21)-64374430 ext 255
Fax:           (86)-(21)-64338357
E-mail: xietao@sunm.shcnc.ac.cn
www: http://202.127.24.111 
------------------------------------------------------


From owner-software@net.bio.net Thu Oct 07 03:08:00 1999
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Reply-To: "Hilton Evans" <hfevans@ici.net>
From: "Hilton Evans" <hfevans_nospam@ici.net>
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Subject: Predict C-13 NMR Shifts
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NMRPen--C-13  NMR Shifts  -- http://home.ici.net/~hfevans/nmrpen.htm


-- 
Hilton Evans
Organic Reactions  -- http://home.ici.net/~hfevans/reactions.htm
ChemPen3D Molecular Mechanics  for Win95/NT --  http://home.ici.net/~hfevans/chempen3d.htm
Chempen Chemical Structure Drawing  -- http://home.ici.net/~hfevans/chempen.htm


From owner-software@net.bio.net Thu Oct 07 03:29:00 1999
Path: biosci!YEAH.NET!lftian
From: lftian@YEAH.NET
Newsgroups: bionet.software
Subject: How to convenient get PHRED?PHRAP/CONSED
Date: 6 Oct 1999 21:29:53 -0700
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Hello everyone,

We are using MegaBase sequencer now.We want to try PHRED package instead of 
Sanger Assembly. 

Could you tell me How to conveniently get the package? I plan to install
them on RedHat Linux,but is it possible for other platforms?

Lifeng Tian
BioDoor Gene Development LTD.
lftian@yeah.net


___________________________________________________________________
辣茩妏蚚厙眢4M諾潔腔轎煤萇赽蚘眊 http://freemail.yeah.net
辣茩蠟隆堐厙眢<<轎煤萇赽膳昜>> http://www.163.com/mail


From owner-software@net.bio.net Thu Oct 07 05:39:00 1999
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From: greg@franklin.burnham-inst.org (Dr. Greg Quinn)
Newsgroups: bionet.software
Subject: Re: How to convenient get PHRED?PHRAP/CONSED
Date: 7 Oct 1999 06:37:58 GMT
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lftian@YEAH.NET wrote:
: Hello everyone,
: 
: We are using MegaBase sequencer now.We want to try PHRED package instead of 
: Sanger Assembly. 
: 
: Could you tell me How to conveniently get the package? I plan to install
: them on RedHat Linux,but is it possible for other platforms?

http://www.phrap.com/phred/

I've set it up on Solaris and it works fine; I believe there are 
commercial ports to Mac (and NT?)

From owner-software@net.bio.net Thu Oct 07 13:47:00 1999
Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.cwix.com!newsfeeds.belnet.be!news.belnet.be!colt.net!Pollux.Teleglobe.net!server-b.cs.interbusiness.it!news.tin.it!not-for-mail
From: madQ <madq968@djeksta.comNOSPAM>
Newsgroups: bionet.software
Subject: Download Ia.n.i.!!! It's free!
Date: 4 Oct 1999 20:47:57 GMT
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Download Ia.n.i. RemoteControlSystem 1.2 beta. It's free!!!
New site: http://members.tripod.com/IaniProject/


From owner-software@net.bio.net Thu Oct 07 20:50:00 1999
Path: biosci!EATWORMS.SWMED.EDU!tim
From: tim@EATWORMS.SWMED.EDU (Tim Niacaris)
Newsgroups: bionet.software
Subject: Primerfinder--A free web based primer design tool
Date: 7 Oct 1999 14:49:45 -0700
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Message-ID: <3.0.6.32.19991007164244.0097cc70@eatworms.swmed.edu>
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Announcing Primerfinder V0.06


Primerfinder is a fast and easy web based primer design program.
Primerfinder can search any sequence you input for primers that meet your
specifications according to several search parameters.  You can specify a
target primer length, annealing temp, percent GC and many other advanced
search parameters.  Additionally, Primerfinder can analyze candidate
primers with Integrated DNA Technology's Oligo Analyzer (powered by
DNASTAR) for possible hairpin and self-dimer formation.  Primerfinder can
also examine primers you have already created by other means with IDT's
Oligo Analyzer.  The main primerfinder search page can be found at:

http://eatworms.swmed.edu/~tim/primerfinder/

A description of Primerfinder and instructions for its use can be found at:

http://eatworms.swmed.edu/~tim/primerfinder/helpfiles/

__________________________________________________________________________

Tim Niacaris    
Department of Molecular Biology
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.  Dallas, TX  75235-9148
E-mail: tim@eatworms.swmed.edu    Home Page: http://eatworms.swmed.edu/~tim

From owner-software@net.bio.net Fri Oct 08 00:15:00 1999
Path: biosci!biosci!not-for-mail
From: adam moore <Adam.Moore@nottingham.ac.uk>
Newsgroups: bionet.software
Subject: Request for SMILES to 2D algorithm
Date: 7 Oct 1999 18:15:42 -0700
Organization: ACS, The University of Nottingham
Lines: 13
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Distribution: world
Message-ID: <Pine.SOL.4.05.9910071623170.673-100000@granby>
NNTP-Posting-Host: net.bio.net

Hi there!

I'm trying to find a script/algorithm/code fragment that will generate a
2D coordinate set from a SMILES formula (e.g. CCc1ccccc1CO)
Please mail anything available to:
adam.moore@stones.com

Adam Moore
Virtual School of Molecular Sciences
School of Pharmaceutical Science, University of Nottingham
http://www.vsms.nottingham.ac.uk/vsms/


From owner-software@net.bio.net Fri Oct 08 01:01:00 1999
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Message-ID: <37FD4E94.B1D5FEFB@mciworld.com>
From: "Jeremy.Parsons" <jeremy.parsons@mciworld.com>
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Subject: Re: sequence trace files format problem
References: <7se2vp$n8v@gazette.bcm.tmc.edu>
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Dear Paula,

It is a Mac JVM problem that is fixed if you install MRJ 2.1.4 and
use the latest IE. I haven't tried the latest Netscape but hope that
the Sun/Netscape/AOL alliance may finally produce a JDK1.1 JVM
that works.

Jeremy Parsons

Paula Burch wrote:

> The sequencing core provides traces to users of various computer
> systems, Mac, Unix, or MS Windows. We have installed a java
> traceviewer that works great in Netscape on the Unix or PC side,
> but fails to work in either Netscape or Internet Explorer on the Mac.
> The easy answer would be to just give our Mac users their own trace
> viewing program, such as the free one from Perkins Elmer.
>
> The problem is that trace files moved to the sequence repository
> machine from the sequencing Mac can be used only by a Mac, not by
> Unix, if tranferred as a Mac binary. If the trace files are moved as
> 'raw data', they work great in the java trace viewing program, but
> are utterly unusable on a Mac.
>
> How can I make 'raw data' trace files work on a Mac? I was told
> something I didn't understand about a missing 'resource fork' that
> the Mac needs. I generally stick to Unix and am mystified. Is
> there any way to fake the resource fork, or any other way to make one
> transfer format work for all three of the more popular computer
> platforms, Mac, Unix, and PC?
>
> We cannot ask the sequencing core personnel to transfer the trace
> files to some labs in Mac binary format and to other labs in 'Raw
> Data' format.
>
> Thanks for any help you can provide....
>
> ________________________________________________________________________
> Paula E. Burch, Ph.D.             Molecular Biology Computation Resource
> Baylor College of Medicine, BCMM M220                voice: 713.798.6023
> One Baylor Plaza, Houston, Texas 77030                 fax: 713.798.4279
> http://mbcr.bcm.tmc.edu/pburch.html            email: pburch@bcm.tmc.edu


From owner-software@net.bio.net Fri Oct 08 03:49:00 1999
Path: biosci!APICE.ORG.CO!agclex
From: agclex@APICE.ORG.CO (alex)
Newsgroups: bionet.software
Subject: in spanish
Date: 7 Oct 1999 21:49:34 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
Lines: 6
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for those of you who wish to visit the colombian academy of sciences, we 
wellcome you all, if you would like to contribute to one of our 
publication please do not heistate to ocntact us, cheers


http://www.accefyn.org.co

From owner-software@net.bio.net Fri Oct 08 05:12:00 1999
Path: biosci!RAGINGBULL.COM!petexy
From: petexy@RAGINGBULL.COM ("Davis")
Newsgroups: bionet.software
Subject: It was complete
Date: 7 Oct 1999 23:12:38 -0700
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From owner-software@net.bio.net Fri Oct 08 07:52:00 1999
Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newsfeed.icl.net!newsfeed.icl.net!newsfeed.nacamar.de!rz.uni-karlsruhe.de!news.uni-stuttgart.de!news.urz.uni-heidelberg.de!news.urz.uni-heidelberg.de!not-for-mail
From: Andreas Bohne <aboh24@gmx.de>
Newsgroups: bionet.software
Subject: Re: Request for SMILES to 2D algorithm
Date: Fri, 08 Oct 1999 10:21:06 +0200
Organization: University of Heidelberg, Germany
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> I'm trying to find a script/algorithm/code fragment that will 
> generate a 2D coordinate set from a SMILES formula (e.g. CCc1ccccc1CO)
http://www2.ccc.uni-erlangen.de/services/gif.html

From owner-software@net.bio.net Fri Oct 08 09:14:00 1999
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From: curiouser@gene.ccmbindia.org ("Malay")
Newsgroups: bionet.software
Subject: Re: How to convenient get PHRED?PHRAP/CONSED
Date: 8 Oct 1999 11:06:59 +0100
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I want to know whether any port to DOS is known. And what is the address?

Malay

----- Original Message -----
From: <lftian@YEAH.NET>
To: <bio-software@hgmp.mrc.ac.uk>
Sent: Thursday, October 07, 1999 9:59 AM
Subject: How to convenient get PHRED?PHRAP/CONSED


: Hello everyone,
:
: We are using MegaBase sequencer now.We want to try PHRED package instead
of
: Sanger Assembly.
:
: Could you tell me How to conveniently get the package? I plan to install
: them on RedHat Linux,but is it possible for other platforms?
:
: Lifeng Tian
: BioDoor Gene Development LTD.
: lftian@yeah.net
:
:
:
: ___________________________________________________________________
: 辣茩妏蚚厙眢4M諾潔腔轎煤萇赽蚘眊 http://freemail.yeah.net
: 辣茩蠟隆堐厙眢<<轎煤萇赽膳昜>> http://www.163.com/mail
:

---

From owner-software@net.bio.net Fri Oct 08 11:06:00 1999
Path: biosci!newsfeed.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!oleane!jussieu.fr!unilim.fr!news.cict.fr!news.u-bordeaux.fr!not-for-mail
From: "PICHON CHRISTOPHE" <pichon_c@hotmail.com>
Newsgroups: bionet.software
Subject: Need ABI377 and 3700 chromatogram file format.
Date: Fri, 8 Oct 1999 20:01:42 +0200
Organization: Universite Bordeaux I
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Hello,

I am searching for a person who can send to me a description of the ABI 377
or/and 3700 data file format, chromatogram picture and AGCT data.

Thanks


From owner-software@net.bio.net Fri Oct 08 11:07:00 1999
Path: biosci!newsfeed.stanford.edu!paloalto-snf1.gtei.net!su-news-hub1.bbnplanet.com!chicago-news-feed1.bbnplanet.com!news.gtei.net!news.itis.com!ebv.oncology.wisc.edu!aiyar
From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar)
Newsgroups: bionet.software
Subject: Re: How to convenient get PHRED?PHRAP/CONSED
Date: 8 Oct 1999 11:55:57 GMT
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-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On 8 Oct 1999 11:06:59 +0100,
    Malay (curiouser@gene.ccmbindia.org) wrote:
>I want to know whether any port to DOS is known. And what is the address?

Not to my knowledge.  However phrap/phred can be compiled with
the cygwin32 compiler, and the mingw32 compiler (with minor changes),
so perhaps they can be compiled with djgpp as well.

For more information on phrap/phred/consed take a look at:
http://bozeman.genome.washington.edu
and
http://www.phrap.com

Later,
Ashok
- -- 
Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research
aiyar@ebv.oncology.wisc.edu
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From owner-software@net.bio.net Fri Oct 08 14:24:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!newsgate.cuhk.edu.hk!newsfeeder.ust.hk!news!not-for-mail
From: "Cyber Judge" <cyber_judge@usa.net>
Newsgroups: alt.es.hackers.software,bionet.software,ied.w95.discussion,ied.y2k.discussion
Subject: Unknow backup file type
Date: Fri, 8 Oct 1999 23:05:49 +0800
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Dear Everyone;

One of our staff members have left our company, he left some BACKUP disks in
his draw. We cannot open it back.

There are 6  1.44MB floppy disks, each disk have a file call cc60703a.001 to
cc60703.006.

Does anyone what backup software it is?
If you know would you tell me what it is, and e-mail me back at

ottolee@hotmail.com

Thank you.


From owner-software@net.bio.net Fri Oct 08 14:46:00 1999
Path: biosci!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.tli.de!news.ndh.net!not-for-mail
From: Armin Ollig <ollig@biofrontera.de>
Newsgroups: bionet.software
Subject: Re: Need ABI377 and 3700 chromatogram file format.
Date: Fri, 08 Oct 1999 17:34:40 +0200
Organization: Biofrontera Pharmaceuticals GmbH
Lines: 23
Message-ID: <37FE0F10.1A6F0ED3@biofrontera.de>
References: <7tkm6t$2n9$1@news.u-bordeaux.fr>
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To: pichon_c@hotmail.com
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PICHON CHRISTOPHE wrote:
> 
> Hello,
> 
> I am searching for a person who can send to me a description of the ABI 377
> or/and 3700 data file format, chromatogram picture and AGCT data.
> 
> Thanks

There's a postscipt document written by Mr. Clark Tibbetts. 
Search altavista for it. 

You may also want to contact ABI directly and ask them for a description
of the format.

Good luck ! ;^]

--armin

--
"To save energy
    the light at the end of the tunnel
         will temporarily be switched off."

From owner-software@net.bio.net Fri Oct 08 17:07:00 1999
Path: biosci!newsfeed.stanford.edu!logbridge.uoregon.edu!news.nero.net!phelpsj_stuff
From: phelpsj_stuff@spam_stuff.bcc.orst.edu (Jim Phelps)
Newsgroups: bionet.software
Subject: Re: sequence trace files format problem
Date: Fri, 08 Oct 1999 10:59:48 -0700
Organization: CGRB
Lines: 24
Message-ID: <phelpsj_stuff-0810991059480001@phelps-3140-c.cordley.orst.edu>
References: <7se2vp$n8v@gazette.bcm.tmc.edu> <37FD4E94.B1D5FEFB@mciworld.com>
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X-Newsreader: MT-NewsWatcher 2.4.4

In article <37FD4E94.B1D5FEFB@mciworld.com>, jparsons@hgmp.mrc.ac.uk wrote:

> Dear Paula,
> 
> It is a Mac JVM problem that is fixed if you install MRJ 2.1.4 and
> use the latest IE. I haven't tried the latest Netscape but hope that
> the Sun/Netscape/AOL alliance may finally produce a JDK1.1 JVM
> that works.


If the JVM fix doesn't work for you, you can try using TAS from Syntax to
transfer your files to the UNIX box.  TAS lets you drag-and-drop your
files.  It preserves all of the Mac attributes but it does convert the
files so UNIX can read them.

This worked for us.

- Jim Phelps

-- 
Director                            /  Computer Support & Planning
Biological Computing Consortium    /                       C.G.R.B.
                 (phelpsj at bcc dot orst dot edu)
Oregon State University,   Center for Gene Research & Biotechnology 

From owner-software@net.bio.net Fri Oct 08 21:12:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!tank.news.pipex.net!pipex!server1.netnews.ja.net!warwick!not-for-mail
From: Web Administrator <webadmin@globin.bio.warwick.ac.uk>
Newsgroups: bionet.software
Subject: ANNOUNCE: PSIPRED Server Update
Date: 8 Oct 1999 22:03:11 GMT
Organization: University of Warwick
Lines: 49
Message-ID: <7tlpmv$n0t$1@wisteria.csv.warwick.ac.uk>
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User-Agent: tin/pre-1.4-980618 (UNIX) (Linux/2.2.10 (i686))


PSIPRED Latest News

http://globin.bio.warwick.ac.uk/psipred

Authors: David Jones, Kevin Bryson & Liam McGuffin

PSIPRED is a Web based protein structure prediction service hosted
by the Protein Bioinformatics Lab at the University of Warwick, U.K.

Three prediction methods are currently implemented. PSIPRED is the
most accurate method currently available for the prediction of protein
secondary structure. MEMSAT2 predicts transmembrane protein structure
and topology from multiple sequence information. GenTHREADER
offers protein tertiary structure prediction by profile-based fold
recognition.

*** NEW THIS MONTH: a facility has been added to generate publication quality
colour cartoon representations of PSIPRED secondary structure results.
*****************************************************************************

Binary versions of the PSIPRED secondary structure prediction software
can also be downloaded for SGI, Linux and Sun systems from the following URL:

ftp://ribosome.bio.warwick.ac.uk/pub/PSIPRED


LICENSING
=========

PSIPRED/MEMSAT/GenTHREADER Server: Free to academics. Commercial users must
obtain a license to access it.

PSIPRED Binaries: Free both to academic and commercial users - however the
program may not be sold or incorporated into a commercial package. Please see
the program documentation for full details on the licensing terms.


REFERENCES
==========

Jones, D.T. (1999) Protein secondary structure prediction based on
position-specific scoring matrices. J. Mol. Biol. 292:195-202.

Jones, D.T. (1999) GenTHREADER: An efficient and reliable protein fold
recognition method for genomic sequences. J. Mol. Biol. 287:797-815.

http://globin.bio.warwick.ac.uk/psipred


From owner-software@net.bio.net Fri Oct 08 21:15:00 1999
Path: biosci!pravda.ucr.edu!ihnp4.ucsd.edu!newsfeed.berkeley.edu!howland.erols.net!vixen.cso.uiuc.edu!not-for-mail
From: Jim Phillips <jim@ks.uiuc.edu>
Newsgroups: bionet.software
Subject: ANNOUNCE: NAMD 2.1b2
Date: Fri, 08 Oct 1999 17:08:43 -0500
Organization: University of Illinois
Lines: 34
Message-ID: <37FE6B6B.5F36EB22@ks.uiuc.edu>
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+--------------------------------------------------------------------+
|                                                                    |
|                  NAMD 2.1b2 Release Announcement                   |
|                                                                    |
+--------------------------------------------------------------------+

                                                   October 8, 1999

The Theoretical Biophysics Group at the University of Illinois is
proud to announce the public release of a new version of NAMD, a
parallel, object-oriented molecular dynamics code designed for
high-performance simulation of large biomolecular systems.  NAMD is
distributed free of charge and includes source code.  NAMD development
is supported by the NIH National Center for Research Resources.

NAMD 2.1b2 is more stable than NAMD 2.0 and adds several new features:

- Mollified impulse multiple timestepping method.

- Faster particle mesh Ewald implementation.

- Periodic boundaries for non-orthogonal cells.

- New interactive molecular dynamics interface to VMD.

NAMD is available from http://www.ks.uiuc.edu/Research/namd/.

The Theoretical Biophysics group encourages NAMD users to be closely
involved in the development process through reporting bugs, contributing
fixes, periodical surveys and via other means.  Any questions or
comments
may be directed to namd@ks.uiuc.edu.

We are eager to hear from you, and thank you for using our software!

From owner-software@net.bio.net Fri Oct 08 23:40:00 1999
Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!not-for-mail
From: Nirav Merchant <nirav@arl.arizona.edu_no_spam>
Newsgroups: bionet.software
Subject: Re: sequence trace files format problem
Date: Fri, 08 Oct 1999 17:18:45 -0700
Organization: Arizona Research Labs, University of Arizona
Lines: 50
Message-ID: <37FE89E5.AC25E99D@arl.arizona.edu_no_spam>
References: <7se2vp$n8v@gazette.bcm.tmc.edu>
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To: Paula Burch <pburch@condor.bcm.tmc.edu>

Paula,
    I am not sure if this will answer you question  ..but we encountered a
similar problems when we developed our "online" ordering and delivery system
for our DNA seq. facility.
    The work around was ...instead using http URL to download the file we
used ftp URL
i.e ftp://dna.arizona.edu/pub/file.cro instead of
http://dna.arizona.edu/file.cro.
    We have users opening these files on mac using Editview and PC users
using chromas/abiview ..unix folks using trev/gcg etc.

regards,
Nirav


Paula Burch wrote:

> The sequencing core provides traces to users of various computer
> systems, Mac, Unix, or MS Windows. We have installed a java
> traceviewer that works great in Netscape on the Unix or PC side,
> but fails to work in either Netscape or Internet Explorer on the Mac.
> The easy answer would be to just give our Mac users their own trace
> viewing program, such as the free one from Perkins Elmer.
>
> The problem is that trace files moved to the sequence repository
> machine from the sequencing Mac can be used only by a Mac, not by
> Unix, if tranferred as a Mac binary. If the trace files are moved as
> 'raw data', they work great in the java trace viewing program, but
> are utterly unusable on a Mac.
>
> How can I make 'raw data' trace files work on a Mac? I was told
> something I didn't understand about a missing 'resource fork' that
> the Mac needs. I generally stick to Unix and am mystified. Is
> there any way to fake the resource fork, or any other way to make one
> transfer format work for all three of the more popular computer
> platforms, Mac, Unix, and PC?
>
> We cannot ask the sequencing core personnel to transfer the trace
> files to some labs in Mac binary format and to other labs in 'Raw
> Data' format.
>
> Thanks for any help you can provide....
>
> ________________________________________________________________________
> Paula E. Burch, Ph.D.             Molecular Biology Computation Resource
> Baylor College of Medicine, BCMM M220                voice: 713.798.6023
> One Baylor Plaza, Houston, Texas 77030                 fax: 713.798.4279
> http://mbcr.bcm.tmc.edu/pburch.html            email: pburch@bcm.tmc.edu


From owner-software@net.bio.net Sat Oct 09 03:17:00 1999
Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!diablo.theplanet.net!colt.net!Pollux.Teleglobe.net!server-b.cs.interbusiness.it!TESORO.GREEN.MinisterodelTesoro-CentroComunicativo.com
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Date: Fri, 8 Oct 1999 17:48:38 +0200 
Message-ID: <04B596965534D31196710000F81EA08901E6E48C@news.tesoro.it>
From: knydnb@rec.uk
Subject: Important issue !  1680   [2/2]
Lines: 2


From owner-software@net.bio.net Sat Oct 09 04:17:00 1999
Path: biosci!BOOM.COM!freetravela
From: freetravela@BOOM.COM
Newsgroups: bionet.software
Subject: Free Vacation when you Request the Info...
Date: 8 Oct 1999 22:17:40 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
Lines: 18
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          GET YOUR FREE VACATION VOUCHER WHEN 
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From owner-software@net.bio.net Sat Oct 09 13:33:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!ctu-gate!news.nctu.edu.tw!news.neto.net!hp1.timenet.net!netnews.hinet.net!news
From: "梁嘉棋" <f84001@ms25.hinet.net>
Newsgroups: bionet.software
Subject: 有關GHOST!!
Date: Sat, 9 Oct 1999 22:25:41 +0800
Organization: DCI HiNet
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請問GHOST 5.1能否將同一個映像檔使用在其他硬碟。


From owner-software@net.bio.net Sat Oct 09 18:45:00 1999
Path: biosci!newsfeed.stanford.edu!logbridge.uoregon.edu!news.indiana.edu!not-for-mail
From: gilbertd@bio.indiana.edu (Don Gilbert)
Newsgroups: bionet.software
Subject: SeqPup, biosequence editor, version 0.9e release
Date: 9 Oct 1999 19:38:41 GMT
Organization: Biology, Indiana University - Bloomington
Lines: 44
Message-ID: <7to5k1$u26$1@flotsam.uits.indiana.edu>
NNTP-Posting-Host: chipmunk.bio.indiana.edu


SeqPup, version 0.9e, October 1999

SeqPup is a biological sequence editor and analysis program.  It
includes links to network services and external analysis
programs.  It is usable on common computer systems that support
the Java runtime environment, including Macintosh, MS-Windows and
X-Windows.

This release is easier to install and use.

Features include
  multiple sequence alignment and single sequence editing
  read and write several sequence file formats 
  sequence feature editing, manipulation and marking in prints
  translate dna/protein, consensus, reverse/complement, and distance methods 
  pretty print of alignments and sequences with boxed and shaded regions
  Internet Sequence Retrieval System (SRS), and NCBI-BLAST searches 
  User Plug-in sequence manipulations and analyses
  User-definable links to external analysis programs, including
    ClustalW multiple alignment, CAP contig assembly, tacg restriction map
  Remote program client-server interface, using CORBA protocol 

Additions to this Java release include sequence document and
feature manipulation and display, enhanced sequence file
handling, enhanced drawing/pretty print methods, including PDF
output, user-developed plug-in methods for sequence analysis and
display (Java classes),  improved single-sequence editing,
improved alignment manipulations.

This application is a work in progress; it has bugs still.  
Your comments are welcome. Email:  seqpup@bio.indiana.edu.

Find this software at
  http://iubio.bio.indiana.edu/soft/molbio/seqpup/java/
  ftp://iubio.bio.indiana.edu/molbio/seqpup/java/ 

[this update superceeds version 0.9c of september]

-- Don

--
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd@bio.indiana.edu

From owner-software@net.bio.net Sun Oct 10 00:52:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!newshub.northeast.verio.net!howland.erols.net!spring.edu.tw!netnews.hinet.net!news
From: wunart@crosswinds.net
Newsgroups: bionet.software
Subject: Active X with Source code for only USD $199
Date: 10 Oct 1999 01:46:02 GMT
Organization: wunart
Lines: 12
Message-ID: <7tor4q$ae@netnews.hinet.net>
NNTP-Posting-Host: 210.242.153.252

Active X with Source code for only USD $199

The Active X for CTI.

It is for Dialogic Analog board -
    D/41H, D/41ESC, VFX/40, D/160SC-LS

It is only USD $199 include source code.

Contact wunart@crosswinds.net  if you need it.


From owner-software@net.bio.net Sun Oct 10 21:42:00 1999
Path: biosci!newsfeed.stanford.edu!skynet.be!bignews.mediaways.net!newsfeed.nettuno.it!server-b.cs.interbusiness.it!news.tin.it!not-for-mail
From: "giuseppe" <mercuzio@tin.it>
Newsgroups: bionet.software
Subject: Z80 COME FUNZIONA
Date: Sun, 10 Oct 1999 23:56:25 +0200
Organization: TIN
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SI


From owner-software@net.bio.net Sun Oct 10 21:52:00 1999
Path: biosci!BOOM.COM!traveling1
From: traveling1@BOOM.COM
Newsgroups: bionet.software
Subject: Automatic Travel Business!
Date: 10 Oct 1999 15:52:17 -0700
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-------------------------------------------------
This mailing list is opt-in only. We are linked 
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to our mailing list. To be removed place your email
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From owner-software@net.bio.net Mon Oct 11 03:11:00 1999
Path: biosci!rutgers!news.sgi.com!news.maxwell.syr.edu!newsfeeds.belnet.be!news.belnet.be!isdnet!proxad.net!Pollux.Teleglobe.net!server-b.cs.interbusiness.it!news.tin.it!not-for-mail
From: madQ <madq968@djeksta.comNOSPAM>
Newsgroups: bionet.software
Subject: Download Ia.n.i.!!! It's free!
Date: 10 Oct 1999 12:15:14 GMT
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Download Ia.n.i. RemoteControlSystem 1.2 beta. It's free!!!
New site: http://jump.to/IaniProject


From owner-software@net.bio.net Mon Oct 11 10:17:00 1999
Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!nntp2.deja.com!nnrp1.deja.com!not-for-mail
From: indies@my-deja.com
Newsgroups: bionet.software
Subject: search free software
Date: Mon, 11 Oct 1999 10:59:40 GMT
Organization: Deja.com - Before you buy.
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X-MyDeja-Info: XMYDJUIDindies

 search free software for collect data to a Sartorius's balancewith a
serail port on my PC.
i test windmill but not good
thanck

--
********************************************
*    Remove the ~ me to contact            *
* Go to F.W.I with  Media Evasion.         *
* http://www.multimania.com/vdelorme       *


Sent via Deja.com http://www.deja.com/
Before you buy.

From owner-software@net.bio.net Mon Oct 11 13:27:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!news-xfer.epix.net!news1.epix.net!not-for-mail
From: "Jeffrey Peter, M.D." <kidsdoc2000@hotmail.com>
Newsgroups: bionet.software
References: <Pine.OSF.3.92.990917170333.29768A-100000@reindeer.mips.biochem.mpg.de> <002a01bf01ef$b154cf00$7b02a8c0@nic.in> <37EADB83.CC021C71@bruxton.com> <003a01bf0823$770bc1c0$7b02a8c0@nic.in> <37F01F7A.82259D0D@bruxton.com>
Subject: Re: C++ gui development
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Date: Mon, 11 Oct 1999 14:20:53 GMT
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Dan Brown wrote in message <37F01F7A.82259D0D@bruxton.com>...
>Malay wrote:
>>
>> I understand the temptation to use JAVA, particularly after the
>> introduction of SWING classes. But is it not pity that the developers in
as
>> powerful language like C++ never thought of writing cross-platform
>> libraries? I think if this trend continues, C++ will lose most of its
>> ardent followers like me to other language like JAVA.
>>
>
>We never found cross-platform libraries for C++ to be very useful. The
>problem is that they could not keep up with user interface changes from
>Microsoft. I believe that this is due to a lack of market: C++
>developers want a C++ class library for use when writing GUI
>applications, and Microsoft provides MFC at no cost with Visual C++.
>This reduces the market for third-party class libraries for GUI
>development sufficiently that the suppliers have a hard time surviving.
>

I used Visual C++ with MFC with very good results (www.msu.edu/~utz, go to
thesis). It was easy to learn and there are some good books out there that
explain it will (I used SAMS's teach yourself Visual C++ 4.0 in 14 days and
Microsoft's Inside Visuall C++, by Kruglinski (for version 5.0)). Of course,
there are more up to date books out there. Plus microsoft has a lot of the
documentation on CDROM and on its web site
>
<stuff deleted>

Jeff Utz


From owner-software@net.bio.net Mon Oct 11 13:28:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!news-xfer.epix.net!news1.epix.net!not-for-mail
From: "Jeffrey Peter, M.D." <kidsdoc2000@hotmail.com>
Newsgroups: bionet.software
References: <Pine.OSF.3.92.990917170333.29768A-100000@reindeer.mips.biochem.mpg.de> <002a01bf01ef$b154cf00$7b02a8c0@nic.in> <37EADB83.CC021C71@bruxton.com> <003a01bf0823$770bc1c0$7b02a8c0@nic.in> <37F01F7A.82259D0D@bruxton.com> <000601bf0f3e$3ef202a0$7b02a8c0@nic.in> <37FA2428.CFCCE29D@bruxton.com> <001701bf0f78$5d74efa0$7b02a8c0@nic.in>
Subject: Re: C++ gui development
Lines: 75
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NNTP-Posting-Date: Mon, 11 Oct 1999 10:21:47 EDT


"Malay" wrote in message <001701bf0f78$5d74efa0$7b02a8c0@nic.in>...
>: The problem is that most software developers want to be paid for their
>: time.
>

Get a graduate student. They are cheap.

Jeffrey Utz

>Sure! But for a non-commercial developer, the appreciation that matters
>most, like in case of any creative work.
>
>: : A company such as Apple, and the UNIX vendors, can subsidise the cost
>of
>: development tools, because it means that more software is available for
>: their platforms. They make their money on the hardware.
>
>But it not always true. The free development tools is a sort of "culture",
>that's been long practised in Unix bandwagon. And more software also means
>more sell of hardware. MS seems to be interested making money out of both
>"the cow" as well as the "milk". That's detrimental when cows are available
>free.
>
>:A company such
>: as Microsoft can make money on sales of Windows, and subsidise the cost
>: of Visual C++ (which I don't believe they do any more).
>
>That's exactly what I say. When Unix vendors can give away their developing
>tools as a part of their operating system. Why not microsoft? Linux is
>rapidly gaining market because of this. Particularly, individual developers
>are more interested in Linux.
>
>:Sun can afford
>: to spend a fortune developing Java (the development of standarized
>: libraries is very expensive), because it increases the market for their
>: servers, and without it, Sun will not exist as Microsoft products become
>: more popular on the desktop.
>
>That's may be true when it comes to "server". But noone can deny that JAVA
>is rapidly becoming an ubiquitous developing environment. SUN created a
>revolution in thinking, may be unknowingly or unintentionally. In the
>coming years, we will definitely see more and more softwares are developed
>in JAVA and Microsoft will lose even the "cow".
>:
>: There is some very good software available at no cost (the GNU tools),
>: where people have donated their time. However, in general, as the cost
>: of software declines relative to the cost of hardware, I expect to see
>: fewer and fewer subsidised development tools.
>
>I completely disagree. I think just the contrary, the developing tools will
>be completely free, as the softwares. And more and more softwares will be
>written by individuals rather than corporates as is happening in
>bioinformatics. Linux will be the operating system, primarily because the
>softwares that comes with it are free, both the tools as well as the
>applications.
>
>:
>: I have been writing computer programs since 1966, and it is my
>: observation that in the computer market there is always a monopolist,
>: and many people do not like that monopolist. However, dislike of a
>: monopolist is insufficient to bring about a new form of computing. So
>: far, that has always been driven by commercial demand.
>:
>
>We are thinking about future. What you said was true in the past. It was a
>"developers market". In future, it will be "user's market".
>
>Malay
>
>
>
>---


From owner-software@net.bio.net Mon Oct 11 14:23:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!newshub.sdsu.edu!franklin.ljcrf.edu!not-for-mail
From: greg@franklin.burnham-inst.org (Dr. Greg Quinn)
Newsgroups: bionet.software
Subject: Re: C++ gui development
Date: 11 Oct 1999 15:22:28 GMT
Organization: COMPUTATIONAL BIOLOGY at The BURNHAM INSTITUTE
Lines: 10
Message-ID: <7tsvbk$hmm$1@franklin.ljcrf.edu>
References: <Pine.OSF.3.92.990917170333.29768A-100000@reindeer.mips.biochem.mpg.de> <002a01bf01ef$b154cf00$7b02a8c0@nic.in> <37EADB83.CC021C71@bruxton.com> <003a01bf0823$770bc1c0$7b02a8c0@nic.in> <37F01F7A.82259D0D@bruxton.com> <000601bf0f3e$3ef202a0$7b02a8c0@nic.in> <37FA2428.CFCCE29D@bruxton.com> <001701bf0f78$5d74efa0$7b02a8c0@nic.in> <%nmM3.989$mR1.186598@news1.epix.net>
NNTP-Posting-Host: franklin.ljcrf.edu
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Jeffrey Peter, M.D. (kidsdoc2000@hotmail.com) wrote:
: 
: "Malay" wrote in message <001701bf0f78$5d74efa0$7b02a8c0@nic.in>...
: >: The problem is that most software developers want to be paid for their
: >: time.
: >
: 
: Get a graduate student. They are cheap.

...or a postdoc; I assume this is flame-bait.

From owner-software@net.bio.net Mon Oct 11 14:34:00 1999
Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!nntp.abs.net!newshub2.home.com!news.home.com!news1.rdc1.on.wave.home.com.POSTED!not-for-mail
From: beta@datacow.com (Ken Gregoire)
Newsgroups: bionet.software
Subject: Need Beta Testers for Portfolio Software c/w Technical
Organization: DataCow Technologies
Reply-To: beta@datacow.com
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NNTP-Posting-Date: Mon, 11 Oct 1999 08:27:22 PDT

Looking for Beta Testers to test EZStock Plus 2.1

EZStock Plus 2.1 includes new Technical Analysis and Indicators
including:
 - Intermarket - Overlays, RSA, Correlation
 - Trends - Trend lines, Bollinger Bands, Moving Average, Exponential
Smoothing, LSQ Lines.
 -  Indicators - RSI, MACD, K%D, PVI, MTM, OBV, CCI, NVI
 - Forecaster - based on GARCH and Spectral Analysis

Technical Analysts welcome!

To obtain EZStock Plus 2.1 Beta
www.datacow.com/download/ezstockplus21.exe

Please send comments, suggestions, bugs to: beta@datacow.com

Ken Gregoire
DataCow Technologies
www.datacow.com

From owner-software@net.bio.net Mon Oct 11 15:24:00 1999
Path: biosci!newsfeed.stanford.edu!logbridge.uoregon.edu!newsfeed.icl.net!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!not-for-mail
From: Ray Hicks <rh208@cus.cam.ac.uk>
Newsgroups: sci.med.laboratory,bionet.cellbiol,bionet.immunology,bionet.software
Subject: New Mac Flow Cytometry Software
Date: Mon, 11 Oct 1999 17:19:02 +0100
Organization: ttp://www.med.cam.ac.uk
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Xref: biosci bionet.cellbiol:12649 bionet.immunology:16800 bionet.software:24369

Announcing FCSPress, a new program for analysis of Flow Cytometric data,
featuring an easy to use interface complete with page layout functions
and saveable worksheets.  You can copy or save (probably the nicest
available) plots and data for  further manipulation in a wide range of
graphics and word processing applications.
FCSPress costs less than a bottle of antibody, or a few hours analysis
time at most facilities, you can use the fully-working demo free for a
month.

Download FCSPress, its documentation  and pricing information from

http://www.FCSPress.com

or e-mail me at

RayH@FCSPress.com

Ray


From owner-software@net.bio.net Mon Oct 11 15:26:00 1999
Path: biosci!newsfeed.stanford.edu!logbridge.uoregon.edu!dca1-hub1.news.digex.net!intermedia!lynx.unm.edu!news.NMSU.Edu!not-for-mail
From: "Donald D. Bustamante" <dbustama@nbif.org>
Newsgroups: bionet.software
Subject: Play Outbreak!
Date: Mon, 11 Oct 1999 09:58:08 -0600
Organization: National Biotechnology Information Facility
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X-Mailer: Mozilla 3.01Gold (WinNT; I)

The National Biotechnology Information Facility is pleased to announce
the availability of Outbreak!, a graphics-rich Internet game which
teaches the use of clinical microbiology skills.  

Visit Outbreak! at http://www.nbif.org/outbreak
-- 
Donald D. Bustamante, Project Manager/Co-PI
National Biotechnology Information Facility
Box 30002, Dept. 3548
Las Cruces, New Mexico USA  88003
(505)-646-5031    FAX:  (505)-522-9373
URL:  http://www.nbif.org

From owner-software@net.bio.net Mon Oct 11 21:42:00 1999
Path: biosci!pravda.ucr.edu!ihnp4.ucsd.edu!newsfeed.berkeley.edu!newsfeed.gamma.ru!Gamma.RU!demos!rosnet!mtu.ru!not-for-mail
From: "慔黨戀" <aloneboy@mtu-net.ru>
Newsgroups: bionet.software
Subject: I`m looking the programm
Date: Mon, 11 Oct 1999 03:36:18 +0300
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     Hello!
  Please, write to me about programm GTWHide v 2.0
  Of course, if somebody knows sonething.

       My  best regards


From owner-software@net.bio.net Mon Oct 11 22:01:00 1999
Path: biosci!bloom-beacon.mit.edu!eecs-usenet-02.mit.edu!netnews.com!newsfeed.gamma.ru!Gamma.RU!Radio-MSU.net!mtu.ru!not-for-mail
From: "慔黨戀" <aloneboy@mtu-net.ru>
Newsgroups: bionet.software,bionet.software.www.
Subject: I`m looking for the programm
Date: Tue, 12 Oct 1999 02:55:09 +0300
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    Hello, everybody!
  I`m looking for the programm  --  GTWHide v2.0 --.
  If you something about it,  send a message to me, please!

           Best regards!     Stay on air!

               aloneboy@mtu-net.ru


From owner-software@net.bio.net Tue Oct 12 01:17:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!feeder.qis.net!newsfeed1.earthlink.net!nntp.earthlink.net!posted-from-earthlink!not-for-mail
From: "Stan Hicks" <intuitivelogic@earthlink.net>
Newsgroups: bionet.software
Subject: New Charting / Data Graphics Software For Windows
Date: Mon, 11 Oct 1999 21:01:55 -0500
X-Posted-Path-Was: not-for-mail
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Message-ID: <7tu4ri$bev$1@ash.prod.itd.earthlink.net>

New! Version 2.5.0! ClickIt Graph http://www.clickitgraph.com

ClickIt Graph is state of the art 32 bit data graphics software for Windows�
95, 98 and NT 4.0. ClickIt Graph is a user friendly full featured data
graphics package that offers over 23 different graph types for business,
engineering and science  presentations. Data is input into a database format
compatible with Microsoft Access� that allows for the ease of use, data
import, and export between different application formats. ClickIt Graph also
supports linking with Microsoft Word� and PowerPoint� 97 and 2000. Transfer
of ClickIt Graph drawn graphs to a Word� document or PowerPoint�
presentation in a consistent presentation quality is as easy as pressing an
F key. Save graphs drawn with ClickIt Graph in a keyword driven database for
fast retrieval of your graphical information. ClickIt Graph supports two and
three-dimensional graph types including line, linear-logarithmic,
logarithmic-linear, logarithmic-logarithmic, scatter, 3D scatter, bar, 3D
bar, pie, 3D pie, 3D tape, 3D surface, polar, area, 3D area, box-whisker,
bubble, candlestick, open-high-low-close, high-low-close, gantt, and data
bound line. CLickIt Graph supports linear regression, polynomial,
logarithmic, exponential, power, inverse power and spline curve fitting.
Best fit, mean, maximum, minimum and standard deviation lines are available
for scatter and line graph types.  Up to 9th order polynomial functions are
supported. Regression equations for line, scatter, linear-logarithmic,
logarithmic-logarithmic, logarithmic-linear, polynomial, power, exponential
and inverse power functions are output to the graph legend and a text file.
Write HTML maps from your data graphs for Web publishing.


From owner-software@net.bio.net Tue Oct 12 15:07:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!newsfeed.tli.de!newscore.gigabell.net!newsfeed.dpn.de!news-out1.f.gtn.com!news-in1.f.gtn.com!news-in1.d.gtn.com!iradj.is-bremen.de!not-for-mail
From: Ilmari Krebs <ik@bdal.de>
Newsgroups: bionet.software
Subject: Re: Request for SMILES to 2D algorithm
Date: Tue, 12 Oct 1999 18:00:41 +0200
Organization: ISB GmbH
Message-ID: <38035B29.C34D771B@bdal.de>
References: <Pine.SOL.4.05.9910071623170.673-100000@granby>
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Try http://vanilla.ice.mpg.de/~stein/projects/SmilesViewer/ e.g.

Ilmari

adam moore wrote:
> 
> Hi there!
> 
> I'm trying to find a script/algorithm/code fragment that will generate a
> 2D coordinate set from a SMILES formula (e.g. CCc1ccccc1CO)
> Please mail anything available to:
> adam.moore@stones.com
> 
> Adam Moore
> Virtual School of Molecular Sciences
> School of Pharmaceutical Science, University of Nottingham
> http://www.vsms.nottingham.ac.uk/vsms/

From owner-software@net.bio.net Tue Oct 12 16:22:00 1999
Path: biosci!newsfeed.stanford.edu!skynet.be!newsfeed.icl.net!oleane!pasteur.fr!not-for-mail
From: Alexis Collette <collette@pasteur.fr>
Newsgroups: bionet.software
Subject: Re: Need ABI377 and 3700 chromatogram file format.
Date: Tue, 12 Oct 1999 19:15:49 +0200
Organization: Institut Pasteur, Paris
Lines: 22
Message-ID: <38036CB7.53497FE6@pasteur.fr>
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You can also try this reference : in it, the authers give some information on
the gel format

Obrien, K. M.
Schageman, J. J.
Major, T. H.
Evans, G. A.
Garner, H. R.
1998    Improving Read Lengths By Recomputing the Matrices Of Model 377 Dna
Sequencers    Biotechniques 24 (6) 1014-1016

PICHON CHRISTOPHE a *crit :

> Hello,
>
> I am searching for a person who can send to me a description of the ABI 377
> or/and 3700 data file format, chromatogram picture and AGCT data.
>
> Thanks

Alexis


From owner-software@net.bio.net Wed Oct 13 02:07:00 1999
Path: biosci!newsfeed.stanford.edu!skynet.be!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!nntp2.deja.com!nnrp1.deja.com!not-for-mail
From: gmei@my-deja.com
Newsgroups: bionet.software
Subject: Uppercase and lowercase DNA letters in Consed window
Date: Wed, 13 Oct 1999 02:53:16 GMT
Organization: Deja.com - Before you buy.
Lines: 12
Message-ID: <7u0s6n$rr2$1@nnrp1.deja.com>
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X-MyDeja-Info: XMYDJUIDgmei

Hi:

When I use Consed to contig DNA sequences, I saw sequences aligned
against each other. But in DNA sequences, some letters are in lower case
and some are in upper case. Does anyone know if there is any meaning of
that?

Thank


Sent via Deja.com http://www.deja.com/
Before you buy.

From owner-software@net.bio.net Wed Oct 13 05:51:00 1999
From: computers@tekx.com
Subject: Product Announcement
Newsgroups: bionet.software
Message-ID: <3D2DEMBX.77R7AC4D@tekx.com>
Date: 12 Oct 1999 23:24:10 -0600
Lines: 17
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Path: biosci!bloom-beacon.mit.edu!news-out.cwix.com!newsfeed.cwix.com!europa.netcrusader.net!192.148.253.68!netnews.com!news-feed.fnsi.net!news-xfer.siscom.net!news.siscom.net!huge.aa.net!205.139.116.162

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From owner-software@net.bio.net Wed Oct 13 07:44:00 1999
Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!newsfeed.icl.net!newsfeed.nacamar.de!newsfeed.tli.de!news.ndh.net!not-for-mail
From: Super-User <ollig@biofrontera.de>
Newsgroups: bionet.software
Subject: Re: Uppercase and lowercase DNA letters in Consed window
Date: Wed, 13 Oct 1999 10:32:39 +0200
Organization: Biofrontera Pharmaceuticals GmbH
Message-ID: <380443A7.9ADFE155@biofrontera.de>
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gmei@my-deja.com wrote:
> 
> Hi:
> 
> When I use Consed to contig DNA sequences, I saw sequences aligned
> against each other. But in DNA sequences, some letters are in lower case
> and some are in upper case. Does anyone know if there is any meaning of
> that?
> 
> Thank
> 
> Sent via Deja.com http://www.deja.com/
> Before you buy.

The uppercase nucleotides  have a better quality value than lowercase
ones.
Try to click at a letter with the mouse cursor and watch the
standart-out (the xterm you started consed in). It will output the
quality value of the nucleotide.

regards,
--armin
--
"To save energy
    the light at the end of the tunnel
         will temporarily be switched off."

From owner-software@net.bio.net Wed Oct 13 16:27:00 1999
Path: biosci!FRODO.MGH.HARVARD.EDU!bongard
From: bongard@FRODO.MGH.HARVARD.EDU ("Deverie K. Bongard-Pierce")
Newsgroups: bionet.software
Subject: How to convenient get PHRED?PHRAP/CONSED
Date: 13 Oct 1999 10:27:19 -0700
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Lines: 14
Sender: daemon@net.bi