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>                                Join Neomorphic, Inc., a fast growing pre-IPO company in the San Francisco
>                                Bay Area where your contributions will play a major role
>                                in the advancement of genomics and drug discovery. We
>                                are a computational biology firm that partners with other
>                                leading organizations, both public and private, in the
>                                battle against disease and illness. Join us and apply
>                                your talent in this key position. We offer a competitive
>                                salary, stock options, health-care benefits, and a liberal
>                                vacation plan.
>
>                                Work with scientists and engineers in a team environment to code and test
>                                applications related to visualization and analysis genomic sequence and
>                                related data. Use a solid understanding of object oriented programming
>                                techniques to maintain, modify and improve upon existing code base of
>                                software and help to develop integration solutions to build our Disease
>                                InformaticsTM platform. The qualified candidate will possess 2+ overall years
>                                of professional experience and a minimum of 1 year of experience with Java.
>                                Candidates for the Programming position will be self-starters who possess the
>                                ability to be productive with minimal supervision and be able to meet assigned
>                                timeframes within the software development lifecycle.
>
>                                Required Skills:
>                                * B.S or M.S in computer science or related field
>                                * 1 year of experience using Java
>                                * Proficiency in use of object oriented programming methodologies and theory
>                                * Client side Java GUI
>                                * Java, JavaBeans, Swing
>                                * Experience in mid to large scale applications development
>                                * UNIX scripting
>                                * Bioinformatics or Biology Background
>
>
>                                Submit resume or CV to : Neomorphic, Inc., 2612 8th Street,
>                                Berkeley, CA 94710; Fax: 510-704-1013;
>                                email (preferred): mailto:vonda@Neomorphic.com EOE
>

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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>

<blockquote TYPE=CITE>
<pre>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Join Neomorphic, Inc., a fast growing pre-IPO company in the San Francisco&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Bay Area where your contributions will play a major role&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; in the advancement of genomics and drug discovery. We&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; are a computational biology firm that partners with other
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; leading organizations, both public and private, in the&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; battle against disease and illness. Join us and apply&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; your talent in this key position. We offer a competitive&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; salary, stock options, health-care benefits, and a liberal&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; vacation plan.&nbsp;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Work with scientists and engineers in a team environment to code and test
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; applications related to visualization and analysis genomic sequence and
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; related data. Use a solid understanding of object oriented programming
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; techniques to maintain, modify and improve upon existing code base of
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; software and help to develop integration solutions to build our Disease
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; InformaticsTM platform. The qualified candidate will possess 2+ overall years
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; of professional experience and a minimum of 1 year of experience with Java.
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Candidates for the Programming position will be self-starters who possess the
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ability to be productive with minimal supervision and be able to meet assigned
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; timeframes within the software development lifecycle.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Required Skills:
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * B.S or M.S in computer science or related field
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * 1 year of experience using Java
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Proficiency in use of object oriented programming methodologies and theory
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Client side Java GUI&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Java, JavaBeans, Swing
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Experience in mid to large scale applications development
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * UNIX scripting&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; * Bioinformatics or Biology Background


&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Submit resume or CV to : Neomorphic, Inc., 2612 8th Street,&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Berkeley, CA 94710; Fax: 510-704-1013;&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; email (preferred): <A HREF="mailto:vonda@Neomorphic.com">mailto:vonda@Neomorphic.com</A> EOE</pre>
</blockquote>
</html>

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From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  1 08:11:52 2000
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From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  1 10:52:33 2000
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From: bortzmeyer@pasteur.fr (Stephane Bortzmeyer)
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Subject: Re: Linux vs Unix for doing bioinformatics
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In article <Pine.SOL.3.96.1000225113218.4072V-100000@cress>,
 Keith Bradnam <keith@thale.nott.ac.uk> writes:

> Does anybody have any experience of performing intensive bioinformatics
> tasks (e.g. running blast searches, serving databases to the outside
> world) on PCs running linux as oppposed to Suns or DECs?

The Subject: is incorrect. Linux is an Unix, like a dog is a mammal or
an applepie is a pie.

And you have to distinguish hardware and software. I ran blast on an
Alpha/Linux. Linux is not PC-specific and the Alpha do not always run
Tru64 (formerly Digital Unix).
 
> We are currently looking to upgrade our Sun servers and are curious
> whether switching to Linux on high-end PCs is a better (and maybe cheaper)
> option for doing bioinformatics.

Did you consider FreeBSD-on-PC also? (No, I didn't try myself but I'm
interested if someone did.)



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Subject: 您知道駭客如何入侵的嗎---駭客教學光碟戴您一窺究竟!!
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-----駭客專家伺服器hkserver工作室駭客教學光碟-----------
89/02/28 
本光碟是為了幫助各位了解駭客入侵電腦的手法及技巧,每個程式都有詳細的中文使用
說明簡單易學易懂
操作容易!!
因本光碟破壞力超強!請不要用於非法用途!!

配備需求
========
Intel(Pentium 166MHz)以上
記憶體 8MB以上
所需硬碟空間 完整安裝300 MB 最小安裝15 MB
所需作業軟體 WINDOWS NT/WORKSTATION/95/98/2000
解壓軟體  ZIP OR RAR FOR WINDOWS


光碟目錄
========
[A區] 入侵程式 #特洛伊程式#
      ^^^^^^^^
           A/1 -Back Orifice
           A/2 -NetBus
           A/3 -Netspy (安裝前請把防毒軟體卸載)
           A/4 -入侵程式的保護與偵除

[B區] ICQ 工具
      ^^^^^^^^
           B/1 -ICQ
           B/2 -ICQ IP / PORT /UIN
           B/3 -ICQ 攻擊/密碼/TRO
           B/4 -ICQ的保護與偵除

[C區] 攻擊&攔截程式
      ^^^^^^^^^^^^^
           C/1 -郵件炸彈/匿名信程式
           C/2 -IP當機
           C/3 -攔截程式網路封包攔截程式
           C/4 -病毒產生器(請小心使用)
           C/5 -攻擊%攔截程式的保護與偵除

[D區] 解密工具
      ^^^^^^^^
           D/1 -文件檔案解密
                           +Word解密程式
                           +Excel解密程式
                           +Zip解密程式
           D/2 -UNIX解密程式$字典式破解(台灣各大ISP皆已UNIX系統為主)
           D/3 -解BIOS密碼
           D/4 一般/撥號破解/電郵密碼破解


[E區] 駭客輔助小程式
      ^^^^^^^^^^^^^^



[F區] 基本電腦與網路收集之網路文件
      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^


[G區] 其他檔案
      ^^^^^^^^

[H區] 特別的文件收集 ( UNDERGROUND )

============================================================================
===========
如想學習駭客技巧這片光碟是您最好的選擇:
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服務信箱 hkserver@ms52.url.com.tw





















From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  1 15:30:20 2000
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From: patrick durand <durand@ncbi.nlm.nih.gov>
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Subject: Octopus 4.1
Date: Wed, 01 Mar 2000 09:45:55 -0500
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Hello,

I've updated Octopus (a graphical BLAST/FASTA parser) to release 4.1.
Octopus implements :
- a full HCA Viewer,
- a new network engine able to talk to Q-BLAST (the new NCBI's BLAST system),
- direct sequence download from Entrez.

More info, download, update :
http://www.lmcp.jussieu.fr/~durand/ 
in the section Softwares.

Patrick


From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  1 16:31:19 2000
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Stephane Bortzmeyer wrote:
> 
> In article <Pine.SOL.3.96.1000225113218.4072V-100000@cress>,
>  Keith Bradnam <keith@thale.nott.ac.uk> writes:
> 
> > Does anybody have any experience of performing intensive bioinformatics
> > tasks (e.g. running blast searches, serving databases to the outside
> > world) on PCs running linux as oppposed to Suns or DECs?
> 
> The Subject: is incorrect. Linux is an Unix, like a dog is a mammal or
> an applepie is a pie.
> 
> And you have to distinguish hardware and software. I ran blast on an
> Alpha/Linux. Linux is not PC-specific and the Alpha do not always run
> Tru64 (formerly Digital Unix).
> 
> > We are currently looking to upgrade our Sun servers and are curious
> > whether switching to Linux on high-end PCs is a better (and maybe cheaper)
> > option for doing bioinformatics.
> 
> Did you consider FreeBSD-on-PC also? (No, I didn't try myself but I'm
> interested if someone did.)

We are running BLAST searches on Linux based PentiumIII-Servers - we
have severe problems (i.e. the server crashes) when we use e.g. blastpgp
and a database which is accessed via NFS. This is a known bug to Linux
as far as I know (If someone knows better please answer). So the best
way to use BLAST is by using locally stored databases and everything is
fine!


From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  1 16:48:10 2000
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From: rh@mblab.gla.ac.uk (Robert Hartley)
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Subject: Artificial Neural Network
Date: Wed, 01 Mar 2000 16:09:04 +0000
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Hello All.
Is there a programme for ANN like NEUframe that is afordable to a student.
EG 100ukp. I want to have ANN annalysis of cell dimensions and other groupings.

Cheers
Bob

-- 
Robert Hartley,
Centre for Cell Engineering,University of Glasgow,UK.
mail: rh@mblab.gla.ac.uk, Tel: ++44 (0)141 330 4756
Web : http://www.gla.ac.uk/Inter/CellEngineering


From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  1 17:10:18 2000
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From: amplicom@my-deja.com
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Subject: Bioinformatics Portal
Date: Wed, 01 Mar 2000 16:57:58 GMT
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A bioinformatics portal at http://www.amplicom.com provides a
comprehensive and searchable informations of genes, proteins, associate
diseases, publications and reagents.

In addition to GeneLinkDB, up-to-date biotech stocks, news, career,
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Sent via Deja.com http://www.deja.com/
Before you buy.


From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  1 17:42:09 2000
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From: Tim Cutts <timc@chiark.greenend.org.uk>
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Subject: Re: Linux vs Unix for doing bioinformatics
Date: 01 Mar 2000 17:32:18 +0000 (GMT)
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In article <38BD45D0.8CE3D50A@embl-heidelberg.de>,
Steffen Schmidt  <schmidt@embl-heidelberg.de> wrote:
>
>We are running BLAST searches on Linux based PentiumIII-Servers - we
>have severe problems (i.e. the server crashes) when we use e.g. blastpgp
>and a database which is accessed via NFS. This is a known bug to Linux
>as far as I know (If someone knows better please answer). So the best
>way to use BLAST is by using locally stored databases and everything is
>fine!

Running BLAST on NFS-mounted directories is a bad idea; BLAST 2 memory
maps the file, and the performance of a mmap'ed file across NFS is
appalling.  Much better to maintain a cache of most recently used
databases on the machine's local disk, and blast that.  In other words,
you have a shell script that does:

if (! have_requested_database)
  while (! have_room_for_requested_database)
    remove least recently used local database
  endwhile
  fetch requested database from it's remote source (e.g. NFS or FTP
  server)
endif
run_blast on local copy

This removes load on your network (absolutely vital if you're using a
farm) and makes the BLAST searches run much more quickly.

As you say, Linux' NFS performance is poor even by NFS' rather poor
standards...

Tim.



From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  1 17:46:01 2000
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From: greg@franklin.burnham-inst.org (Dr. Greg Quinn)
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Subject: Re: Linux vs Unix for doing bioinformatics
Date: 1 Mar 2000 17:50:46 GMT
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A lot of folks are using Linux for intensive bioinformtics uses, and I've 
recently started to do this on a quad pentium box; it seems to work well, 
but as the other responder suggested, there are problems. My gut feeling 
is that the implementations of Linux you'll likely to be using are not 
really to the level of commercial software such as Intel Solaris. I got a 
communication a while back from some folks at NCBI in which they 
indicated that they were or had set up clusters of pentiums for running 
blast jobs, but using X86 Solaris. A big practical advantage for Linux is 
that bioinformatics executables for Linux are everywhere, but rarely 
found for X86 Sol, or FreeBSD (another UNIX flavor which ISP's use on 
pentiums; generally, for a bunch of reasons including stability, security 
and ability to handle high load, ISP's don't touch solaris). Another big 
problem is that Linux doesn't have a reliable version of the 'dump' 
program, so you're usually left backing up with tar (taper, etc), which 
isn't a wonderful alternative. To be honest, if I was starting from 
scratch again (and I may do that), I wouldn't use Linux, but Solaris X86 
or FreeBSD..... probably Solaris, which is free to academics now.
My 0.02c

Keith Bradnam (keith@thale.nott.ac.uk) wrote:
: 
: 
: Hello,
: 
: Does anybody have any experience of performing intensive bioinformatics
: tasks (e.g. running blast searches, serving databases to the outside
: world) on PCs running linux as oppposed to Suns or DECs?
: 
: We are currently looking to upgrade our Sun servers and are curious
: whether switching to Linux on high-end PCs is a better (and maybe cheaper)
: option for doing bioinformatics.
: 
: Thanks in advance,
: 
: Keith
: 
: 
: ~  Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR)
: ~  Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/
: ~  University Park, University of Nottingham, NG7 2RD, UK
: ~  Tel: (0115) 951 3091 
: 
: 

-- 
*****************************************
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-bio-software@hgmp.mrc.ac.uk  Wed Mar  1 18:17:07 2000
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From: Tim Cutts <timc@chiark.greenend.org.uk>
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In article <89isp9$b9e$1@ezili.sis.pasteur.fr>,
Stephane Bortzmeyer <bortzmeyer@pasteur.fr> wrote:
>
>The Subject: is incorrect. Linux is an Unix, like a dog is a mammal or
>an applepie is a pie.

Although I agree with you in spirit, the pedantic truth is that Linux is
not Unix; it is a unix-like operating system, but it's not unix.

The description in most Linux distributions carefully avoids calling it
unix.  For example, the Debian FAQ says:

"Linux is the kernel of a Unix-like operating system"

www.linux.org says:

"Linux is a free Unix-type operating system..."

Neither site says that Linux *is* unix.

It's something that needs bearing in mind, since it could potentially
make a difference to software portability and so on.

Right, that's enough pedantry.  You can now go back to calling Linux
unix and I won't care.  :-)

Tim.



From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  1 18:22:10 2000
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In article <Pine.SOL.3.96.1000225113218.4072V-100000@cress>,
Keith Bradnam  <keith@thale.nott.ac.uk> wrote:
>
>
>Hello,
>
>Does anybody have any experience of performing intensive bioinformatics
>tasks (e.g. running blast searches, serving databases to the outside
>world) on PCs running linux as oppposed to Suns or DECs?
>
>We are currently looking to upgrade our Sun servers and are curious
>whether switching to Linux on high-end PCs is a better (and maybe cheaper)
>option for doing bioinformatics.

There are a couple of performance issues:

1)  SMP performance on Linux is not as good as something like Solaris.
2)  Most PC motherboards can't take much RAM (usually only 768 MB or
    1GB).  This is simply not enough for many bioinformatics programs.

3)  On Intel platforms, Linux is a 32-bit OS, which means that it can't
    handle files greater than 2.1 GB in size.  This could be a problem for
    you.  Linux on alpha (I believe) is 64-bit and does not have this
    issue.


Despite these limitations, the price/performancs of Linux on Intel
still beats any commercial vendor.

If you can split your work into small enough chunks that the low RAM
amount of the PC architecture is not a problem, then the Intel solution
is a winner.

Tim.



From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  1 18:35:59 2000
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From: greg@franklin.burnham-inst.org (Dr. Greg Quinn)
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Subject: Re: Linux vs Unix for doing bioinformatics
Date: 1 Mar 2000 18:41:12 GMT
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Dr. Greg Quinn (greg@franklin.burnham-inst.org) wrote:
: and ability to handle high load, ISP's don't touch solaris). Another big 
                                                     ^^^^^^^
That should have read "Linux"; s'what happens if you write replies just 
after waking up.... 


From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  1 19:16:06 2000
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On Wed, 1 Mar 2000, Steffen Schmidt wrote:

> Stephane Bortzmeyer wrote:
> > 
> >  Keith Bradnam <keith@thale.nott.ac.uk> writes:
> > 
> > > Does anybody have any experience of performing intensive bioinformatics
> > > tasks (e.g. running blast searches, serving databases to the outside
> > > world) on PCs running linux as oppposed to Suns or DECs?

> We are running BLAST searches on Linux based PentiumIII-Servers - we
> have severe problems (i.e. the server crashes) when we use e.g. blastpgp
> and a database which is accessed via NFS. This is a known bug to Linux
> as far as I know (If someone knows better please answer). So the best
> way to use BLAST is by using locally stored databases and everything is
> fine!

We have found that for the fasta package, threaded memory allocation is
flakey under Linux.  We have not experienced these memory problems under
any other OS version (and note that the Linux problems are sporadic and
specific only to threaded versions of the fasta programs).

On the otherhand, our PVM- and MPI-enabled versions of the fasta programs
work great on a distributed linux clusters (ours is quite big, and the
databases are shared via NFS with no problems).

So Linux may not yet be the best solution for everyone.

-Aaron

-- 
 o ~   ~   ~   ~   ~   ~  o
/ Aaron J Mackey           \
\  Dr. Pearson Laboratory  / 
 \ University of Virginia  \     
 /  (804) 924-2821          \
 \  amackey@virginia.edu    /
  o ~   ~   ~   ~   ~   ~  o




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From owner-bio-software@hgmp.mrc.ac.uk  Thu Mar  2 07:40:05 2000
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From: joe@evolution.genetics.washington.edu (Joe Felsenstein)
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Subject: Re: Linux vs Unix for doing bioinformatics
Date: 2 Mar 2000 07:24:34 GMT
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Summary: Linux is Unix, and isn't
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In article <Rit*4D1lo@news.chiark.greenend.org.uk>,
Tim Cutts  <timc@chiark.greenend.org.uk> wrote:
>In article <89isp9$b9e$1@ezili.sis.pasteur.fr>,
>Stephane Bortzmeyer <bortzmeyer@pasteur.fr> wrote:
>>
>>The Subject: is incorrect. Linux is an Unix, like a dog is a mammal or
>>an applepie is a pie.
>
>Although I agree with you in spirit, the pedantic truth is that Linux is
>not Unix; it is a unix-like operating system, but it's not unix.

He cites various FAQs and web pages.  Those were written to ensure that
no lawyer will bother these Linux organizations.

>From a legal viewpoint, Linux isn't Unix.  From a functional viewpoint,
for the purposes most of us use it for, it is Unix.  We find some source
code written to work on Unix, which does something bioinformatic.  We want to
know whether it will work on Linux.  If we try it on Windows98, it
won't work.   If we try it on MacOS, it won't.  If we try it on Linux
it usually will.

For the bioinformatic Unix source code stuff I want to run, it usually works
fine on Linux, and is less likely to run on my Digital Unix system, which
is one that has the approval of the lawyers.   Mostly that's because of
32/64 bit issues, which aren't affected but what some lawyer thinks is Unix.

(Ok, I'm quibbling.  This thread has been interesting and I have
enjoyed the helpful discussion of how well or not Linux systems work for
computational molecular biology.)

>Right, that's enough pedantry.  You can now go back to calling Linux
>unix and I won't care.  :-)

Fair enough.

-- 
Joe Felsenstein         joe@genetics.washington.edu
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA


From owner-bio-software@hgmp.mrc.ac.uk  Thu Mar  2 09:03:08 2000
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In article <6lp*iu1lo@news.chiark.greenend.org.uk>,
	Tim Cutts <timc@chiark.greenend.org.uk> writes:
> 
> Running BLAST on NFS-mounted directories is a bad idea; BLAST 2 memory
> maps the file, and the performance of a mmap'ed file across NFS is
> appalling.

Indeed? We run blast across nfs; once the file is pulled across into
memory then the machines in the farm run flat out with no network
traffic (until they need to get another database that isn't in memory).

-- 
-Peter Tribble
HGMP Computing Services
http://www.hgmp.mrc.ac.uk/~ptribble/


From owner-bio-software@hgmp.mrc.ac.uk  Thu Mar  2 09:10:32 2000
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From: Ronald Govaert <Ronald.Govaert@hydro.com>
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Subject: software
Date: Thu, 02 Mar 2000 09:59:57 +0100
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Ik zoek een copy van Lotus Smartsuite 9.5 Nederlands en Lotus Notes
Nederlands
govaert2@wish.net



From owner-bio-software@hgmp.mrc.ac.uk  Thu Mar  2 09:21:37 2000
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From: Nicolas Le Novere <nl223@cus.cam.ac.uk>
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Subject: Re: Linux vs Unix for doing bioinformatics
Date: Thu, 02 Mar 2000 09:06:58 +0000
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Tim Cutts wrote:

> There are a couple of performance issues:
> 
> 1)  SMP performance on Linux is not as good as something like Solaris.
> 2)  Most PC motherboards can't take much RAM (usually only 768 MB or
>     1GB).  This is simply not enough for many bioinformatics programs.
 
http://www.beowulf.org/

> 3)  On Intel platforms, Linux is a 32-bit OS, which means that it can't
>     handle files greater than 2.1 GB in size.  This could be a problem for
>     you.  Linux on alpha (I believe) is 64-bit and does not have this
>     issue.

http://www.linuxia64.org/
 

--
Dr Nicolas Le Nov鋨e                   e-mail: nl223@cus.cam.ac.uk 
Dpt Zoology, Univ Cambridge, Downing street, Cambridge CB2 3EJ, UK
http://www.pasteur.fr/recherche/unites/neubiomol/ 
tel: +44 1223 336623                          fax: +44 1223 336676


From owner-bio-software@hgmp.mrc.ac.uk  Thu Mar  2 12:47:13 2000
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From: nospamplease.plebrun@fysp1.vub.ac.be (Philippe Lebrun)
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In article <rh-0103001609040001@a6-curtis.ibls.gla.ac.uk>,
	rh@mblab.gla.ac.uk (Robert Hartley) writes:
> Hello All.
> Is there a programme for ANN like NEUframe that is afordable to a student.
> EG 100ukp. I want to have ANN annalysis of cell dimensions and 
> other groupings.
>

There is a contributed neural network module in Scilab
(http://www-rocq.inria.fr/scilab/). Or else the Stuttgart Neural
Network simulator, but I can't find the address right now.

-philippe



From owner-bio-software@hgmp.mrc.ac.uk  Thu Mar  2 14:01:46 2000
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From: Aaron J Mackey <ajm6q@virginia.edu>
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On 2 Mar 2000, Peter C. Tribble wrote:

> In article <6lp*iu1lo@news.chiark.greenend.org.uk>,
> 	Tim Cutts <timc@chiark.greenend.org.uk> writes:
> > 
> > Running BLAST on NFS-mounted directories is a bad idea; BLAST 2 memory
> > maps the file, and the performance of a mmap'ed file across NFS is
> > appalling.
> 
> Indeed? We run blast across nfs; once the file is pulled across into
> memory then the machines in the farm run flat out with no network
> traffic (until they need to get another database that isn't in memory).

This is also our experience, whether we use memory-mapped databases or not
(page buffers actually seem to keep much of the data around, reducing the
need to re-read the database on subsequence executions in the absence of
memory-mapped databases).

When we run a farm-tasking implementation of fasta/ssearch/blast across
our cluster and use NFS-shared databases, the first database read is very
slow, to be sure.  But subsequence performance is remarkably fast (and I'm
considering 100's of processors here, by the way ...)  I've also tried
copying the databases to each machine's local /tmp directory and running
all the searches and while it's true that the first search takes far less
time, the subsequent searches all run about the same speed, which for a
large "database vs. database" type of run equates to not much difference
at all between NFS and locally mounted databases (and actually, given all
the copying time required to get the database onto each of the machines,
it may be a negative to go that route, unless your database is very
static).

But this has little to do with Linux vs UNIX.

-Aaron

-- 
 o ~   ~   ~   ~   ~   ~  o
/ Aaron J Mackey           \
\  Dr. Pearson Laboratory  / 
 \ University of Virginia  \     
 /  (804) 924-2821          \
 \  amackey@virginia.edu    /
  o ~   ~   ~   ~   ~   ~  o




From owner-bio-software@hgmp.mrc.ac.uk  Thu Mar  2 14:37:05 2000
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From: Keith Bradnam <keith@thale.life.nottingham.ac.uk>
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Hello,

Thanks to everyone who has emailed me directly or responded via this
newsgroup regarding this issue of Linux and bioinformatics.  I wasn't
expecting so many people to take such a deep interest in this subject, and
it has been interesting to watch the posts fly back and forth.  At times
this seems to have sparked off some lively debate!

I guess my initial question was posted to find out whether people *are*
doing bioinformatics using Linux (on PCs) and the answer is yes.  Whether
that is the best solution for our particular group remains to be seen (I don't 
think we quite have enough space in our lab for 20 or so PCs!).

However, at least we know now that should we pursue a Linux/PC
solution then there are others out there who may be able to help us with
any problems.


Thanks again,

Keith

~  Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR)
~  Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/
~  University Park, University of Nottingham, NG7 2RD, UK
~  Tel: (0115) 951 3091 




From owner-bio-software@hgmp.mrc.ac.uk  Thu Mar  2 16:13:55 2000
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From: pearce@subdimensionTNT.com (pearce)
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Subject: I need the PCO3D software package
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I am lookig for the PCO3D software package to use in my analysis of
RAPD DNA fragments.  It is put out by Robert P. Adams from Baylor
University, but I am unable to contact him or find any references to
this software package on the web.  I need the software to do a
Principal Coordinates Analysis (PCoA or PCO) of my dataset.  

If you know how to obtain a copy, please conatct me ASAP (note that my
reply address is spam-proofed).

If you know a of another software package that would do this type of
analysis, please forward that along as well.

Thanks in Advance,

Pearce

NOTICE: Reomove TNT to reply
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From owner-bio-software@hgmp.mrc.ac.uk  Thu Mar  2 19:30:17 2000
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From: patrick durand <durand@ncbi.nlm.nih.gov>
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Subject: HCA plot
Date: Thu, 02 Mar 2000 14:18:31 -0500
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Hello,

For those of you using the Hydrophobic Clutser Analysis (HCA) method
(http://www.lmcp.jussieu.fr/~mornon/sequence.html for more info
about HCA), I've written a Java software, Turtle, able to display 
HCA plots in a Web browser. This applet is also available as a real 
Java 2 application.

More info about Turtle is available on my web site:

http://www.multimania.com/pdurand/HtmlDoc/software/turtle/index.html


-- Patrick


From owner-bio-software@hgmp.mrc.ac.uk  Thu Mar  2 20:02:45 2000
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From: chevreux@mbp-lserv1.inet.dkfz-heidelberg.de (Bastien Chevreux)
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            Deutsches Krebsforschungszentrum Heidelberg
              German Cancer Research Centre Heidelberg

                           MIRA V1.4.0rc1
	        a DNA shotgun fragment assembler

                     written in 1998-2000 by
                        Bastien Chevreux


      EdIt trace file analysis and contig editing routines 
             written in 1998-2000 by Thomas Pfisterer



MIRA is a DNA shotgun sequence data assembly program capable of
assembling megabase projects which takes reads/sequences gained by (gel or
capillary) electrophoresis experiments and defined in the Staden
experiment (EXP), Sanger CAF or even FASTA file format as input and
assembles them into contigs. SCF signal electrophoresis trace files are
used, if present, to adjudicate between contradicting stretches of bases
in reads and discriminating different repeat types. The resulting assembly
is being written as standard CAF file which can easily be imported into
numerous finishing tools like GAP4.

We provide two versions of MIRA. One uses the automatic contig editor
EdIt that has been trained on standard ABI traces (mira_j), the other
version has been trained on ALF traces (mira_l).

Two additional tools are also provided with the package:
(1) scf_cut can trim SCF files
(2) convert_project can convert EXPs to CAF and FASTA; and CAF to 
    HTML format.

The canonical homepage of MIRA and EdIt, including download
possibilities, is:

            http://www.dkfz-heidelberg.de/mbp-ased/

A complete documentation can be found in the 'doc' directory of the
tarballs as HTML, texinfo and man page. Please mail suggestions,
critics, bug reports etc. to b.chevreux@dkfz-heidelberg.de
or t.pfisterer@dkfz-heidelberg.de

This will be the last release of a MIRA 1.x version except for
maintenance releases in case of heavy bugs (which we do not expect) as
work is shifting toward MIRA 2. We'd hereby like to thank the feedback
contributors from all over the world and declare open the wish list for
the next version of MIRA.

Have fun :-)
              Bastien Chevreux

-------------------------------------------------------------------------------
   Dipl.-Inform. Med. Bastien Chevreux  --  b.chevreux@dkfz-heidelberg.de 
 Deutsches Krebsforschungszentrum Heidelberg -- Abteilung Molekulare Biophysik 
    Im Neuenheimer Feld 280 -- 69120 Heidelberg -- Phone: +49 6221 42 2336
-------------------------------------------------------------------------------
    -It's mine.  =Nope, it's my one.   *CRASH*   =Alright. It WAS yours.


From owner-bio-software@hgmp.mrc.ac.uk  Fri Mar  3 10:13:53 2000
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> 
> But this has little to do with Linux vs UNIX.
> 

Our severe NFS problems occur only on Linux machines (have you ever
tried to copy a very large file while doing blast-searches against a
NFS-shared database?) - the load of blast on its own is about 4,12
Mbyte/s and when you then copy a file via NFS....
By the way - which NFS-server do you use (the kernelNFS or the UserNFS?)


From owner-bio-software@hgmp.mrc.ac.uk  Fri Mar  3 10:25:30 2000
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Hi,

I'm thinking of working this thread into an article for the 'Biochemist' 
- if none of the authors object.  I may have to quote some posts which 
obviously brings up copyright issues.

But anyway, I'm assuming that the arguments for/against linux on PC 
apply to Linux on PPC too??  Does anyone have any data for this?

R

-- 
Richard P. Grant MA DPhil          
Structural Studies Group, MRC-LMB
http://www2.mrc-lmb.cam.ac.uk/personal/rpg/index.html
Please reply to rpg 'at' mrc-lmb.cam.ac.uk


From owner-bio-software@hgmp.mrc.ac.uk  Fri Mar  3 11:35:40 2000
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In article <rgrant-E1E6E4.10252503032000@nntp-serv.cam.ac.uk>,
 "Richard P. Grant" <rgrant@netscape.net> writes:

> But anyway, I'm assuming that the arguments for/against linux on PC 
> apply to Linux on PPC too?? 

Probably not:

- hardware with PowerPC is more expensive so you lose the advantage of
using Taiwan-made cheap PCs. And the PowerPC is 32-bits like the i386.

- Linux and the applications it runs are less stable on the PowerPC. I
am still not able to compile a kernel on my PowerMacintosh, even if I
did it without trouble on dozens of PCs. Many applications programs
suffer, too, specially those who believe that char is signed.



From owner-bio-software@hgmp.mrc.ac.uk  Fri Mar  3 14:20:24 2000
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From: Damir Zucic <zucic@drava.etfos.hr>
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Keith Bradnam <keith@thale.nott.ac.uk> wrote:

> However, at least we know now that should we pursue a Linux/PC
> solution then there are others out there who may be able to help us with
> any problems.

In just few years, the amount of free and commercial software for bioinformatics
on Linux will be significantly larger. I will, for example, release a free, 
open source molecular visualisation program, which will be capable to load
large macromolecules, show it in different ways etc... 

see http://pref.etfos.hr/garlic





From owner-bio-software@hgmp.mrc.ac.uk  Fri Mar  3 15:28:06 2000
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In article <89ognt$neb$2@bagan.srce.hr>,
	Damir Zucic <zucic@drava.etfos.hr> writes:
> 
> In just few years, the amount of free and commercial software for bioinformatics
> on Linux will be significantly larger. I will, for example, release a free, 
> open source molecular visualisation program, which will be capable to load
> large macromolecules, show it in different ways etc... 

Which has nothing to do with Linux, as any competently written program
will run on the regular unix flavours as well. (And vice-versa.)

-- 
-Peter Tribble
HGMP Computing Services
http://www.hgmp.mrc.ac.uk/~ptribble/


From owner-bio-software@hgmp.mrc.ac.uk  Fri Mar  3 16:52:40 2000
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Subject: Announcement: BioCoRe
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Urbana, Illinois - The Theoretical Biophysics Group at the
University of Illinois is proud to announce the initial public release
of BioCoRE, a collaborative research environment.  BioCoRE software is
freely available for use at the Theoretical Biophysics Group website.
BioCoRE development is supported by the NIH National Center for
Research Resources.

Modern computational structural biology requires scientists to employ a
wide range of tools and techniques to solve complex problems while
keeping accurate and complete records of research activities.
Additional complications are introduced by the need to effectively
engage in interdisciplinary collaborations with geographically
dispersed colleagues. The software BioCoRE, a collaborative research
environment for molecular modeling and simulations, addresses these
challenges.

Initial design work has led to a web-based architecture focused on four
primary interface paradigms:

  + a WORKBENCH interface includes features for controlling molecular
modeling, simulation, and bioinformatics tools with convenient and
uniform access to collaboratory data.  Initial tools in this category
include the ability to start and monitor molecular dynamics simulations
via a web browser interface.

  + a NOTEBOOK interface automates recording of research activities.
Initial tools in this category include a notebook tool which can be used
by researchers to engage in offline discussions as well as review and
search the entire text of any prior chat session.

  + a CONFERENCE interface enables scientists to discuss their research
across distances in real time or time-delayed sessions and will spawn
software for teleconferencing and synchronized visualization of shared
data at distant sites.  Initially, this category includes a text-based
chat mechanism where the researchers can choose topics and converse with
other researchers who are working on the same project.

  + a DOCUMENTS interface permits the preparation of multi-author
documents in a cross-platform revision control system.

BioCoRE consists of html and javascript and java where needed.

For additional information, please visit the BioCoRE website at
<http://www.ks.uiuc.edu/Research/collaboratory/>.

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

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





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From: Marcel Turcotte <turcotte@fir.lif.icnet.uk>
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It would help if people could include which release of Linux they are
using and the type/speed of network.

We have a cluster of 25 PIII/500MHz/128Mb connected to a Cisco switch
full-duplex 100Mbit/s, we should have more information to share over
the next few weeks (comparative genomics using psi-blast), but so far
the bottleneck seems to be the speed the local ide disk and not the
network/NFS.  We are running RH 6.1 and I've been told that NFS has
been much improved/rewritten (I need to check on that though).

Just my $.02
M.

 Steffen Schmidt <schmidt@embl-heidelberg.de> writes:

 [...]

 > We are running BLAST searches on Linux based PentiumIII-Servers - we
 > have severe problems (i.e. the server crashes) when we use e.g. blastpgp
 > and a database which is accessed via NFS. This is a known bug to Linux
 > as far as I know (If someone knows better please answer). So the best
 > way to use BLAST is by using locally stored databases and everything is
 > fine!

-- 

Marcel Turcotte                          Biomolecular Modelling Laboratory
M.Turcotte@icrf.icnet.uk                 Imperial Cancer Research Fund
[44|0]-171-269-3348/3258 Phone/Fax       PO Box 123, 44 Lincoln's Inn Fields
http://www.bmm.icnet.uk/people/turcotte  London WC2A 3PX, England


From owner-bio-software@hgmp.mrc.ac.uk  Fri Mar  3 22:02:10 2000
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From: Tim Cutts <timc@chiark.greenend.org.uk>
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Subject: Re: Linux vs Unix for doing bioinformatics
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In article <38BE2F32.3088CDEA@cus.cam.ac.uk>,
Nicolas Le Novere  <nl223@cus.cam.ac.uk> wrote:
>Tim Cutts wrote:
>
>> There are a couple of performance issues:
>> 
>> 1)  SMP performance on Linux is not as good as something like Solaris.
>> 2)  Most PC motherboards can't take much RAM (usually only 768 MB or
>>     1GB).  This is simply not enough for many bioinformatics programs.
> 
>http://www.beowulf.org/

So what?  I have a number of pieces of software which require a working
set in excess of 1 GB in order to avoid swapping (I deal with some very
large datasets), having a cluster of smaller machines doesn't help in
this context; the individual nodes in the cluster would still have the
problem that they'd be swapping to death and performance would be poor.
I need nodes with large physical RAM, which at the moment still means
commercial UNIX vendors.

>> 3)  On Intel platforms, Linux is a 32-bit OS, which means that it can't
>>     handle files greater than 2.1 GB in size.  This could be a problem for
>>     you.  Linux on alpha (I believe) is 64-bit and does not have this
>>     issue.
>
>http://www.linuxia64.org/

Yes, but the Itanium processor isn't here yet.  On mass commodity PCs
based around the Pentium II/III, 32-bits is still the limit.

Tim.



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From: spam@127.0.0.1 (Bernard Murray, PhD)
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Date: Fri, 03 Mar 2000 12:30:17 -0700
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In article <89olm2$39s$1@niobium.hgmp.mrc.ac.uk>, ptribble@hgmp.mrc.ac.uk
(Peter C. Tribble) wrote:

> In article <89ognt$neb$2@bagan.srce.hr>,
>         Damir Zucic <zucic@drava.etfos.hr> writes:
> > 
> > In just few years, the amount of free and commercial software for
bioinformatics
> > on Linux will be significantly larger. I will, for example, release a free, 
> > open source molecular visualisation program, which will be capable to load
> > large macromolecules, show it in different ways etc... 
> 
> Which has nothing to do with Linux, as any competently written program
> will run on the regular unix flavours as well. (And vice-versa.)

However, distributors who supply binary-only programs still neglect
Linux at the moment so I believe Damir was indicating that this may
change in the future.

This also highlights one of the other advantages of Linux (and *BSD
distributions) occupying a larger mindset - a wider appreciation of
open source software.  Certainly people in the past would happily
hand out source code for bioinformatics-related programs but only
those with access to UNIX boxes would have the chance to run them.
As Linux has taken hold the open source philosophy has also been
propagated so even if you are running a commercial OS (even if
freely distributed like Solaris) you are (hopefully) more likely
to share your code.

   Bernard

P.S. Garlic looks real nice, Damir.

-- 
Bernard P. Murray, PhD
bpmurray at cgl . ucsf . edu
Department of Cellular & Molecular Pharmacology, UCSF


From owner-bio-software@hgmp.mrc.ac.uk  Sat Mar  4 08:19:29 2000
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From: karplus@cse.ucsc.edu (Kevin Karplus)
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Julie Thompson-Maaloum <julie@titus.u-strasbg.fr> wondered what my
alignments of 10,000 sequences looked like.  Well, they are generally
fairly redundant.  Although each sequence is unique (from NCBI's NR
protein database), they often have a lot in common.  I have large
alignments of immunoglobulins and of zinc fingers.  Perhaps the least
diverse alignment started with 1ce4A, which is a domain of an HIV coat
protein.  There are over 16000 similar sequences in NR, with only tiny
differences---I think that reducing to sequences which have no more
than 90% similarity would reduce this set to one sequence.

-- 
Kevin Karplus 	karplus@cse.ucsc.edu	http://www.cse.ucsc.edu/~karplus
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck
Anything below this line is junk added by others without my approval.


From owner-bio-software@hgmp.mrc.ac.uk  Sat Mar  4 20:47:21 2000
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---


From owner-bio-software@hgmp.mrc.ac.uk  Sun Mar  5 08:01:14 2000
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From: dfhk@ms50.url.com.tw
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Subject: [駭客新聞]----Pretty Park電腦病毒快速擴散
Date: 5 Mar 2000 08:00:52 GMT
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sorry......打擾了!!
====================================================================
***請認明正宗防止駭客'dfhk'(dfhk@ms50.url.com.tw)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!!
=========================================================

Pretty Park電腦病毒快速擴散 

[駭客新聞]
3/5/2000 
Pretty Park電腦病毒快速擴散 

小心您的電子郵件附加檔，這個命名為”prettypark.exe”的病毒，自二月中發現後，最近數日各個
電腦感染率急遽升高。 

根據Network Associates表示，”prettypark.exe”雖不致刪除或更改檔案，但每卅分鐘卻會自動按
照電子郵件通訊錄上所列地址將病毒本身傳送出去一次，結果造成整個網路全面當機。目前已有十二
家企業和政府網路受到感染。 此一病毒正式名稱為”W32/Pretty.worm.unp”。 

 

========================================================================================================
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@ms50.url.com.tw



From owner-bio-software@hgmp.mrc.ac.uk  Sun Mar  5 09:45:04 2000
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C'est un message de format MIME en plusieurs parties.

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cherche belgium
music maker 5
music studio 5
gravure nero
video capture

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From owner-bio-software@hgmp.mrc.ac.uk  Mon Mar  6 05:57:18 2000
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From: "Marcel Dinger" <marcel@ihug.co.nz>
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GENAMICS EXPRESSION: The Next Generation of Sequence Analysis Software

If you've gotten tired of the complexity of current sequence analysis programs,
we strongly recommend you take a look at Expression. We promise that you will be
amazed at how simple both basic and complex sequence analysis problems can be
solved with Expression.

Genamics Expression is a revolutionary new Windows application for DNA and
protein sequence analysis. Utilising a novel interface, Expression makes complex
computational analyses of sequence information incredibly simple. Expression
uses the very latest computing technology to set new standards in the way
sequences are analysed.

A fully-featured demo of Genamics Expression can be downloaded from
http://genamics.com/expression/download.htm

Feature Summary:
  Sequence Annotation
  Graphical Sequence Map
  Degenerate DNA and Amino Acid Sequence Support
  Restriction Analysis
  Primer Design and Analysis
  ORF Prediction
  Pattern Finding
  Reverse Translation
  GenBank Searching
  Pattern and Motif Identification
  Multiple Sequence Alignment
  Protein Structure Prediction
  Lightning-fast Algorithms
  Plugin Architecture for Developers

More details, including screenshots and tutorials, for Expression can be found
at http://genamics.com/expression/
We welcome your feedback.

Marcel Dinger,
Genamics.





From owner-bio-software@hgmp.mrc.ac.uk  Mon Mar  6 08:40:25 2000
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In article <89o81v$97a$1@ezili.sis.pasteur.fr>, bortzmeyer@pasteur.fr 
(Stephane Bortzmeyer) wrote:

> In article <rgrant-E1E6E4.10252503032000@nntp-serv.cam.ac.uk>,
>  "Richard P. Grant" <rgrant@netscape.net> writes:
> 
> > But anyway, I'm assuming that the arguments for/against linux on PC 
> > apply to Linux on PPC too?? 
> 
> Probably not:
> 
> - hardware with PowerPC is more expensive so you lose the advantage of
> using Taiwan-made cheap PCs. 

But the point is we have thousands of macs sitting around not using 
anything like their full potential - I'm thinking of dual boot systems 
for use in the working lab, not a computer room stuffed full of gubbins.

> And the PowerPC is 32-bits like the i386.

Eh?  The PII/III is 32 bit.

> 
> - Linux and the applications it runs are less stable on the PowerPC. I
> am still not able to compile a kernel on my PowerMacintosh, even if I
> did it without trouble on dozens of PCs.

With respect, I would like to see n > 1 because I am sure there are 
people around who run Linux on PPCs.

Cheers,

Richard

-- 
Richard P. Grant MA DPhil          
Structural Studies Group, MRC-LMB
http://www2.mrc-lmb.cam.ac.uk/personal/rpg/index.html
Please reply to rpg 'at' mrc-lmb.cam.ac.uk


From owner-bio-software@hgmp.mrc.ac.uk  Mon Mar  6 11:50:14 2000
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Bernard Murray, PhD <spam@127.0.0.1> wrote:
> In article <89olm2$39s$1@niobium.hgmp.mrc.ac.uk>, ptribble@hgmp.mrc.ac.uk
> (Peter C. Tribble) wrote:
> This also highlights one of the other advantages of Linux (and *BSD
> distributions) occupying a larger mindset - a wider appreciation of
> open source software.  ... ... ...

There is one more thing: open source allows us to check the mathematical
formulas (well, at least in theory), otherwise you may get some results which
may be based on bad physics, chemistry etc.


> P.S. Garlic looks real nice, Damir.

Thanks. Are you interested to try garlic these days? Documentation is missing,
but I can write some brief instructions and put everything to my ftp site, if
some people would like to try the program and send me some comments and
suggestions.



From owner-bio-software@hgmp.mrc.ac.uk  Mon Mar  6 15:23:28 2000
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From: chevreux@mbp-lserv1.inet.dkfz-heidelberg.de (Bastien Chevreux)
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On 2 Mar 2000 12:26:28 GMT, Philippe Lebrun
<nospamplease.plebrun@fysp1.vub.ac.be> wrote: 
>In article <rh-0103001609040001@a6-curtis.ibls.gla.ac.uk>,
>	rh@mblab.gla.ac.uk (Robert Hartley) writes:
>> Hello All.
>> Is there a programme for ANN like NEUframe that is afordable to a student.
>> EG 100ukp. I want to have ANN annalysis of cell dimensions and 
>> other groupings.
>There is a contributed neural network module in Scilab
>(http://www-rocq.inria.fr/scilab/). Or else the Stuttgart Neural
>Network simulator, but I can't find the address right now.

http://inf.informatik.uni-stuttgart.de:80/ipvr/bv/projekte/snns/

Salut,
       Bastien

-------------------------------------------------------------------------------
   Dipl.-Inform. Med. Bastien Chevreux  --  b.chevreux@dkfz-heidelberg.de 
 Deutsches Krebsforschungszentrum Heidelberg -- Abteilung Molekulare Biophysik 
    Im Neuenheimer Feld 280 -- 69120 Heidelberg -- Phone: +49 6221 42 2336
-------------------------------------------------------------------------------
    -It's mine.  =Nope, it's my one.   *CRASH*   =Alright. It WAS yours.


From owner-bio-software@hgmp.mrc.ac.uk  Mon Mar  6 21:20:34 2000
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Chemical Structure Drawing,
Molecular Mechanics for Windows,
C-13 NMR Shift Prediction for Windows,
http://home.ici.net/~hfevans/chempen.htm



From owner-bio-software@hgmp.mrc.ac.uk  Mon Mar  6 23:26:11 2000
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From: lisa_crawford@cmagroup.com
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Subject: Colorado; Sr. Software Engineer; NT, C++, DICOM, Imaging
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Colorado; Sr. Software Engineer; NT, C++, DICOM, Imaging

**We are also working similar medical imaging software positions for clients 
in NE USA, Midwest, PNW, CA and BC Canada.  

-Senior Software Engineer
-Greater Denver/Boulder
-Salaried, Full-Time, Excellent Benefits 
(Relocation Assistance Available)

Medical DICOM knowledge important. 
Experience with C/C++ and NT required. 
Image manipulation, compression, edge detection, analysis, all good things 
to have. 




Please refer to JO# 7657RJS in your response.

lisa_crawford@cmagroup.com 

Lisa Crawford
Sr. Researcher & Associate Recruiter
ljc@cmagroup.com
IT & Software Solutions Team
Career Marketing Associates



From owner-bio-software@hgmp.mrc.ac.uk  Tue Mar  7 09:46:56 2000
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From: gwilliam@hgmp.mrc.ac.uk (Gary Williams)
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We are seeing increasing numbers of BLAST searches failing like this:

---------------------------------------------------------------------------
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= Z92844, 151798 bases, CBD5EE91 checksum.
         (151,798 letters)

Database: new
           312,486 sequences; 300,934,448 total letters

Searching.......................................
---------------------------------------------------------------------------

With no further output or error messages.
It exits with a status value of 1.

We are running BLAST on SPARC and Intel machines with Solaris.
We have large amounts of swap space available.
(For example: Memory: 5120M real, 153M free, 322M swap in use, 12G swap free)

The query sequence size and database size of some typical failed searches
are as follows:

Query		Database
-----		--------
129,429		2,950,329,007
193,974		2,950,329,007
151,798		  300,934,448
151,798		2,950,329,007
183,521		2,950,329,007
151,798		  300,934,448
151,798		2,950,329,007
 14,931		   87,398,758
 30,000		   87,398,758
100,000		1,607,027,821
100,000		   87,398,758
283,438		  105,694,337
104,147		2,507,032,618

Is anyone else seeing this sort of thing?

Does anyone have any idaes as to the cause or cure?

Thanks,
Gary

Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams@hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK

---


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Subject: Re: BLAST jobs crashing - any ideas?
Date: Tue, 07 Mar 2000 18:27:52 +0000
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This message has been posted by:  Arne Mueller <a.mueller@REMOVE-THIS-TO-SENDicrf.icnet.uk>

Gary Williams wrote:
> 
> We are seeing increasing numbers of BLAST searches failing like this:
> 
> ---------------------------------------------------------------------------
> Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
> "Gapped BLAST and PSI-BLAST: a new generation of protein database search
> programs",  Nucleic Acids Res. 25:3389-3402.
> 
> Query= Z92844, 151798 bases, CBD5EE91 checksum.
>          (151,798 letters)
> 
> Database: new
>            312,486 sequences; 300,934,448 total letters
> 
> Searching.......................................
> ---------------------------------------------------------------------------
> 
> With no further output or error messages.
> It exits with a status value of 1.

Hi All,

I had problems with blast version 2.0.6 (I guess), sometimes it crashed
and it took me while to look at the syslog of our server to find out
that it was killed by the operating system (IRIX 6.5). 

The reason was that blastpgp installed a signal handler to catch
segmentation faults and this handler itself caused a segmentation fault.
To prevent an endless recoursion it was killed by the os (that was the
message in the syslog). It's along time ago and I don't realy remember
;-( but I think blastpgp was terminated without printing any message.

Is there anything in your syslog?
 
	good luck,

	Arne

-- 
Arne Mueller
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund
44 Lincoln's Inn Fields
London WC2A 3PX, U.K.
phone : +44-(0)171 2693405      | fax :+44-(0)171-269-3534
email : a.mueller@icrf.icnet.uk | http://www.bmm.icnet.uk


From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  8 09:10:51 2000
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From: njoly@pasteur.fr (Nicolas Joly)
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Subject: Re: BLAST jobs crashing - any ideas?
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Gary Williams <gwilliam@hgmp.mrc.ac.uk> 嶰rit :
> 
> We are seeing increasing numbers of BLAST searches failing like this:
> 
> ---------------------------------------------------------------------------
> Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
> "Gapped BLAST and PSI-BLAST: a new generation of protein database search
> programs",  Nucleic Acids Res. 25:3389-3402.
> 
> Query= Z92844, 151798 bases, CBD5EE91 checksum.
>          (151,798 letters)
> 
> Database: new
>            312,486 sequences; 300,934,448 total letters
> 
> Searching.......................................
> ---------------------------------------------------------------------------
> 
> With no further output or error messages.
> It exits with a status value of 1.
> 
> We are running BLAST on SPARC and Intel machines with Solaris.
> We have large amounts of swap space available.
> (For example: Memory: 5120M real, 153M free, 322M swap in use, 12G swap free)
> 
> Is anyone else seeing this sort of thing?

We noticed this behaviour under Digital Unix v4.0f too, with the lastest
blast v2.0.11
 
> Does anyone have any idaes as to the cause or cure?

It seems to be platform independant ... ;-)

-- 
Nicolas Joly

Informatique Scientifique
Institut Pasteur, Paris.


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hi
    I am presently using 141.44.20.80 for downloading my news items.  But
unfortunately I don't have post access to this server.  Does anybody know of
any server where Post access is possible or atleast can somebody give me a
post access to some newsgroup server.
    thank you
sincerley
jayakumar

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R. JAYAKUMAR
CSIR- Senior Research Fellow
Dept. of Molecular Microbiology,
School of Biotechnology,
Madurai Kamaraj University,
Madurai - 625 021.
India
email: jakku@usaf.org
tel: +91-452-858471-374
efax: (603)-688-4665
web: http://members.tripod.com/~jakspage
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"There is a possible even in imPOSSIBLE"
a

---


From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  8 13:10:13 2000
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In article <002e01bf88f9$a2279300$8c01a8c0@tn.nic.in>,
  jakku@mrna.tn.nic.in ("R. Jayakumar") wrote:
> hi
>     I am presently using 141.44.20.80 for downloading my news items.
But
> unfortunately I don't have post access to this server.

Try a web interface like http://www.deja.com/usenet/.

   -- Petr

_________________________________________________________
Petr Kuzmic, Ph.D. * http://www.biokin.com
B i o K i n   Ltd. * Consulting and Software Developement


Does anybody
know of
> any server where Post access is possible or atleast can somebody give
me a
> post access to some newsgroup server.
>     thank you
> sincerley
> jayakumar
>
>
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
||||
>
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
||||
> ||||
> R. JAYAKUMAR
> CSIR- Senior Research Fellow
> Dept. of Molecular Microbiology,
> School of Biotechnology,
> Madurai Kamaraj University,
> Madurai - 625 021.
> India
> email: jakku@usaf.org
> tel: +91-452-858471-374
> efax: (603)-688-4665
> web: http://members.tripod.com/~jakspage
>
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
||||
>
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||||
> ||||
> "There is a possible even in imPOSSIBLE"
> a
>
> ---
>


Sent via Deja.com http://www.deja.com/
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From owner-bio-software@hgmp.mrc.ac.uk  Wed Mar  8 13:47:51 2000
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