[Biodevelopers] bioinformatics and .NET

Margolin, Adam margolia at wharton.upenn.edu
Tue May 27 12:21:36 EDT 2003


At the risk of sounding heretical, I think that .NET could an excellent environment for developing bioinformatics applications.  The platform is designed for interoperability between different languages, and you can write in Perl, C++, and C# all in the same environment.  I am doubtful that this will catch on due to other factors, but if a Bio C# project does begin please keep me informed.

We might also want to look into the possibilities of 1) using the .NET tool that converts Java to C# (although people may raise objection to this)  2)  Creating something like Bio .NET by compiling a (perhaps already existing) bioinformatics library to .NET byte code that can then be accessed by any .NET supported language. 

Does anybody have any thoughts on what Microsoft's role with be in bioinformatics?

-Adam


-----Original Message-----
From: biodevelopers-request at bioinformatics.org [mailto:biodevelopers-request at bioinformatics.org] 
Sent: Tuesday, May 27, 2003 11:54 AM
To: biodevelopers at bioinformatics.org
Subject: Biodevelopers digest, Vol 1 #113 - 4 msgs

Send Biodevelopers mailing list submissions to
	biodevelopers at bioinformatics.org

To subscribe or unsubscribe via the World Wide Web, visit
	https://bioinformatics.org/mailman/listinfo/biodevelopers
or, via email, send a message with subject or body 'help' to
	biodevelopers-request at bioinformatics.org

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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Biodevelopers digest..."


Today's Topics:

   1. Re: Re: Biodevelopers digest, Vol 1 #111 - 1 msg (Daniel Wetzler)
   2. Urbigene Package (=?iso-8859-1?q?Pierre=20LINDENBAUM?=)
   3. About Bio C# and me (David Leader)
   4. RE: Re: Biodevelopers digest, Vol 1 #111 - 1 msg (Blair Jennings)

--__--__--

Message: 1
Date: Mon, 26 May 2003 15:27:13 +0200
From: Daniel Wetzler <Daniel.Wetzler at uni-koeln.de>
To: biodevelopers at bioinformatics.org
Subject: Re: [Biodevelopers] Re: Biodevelopers digest, Vol 1 #111 - 1 msg
Reply-To: biodevelopers at bioinformatics.org

Hallo,

I think that C# will become sooner or later a propietary solution
like e.G. VB.
C# is maintained by Microsoft and they are responsible for future
enhancements of the language. And I don't think that they will
support other platforms than Windows and they won't espiacally support
Linux/Unix after C# having gained a bigger part of the market.

So I would propose to develop a C++ Library since such a Library could be
supported on several platforms.

Greetings,

Daniel




Fangxia Li schrieb:

>Hey, Bio Dev Guru,
>
>I am a Java Developer instead, while interested at C#.
>I want to know exactly what kind of projects are there
>in your mind. 
>
>Brief about me: I am M.D. studying biology signal
>transduction etc at Thomas Jefferson Hosptial. I got
>my M.S degree at computer science and gained 2 years
>programming experience in IT industry. Looking for a
>better way to contribute to bioinformatics
>projects...8-)
>
>Regards,
>
>Scott Lee
>--- arun a <arunnuraa at linuxmail.org> wrote:
>  
>
>>Hai 
>>   I am from Bharathiar University, India. I am also
>>interested to participate int Bio C#. I know some
>>computer programing. Can u accept my invitation.
>>
>>From: biodevelopers-request at bioinformatics.org
>>Date: Sun, 25 May 2003 12:01:49 -0400 (EDT) 
>>To: biodevelopers at bioinformatics.org
>>Subject: Biodevelopers digest, Vol 1 #111 - 1 msg
>>
>>Re: Send Biodevelopers mailing list submissions to
>>Re: 	biodevelopers at bioinformatics.org
>>Re: 
>>Re: To subscribe or unsubscribe via the World Wide
>>Web, visit
>>Re: 
>>
>>    
>>
>https://bioinformatics.org/mailman/listinfo/biodevelopers
>  
>
>>Re: or, via email, send a message with subject or
>>body 'help' to
>>Re: 	biodevelopers-request at bioinformatics.org
>>Re: 
>>Re: You can reach the person managing the list at
>>Re: 	biodevelopers-admin at bioinformatics.org
>>Re: 
>>Re: When replying, please edit your Subject line so
>>it is more specific
>>Re: than "Re: Contents of Biodevelopers digest..."
>>Re: 
>>Re: 
>>Re: Today's Topics:
>>Re: 
>>Re:    1. About Bio C# and me (Serge Gregorio)
>>Re: 
>>Re: -- __--__-- 
>>Re: 
>>Re: Message: 1
>>Re: To: biodevelopers at bioinformatics.org
>>Re: Date: Sun, 25 May 2003 03:34:47 +0800
>>Re: From: "Serge Gregorio"
>><d.gregorio at eudoramail.com>
>>Re: Organization: Lycos Mail 
>>(http://www.mail.eudoramail.com)
>>Re: Subject: [Biodevelopers] About Bio C# and me
>>Re: Reply-To: biodevelopers at bioinformatics.org
>>Re: 
>>Re: >Scott:
>>Re: 
>>Re: >Hey, Serge,
>>Re: >Where you from, get us some info about you,
>>thanks! 
>>Re: 
>>Re: Hello Scott!  I'm an IT pro from Manila,
>>Philippines.  I'm into PHP, VB, Oracle, etc.  I'm a
>>relatively new "recruit/convert" to bioinformatics. 
>>More about me at:
>>Re: 
>>Re:    http://genephp.sf.net 
>>Re: 
>>Re: >Jaroslaw:
>>Re:  
>>Re: >What do you think about starting a Bio C++
>>project? >AFAIK there is now such at the moment and
>>I know lot >of people working in bioinformatics and
>>using C++.
>>Re: 
>>Re: Nice idea... I use occasionally use C++
>>myself... but
>>Re: for the sole purpose of learning a new language,
>>I'd prefer joining a Bio C# or maybe a Bio
>>Coldfusion? =)
>>Re: 
>>Re: Regards,
>>Re: 
>>Re: Serge Gregorio
>>Re: 
>>Re: 
>>Re: Need a new email address that people can
>>remember
>>Re: Check out the new EudoraMail at
>>Re: http://www.eudoramail.com
>>Re: 
>>Re: 
>>Re: -- __--__-- 
>>Re: 
>>Re: _______________________________________________
>>Re: Biodevelopers mailing list
>>Re: Biodevelopers at bioinformatics.org
>>Re:
>>
>>    
>>
>https://bioinformatics.org/mailman/listinfo/biodevelopers
>  
>
>>Re: 
>>Re: 
>>Re: End of Biodevelopers Digest
>>
>>
>>
>>.-. .-.   .-. .-.   .-. .-.   .-. .-.   .-. .-.  
>>.-. .-.   .-. .-.
>> /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\
>>/|||X|||\ /|||X|||\
>>X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/
>>\|||X|||/ \|||X|||/ \|||X
>> `-'   `-' `-'   `-' `-'   `-' `-'   `-' `-'   `-'
>>`-'   `-' `-'   `-'
>>Arun.A.P
>>C/O Prof.M.R.N.Murthy,
>>Dept of Molecular Biophysics,
>>Indian Institute of Science,
>>Bangalore -12
>>91 80 2932458
>>.-. .-.   .-. .-.   .-. .-.   .-. .-.   .-. .-.  
>>.-. .-.   .-. .-.
>> /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\
>>/|||X|||\ /|||X|||\
>>X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/
>>\|||X|||/ \|||X|||/ \|||X
>> `-'   `-' `-'   `-' `-'   `-' `-'   `-' `-'   `-'
>>`-'   `-' `-'   `-'
>>
>>
>>-- 
>>______________________________________________
>>http://www.linuxmail.org/
>>Now with e-mail forwarding for only US$5.95/yr
>>
>>Powered by Outblaze
>>_______________________________________________
>>Biodevelopers mailing list
>>Biodevelopers at bioinformatics.org
>>
>>    
>>
>https://bioinformatics.org/mailman/listinfo/biodevelopers
>
>
>__________________________________
>Do you Yahoo!?
>The New Yahoo! Search - Faster. Easier. Bingo.
>http://search.yahoo.com
>_______________________________________________
>Biodevelopers mailing list
>Biodevelopers at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/biodevelopers
>
>  
>



--__--__--

Message: 2
Date: Mon, 26 May 2003 10:56:38 +0200 (CEST)
From: =?iso-8859-1?q?Pierre=20LINDENBAUM?= <plindenbaum at yahoo.fr>
To: biodevelopers at bioinformatics.org
Subject: [Biodevelopers] Urbigene Package
Reply-To: biodevelopers at bioinformatics.org

hello all,

The Urbigene Package contains modest C++ tools for
molecular biology I wrote at the INTEGRAGEN company.
As a subset of those tools do not present any
commercial interest so I've been allowed to release it
to the scientific community as an open source package
under the GNU General Public License (GPL). You'll
find sources for parsing blast results in XML format,
the new versions of the CloneIt program, filters for
FASTA sequences, for PRIMER3 output... etc...

(There are also programs that are not dedicated to
biology but may be of general interest. For example
PIVOT creates cross tables from delimited files,
GeneticProg tries to find an equation that fits
experimental values, etc...)

The package is available at:

                  http://www.urbigene.com


Usage Example
Consider the following script:


#This script takes as input the chromosome 22 from the
goldenpath
#It then digests the whole chromosome by NotI
#cuts the boundaries by 6 bases,
#keeps fragments between 100 bases and 10Kb,
#keeps fragments containing a CA repeat,
#keeps fragments where %GC is between 40 and 60%,
#just keeps the 10 first sequences,
#converts the sequences as an input for primer3
#launches primer3
#converts the amplified fragments to FASTA
#blast those fragments against the whole goldenpath
#retains BLAST HSP where score is lower than 10 or
greater then 50
#converts the output to text
#transforms this text to XML
#keeps the 50 first lines
#

BIN=./bin/
${BIN}/fastaretrieve -chr 22 -entry
/env/ig/pubdb/mirror/golden_path/14nov2002/chromosomes/entry_points.csv
|
${BIN}/fastadigest -e NotI |
${BIN}/fastacrop -5 6 -3 6 |
${BIN}/fastasize -m 100 -M 100000 |
${BIN}/fastaslice -e 5000 -n 10000 |
${BIN}/fastafind -s CACACACACACA -print T |
${BIN}/fastagc -min 40 -max 60 -sort T |
${BIN}/fastahead |
${BIN}/fasta2primer3 -max-stgy 1 -gc-min 20 -gc-max 80
-max-size 2000 | 
primer3 |
${BIN}/primer3tofasta | 
blastall -e 10 -p blastn -d
/env/ig/pubdb/blastdb/GP10apr2003/gp10apr2003 -m 7 |
#${BIN}/blastlisp -e
'or(lt(hsp.score(),10),gt(hsp.score(),50))' |
${BIN}/blast2txt |
${BIN}/text2xml |
head -n 50 > demo.txt


Result will be 



//iteration
######################################################################
22:0-47748584(+)|restriction_fragment[NotI(35516844)-NotI(35580318):63482]|crop_5(6)crop_3(6)|size_filter(100-100000)|slice(50000-59999)|gc(41.53%)|pcr_0(34-884:851
pb) primer_left(TTCCAAAGTGCTGGGATTATAG)
primer_right(TCTGGGATTTTCCAGAGGTATAG)	len:851

####################################################################>
build33|chr22|slice(37101000-37250999)	len:150000
Object:94394-95244	Query:1-851	830	0
                                                      
  .....>       	build33|chr22|slice(37101000-37250999)
len:150000	Object:47208-47286	Query:682-761	32
1.48067e-07
 ..>                                                  
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:138640-138677	Query:3-40	30
2.31183e-06
 <..                                                  
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:88694-88734	Query:43-3	29
9.13492e-06
 <..                                                  
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:113943-113983	Query:43-3	29
9.13492e-06
 <.                                                   
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:16320-16349	Query:32-3	26
0.000563575
 <..                                                  
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:76801-76838	Query:40-3	26
0.000563575
 <..                                                  
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:104040-104080	Query:43-3	25
0.0022269
 <.                                                   
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:132737-132766	Query:32-3	22	0.137388
 <.                                                   
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:71167-71196	Query:32-3	22	0.137388
 <.                                                   
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:142101-142130	Query:32-3	22	0.137388
 <.                                                   
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:127879-127904	Query:28-3	22	0.137388
 .>                                                   
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:82934-82963	Query:3-32	22	0.137388
 <.                                                   
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:53573-53602	Query:32-3	22	0.137388
 <.                                                   
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:62190-62219	Query:32-3	22	0.137388
 .>                                                   
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:33547-33576	Query:3-32	22	0.137388
 ..>                                                  
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:94134-94171	Query:3-40	22	0.137388
 <..                                                  
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:95472-95509	Query:40-3	22	0.137388
 .>                                                   
               	build33|chr22|slice(37101000-37250999)
len:150000	Object:121477-121506	Query:3-32	22	0.137388
(...


Enjoy
Pierre Lindenbaum PhD





___________________________________________________________
Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en français !
Yahoo! Mail : http://fr.mail.yahoo.com

--__--__--

Message: 3
Date: Tue, 27 May 2003 10:32:40 +0100
To: biodevelopers at bioinformatics.org
From: David Leader <d.leader at bio.gla.ac.uk>
Subject: [Biodevelopers] About Bio C# and me
Reply-To: biodevelopers at bioinformatics.org

Serge and Arun. Why would you want to use C# to develop 
bioinformatics software? I don't know much about it but I thought it 
was Windows only.

David
-- 
_______________________________________________________________
  David P.Leader, Biochemistry and Molecular Biology
  Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK
  Phone: +44 41 330-5905                d.leader at bio.gla.ac.uk
            http://doolittle.ibls.gla.ac.uk/leader
_______________________________________________________________

    

--__--__--

Message: 4
From: Blair Jennings <blair.jennings at lionbioscience.com>
To: "'biodevelopers at bioinformatics.org'" <biodevelopers at bioinformatics.org>
Subject: RE: [Biodevelopers] Re: Biodevelopers digest, Vol 1 #111 - 1 msg
Date: Tue, 27 May 2003 08:49:29 -0700
Reply-To: biodevelopers at bioinformatics.org

This message is in MIME format. Since your mail reader does not understand
this format, some or all of this message may not be legible.

------_=_NextPart_001_01C32467.8EFE7CA0
Content-Type: text/plain;
	charset="iso-8859-1"

Not possible C# has been approved by the ECMA standards board (and will soon
be an ISO standard); this means that anyone can write their own
implementation of C# without having to license it from Microsoft (not true
with Java and Sun my biggest complaint about Java). 

Also go look at the mono project (www.go-mono.com) it is a port of .NET to
UNIX (currently linux, solaris and Mac). 


Can anyone fill me in about the Bio C# project. I've been writing in it for
1.5 years; have an extensive background in Biological Chemistry and would
like to help out.

Blair Jennings
Software Engineer
Lion bioscience


-----Original Message-----
From: Daniel Wetzler [mailto:Daniel.Wetzler at uni-koeln.de]
Sent: Monday, May 26, 2003 6:27 AM
To: biodevelopers at bioinformatics.org
Subject: Re: [Biodevelopers] Re: Biodevelopers digest, Vol 1 #111 - 1
msg


Hallo,

I think that C# will become sooner or later a propietary solution
like e.G. VB.
C# is maintained by Microsoft and they are responsible for future
enhancements of the language. And I don't think that they will
support other platforms than Windows and they won't espiacally support
Linux/Unix after C# having gained a bigger part of the market.

So I would propose to develop a C++ Library since such a Library could be
supported on several platforms.

Greetings,

Daniel




Fangxia Li schrieb:

>Hey, Bio Dev Guru,
>
>I am a Java Developer instead, while interested at C#.
>I want to know exactly what kind of projects are there
>in your mind. 
>
>Brief about me: I am M.D. studying biology signal
>transduction etc at Thomas Jefferson Hosptial. I got
>my M.S degree at computer science and gained 2 years
>programming experience in IT industry. Looking for a
>better way to contribute to bioinformatics
>projects...8-)
>
>Regards,
>
>Scott Lee
>--- arun a <arunnuraa at linuxmail.org> wrote:
>  
>
>>Hai 
>>   I am from Bharathiar University, India. I am also
>>interested to participate int Bio C#. I know some
>>computer programing. Can u accept my invitation.
>>
>>From: biodevelopers-request at bioinformatics.org
>>Date: Sun, 25 May 2003 12:01:49 -0400 (EDT) 
>>To: biodevelopers at bioinformatics.org
>>Subject: Biodevelopers digest, Vol 1 #111 - 1 msg
>>
>>Re: Send Biodevelopers mailing list submissions to
>>Re: 	biodevelopers at bioinformatics.org
>>Re: 
>>Re: To subscribe or unsubscribe via the World Wide
>>Web, visit
>>Re: 
>>
>>    
>>
>https://bioinformatics.org/mailman/listinfo/biodevelopers
>  
>
>>Re: or, via email, send a message with subject or
>>body 'help' to
>>Re: 	biodevelopers-request at bioinformatics.org
>>Re: 
>>Re: You can reach the person managing the list at
>>Re: 	biodevelopers-admin at bioinformatics.org
>>Re: 
>>Re: When replying, please edit your Subject line so
>>it is more specific
>>Re: than "Re: Contents of Biodevelopers digest..."
>>Re: 
>>Re: 
>>Re: Today's Topics:
>>Re: 
>>Re:    1. About Bio C# and me (Serge Gregorio)
>>Re: 
>>Re: -- __--__-- 
>>Re: 
>>Re: Message: 1
>>Re: To: biodevelopers at bioinformatics.org
>>Re: Date: Sun, 25 May 2003 03:34:47 +0800
>>Re: From: "Serge Gregorio"
>><d.gregorio at eudoramail.com>
>>Re: Organization: Lycos Mail 
>>(http://www.mail.eudoramail.com)
>>Re: Subject: [Biodevelopers] About Bio C# and me
>>Re: Reply-To: biodevelopers at bioinformatics.org
>>Re: 
>>Re: >Scott:
>>Re: 
>>Re: >Hey, Serge,
>>Re: >Where you from, get us some info about you,
>>thanks! 
>>Re: 
>>Re: Hello Scott!  I'm an IT pro from Manila,
>>Philippines.  I'm into PHP, VB, Oracle, etc.  I'm a
>>relatively new "recruit/convert" to bioinformatics. 
>>More about me at:
>>Re: 
>>Re:    http://genephp.sf.net 
>>Re: 
>>Re: >Jaroslaw:
>>Re:  
>>Re: >What do you think about starting a Bio C++
>>project? >AFAIK there is now such at the moment and
>>I know lot >of people working in bioinformatics and
>>using C++.
>>Re: 
>>Re: Nice idea... I use occasionally use C++
>>myself... but
>>Re: for the sole purpose of learning a new language,
>>I'd prefer joining a Bio C# or maybe a Bio
>>Coldfusion? =)
>>Re: 
>>Re: Regards,
>>Re: 
>>Re: Serge Gregorio
>>Re: 
>>Re: 
>>Re: Need a new email address that people can
>>remember
>>Re: Check out the new EudoraMail at
>>Re: http://www.eudoramail.com
>>Re: 
>>Re: 
>>Re: -- __--__-- 
>>Re: 
>>Re: _______________________________________________
>>Re: Biodevelopers mailing list
>>Re: Biodevelopers at bioinformatics.org
>>Re:
>>
>>    
>>
>https://bioinformatics.org/mailman/listinfo/biodevelopers
>  
>
>>Re: 
>>Re: 
>>Re: End of Biodevelopers Digest
>>
>>
>>
>>.-. .-.   .-. .-.   .-. .-.   .-. .-.   .-. .-.  
>>.-. .-.   .-. .-.
>> /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\
>>/|||X|||\ /|||X|||\
>>X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/
>>\|||X|||/ \|||X|||/ \|||X
>> `-'   `-' `-'   `-' `-'   `-' `-'   `-' `-'   `-'
>>`-'   `-' `-'   `-'
>>Arun.A.P
>>C/O Prof.M.R.N.Murthy,
>>Dept of Molecular Biophysics,
>>Indian Institute of Science,
>>Bangalore -12
>>91 80 2932458
>>.-. .-.   .-. .-.   .-. .-.   .-. .-.   .-. .-.  
>>.-. .-.   .-. .-.
>> /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\
>>/|||X|||\ /|||X|||\
>>X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/
>>\|||X|||/ \|||X|||/ \|||X
>> `-'   `-' `-'   `-' `-'   `-' `-'   `-' `-'   `-'
>>`-'   `-' `-'   `-'
>>
>>
>>-- 
>>______________________________________________
>>http://www.linuxmail.org/
>>Now with e-mail forwarding for only US$5.95/yr
>>
>>Powered by Outblaze
>>_______________________________________________
>>Biodevelopers mailing list
>>Biodevelopers at bioinformatics.org
>>
>>    
>>
>https://bioinformatics.org/mailman/listinfo/biodevelopers
>
>
>__________________________________
>Do you Yahoo!?
>The New Yahoo! Search - Faster. Easier. Bingo.
>http://search.yahoo.com
>_______________________________________________
>Biodevelopers mailing list
>Biodevelopers at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/biodevelopers
>
>  
>


_______________________________________________
Biodevelopers mailing list
Biodevelopers at bioinformatics.org
https://bioinformatics.org/mailman/listinfo/biodevelopers

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<META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; =
charset=3Diso-8859-1">
<META NAME=3D"Generator" CONTENT=3D"MS Exchange Server version =
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<TITLE>RE: [Biodevelopers] Re: Biodevelopers digest, Vol 1 #111 - 1 =
msg</TITLE>
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<BODY>

<P><FONT SIZE=3D2>Not possible C# has been approved by the ECMA =
standards board (and will soon be an ISO standard); this means that =
anyone can write their own implementation of C# without having to =
license it from Microsoft (not true with Java and Sun my biggest =
complaint about Java). </FONT></P>

<P><FONT SIZE=3D2>Also go look at the mono project (www.go-mono.com) it =
is a port of .NET to UNIX (currently linux, solaris and Mac). </FONT>
</P>
<BR>

<P><FONT SIZE=3D2>Can anyone fill me in about the Bio C# project. I've =
been writing in it for 1.5 years; have an extensive background in =
Biological Chemistry and would like to help out.</FONT></P>

<P><FONT SIZE=3D2>Blair Jennings</FONT>
<BR><FONT SIZE=3D2>Software Engineer</FONT>
<BR><FONT SIZE=3D2>Lion bioscience</FONT>
</P>
<BR>

<P><FONT SIZE=3D2>-----Original Message-----</FONT>
<BR><FONT SIZE=3D2>From: Daniel Wetzler [<A =
HREF=3D"mailto:Daniel.Wetzler at uni-koeln.de">mailto:Daniel.Wetzler at uni-ko=
eln.de</A>]</FONT>
<BR><FONT SIZE=3D2>Sent: Monday, May 26, 2003 6:27 AM</FONT>
<BR><FONT SIZE=3D2>To: biodevelopers at bioinformatics.org</FONT>
<BR><FONT SIZE=3D2>Subject: Re: [Biodevelopers] Re: Biodevelopers =
digest, Vol 1 #111 - 1</FONT>
<BR><FONT SIZE=3D2>msg</FONT>
</P>
<BR>

<P><FONT SIZE=3D2>Hallo,</FONT>
</P>

<P><FONT SIZE=3D2>I think that C# will become sooner or later a =
propietary solution</FONT>
<BR><FONT SIZE=3D2>like e.G. VB.</FONT>
<BR><FONT SIZE=3D2>C# is maintained by Microsoft and they are =
responsible for future</FONT>
<BR><FONT SIZE=3D2>enhancements of the language. And I don't think that =
they will</FONT>
<BR><FONT SIZE=3D2>support other platforms than Windows and they won't =
espiacally support</FONT>
<BR><FONT SIZE=3D2>Linux/Unix after C# having gained a bigger part of =
the market.</FONT>
</P>

<P><FONT SIZE=3D2>So I would propose to develop a C++ Library since =
such a Library could be</FONT>
<BR><FONT SIZE=3D2>supported on several platforms.</FONT>
</P>

<P><FONT SIZE=3D2>Greetings,</FONT>
</P>

<P><FONT SIZE=3D2>Daniel</FONT>
</P>
<BR>
<BR>
<BR>

<P><FONT SIZE=3D2>Fangxia Li schrieb:</FONT>
</P>

<P><FONT SIZE=3D2>&gt;Hey, Bio Dev Guru,</FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;I am a Java Developer instead, while interested =
at C#.</FONT>
<BR><FONT SIZE=3D2>&gt;I want to know exactly what kind of projects are =
there</FONT>
<BR><FONT SIZE=3D2>&gt;in your mind. </FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;Brief about me: I am M.D. studying biology =
signal</FONT>
<BR><FONT SIZE=3D2>&gt;transduction etc at Thomas Jefferson Hosptial. I =
got</FONT>
<BR><FONT SIZE=3D2>&gt;my M.S degree at computer science and gained 2 =
years</FONT>
<BR><FONT SIZE=3D2>&gt;programming experience in IT industry. Looking =
for a</FONT>
<BR><FONT SIZE=3D2>&gt;better way to contribute to =
bioinformatics</FONT>
<BR><FONT SIZE=3D2>&gt;projects...8-)</FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;Regards,</FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;Scott Lee</FONT>
<BR><FONT SIZE=3D2>&gt;--- arun a &lt;arunnuraa at linuxmail.org&gt; =
wrote:</FONT>
<BR><FONT SIZE=3D2>&gt;&nbsp; </FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Hai </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;&nbsp;&nbsp; I am from Bharathiar =
University, India. I am also</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;interested to participate int Bio C#. I know =
some</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;computer programing. Can u accept my =
invitation.</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;From: =
biodevelopers-request at bioinformatics.org</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Date: Sun, 25 May 2003 12:01:49 -0400 (EDT) =
</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;To: biodevelopers at bioinformatics.org</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Subject: Biodevelopers digest, Vol 1 #111 - =
1 msg</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Send Biodevelopers mailing list =
submissions to</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: &nbsp; =
biodevelopers at bioinformatics.org</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: To subscribe or unsubscribe via the =
World Wide</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Web, visit</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;&nbsp;&nbsp;&nbsp; </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;<A =
HREF=3D"https://bioinformatics.org/mailman/listinfo/biodevelopers" =
TARGET=3D"_blank">https://bioinformatics.org/mailman/listinfo/biodevelop=
ers</A></FONT>
<BR><FONT SIZE=3D2>&gt;&nbsp; </FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: or, via email, send a message with =
subject or</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;body 'help' to</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: &nbsp; =
biodevelopers-request at bioinformatics.org</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: You can reach the person managing the =
list at</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: &nbsp; =
biodevelopers-admin at bioinformatics.org</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: When replying, please edit your Subject =
line so</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;it is more specific</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: than &quot;Re: Contents of Biodevelopers =
digest...&quot;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Today's Topics:</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re:&nbsp;&nbsp;&nbsp; 1. About Bio C# and me =
(Serge Gregorio)</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: -- __--__-- </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Message: 1</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: To: =
biodevelopers at bioinformatics.org</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Date: Sun, 25 May 2003 03:34:47 =
+0800</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: From: &quot;Serge Gregorio&quot;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;&lt;d.gregorio at eudoramail.com&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Organization: Lycos Mail </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;(<A HREF=3D"http://www.mail.eudoramail.com" =
TARGET=3D"_blank">http://www.mail.eudoramail.com</A>)</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Subject: [Biodevelopers] About Bio C# =
and me</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Reply-To: =
biodevelopers at bioinformatics.org</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: &gt;Scott:</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: &gt;Hey, Serge,</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: &gt;Where you from, get us some info =
about you,</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;thanks! </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Hello Scott!&nbsp; I'm an IT pro from =
Manila,</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Philippines.&nbsp; I'm into PHP, VB, Oracle, =
etc.&nbsp; I'm a</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;relatively new &quot;recruit/convert&quot; =
to bioinformatics. </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;More about me at:</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re:&nbsp;&nbsp;&nbsp; <A =
HREF=3D"http://genephp.sf.net" =
TARGET=3D"_blank">http://genephp.sf.net</A> </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: &gt;Jaroslaw:</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re:&nbsp; </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: &gt;What do you think about starting a =
Bio C++</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;project? &gt;AFAIK there is now such at the =
moment and</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;I know lot &gt;of people working in =
bioinformatics and</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;using C++.</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Nice idea... I use occasionally use =
C++</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;myself... but</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: for the sole purpose of learning a new =
language,</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;I'd prefer joining a Bio C# or maybe a =
Bio</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Coldfusion? =3D)</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Regards,</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Serge Gregorio</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Need a new email address that people =
can</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;remember</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Check out the new EudoraMail at</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: <A HREF=3D"http://www.eudoramail.com" =
TARGET=3D"_blank">http://www.eudoramail.com</A></FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: -- __--__-- </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: =
_______________________________________________</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Biodevelopers mailing list</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: Biodevelopers at bioinformatics.org</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re:</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;&nbsp;&nbsp;&nbsp; </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;<A =
HREF=3D"https://bioinformatics.org/mailman/listinfo/biodevelopers" =
TARGET=3D"_blank">https://bioinformatics.org/mailman/listinfo/biodevelop=
ers</A></FONT>
<BR><FONT SIZE=3D2>&gt;&nbsp; </FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Re: End of Biodevelopers Digest</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;.-. .-.&nbsp;&nbsp; .-. .-.&nbsp;&nbsp; .-. =
.-.&nbsp;&nbsp; .-. .-.&nbsp;&nbsp; .-. .-.&nbsp; </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;.-. .-.&nbsp;&nbsp; .-. .-.</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ =
/|||X|||\</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;/|||X|||\ /|||X|||\</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;X|||/ \|||X|||/ \|||X|||/ \|||X|||/ =
\|||X|||/</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;\|||X|||/ \|||X|||/ \|||X</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; `-'&nbsp;&nbsp; `-' `-'&nbsp;&nbsp; `-' =
`-'&nbsp;&nbsp; `-' `-'&nbsp;&nbsp; `-' `-'&nbsp;&nbsp; `-'</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;`-'&nbsp;&nbsp; `-' `-'&nbsp;&nbsp; =
`-'</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Arun.A.P</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;C/O Prof.M.R.N.Murthy,</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Dept of Molecular Biophysics,</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Indian Institute of Science,</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Bangalore -12</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;91 80 2932458</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;.-. .-.&nbsp;&nbsp; .-. .-.&nbsp;&nbsp; .-. =
.-.&nbsp;&nbsp; .-. .-.&nbsp;&nbsp; .-. .-.&nbsp; </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;.-. .-.&nbsp;&nbsp; .-. .-.</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ =
/|||X|||\</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;/|||X|||\ /|||X|||\</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;X|||/ \|||X|||/ \|||X|||/ \|||X|||/ =
\|||X|||/</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;\|||X|||/ \|||X|||/ \|||X</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; `-'&nbsp;&nbsp; `-' `-'&nbsp;&nbsp; `-' =
`-'&nbsp;&nbsp; `-' `-'&nbsp;&nbsp; `-' `-'&nbsp;&nbsp; `-'</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;`-'&nbsp;&nbsp; `-' `-'&nbsp;&nbsp; =
`-'</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;-- </FONT>
<BR><FONT =
SIZE=3D2>&gt;&gt;______________________________________________</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;<A HREF=3D"http://www.linuxmail.org/" =
TARGET=3D"_blank">http://www.linuxmail.org/</A></FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Now with e-mail forwarding for only =
US$5.95/yr</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Powered by Outblaze</FONT>
<BR><FONT =
SIZE=3D2>&gt;&gt;_______________________________________________</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Biodevelopers mailing list</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;Biodevelopers at bioinformatics.org</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt;&nbsp;&nbsp;&nbsp; </FONT>
<BR><FONT SIZE=3D2>&gt;&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;<A =
HREF=3D"https://bioinformatics.org/mailman/listinfo/biodevelopers" =
TARGET=3D"_blank">https://bioinformatics.org/mailman/listinfo/biodevelop=
ers</A></FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;__________________________________</FONT>
<BR><FONT SIZE=3D2>&gt;Do you Yahoo!?</FONT>
<BR><FONT SIZE=3D2>&gt;The New Yahoo! Search - Faster. Easier. =
Bingo.</FONT>
<BR><FONT SIZE=3D2>&gt;<A HREF=3D"http://search.yahoo.com" =
TARGET=3D"_blank">http://search.yahoo.com</A></FONT>
<BR><FONT =
SIZE=3D2>&gt;_______________________________________________</FONT>
<BR><FONT SIZE=3D2>&gt;Biodevelopers mailing list</FONT>
<BR><FONT SIZE=3D2>&gt;Biodevelopers at bioinformatics.org</FONT>
<BR><FONT SIZE=3D2>&gt;<A =
HREF=3D"https://bioinformatics.org/mailman/listinfo/biodevelopers" =
TARGET=3D"_blank">https://bioinformatics.org/mailman/listinfo/biodevelop=
ers</A></FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&nbsp; </FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
</P>
<BR>

<P><FONT =
SIZE=3D2>_______________________________________________</FONT>
<BR><FONT SIZE=3D2>Biodevelopers mailing list</FONT>
<BR><FONT SIZE=3D2>Biodevelopers at bioinformatics.org</FONT>
<BR><FONT SIZE=3D2><A =
HREF=3D"https://bioinformatics.org/mailman/listinfo/biodevelopers" =
TARGET=3D"_blank">https://bioinformatics.org/mailman/listinfo/biodevelop=
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