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<TITLE>Re: [BiO BB] DNA Strider</TITLE>
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<DIV><SPAN class=282130713-05042004><FONT face=Arial color=#0000ff
size=2>Joel,</FONT></SPAN></DIV>
<DIV><SPAN class=282130713-05042004><FONT face=Arial color=#0000ff size=2>I
write a short piece in every issue of The Scientist magazine called Software
Watch that features an open source biology software program. I'm interested in
hearing more about the system you mention as a possible item about which I could
write. We have a lead time of as much as two months, so embargoing our coverage
is no problem. Can you send me any information about the
system?</FONT></SPAN></DIV>
<DIV><SPAN class=282130713-05042004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=282130713-05042004>
<P><FONT face=Arial size=2>Sam Jaffe</FONT> <BR><FONT face=Arial
size=2>Associate Editor</FONT> <BR><FONT face=Arial size=2>The Scientist
Magazine (www.the-scientist.com)</FONT> <BR><FONT face=Arial size=2>3535 Market
St.</FONT> <BR><FONT face=Arial size=2>Second Floor</FONT> <BR><FONT face=Arial
size=2>Philadelphia, PA, 19104</FONT> <BR><FONT face=Arial size=2>215 386 9601
x.3015</FONT> <BR><FONT face=Arial size=2>sjaffe@the-scientist.com</FONT>
</P></SPAN></DIV>
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<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B> Joel Dudley
[mailto:Joel.Dudley@asu.edu]<BR><B>Sent:</B> Monday, April 05, 2004 4:56
PM<BR><B>To:</B> bio_bulletin_board@bioinformatics.org<BR><B>Subject:</B> RE:
[BiO BB] DNA Strider<BR><BR></FONT></DIV>
<DIV>Several such systems are already under development and released in the
private sector. I know of a soon to be open-source project that has
all of these features and is already quite mature. You should hear about it in
a month or so.</DIV>
<DIV> </DIV>
<DIV>- Joel</DIV>
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<DIV><FONT size=2>-----Original Message----- <BR><B>From:</B>
bio_bulletin_board-admin@bioinformatics.org on behalf of Marcos
Oliveira de Carvalho <BR><B>Sent:</B> Tue 3/30/2004 5:21 PM <BR><B>To:</B>
bio_bulletin_board@bioinformatics.org <BR><B>Cc:</B> <BR><B>Subject:</B> Re:
[BiO BB] DNA Strider<BR><BR></FONT></DIV><BR>
<P><FONT size=2>It would be nice to have a bioinformatics IDRE ( Integrated
Development<BR>and Research Environment) with some basic features
(sequence<BR>visualization, editing, annotation, data management, etc...)
and a well<BR>designed plug-in API, for easy extension. An idea could be
build it on top<BR>of the NetBeans platform , and with java we get
platform-independent<BR>software. (with other languages too, but java do the
job)<BR>One can suggest add bindings with python/perl/ruby/java and theirs
Bio*<BR>libraries, interfaces to bioinformatics tools, including
output capture<BR>(emboss, phred, phrap, BLAST, FASTA,
Clustal,R/bioconductor, Mummer,...) .<BR>Also interfaces to webservices and
data retrieving from major databases.<BR>Well, there are lots of
possibilities.<BR><BR>cheers<BR>Marcos<BR><BR><BR><BR>On Tue, 30 Mar 2004
18:30:36 -0500, Ryan Golhar
<ryangolhar@hotmail.com><BR>wrote:<BR><BR>> You know, I'm
constantly finding different programs to perform different<BR>>
tasks. Either client applications, or web-based. Some run on
Linux,<BR>> others Windows.<BR>><BR>> I would like to see 1
application for multiple platforms to performs dna<BR>> sequence
analysis. I started writing something in Java to do this but<BR>>
haven't touched in awhile.<BR>><BR>> I'm wondering how many people
would be interested in helping to develop<BR>> a
platform-independent application to perform all sorts of sequence<BR>>
analysis - alignments, snp analysis, assembly, etc. Sort of like
GCG,<BR>> but free and actually user-friendly and useful. If people
are<BR>> interested, I think we should talk about a framework and start
building<BR>> something as needed.<BR>><BR>> Any
comments?<BR>><BR>> -----<BR>> Ryan Golhar<BR>> Computational
Biologist<BR>> The Informatics Institute at<BR>> The University of
Medicine & Dentistry of NJ<BR>><BR>> Phone: 973-972-5034<BR>>
Fax: 973-972-7412<BR>> Email: golharam@umdnj.edu<BR>><BR>>
-----Original Message-----<BR>> From:
bio_bulletin_board-admin@bioinformatics.org<BR>> [<A
href="mailto:bio_bulletin_board-admin@bioinformatics.org">mailto:bio_bulletin_board-admin@bioinformatics.org</A>]
On Behalf Of<BR>> Yannick Wurm<BR>> Sent: Tuesday, March 30, 2004
10:05 AM<BR>> To: bio_bulletin_board@bioinformatics.org<BR>> Subject:
[BiO BB] DNA Strider<BR>><BR>><BR>> Hi,<BR>> I'm a student in
Bioinformatics and Modeling at a French engineering<BR>> school in Lyon,
France (<A
href="http://biosciences.insa-lyon.fr">http://biosciences.insa-lyon.fr</A>).
Currently in<BR>> my last year, I'm currently doing a six month
internship in a C.<BR>> elegans lab at McGill University in
Montreal.<BR>> The lab's computer are Macs, and besides standard
browsing, word<BR>> processing and image processing, lab members also use
them to aid them<BR>> in their molecular biology work.<BR>> One of the
programs they use is called DNA Strider. This piece of<BR>> software has
not been updated in a long time (probably since Apple's<BR>> System 6.x -
window sizes are fixed to the small old mac screen size!)<BR>> and could
require a face-lift.<BR>><BR>> In the lab, it is mainly used for
managing and manipulating sequences<BR>> of genes, primers and
constructs. The main features of interest here<BR>> are:<BR>>
- Sequence
management<BR>> - Graphical (circular or
linear) restriction maps of a given<BR>> sequence (or part of it),
showing restriction site data concerning the<BR>> part or whole sequence
(for each enzyme, you get the number of<BR>> restriction sites, and the
obtained fragement sizes)<BR>> - Reverse
complementary sequence<BR>> - Quick and
simple alignment between two sequences<BR>><BR>> I've searched the web
and could not find an all-in-one package that<BR>> seemed as user
friendly and coherent as DNA Strider. Individual web<BR>> sites and
software tools do offer these features, but<BR>>
- the internet is slow (you click and need to
wait before<BR>> getting your<BR>> result)<BR>>
- having everything in one place is
nice<BR>><BR>> Sequence Analysis (for Mac OS X) <A
href="http://informagen.com/SA/">http://informagen.com/SA/</A> seems to
be<BR>> aiming to do what DNA Strider does, but is still very young
(and<BR>> closed-source, but thats a different debate).<BR>><BR>>
<A href="http://www.mekentosj.com/">http://www.mekentosj.com/</A> has some
very nice tools as well, but they're<BR>> very
problem-specific.<BR>><BR>> Have I missed something? Is there a really
cool java app or web<BR>> software (that I could install locally for
speed) that would replace<BR>> DNA Strider? What does your molecular
biology lab use in for it's day<BR>> to day work?<BR>> Oh and buying
something expensive is not a solution.<BR>><BR>> Thanks for any
leads,<BR>><BR>> Yannick.<BR>><BR>> \\\\\\\\\\\\\\\\\\\<BR>>
\\ <A href="http://yannick.poulet.org">http://yannick.poulet.org</A>
icq: 22044361<BR>> \\ idh@poulet.org tel:
++33.6.16.41.71.92<BR>><BR>>
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