[BiO BB] RE: [BiO BB] DNA Strider

Tue Apr 6 09:09:00 EDT 2004

Joel,
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?

Sam Jaffe 
Associate Editor 
The Scientist Magazine (www.the-scientist.com) 
3535 Market St. 
Second Floor 
Philadelphia, PA, 19104 
215 386 9601 x.3015 
sjaffe at the-scientist.com 

-----Original Message-----
From: Joel Dudley [mailto:Joel.Dudley at asu.edu]
Sent: Monday, April 05, 2004 4:56 PM
To: bio_bulletin_board at bioinformatics.org
Subject: RE: [BiO BB] DNA Strider

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.

- Joel

-----Original Message----- 
From: bio_bulletin_board-admin at bioinformatics.org on behalf of Marcos
Oliveira de Carvalho 
Sent: Tue 3/30/2004 5:21 PM 
To: bio_bulletin_board at bioinformatics.org 
Cc: 
Subject: Re: [BiO BB] DNA Strider

It would be nice to have a bioinformatics IDRE ( Integrated Development
and Research Environment) with some basic features (sequence
visualization, editing, annotation, data management, etc...) and a well
designed plug-in API, for easy extension. An idea could be build it on top
of the NetBeans platform , and with java we get platform-independent
software. (with other languages too, but java do the job)
One can suggest add bindings with python/perl/ruby/java and theirs Bio*
libraries, interfaces  to bioinformatics tools, including output capture
(emboss, phred, phrap, BLAST, FASTA, Clustal,R/bioconductor, Mummer,...) .
Also interfaces to webservices and data retrieving from major databases.
Well, there are lots of possibilities.

cheers
Marcos

On Tue, 30 Mar 2004 18:30:36 -0500, Ryan Golhar <ryangolhar at hotmail.com>
wrote:

> You know, I'm constantly finding different programs to perform different
> tasks.  Either client applications, or web-based.  Some run on Linux,
> others Windows.
>
> I would like to see 1 application for multiple platforms to performs dna
> sequence analysis.  I started writing something in Java to do this but
> haven't touched in awhile.
>
> I'm wondering how many people would be interested in helping to develop
> a  platform-independent application to perform all sorts of sequence
> analysis - alignments, snp analysis, assembly, etc.  Sort of like GCG,
> but free and actually user-friendly and useful.  If people are
> interested, I think we should talk about a framework and start building
> something as needed.
>
> Any comments?
>
> -----
> Ryan Golhar
> Computational Biologist
> The Informatics Institute at
> The University of Medicine & Dentistry of NJ
>
> Phone: 973-972-5034
> Fax: 973-972-7412
> Email: golharam at umdnj.edu
>
> -----Original Message-----
> From: bio_bulletin_board-admin at bioinformatics.org
> [ mailto:bio_bulletin_board-admin at bioinformatics.org
<mailto:bio_bulletin_board-admin at bioinformatics.org> ] On Behalf Of
> Yannick Wurm
> Sent: Tuesday, March 30, 2004 10:05 AM
> To: bio_bulletin_board at bioinformatics.org
> Subject: [BiO BB] DNA Strider
>
>
> Hi,
> I'm a student in Bioinformatics and Modeling at a French engineering
> school in Lyon, France ( http://biosciences.insa-lyon.fr
<http://biosciences.insa-lyon.fr> ). Currently in
> my last year, I'm currently doing a six month internship in a C.
> elegans lab at McGill University in Montreal.
> The lab's computer are Macs, and besides standard browsing, word
> processing and image processing, lab members also use them to aid them
> in their molecular biology work.
> One of the programs they use is called DNA Strider. This piece of
> software has not been updated in a long time (probably since Apple's
> System 6.x - window sizes are fixed to the small old mac screen size!)
> and could require a face-lift.
>
> In the lab, it is mainly used for managing and manipulating sequences
> of genes, primers and constructs. The main features of interest here
> are:
>       - Sequence management
>      - Graphical (circular or linear) restriction maps of a given
> sequence (or part of it), showing restriction site data concerning the
> part or whole sequence (for each enzyme, you get the number of
> restriction sites, and the obtained fragement sizes)
>       - Reverse complementary sequence
>       - Quick and simple alignment between two sequences
>
> I've searched the web and could not find an all-in-one package that
> seemed as user friendly and coherent as DNA Strider. Individual web
> sites and software tools do offer these features, but
>       - the internet is slow (you click and need to wait before
> getting your
> result)
>       - having everything in one place is nice
>
> Sequence Analysis (for Mac OS X) http://informagen.com/SA/
<http://informagen.com/SA/>  seems to be
> aiming to do what DNA Strider does, but is still very young (and
> closed-source, but thats a different debate).
>
> http://www.mekentosj.com/ <http://www.mekentosj.com/>  has some very nice
tools as well, but they're
> very problem-specific.
>
> Have I missed something? Is there a really cool java app or web
> software (that I could install locally for speed) that would replace
> DNA Strider? What does your molecular biology lab use in for it's day
> to day work?
> Oh and buying something expensive is not a solution.
>
> Thanks for any leads,
>
> Yannick.
>
> \\\\\\\\\\\\\\\\\\\
> \\  http://yannick.poulet.org <http://yannick.poulet.org>  icq: 22044361
> \\  idh at poulet.org  tel: ++33.6.16.41.71.92
>
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the torch which illuminates the world. "
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